Papers citing PR2

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., … Christen, R. (2013). The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(D1), D597–D604. https://doi.org/10.1093/nar/gks1160

References are available as a Zotero group

2022

Anderson, S. and L. Thompson (2022). “Optimizing an enclosed bead beating extraction method for microbial and fish environmental DNA”. In: Environmental DNA 4.2, pp. 291-303. DOI: 10.1002/edn3.251.

Bachy, C., L. Sudek, C. Choi, et al. (2022). “Phytoplankton surveys in the arctic fram strait demonstrate the tiny eukaryotic alga micromonas and other picoprasinophytes contribute to deep sea export”. In: Microorganisms 10.5. DOI: 10.3390/microorganisms10050961.

Bai, R., M. Zhou, Y. Guo, et al. (2022). “Long-term mowing reinforces connections between soil microbial and plant communities in a temperate steppe”. In: Plant and Soil. DOI: 10.1007/s11104-022-05374-9.

Biard, T. (2022). “Diversity and ecology of Radiolaria in modern oceans”. In: Environmental Microbiology. DOI: 10.1111/1462-2920.16004.

Blais, M., A. Matveev, C. Lovejoy, et al. (2022). “Size-fractionated microbiome structure in subarctic rivers and a coastal plume across DOC and salinity gradients”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.760282.

Bock, C., J. Olefeld, J. Vogt, et al. (2022). “Phylogenetic and functional diversity of Chrysophyceae in inland waters”. In: Organisms Diversity and Evolution 22.2, pp. 327-341. DOI: 10.1007/s13127-022-00554-y.

Brasell, K., X. Pochon, J. Howarth, et al. (2022). “Shifts in DNA yield and biological community composition in stored sediment: Implications for paleogenomic studies”. In: Metabarcoding and Metagenomics 6. DOI: 10.3897/mbmg.6.78128.

Briscoe, A., S. Nichols, H. Hartikainen, et al. (2022). “High-throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds”. In: Molecular Ecology Resources 22.4, pp. 1303-1318. DOI: 10.1111/1755-0998.13548.

Cahoon, A. and R. VanGundy (2022). “Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves”. In: Environmental Microbiology Reports. DOI: 10.1111/1758-2229.13060.

Capo, E., M. Monchamp, M. Coolen, et al. (2022). “Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential”. In: Environmental Microbiology. DOI: 10.1111/1462-2920.15913.

Cho, A., D. Tikhonenkov, E. Hehenberger, et al. (2022). “Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles”. In: Molecular Phylogenetics and Evolution 171. DOI: 10.1016/j.ympev.2022.107468.

Couch, C., J. Sanders, D. Sweitzer, et al. (2022). “The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens)”. In: Proceedings of the Royal Society B: Biological Sciences 289.1972. DOI: 10.1098/rspb.2022.0079.

De Gruyter, J., J. Weedon, E. Elst, et al. (2022). “Arbuscular mycorrhizal inoculation and plant response strongly shape bacterial and eukaryotic soil community trajectories”. In: Soil Biology and Biochemistry 165. DOI: 10.1016/j.soilbio.2021.108524.

Djaoudi, K., J. Onrubia, A. Boukra, et al. (2022). “Seawater copper content controls biofilm bioaccumulation and microbial community on microplastics”. In: Science of the Total Environment 814. DOI: 10.1016/j.scitotenv.2021.152278.

Duerschlag, J., W. Mohr, T. Ferdelman, et al. (2022). “Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean”. In: ISME Journal 16.2, pp. 465-476. DOI: 10.1038/s41396-021-01072-z.

Dumack, K., O. Ferlian, D. Morselli Gysi, et al. (2022). “Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests”. In: Biological Invasions 24.5, pp. 1345-1357. DOI: 10.1007/s10530-021-02726-x.

Durán, P., J. Flores-Uribe, K. Wippel, et al. (2022). “Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota”. In: Nature Communications 13.1. DOI: 10.1038/s41467-022-28055-8.

Durkin, C., I. Cetinic, M. Estapa, et al. (2022). “Tracing the path of carbon export in the ocean though DNA sequencing of individual sinking particles”. In: ISME Journal. DOI: 10.1038/s41396-022-01239-2.

Eshghi Sahraei, S., B. Furneaux, K. Kluting, et al. (2022). “Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding”. In: Ecology and Evolution 12.3. DOI: 10.1002/ece3.8676.

Fall, F., H. Sanguin, D. Fall, et al. (2022). “Changes in intraspecific diversity of the arbuscular mycorrhizal community involved in Plantinteractions between sporobolus robustus kunth and prosopis juliflora (swartz) DC along an environmental gradient”. In: Microbial Ecology 83.4, pp. 886-898. DOI: 10.1007/s00248-021-01779-8.

Ferreira, M. and D. Cleary (2022). “Microeukaryotic communities of golf-ball sponges inside and outside of marine lakes”. In: Journal of Sea Research 180. DOI: 10.1016/j.seares.2021.102151.

Fiore-Donno, A., Z. Human, M. Å tursová, et al. (2022). “Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition”. In: Soil Biology and Biochemistry 168. DOI: 10.1016/j.soilbio.2022.108628.

Fournier, I., C. Lovejoy, and W. Vincent (2022). “Road salt versus urban snow effects on lake microbial communities”. In: Microorganisms 10.4. DOI: 10.3390/microorganisms10040803.

Freudenthal, J., F. Ju, H. Bürgmann, et al. (2022). “Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal”. In: Microbiome 10.1. DOI: 10.1186/s40168-022-01225-y.

Fuchsman, C., L. Cherubini, and M. Hays (2022). “An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N2-producing bacteria”. In: Environmental Microbiology 24.4, pp. 1790-1804. DOI: 10.1111/1462-2920.15893.

Funaki, H., C. Gaonkar, T. Kataoka, et al. (2022). “Horizontal and vertical distribution of Gambierdiscus spp. (Dinophyceae) including novel phylotypes in Japan identified by 18S rDNA metabarcoding”. In: Harmful Algae 111. DOI: 10.1016/j.hal.2021.102163.

Gibson, K., H. Song, and N. Chen (2022). “Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China”. In: Harmful Algae 114. DOI: 10.1016/j.hal.2022.102217.

Girard, E., A. Langerak, J. Jompa, et al. (2022). “Mitochondrial cytochrome oxidase subunit 1: A promising molecular marker for species identification in foraminifera”. In: Frontiers in Marine Science 9. DOI: 10.3389/fmars.2022.809659.

Guo, S., C. Tao, A. Jousset, et al. (2022). “Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health”. In: ISME Journal. DOI: 10.1038/s41396-022-01244-5.

Hörstmann, C., P. Buttigieg, U. John, et al. (2022). “Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales”. In: Environmental Microbiology 24.1, pp. 404-419. DOI: 10.1111/1462-2920.15832.

Hu, J., M. Gebremikael, B. Tytgat, et al. (2022). “Combined selective gamma irradiation and pulverized soil inoculation for ecologically relevant soil microfauna studies”. In: Applied Soil Ecology 169. DOI: 10.1016/j.apsoil.2021.104223.

James, C., A. Barton, L. Allen, et al. (2022). “Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region”. In: Nature Communications 13.1. DOI: 10.1038/s41467-022-30139-4.

Jamieson, T., H. Whiley, J. Gascooke, et al. (2022). “Can aggregate-associated organisms influence the fouling in a SWRO desalination plant?” In: Microorganisms 10.4. DOI: 10.3390/microorganisms10040682.

Keck, F., R. Blackman, R. Bossart, et al. (2022). “Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment”. In: Molecular Ecology 31.6, pp. 1820-1835. DOI: 10.1111/mec.16364.

Kitagami, Y., K. Obase, and Y. Matsuda (2022). “High-throughput sequencing and conventional morphotyping show different soil nematode assemblages but similar community responses to altitudinal gradients on Mt. Ibuki, Japan”. In: Pedobiologia 90. DOI: 10.1016/j.pedobi.2021.150788.

Krabberød, A., I. Deutschmann, M. Bjorbækmo, et al. (2022). “Long-term patterns of an interconnected core marine microbiota”. In: Environmental Microbiomes 17.1. DOI: 10.1186/s40793-022-00417-1.

Lansac-Tôha, F., P. Buosi, M. Baumgartner, et al. (2022). “Molecular insight reveals broad-scale spatial patterns in floodplain ciliate assemblages, whereas morphology reflects local environmental controls”. In: Freshwater Science. DOI: 10.1086/719992.

Lapeyra Martin, J., U. John, C. Royer, et al. (2022). “Fantastic beasts: Unfolding mixoplankton temporal variability in the belgian coastal zone through DNA-Metabarcoding”. In: Frontiers in Marine Science 9. DOI: 10.3389/fmars.2022.786787.

Lara, E., D. Singer, and S. Geisen (2022). “Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA-based studies”. In: Environmental Microbiology. DOI: 10.1111/1462-2920.16019.

Latz, M., V. Grujcic, S. Brugel, et al. (2022). “Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing”. In: Molecular Ecology Resources. DOI: 10.1111/1755-0998.13623.

Leray, M., N. Knowlton, and R. Machida (2022). “MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences”. In: Environmental DNA. DOI: 10.1002/edn3.303.

Li, H., D. Zhu, A. Sun, et al. (2022). “Effects of soil protists on the antibiotic resistome under long term fertilization”. In: Environmental Pollution 307. DOI: 10.1016/j.envpol.2022.119516.

Li, Q., K. Edwards, C. Schvarcz, et al. (2022). “Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus”. In: ISME Journal. DOI: 10.1038/s41396-022-01204-z.

Li, Y., R. Yang, L. Guo, et al. (2022). “The composition, biotic network, and assembly of plastisphere protistan taxonomic and functional communities in plastic-mulching croplands”. In: Journal of Hazardous Materials 430. DOI: 10.1016/j.jhazmat.2022.128390.

Li, Z., A. Sun, X. Liu, et al. (2022). “Climate warming increases the proportions of specific antibiotic resistance genes in natural soil ecosystems”. In: Journal of Hazardous Materials 430. DOI: 10.1016/j.jhazmat.2022.128442.

Liu, S., Z. Cui, Y. Zhao, et al. (2022). “Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay”. In: Water Research 218. DOI: 10.1016/j.watres.2022.118488.

Liu, Y., D. Li, H. Gao, et al. (2022). “Regulation of soil micro-foodwebs to root secondary metabolites in cultivated and wild licorice plants”. In: Science of the Total Environment 828. DOI: 10.1016/j.scitotenv.2022.154302.

Metz, S., P. Huber, V. Accattatis, et al. (2022). “Freshwater protists: unveiling the unexplored in a large floodplain system”. In: Environmental Microbiology 24.4, pp. 1731-1745. DOI: 10.1111/1462-2920.15838.

Minardi, D., D. Ryder, J. del Campo, et al. (2022). “Improved high throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples”. In: Molecular Ecology Resources 22.2, pp. 664-678. DOI: 10.1111/1755-0998.13509.

Moreno-Mesonero, L., I. Amorós, Y. Moreno, et al. (2022). “Simultaneous detection of less frequent waterborne parasitic protozoa in reused wastewater using amplicon sequencing and qPCR techniques”. In: Journal of Environmental Management 314. DOI: 10.1016/j.jenvman.2022.115029.

Moynihan, M., N. Goodkin, K. Morgan, et al. (2022). “Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef”. In: ISME Journal 16.1, pp. 233-246. DOI: 10.1038/s41396-021-01054-1.

Nguyen, B., Q. Chen, J. He, et al. (2022). “Livestock manure spiked with the antibiotic tylosin significantly altered soil protist functional groups”. In: Journal of Hazardous Materials 427. DOI: 10.1016/j.jhazmat.2021.127867.

Okamoto, N., P. Keeling, B. Leander, et al. (2022). “Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location”. In: Molecular Ecology 31.11, pp. 3210-3227. DOI: 10.1111/mec.16453.

Oliva, A., R. Garner, D. Walsh, et al. (2022). “The occurrence of potentially pathogenic fungi and protists in Canadian lakes predicted using geomatics, in situ and satellite-derived variables: Towards a tele-epidemiological approach”. In: Water Research 209. DOI: 10.1016/j.watres.2021.117935.

Pierella Karlusich, J., E. Pelletier, L. Zinger, et al. (2022). “A robust approach to estimate relative phytoplankton cell abundances from metagenomes”. In: Molecular Ecology Resources. DOI: 10.1111/1755-0998.13592.

Potvin, M., M. Rautio, and C. Lovejoy (2022). “Freshwater microbial eukaryotic core communities, open-water and under-ice specialists in southern victoria island lakes (ekaluktutiak, NU, canada)”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.786094.

Qi, Q., C. Hu, J. Lin, et al. (2022). “Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks”. In: Environmental Pollution 306. DOI: 10.1016/j.envpol.2022.119406.

Reid, B., J. Servis, M. Timmers, et al. (2022). “18S rDNA amplicon sequence data (V1-V3) of the palmyra atoll national wildlife refuge, central pacific”. In: Metabarcoding and Metagenomics 6, pp. 89-99. DOI: 10.3897/mbmg.6.78762.

Resch, M., M. Schütz, R. Ochoa-Hueso, et al. (2022). “Long-term recovery of above- and below-ground interactions in restored grasslands after topsoil removal and seed addition”. In: Journal of Applied Ecology. DOI: 10.1111/1365-2664.14145.

Rii, Y., L. Peoples, D. Karl, et al. (2022). “Seasonality and episodic variation in picoeukaryote diversity and structure reveal community resilience to disturbances in the North Pacific Subtropical Gyre”. In: Limnology and Oceanography 67.S1, pp. S331-S351. DOI: 10.1002/lno.11916.

Romdhane, S., A. Spor, S. Banerjee, et al. (2022). “Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity”. In: Environmental Microbiomes 17.1. DOI: 10.1186/s40793-021-00396-9.

Salmaso, N., V. Vasselon, F. Rimet, et al. (2022). “DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region”. In: Science of the Total Environment 834. DOI: 10.1016/j.scitotenv.2022.155175.

Selak, L., H. Osterholz, I. Stankovic, et al. (2022). “Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake”. In: Environmental Microbiology 24.5, pp. 2282-2298. DOI: 10.1111/1462-2920.15924.

Stefanni, S., L. Mirimin, D. Stankovic, et al. (2022). “Framing cutting-edge integrative deep-sea biodiversity monitoring via environmental DNA and optoacoustic augmented infrastructures”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.797140.

Sun, F., X. Xia, M. Simon, et al. (2022). “Anticyclonic eddy driving significant changes in prokaryotic and eukaryotic communities in the south china sea”. In: Frontiers in Marine Science 9. DOI: 10.3389/fmars.2022.773548.

Sun, P., Y. Liao, Y. Wang, et al. (2022). “Contrasting community composition and co-occurrence relationships of the active pico-sized haptophytes in the surface and subsurface chlorophyll maximum layers of the arctic ocean in summer”. In: Microorganisms 10.2. DOI: 10.3390/microorganisms10020248.

Sun, P., Y. Wang, X. Huang, et al. (2022). “Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities”. In: Water Research 215. DOI: 10.1016/j.watres.2022.118274.

Suter, E., M. Pachiadaki, G. Taylor, et al. (2022). “Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.764605.

Vannoni, M., V. Créach, D. Ryder, et al. (2022). “Resilience of a microphytobenthos community from the Severn Estuary, UK, to chlorination: A mesocosm approach”. In: Marine Pollution Bulletin 176. DOI: 10.1016/j.marpolbul.2022.113443.

Vasar, M., J. Davison, S. Sepp, et al. (2022). “Global soil microbiomes: A new frontline of biome-ecology research”. In: Global Ecology and Biogeography 31.6, pp. 1120-1132. DOI: 10.1111/geb.13487.

Vaulot, D., S. Geisen, F. Mahé, et al. (2022). “pr2-primers: An 18S rRNA primer database for protists”. In: Molecular Ecology Resources 22.1, pp. 168-179. DOI: 10.1111/1755-0998.13465.

Wang, Y., X. Li, Y. Chi, et al. (2022). “Changes of the freshwater microbial community structure and assembly processes during different sample storage conditions”. In: Microorganisms 10.6. DOI: 10.3390/microorganisms10061176.

Wu, B., L. Zhou, S. Liu, et al. (2022). “Biogeography of soil protistan consumer and parasite is contrasting and linked to microbial nutrient mineralization in forest soils at a wide-scale”. In: Soil Biology and Biochemistry 165. DOI: 10.1016/j.soilbio.2021.108513.

Wu, C., Y. Chao, L. Shu, et al. (2022). “Interactions between soil protists and pollutants: An unsolved puzzle”. In: Journal of Hazardous Materials 429. DOI: 10.1016/j.jhazmat.2022.128297.

Xiong, W., M. Delgado-Baquerizo, Q. Shen, et al. (2022). “Pedogenesis shapes predator-prey relationships within soil microbiomes”. In: Science of the Total Environment 828. DOI: 10.1016/j.scitotenv.2022.154405.

Xu, D., H. Kong, E. Yang, et al. (2022). “Spatial dynamics of active microeukaryotes along a latitudinal gradient: Diversity, assembly process, and co-occurrence relationships”. In: Environmental Research 212. DOI: 10.1016/j.envres.2022.113234.

Yin, Y., M. Li, C. Yang, et al. (2022). “Phagotrophic protists can change microbial nitrogen conversion patterns during swine manure composting”. In: Biomass Conversion and Biorefinery. DOI: 10.1007/s13399-022-02318-2.

Yung, C., E. Redondo, F. Sanchez, et al. (2022). “Diversity and evolution of mamiellophyceae: Early-diverging phytoplanktonic green algae containing many cosmopolitan species”. In: Journal of Marine Science and Engineering 10.2. DOI: 10.3390/jmse10020240.

Zafeiropoulos, H., S. Paragkamian, S. Ninidakis, et al. (2022). “PREGO: A literature and data-mining resource to associate microorganisms, biological processes, and environment types”. In: Microorganisms 10.2. DOI: 10.3390/microorganisms10020293.

Zhao, H., Z. Zhang, S. Nair, et al. (2022). “Vertically exported phytoplankton (¡ 20 µm) and their correlation network with bacterioplankton along a deep-sea seamount”. In: Frontiers in Marine Science 9. DOI: 10.3389/fmars.2022.862494.

Zhao, Z., H. Li, Y. Sun, et al. (2022). “How habitat heterogeneity shapes bacterial and protistan communities in temperate coastal areas near estuaries”. In: Environmental Microbiology 24.4, pp. 1775-1789. DOI: 10.1111/1462-2920.15892.

2021

Abdullah Al, M., Y. Xue, P. Xiao, et al. (2021). “DNA metabarcoding reveals the significant influence of anthropogenic effects on microeukaryotic communities in urban waterbodies”. In: Environmental Pollution 285. DOI: 10.1016/j.envpol.2021.117336.

Acinas, S., P. Sánchez, G. Salazar, et al. (2021). “Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities”. In: Communications Biology 4.1. DOI: 10.1038/s42003-021-02112-2.

Armbrecht, L., G. Hallegraeff, C. Bolch, et al. (2021). “Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-82578-6.

Asiloglu, R., K. Shiroishi, K. Suzuki, et al. (2021). “Soil properties have more significant effects on the community composition of protists than the rhizosphere effect of rice plants in alkaline paddy field soils”. In: Soil Biology and Biochemistry 161. DOI: 10.1016/j.soilbio.2021.108397.

Beng, K., J. Wolinska, E. Funke, et al. (2021). “Temporal dynamics of freshwater planktonic parasites inferred using a DNA metabarcoding time-series”. In: Parasitology 148.13, pp. 1602-1611. DOI: 10.1017/S0031182021001293.

Bonfantine, K., S. Trevathan-Tackett, T. Matthews, et al. (2021). “Dumpster diving for diatom plastid 16S rRNA genes”. In: PeerJ 9. DOI: 10.7717/peerj.11576.

Brandt, M., F. Pradillon, B. Trouche, et al. (2021). “Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-86396-8.

Bruhn, C., S. Wohlrab, B. Krock, et al. (2021). “Seasonal plankton succession is in accordance with phycotoxin occurrence in Disko Bay, West Greenland”. In: Harmful Algae 103. DOI: 10.1016/j.hal.2021.101978.

Burki, F., M. Sandin, and M. Jamy (2021). “Diversity and ecology of protists revealed by metabarcoding”. In: Current Biology 31.19, pp. R1267-R1280. DOI: 10.1016/j.cub.2021.07.066.

Canino, A., A. Bouchez, C. Laplace-Treyture, et al. (2021). “Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations”. In: Metabarcoding and Metagenomics 5, pp. 199-205. DOI: 10.3897/mbmg.5.74096.

Capo, E., C. Giguet-Covex, A. Rouillard, et al. (2021). “Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations”. In: Quaternary 4.1. DOI: 10.3390/quat4010006.

Casey, J., E. Ransome, A. Collins, et al. (2021). “DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity”. In: Environmental DNA 3.6, pp. 1229-1246. DOI: 10.1002/edn3.245.

Castagna, A., H. Dierssen, E. Organelli, et al. (2021). “Optical detection of harmful algal blooms in the belgian coastal zone: A cautionary tale of chlorophyll c3”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.770340.

Catlett, D., K. Son, and C. Liang (2021). “EnsembleTax: An R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences”. In: PeerJ 9. DOI: 10.7717/peerj.11865.

Cecchetto, M., A. Di Cesare, E. Eckert, et al. (2021). “Antarctic coastal nanoplankton dynamics revealed by metabarcoding of desalination plant filters: Detection of short-term events and implications for routine monitoring”. In: Science of the Total Environment 757. DOI: 10.1016/j.scitotenv.2020.143809.

Ceja-Navarro, J., Y. Wang, D. Ning, et al. (2021). “Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop”. In: Microbiome 9.1. DOI: 10.1186/s40168-021-01042-9.

Chang, F., J. Yang, A. Liu, et al. (2021). “Community assembly processes as a mechanistic explanation of the predator-prey diversity relationship in marine microbes”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.651565.

Charvet, S., E. Kim, A. Subramaniam, et al. (2021). “Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-95676-2.

Chen, B., W. Xiong, J. Qi, et al. (2021). “Trophic interrelationships drive the biogeography of protistan community in agricultural ecosystems”. In: Soil Biology and Biochemistry 163. DOI: 10.1016/j.soilbio.2021.108445.

Chen, J., L. Dong, X. Ma, et al. (2021). “Microbial community monitoring in baiyangdian lake based on eDNA technology [基于 eDNA 技术的白洋淀微型生物群落盒测]”. In: Journal of Agro-Environment Science 40.9, pp. 1773-1786. DOI: 10.11654/jaes.2021-0632.

Chen, Y., Q. Xu, K. Gibson, et al. (2021). “Metabarcoding dissection of harmful algal bloom species in the East China Sea off Southern Zhejiang Province in late spring”. In: Marine Pollution Bulletin 169. DOI: 10.1016/j.marpolbul.2021.112586.

Choe, Y., M. Kim, and Y. Lee (2021). “Distinct microbial communities in adjacent rock and soil substrates on a high arctic polar desert”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.607396.

Chrismas, N., R. Allen, A. Hollingsworth, et al. (2021). “Complex photobiont diversity in the marine lichen Lichina pygmaea”. In: Journal of the Marine Biological Association of the United Kingdom 101.4, pp. 667-674. DOI: 10.1017/S002531542100062X.

Christaki, U., I. Skouroliakou, A. Delegrange, et al. (2021). “Microzooplankton diversity and potential role in carbon cycling of contrasting Southern Ocean productivity regimes”. In: Journal of Marine Systems 219. DOI: 10.1016/j.jmarsys.2021.103531.

Cohen, N., M. McIlvin, D. Moran, et al. (2021). “Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean”. In: Nature Microbiology 6.2, pp. 173-186. DOI: 10.1038/s41564-020-00814-7.

Cohen, N., A. Noble, D. Moran, et al. (2021). “Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean”. In: Biogeosciences (Online) 18.19, pp. 5397-5422. DOI: 10.5194/bg-18-5397-2021.

Cordier, T., L. Alonso-Sáez, L. Apothéloz-Perret-Gentil, et al. (2021). “Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap”. In: Molecular Ecology 30.13, pp. 2937-2958. DOI: 10.1111/mec.15472.

Cui, Z., Q. Xu, K. Gibson, et al. (2021). “Metabarcoding analysis of harmful algal bloom species in the Changjiang Estuary, China”. In: Science of the Total Environment 782. DOI: 10.1016/j.scitotenv.2021.146823.

D'iaz-Torres, O., J. de Anda, O. Lugo-Melchor, et al. (2021). “Rapid changes in the phytoplankton community of a subtropical, shallow, hypereutrophic lake during the rainy season”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.617151.

Dai, Z., X. Lv, B. Ma, et al. (2021). “Concurrent and rapid recovery of bacteria and protist communities in Canadian boreal forest ecosystems following wildfire”. In: Soil Biology and Biochemistry 163. DOI: 10.1016/j.soilbio.2021.108452.

David, G., D. Moreira, G. Reboul, et al. (2021). “Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake”. In: Environmental Microbiology 23.3, pp. 1436-1451. DOI: 10.1111/1462-2920.15346.

De Mesquita, C., L. Nichols, M. Gebert, et al. (2021). “Structure of chimpanzee gut microbiomes across tropical Africa”. In: mSystems 6.3. DOI: 10.1128/mSystems.01269-20.

Degenhardt, J., S. Khodami, F. Milke, et al. (2021). “The three domains of life within the discharge area of a shallow subterranean estuary at a high energy beach”. In: Frontiers in Environmental Science 9. DOI: 10.3389/fenvs.2021.642098.

Deutschmann, I., G. Lima-Mendez, A. Krabberød, et al. (2021). “Disentangling environmental effects in microbial association networks”. In: Microbiome 9.1. DOI: 10.1186/s40168-021-01141-7.

Di Capua, I., R. Piredda, M. Mazzocchi, et al. (2021). “Metazoan diversity and seasonality through eDNA metabarcoding at a Mediterranean long-term ecological research site”. In: ICES Journal of Marine Science 78.9, pp. 3303-3316. DOI: 10.1093/icesjms/fsab059.

Diner, R., D. Kaul, A. Rabines, et al. (2021). “Pathogenic vibrio species are associated with distinct environmental niches and planktonic taxa in southern california (usa) aquatic microbiomes”. In: mSystems 6.4. DOI: 10.1128/mSystems.00571-21.

Doliwa, A., M. Dunthorn, E. Rassoshanska, et al. (2021). “Identifying potential hosts of short-branch microsporidia”. In: Microbial Ecology 82.2, pp. 549-553. DOI: 10.1007/s00248-020-01657-9.

Dubuffet, A., M. Chauvet, A. Moné, et al. (2021). “A phylogenetic framework to investigate the microsporidian communities through metabarcoding and its application to lake ecosystems”. In: Environmental Microbiology 23.8, pp. 4344-4359. DOI: 10.1111/1462-2920.15618.

Dumack, K. and M. Bonkowski (2021). “Protists in the plant microbiome: an untapped field of research”. In: Methods in Molecular Biology 2232, pp. 77-84. DOI: 10.1007/978-1-0716-1040-4_8.

Egge, E., S. Elferink, D. Vaulot, et al. (2021). “An 18S V4 rRNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000m depth”. In: Earth System Science Data 13.10, pp. 4913-4928. DOI: 10.5194/essd-13-4913-2021.

Fermani, P., S. Metz, V. Balagué, et al. (2021). “Microbial eukaryote assemblages and potential novel diversity in four tropical East African Great Lakes”. In: FEMS Microbiology Ecology 97.9. DOI: 10.1093/femsec/fiab114.

Forster, D., Z. Qu, G. Pitsch, et al. (2021). “Lake ecosystem robustness and resilience inferred from a climate-stressed protistan plankton network”. In: Microorganisms 9.3, pp. 1-20. DOI: 10.3390/microorganisms9030549.

Fournier, I., C. Lovejoy, and W. Vincent (2021). “Changes in the community structure of under-ice and open-water microbiomes in urban lakes exposed to road salts”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.660719.

Francioli, D., G. Lentendu, S. Lewin, et al. (2021). “DNA metabarcoding for the characterization of terrestrial microbiota—pitfalls and solutions”. In: Microorganisms 9.2, pp. 1-29. DOI: 10.3390/microorganisms9020361.

Freyria, N., N. Joli, and C. Lovejoy (2021). “A decadal perspective on north water microbial eukaryotes as Arctic Ocean sentinels”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-87906-4.

Ganser, M., D. Forster, W. Liu, et al. (2021). “Genetic diversity in marine planktonic ciliates (alveolata, ciliophora) suggests distinct geographical patterns data from chinese and european coastal waters”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.643822.

Gauthier, J., D. Walsh, D. Selbie, et al. (2021). “Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36-month time series from a temperate monomictic lake”. In: Limnology and Oceanography 66.8, pp. 3020-3039. DOI: 10.1002/lno.11856.

Genitsaris, S., N. Stefanidou, Y. Beeri-Shlevin, et al. (2021). “Air-dispersed aquatic microorganisms show establishment and growth preferences in different freshwater colonisation habitats”. In: FEMS Microbiology Ecology 97.9. DOI: 10.1093/femsec/fiab122.

Glasner, B., C. Henr'iquez-Castillo, F. Alfaro, et al. (2021). “Decoupling of biotic and abiotic patterns in a coastal area affected by chronic metal micronutrients disturbances”. In: Marine Pollution Bulletin 166. DOI: 10.1016/j.marpolbul.2020.111608.

Gong, X., X. Chen, S. Geisen, et al. (2021). “Agricultural habitats are dominated by rapidly evolving nematodes revealed through phylogenetic comparative methods”. In: Soil Biology and Biochemistry 155. DOI: 10.1016/j.soilbio.2021.108183.

González-Pleiter, M., D. Velázquez, M. Casero, et al. (2021). “Microbial colonizers of microplastics in an Arctic freshwater lake”. In: Science of the Total Environment 795. DOI: 10.1016/j.scitotenv.2021.148640.

Gottschling, M., L. Czech, F. Mahé, et al. (2021). “The windblown: Possible explanations for dinophyte DNA in forest soils”. In: Journal of Eukaryotic Microbiology 68.1. DOI: 10.1111/jeu.12833.

Greco, M., R. Morard, and M. Kucera (2021). “Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community”. In: Journal of Plankton Research 43.2, pp. 113-125. DOI: 10.1093/plankt/fbab015.

Guo, S., W. Xiong, X. Hang, et al. (2021). “Protists as main indicators and determinants of plant performance”. In: Microbiome 9.1. DOI: 10.1186/s40168-021-01025-w.

Hamard, S., R. Céréghino, M. Barret, et al. (2021). “Contribution of microbial photosynthesis to peatland carbon uptake along a latitudinal gradient”. In: Journal of Ecology 109.9, pp. 3424-3441. DOI: 10.1111/1365-2745.13732.

Hamilton, M., M. Mascioni, E. Hehenberger, et al. (2021). “Spatiotemporal variations in antarctic protistan communities highlight phytoplankton diversity and seasonal dominance by a novel cryptophyte lineage”. In: mBio 12.6. DOI: 10.1128/mBio.02973-21.

Herrera, G., L. Vega, M. Patarroyo, et al. (2021). “Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-90380-7.

Hervé, V., J. Lambourdière, M. René-Trouillefou, et al. (2021). “Sargassum differentially shapes the microbiota composition and diversity at coastal tide sites and inland storage sites on caribbean islands”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.701155.

Hii, K., M. Mohd-Din, Z. Luo, et al. (2021). “Diverse harmful microalgal community assemblages in the Johor Strait and the environmental effects on its community dynamics”. In: Harmful Algae 107. DOI: 10.1016/j.hal.2021.102077.

Hilton, S., E. Picot, S. Schreiter, et al. (2021). “Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale”. In: Microbiome 9.1. DOI: 10.1186/s40168-020-00972-0.

Hohlfeld, M., A. Schoenle, and H. Arndt (2021). “Horizontal and vertical small-scale patterns of protist communities at the Atlantic deep-sea floor”. In: Deep-Sea Research Part I: Oceanographic Research Papers 171. DOI: 10.1016/j.dsr.2021.103515.

Hörstmann, C., E. Raes, P. Buttigieg, et al. (2021). “Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean”. In: Biogeosciences (Online) 18.12, pp. 3733-3749. DOI: 10.5194/bg-18-3733-2021.

Hu, S., E. Herrera, A. Smith, et al. (2021). “Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents”. In: Proceedings of the National Academy of Sciences of the United States of America 118.29. DOI: 10.1073/pnas.2102674118.

Huang, H., Q. Xu, K. Gibson, et al. (2021). “Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis”. In: Harmful Algae 106. DOI: 10.1016/j.hal.2021.102066.

Huang, X., J. Wang, K. Dumack, et al. (2021). “Protists modulate fungal community assembly in paddy soils across climatic zones at the continental scale”. In: Soil Biology and Biochemistry 160. DOI: 10.1016/j.soilbio.2021.108358.

Iniesto, M., D. Moreira, G. Reboul, et al. (2021). “Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient”. In: Environmental Microbiology 23.1, pp. 51-68. DOI: 10.1111/1462-2920.15252.

Irion, S., U. Christaki, H. Berthelot, et al. (2021). “Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean”. In: ISME Journal 15.9, pp. 2509-2522. DOI: 10.1038/s41396-021-00915-z.

Izaguirre, I., F. Unrein, M. Schiaffino, et al. (2021). “Phylogenetic diversity and dominant ecological traits of freshwater Antarctic Chrysophyceae”. In: Polar Biology 44.5, pp. 941-957. DOI: 10.1007/s00300-021-02850-3.

Jamieson, T., S. Balzano, C. Le Lan, et al. (2021). “Survival of the fittest: Prokaryotic communities within a SWRO desalination plant”. In: Desalination 514. DOI: 10.1016/j.desal.2021.115152.

Jauss, R., A. Nowack, S. Walden, et al. (2021). “To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies”. In: European Journal of Protistology 80. DOI: 10.1016/j.ejop.2021.125805.

Joglar, V., X. Álvarez-Salgado, A. Gago-Martinez, et al. (2021). “Cobalamin and microbial plankton dynamics along a coastal to offshore transect in the Eastern North Atlantic Ocean”. In: Environmental Microbiology 23.3, pp. 1559-1583. DOI: 10.1111/1462-2920.15367.

Joglar, V., B. Pontiller, S. Mart'inez-Garc'ia, et al. (2021). “Microbial plankton community structure and function responses to vitamin B12and B1Amendments in an upwelling system”. In: Applied and Environmental Microbiology 87.22. DOI: 10.1128/AEM.01525-21.

Käse, L., K. Metfies, A. Kraberg, et al. (2021). “Metabarcoding analysis suggests that flexible food web interactions in the eukaryotic plankton community are more common than specific predator-prey relationships at Helgoland Roads, North Sea”. In: ICES Journal of Marine Science 78.9, pp. 3372-3386. DOI: 10.1093/icesjms/fsab058.

Käse, L., K. Metfies, S. Neuhaus, et al. (2021). “Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?” In: PLoS ONE 16.1 January. DOI: 10.1371/journal.pone.0244817.

Kawachi, M., T. Nakayama, M. Kayama, et al. (2021). “Rappemonads are haptophyte phytoplankton”. In: Current Biology 31.11, pp. 2395-2403.e4. DOI: 10.1016/j.cub.2021.03.012.

Kawamoto, Y., H. Kato, Y. Nagata, et al. (2021). “Microbial communities developing within bulk sediments under fish carcasses on a tidal flat”. In: PLoS ONE 16.2 February. DOI: 10.1371/journal.pone.0247220.

Kobari, T., Y. Tokumo, I. Sato, et al. (2021). “Metabarcoding analysis of trophic sources and linkages in the plankton community of the Kuroshio and neighboring waters”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-02083-8.

Kulaš, A., V. Gulin, R. Matonickin Kepcija, et al. (2021). “Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case”. In: Ecological Indicators 124. DOI: 10.1016/j.ecolind.2021.107430.

Lambert, S., J. Lozano, F. Bouget, et al. (2021). “Seasonal marine microorganisms change neighbours under contrasting environmental conditions”. In: Environmental Microbiology 23.5, pp. 2592-2604. DOI: 10.1111/1462-2920.15482.

Latorre, F., I. Deutschmann, A. Labarre, et al. (2021). “Niche adaptation promoted the evolutionary diversification of tiny ocean predators”. In: Proceedings of the National Academy of Sciences of the United States of America 118.25. DOI: 10.1073/pnas.2020955118.

Lattaud, J., S. Balzano, M. van der Meer, et al. (2021). “Sources and seasonality of long-chain diols in a temperate lake (Lake Geneva)”. In: Organic Geochemistry 156. DOI: 10.1016/j.orggeochem.2021.104223.

Lee, S., D. Lee, H. Kang, et al. (2021). “Analysis of in vitro digestion using human gut microbiota in adult and elderly individuals”. In: Food Chemistry 362. DOI: 10.1016/j.foodchem.2021.130228.

Lejzerowicz, F., A. Gooday, I. Barrenechea Angeles, et al. (2021). “Eukaryotic biodiversity and spatial patterns in the clarion-clipperton zone and other abyssal regions: Insights from sediment DNA and RNA metabarcoding”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.671033.

Lentendu, G. and M. Dunthorn (2021). “Phylogenetic relatedness drives protist assembly in marine and terrestrial environments”. In: Global Ecology and Biogeography 30.7, pp. 1532-1544. DOI: 10.1111/geb.13317.

Li, F., A. Sun, X. Jiao, et al. (2021). “Specific protistan consumers and parasites are responsive to inorganic fertilization in rhizosphere and bulk soils”. In: Journal of Soils and Sediments 21.12, pp. 3801-3812. DOI: 10.1007/s11368-021-03052-4.

Li, F., Y. Zhang, F. Altermatt, et al. (2021). “Consideration of multitrophic biodiversity and ecosystem functions improves indices on river ecological status”. In: Environmental Science and Technology 55.24, pp. 16434-16444. DOI: 10.1021/acs.est.1c05899.

Li, R., C. Hu, J. Wang, et al. (2021). “Biogeographical distribution and community assembly of active protistan assemblages along an estuary to a basin transect of the northern south China sea”. In: Microorganisms 9.2, pp. 1-20. DOI: 10.3390/microorganisms9020351.

Liu, S., M. Zhang, Y. Zhao, et al. (2021). “Biodiversity and spatial-temporal dynamics of margalefidinium species in jiaozhou bay, China”. In: International Journal of Environmental Research and Public Health 18.21. DOI: 10.3390/ijerph182111637.

Liu, X., N. Xie, M. Bai, et al. (2021). “Composition change and decreased diversity of microbial eukaryotes in the coastal upwelling waters of South China Sea”. In: Science of the Total Environment 795. DOI: 10.1016/j.scitotenv.2021.148892.

Ma, Y., Y. Pan, Q. Liu, et al. (2021). “Co-occurrence patterns and assembly processes of microeukaryotic communities in a semi-enclosed aquaculture bay”. In: Continental Shelf Research 228. DOI: 10.1016/j.csr.2021.104550.

Majaneva, M., J. Rintala, and J. Blomster (2021). “Taxonomically and functionally distinct ciliophora assemblages inhabiting baltic sea ice”. In: Microbial Ecology. DOI: 10.1007/s00248-021-01915-4.

Martini, S., F. Larras, A. Boyé, et al. (2021). “Functional trait-based approaches as a common framework for aquatic ecologists”. In: Limnology and Oceanography 66.3, pp. 965-994. DOI: 10.1002/lno.11655.

McLennan, K., R. Ruvindy, M. Ostrowski, et al. (2021). “Assessing the use of molecular barcoding and QPCR for investigating the ecology of prorocentrum minimum (Dinophyceae), a harmful algal species”. In: Microorganisms 9.3, pp. 1-20. DOI: 10.3390/microorganisms9030510.

McNichol, J., P. Berube, S. Biller, et al. (2021). “Evaluating and improving small subunit rrna pcr primer coverage for bacteria, archaea, and eukaryotes using metagenomes from global ocean surveys”. In: mSystems 6.3. DOI: 10.1128/mSystems.00565-21.

Meng, L., H. Endo, R. Blanc-Mathieu, et al. (2021). “Quantitative assessment of nucleocytoplasmic large DNA virus and host interactions predicted by co-occurrence analyses”. In: mSphere 6.2, pp. 1-18. DOI: 10.1128/mSphere.01298-20.

Meredith, C., J. Hoffman, A. Trebitz, et al. (2021). “Evaluating the performance of DNA metabarcoding for assessment of zooplankton communities in Western Lake Superior using multiple markers”. In: Metabarcoding and Metagenomics 5, pp. 83-97. DOI: 10.3897/MBMG.5.64735.

Michealsamy, A., L. Thangamani, G. Manivel, et al. (2021). “Current research and applications of meta-omics stratagems in bioremediation: A bird’s-eye view”. In: Journal of Applied Biotechnology Reports 8.2, pp. 109-115. DOI: 10.30491/jabr.2020.237662.1248.

Mikryukov, V., O. Dulya, G. Likhodeevskii, et al. (2021). “Analysis of ecological networks in multicomponent communities of microorganisms: Possibilities, limitations, and potential errors”. In: Russian Journal of Ecology 52.3, pp. 188-200. DOI: 10.1134/S1067413621030085.

Mo, Y., F. Peng, X. Gao, et al. (2021). “Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir”. In: Microbiome 9.1. DOI: 10.1186/s40168-021-01079-w.

Mthethwa, N., I. Amoah, P. Reddy, et al. (2021). “A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives”. In: Journal of Microbiological Methods 187. DOI: 10.1016/j.mimet.2021.106269.

Neupane, S., C. Saski, and D. Nayduch (2021). “House fly larval grazing alters dairy cattle manure microbial communities”. In: BMC Microbiology 21.1. DOI: 10.1186/s12866-021-02418-5.

Nguyen, B., Q. Chen, Z. Yan, et al. (2021). “Distinct factors drive the diversity and composition of protistan consumers and phototrophs in natural soil ecosystems”. In: Soil Biology and Biochemistry 160. DOI: 10.1016/j.soilbio.2021.108317.

Novotny, A., S. Zamora-Terol, and M. Winder (2021). “DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species”. In: Proceedings of the Royal Society B: Biological Sciences 288.1953. DOI: 10.1098/rspb.2021.0908.

Nowinski, B. and M. Moran (2021). “Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater”. In: Nature Microbiology 6.4, pp. 524-532. DOI: 10.1038/s41564-020-00851-2.

Obertegger, U., M. Pindo, and G. Flaim (2021). “Do inferences about freshwater phytoplankton communities change when based on microscopy or high-throughput sequencing data?” In: Freshwater Biology 66.4, pp. 640-655. DOI: 10.1111/fwb.13667.

Ollison, G., S. Hu, L. Mesrop, et al. (2021). “Come rain or shine: Depth not season shapes the active protistan community at station ALOHA in the North Pacific Subtropical Gyre”. In: Deep-Sea Research Part I: Oceanographic Research Papers 170. DOI: 10.1016/j.dsr.2021.103494.

Pappalardo, P., A. Collins, K. Pagenkopp Lohan, et al. (2021). “The role of taxonomic expertise in interpretation of metabarcoding studies”. In: ICES Journal of Marine Science 78.9, pp. 3397-3410. DOI: 10.1093/icesjms/fsab082.

Pauli, N., K. Metfies, E. Pakhomov, et al. (2021). “Selective feeding in Southern Ocean key grazers—diet composition of krill and salps”. In: Communications Biology 4.1. DOI: 10.1038/s42003-021-02581-5.

Pearman, J., U. von Ammon, O. Laroche, et al. (2021). “Metabarcoding as a tool to enhance marine surveillance of nonindigenous species in tropical harbors: A case study in Tahiti”. In: Environmental DNA 3.1, pp. 173-189. DOI: 10.1002/edn3.154.

Picot, E., C. Hale, S. Hilton, et al. (2021). “Contrasting responses of rhizosphere bacterial, fungal, protist, and nematode communities to nitrogen fertilization and crop genotype in field grown oilseed rape (brassica napus)”. In: Frontiers in Sustainable Food Systems 5. DOI: 10.3389/fsufs.2021.613269.

Ramírez, A., G. Herrera, M. Muñoz, et al. (2021). “Describing the intestinal microbiota of holstein fasciola-positive and-negative cattle from a hyperendemic area of fascioliasis in central colombia”. In: PLoS Neglected Tropical Diseases 15.8. DOI: 10.1371/journal.pntd.0009658.

Ramond, P., R. Siano, S. Schmitt, et al. (2021). “Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-82071-0.

Reñé, A., N. Timoneda, N. Sampedro, et al. (2021). “Host preferences of coexisting Perkinsea parasitoids during coastal dinoflagellate blooms”. In: Molecular Ecology 30.10, pp. 2417-2433. DOI: 10.1111/mec.15895.

Ricci, F., A. Fordyce, W. Leggat, et al. (2021). “Multiple techniques point to oxygenic phototrophs dominating the Isopora palifera skeletal microbiome”. In: Coral reefs (Online) 40.2, pp. 275-282. DOI: 10.1007/s00338-021-02068-z.

Rimet, F., E. Aylagas, A. Borja, et al. (2021). “Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life”. In: Metabarcoding and Metagenomics 5, pp. 17-33. DOI: 10.3897/mbmg.5.58056.

Roshan, S., K. Dumack, M. Bonkowski, et al. (2021). “Taxonomic and functional diversity of heterotrophic protists (Cercozoa and endomyxa) from biological soil crusts”. In: Microorganisms 9.2, pp. 1-14. DOI: 10.3390/microorganisms9020205.

Rüger, L., K. Feng, K. Dumack, et al. (2021). “Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (zea mays L.)”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.614501.

Sakamoto, T. and J. Ortega (2021). “Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree”. In: BMC Bioinformatics 22.1. DOI: 10.1186/s12859-021-04304-3.

Schiwitza, S. and F. Nitsche (2021). “A needle in the haystack mapping sequences to morphology exemplified by the loricate choanoflagellate enibas thessalia sp. nov. (acanthoecida, acanthoecidae)”. In: Protist 172.1. DOI: 10.1016/j.protis.2020.125782.

Schoenle, A., M. Hohlfeld, K. Hermanns, et al. (2021). “High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans”. In: Communications Biology 4.1. DOI: 10.1038/s42003-021-02012-5.

Shemi, A., U. Alcolombri, D. Schatz, et al. (2021). “Dimethyl sulfide mediates microbial predatorprey interactions between zooplankton and algae in the ocean”. In: Nature Microbiology 6.11, pp. 1357-1366. DOI: 10.1038/s41564-021-00971-3.

Shi, J., Y. Lei, H. Li, et al. (2021). “NGS-metabarcoding revealing novel foraminiferal diversity in the Western Pacific Magellan Seamount sediments”. In: Journal of Oceanology and Limnology 39.5, pp. 1718-1729. DOI: 10.1007/s00343-021-0427-0.

Shore, A., R. Day, J. Stewart, et al. (2021). “Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions”. In: Applied and Environmental Microbiology 87.6, pp. 1-18. DOI: 10.1128/AEM.02189-20.

Siano, R., M. Lassudrie, P. Cuzin, et al. (2021). “Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution”. In: Current Biology 31.12, pp. 2682-2689.e7. DOI: 10.1016/j.cub.2021.03.079.

Singer, D., C. Seppey, G. Lentendu, et al. (2021). “Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems”. In: Environment International 146. DOI: 10.1016/j.envint.2020.106262.

Snyder, R., J. Moss, L. Santoferrara, et al. (2021). “Ciliate microzooplankton from the northeastern gulf of mexico”. In: ICES Journal of Marine Science 78.9, pp. 3356-3371. DOI: 10.1093/icesjms/fsab002.

Soler, P., L. Moreno-Mesonero, A. Zornoza, et al. (2021). “Characterization of eukaryotic microbiome and associated bacteria communities in a drinking water treatment plant”. In: Science of the Total Environment 797. DOI: 10.1016/j.scitotenv.2021.149070.

Steven, B., J. LaReau, S. Taerum, et al. (2021). “What’s under the christmas tree? A soil sulfur amendment lowers soil pH and alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits”. In: Microbiology Spectrum 9.1, pp. 1-14. DOI: 10.1128/Spectrum.00166-21.

Sun, A., X. Jiao, Q. Chen, et al. (2021). “Fertilization alters protistan consumers and parasites in crop-associated microbiomes”. In: Environmental Microbiology 23.4, pp. 2169-2183. DOI: 10.1111/1462-2920.15385.

Sun, P., X. Huang, Y. Wang, et al. (2021). “Protistan-bacterial microbiota exhibit stronger species sorting and greater network connectivity offshore than nearshore across a coast-to-basin continuum”. In: mSystems 6.5. DOI: 10.1128/mSystems.00100-21.

Sun, P., S. Zhang, Y. Wang, et al. (2021). “Biogeographic role of the kuroshio current intrusion in the microzooplankton community in the boundary zone of the northern south china sea”. In: Microorganisms 9.5. DOI: 10.3390/microorganisms9051104.

Thioye, B., H. Sanguin, A. Kane, et al. (2021). “Mycorrhizal inoculation increases fruit production without disturbance of native arbuscular mycorrhizal community in jujube tree orchards (Senegal)”. In: Symbiosis (Philadelphia, Pa.) 83.3, pp. 361-372. DOI: 10.1007/s13199-021-00757-5.

Thompson, A. (2021). “Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices”. In: Polar Biology 44.8, pp. 1467-1484. DOI: 10.1007/s00300-021-02896-3.

Thompson, A., A. Roth-monzón, Z. Aanderud, et al. (2021). “Phagotrophic protists and their associates: Evidence for preferential grazing in an abiotically driven soil ecosystem”. In: Microorganisms 9.8. DOI: 10.3390/microorganisms9081555.

Trefault, N., R. De la Iglesia, M. Moreno-Pino, et al. (2021). “Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-020-80568-8.

Vega, L., G. Herrera, M. Munoz, et al. (2021). “Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis”. In: PLoS ONE 16.3 March. DOI: 10.1371/journal.pone.0248185.

Vega, L., J. Jaimes, D. Morales, et al. (2021). “Microbial communities’ characterization in urban recreational surface waters using next generation sequencing”. In: Microbial Ecology 81.4, pp. 847-863. DOI: 10.1007/s00248-020-01649-9.

Vernette, C., N. Henry, J. Lecubin, et al. (2021). “The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms”. In: Molecular Ecology Resources 21.4, pp. 1347-1358. DOI: 10.1111/1755-0998.13322.

Vilne, B., L. Granti-Ievi, J. , et al. (2021). “Investigating bacterial and free-living protozoa diversity in biofilms of hot water pipes of apartment buildings in the city of riga (latvia)”. In: Frontiers in Water 3. DOI: 10.3389/frwa.2021.799840.

Walden, S., R. Jauss, K. Feng, et al. (2021). “On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies”. In: FEMS Microbiology Ecology 97.7. DOI: 10.1093/femsec/fiab081.

Walker, L., T. Hoppe, and M. Silliker (2021). Molecular techniques and current research approaches , pp. 195-229. DOI: 10.1016/B978-0-12-824281-0.00006-3.

Wang, C., A. Masoudi, M. Wang, et al. (2021). “Land-use types shape soil microbial compositions under rapid urbanization in the Xiong’an New Area, China”. In: Science of the Total Environment 777. DOI: 10.1016/j.scitotenv.2021.145976.

Wang, C., W. Zhu, P. Strong, et al. (2021). “Disentangling the effects of physicochemical, genetic, and microbial properties on phase-driven resistome dynamics during multiple manure composting processes”. In: Environmental Science and Technology 55.21, pp. 14732-14745. DOI: 10.1021/acs.est.1c03933.

Wang, K., Y. Huang, M. Majaneva, et al. (2021). “Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution”. In: Nature Communications 12.1. DOI: 10.1038/s41467-020-20187-z.

Wilms, S. (2021). “A beginner’s guide on integrating *Omics approaches to study marine microbial communities: Details and discussions from sample collection to bioinformatics analysis”. In: Frontiers in Marine Science 8. DOI: 10.3389/fmars.2021.692538.

Xiong, W., A. Jousset, R. Li, et al. (2021). “A global overview of the trophic structure within microbiomes across ecosystems”. In: Environment International 151. DOI: 10.1016/j.envint.2021.106438.

Xu, Q., C. Wang, K. Xu, et al. (2021). “Metabarcoding analysis of harmful algal bloom species in the western pacific seamount regions”. In: International Journal of Environmental Research and Public Health 18.21. DOI: 10.3390/ijerph182111470.

Yang, J., J. Lv, Q. Liu, et al. (2021). “Seasonal and spatial patterns of eukaryotic phytoplankton communities in an urban river based on marker gene”. In: Scientific Reports 11.1. DOI: 10.1038/s41598-021-02183-5.

Yap, W., A. Switzer, C. Gouramanis, et al. (2021). “Environmental DNA signatures distinguish between tsunami and storm deposition in overwash sand”. In: Communications Earth and Environment 2.1. DOI: 10.1038/s43247-021-00199-3.

Yeh, Y., J. McNichol, D. Needham, et al. (2021). “Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S”. In: Environmental Microbiology 23.6, pp. 3240-3250. DOI: 10.1111/1462-2920.15553.

Zamora-Terol, S., A. Novotny, and M. Winder (2021). “Molecular evidence of host-parasite interactions between zooplankton and Syndiniales”. In: Aquatic Ecology 55.1, pp. 125-134. DOI: 10.1007/s10452-020-09816-3.

Zhang, J., P. Xing, M. Niu, et al. (2021). “Taxonomic compositions and co-occurrence relationships of protists in bulk soil and rhizosphere of soybean fields in different regions of china”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.738129.

Zhang, L., S. Xu, Z. Zhao, et al. (2021). “Precision of eDNA metabarcoding technology for biodiversity monitoring of eukaryotic phytoplankton in lakes [环境DNA宏条形码盒测湖泊真核浮游植物的精准性]”. In: Huanjing Kexue/Environmental Science 42.2, pp. 796-807. DOI: 10.13227/j.hjkx.202007236.

Zhang, S., X. Xia, Y. Ke, et al. (2021). “Population dynamics and interactions of Noctiluca scintillans and Mesodinium rubrum during their successive blooms in a subtropical coastal water”. In: Science of the Total Environment 755. DOI: 10.1016/j.scitotenv.2020.142349.

Zhang, Y., N. Huang, M. Wang, et al. (2021). “Microbial eukaryotes associated with sediments in deep-sea cold seeps”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.782004.

Zhao, F., S. Filker, C. Wang, et al. (2021). “Bathymetric gradient shapes the community composition rather than the species richness of deep-sea benthic ciliates”. In: Science of the Total Environment 755. DOI: 10.1016/j.scitotenv.2020.142623.

Zhao, F., Y. Wang, S. Zheng, et al. (2021). “Patterns and drivers of microeukaryotic distribution along the North Equatorial Current from the Central Pacific Ocean to the South China Sea”. In: Marine Pollution Bulletin 165. DOI: 10.1016/j.marpolbul.2021.112091.

Zheng, X., K. Zhang, T. Yang, et al. (2021). “Sediment resuspension drives protist metacommunity structure and assembly in grass carp (Ctenopharyngodon idella) aquaculture ponds”. In: Science of the Total Environment 764. DOI: 10.1016/j.scitotenv.2020.142840.

Zhou, Y., B. Sun, B. Xie, et al. (2021). “Warming reshaped the microbial hierarchical interactions”. In: Global Change Biology 27.24, pp. 6331-6347. DOI: 10.1111/gcb.15891.

Zou, K., R. Wang, S. Xu, et al. (2021). “Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence”. In: Water Research 200. DOI: 10.1016/j.watres.2021.117294.

2020

Živaljić, S., A. Scherwass, A. Schoenle, et al. (2020). “A barotolerant ciliate isolated from the abyssal deep sea of the North Atlantic: Euplotes dominicanus sp. n. (Ciliophora, Euplotia)”. In: European Journal of Protistology 73. DOI: 10.1016/j.ejop.2019.125664.

Abdala Asbun, A., M. Besseling, S. Balzano, et al. (2020). “Cascabel: A scalable and versatile amplicon sequence data analysis pipeline delivering reproducible and documented results”. In: Frontiers in Genetics 11. DOI: 10.3389/fgene.2020.489357.

Allen, R., T. Summerfield, K. Currie, et al. (2020). “Distinct processes structure bacterioplankton and protist communities across an oceanic front”. In: Aquatic Microbial Ecology 85, pp. 19-34. DOI: 10.3354/AME01938.

Alric, B., C. ter Braak, Y. Desdevises, et al. (2020). “Investigating microbial associations from sequencing survey data with co-correspondence analysis”. In: Molecular Ecology Resources 20.2, pp. 468-480. DOI: 10.1111/1755-0998.13126.

Ammon, U. von, A. Jeffs, A. Zaiko, et al. (2020). “A portable cruising speed net: Expanding global collection of sea surface plankton data”. In: Frontiers in Marine Science 7. DOI: 10.3389/fmars.2020.615458.

Anderson, S. and E. Harvey (2020). “Temporal variability and ecological interactions of parasitic marine syndiniales in coastal protist communities”. In: mSphere 5.3. DOI: 10.1128/mSphere.00209-20.

Annenkova, N., C. Giner, and R. Logares (2020). “Tracing the origin of planktonic protists in an ancient lake”. In: Microorganisms 8.4. DOI: 10.3390/microorganisms8040543.

Armbrecht, L. (2020). “The potential of sedimentary ancient DNA to reconstruct past ocean ecosystems”. In: Oceanography 33.2, pp. 116-123. DOI: 10.5670/oceanog.2020.211.

Arsenieff, L., F. Le Gall, F. Rigaut-Jalabert, et al. (2020). “Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel”. In: ISME Journal 14.8, pp. 1966-1981. DOI: 10.1038/s41396-020-0659-6.

Atienza, S., M. Guardiola, K. Præbel, et al. (2020). “DNA metabarcoding of deep-sea sediment communities using COI: Community assessment, spatio-temporal patterns and comparison with 18S rDNA”. In: Diversity 12.4. DOI: 10.3390/D12040123.

Barrenechea Angeles, I., F. Lejzerowicz, T. Cordier, et al. (2020). “Planktonic foraminifera eDNA signature deposited on the seafloor remains preserved after burial in marine sediments”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-77179-8.

Bastida, F., D. Eldridge, S. Abades, et al. (2020). “Climatic vulnerabilities and ecological preferences of soil invertebrates across biomes”. In: Molecular Ecology 29.4, pp. 752-761. DOI: 10.1111/mec.15299.

Beam, J., S. George, N. Record, et al. (2020). “Mud, microbes, and macrofauna: Seasonal dynamics of the iron biogeochemical cycle in an intertidal mudflat”. In: Frontiers in Marine Science 7. DOI: 10.3389/fmars.2020.562617.

Bird, C., M. Schweizer, A. Roberts, et al. (2020). “The genetic diversity, morphology, biogeography, and taxonomic designations of Ammonia (Foraminifera) in the Northeast Atlantic”. In: Marine Micropaleontology 155. DOI: 10.1016/j.marmicro.2019.02.001.

Botnen, S., E. Thoen, P. Eidesen, et al. (2020). “Community composition of arctic root-associated fungi mirrors host plant phylogeny”. In: FEMS Microbiology Ecology 96.11. DOI: 10.1093/femsec/fiaa185.

Busseni, G., L. Caputi, R. Piredda, et al. (2020). “Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean”. In: Global Ecology and Biogeography 29.11, pp. 1915-1928. DOI: 10.1111/geb.13161.

Cai, R., E. Kayal, C. Alves-de-Souza, et al. (2020). “Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-59524-z.

Canals, O., A. Obiol, I. Muhovic, et al. (2020). “Ciliate diversity and distribution across horizontal and vertical scales in the open ocean”. In: Molecular Ecology 29.15, pp. 2824-2839. DOI: 10.1111/mec.15528.

Carley, L., R. Panchagavi, X. Song, et al. (2020). “Long-term effects of copper nanopesticides on soil and sediment community diversity in two outdoor mesocosm experiments”. In: Environmental Science and Technology 54.14, pp. 8878-8889. DOI: 10.1021/acs.est.0c00510.

Catlett, D., P. Matson, C. Carlson, et al. (2020). “Evaluation of accuracy and precision in an amplicon sequencing workflow for marine protist communities”. In: Limnology and Oceanography: Methods 18.1, pp. 20-40. DOI: 10.1002/lom3.10343.

Clark, D., C. Pilditch, J. Pearman, et al. (2020). “Environmental DNA metabarcoding reveals estuarine benthic community response to nutrient enrichment Evidence from an in-situ experiment”. In: Environmental Pollution 267. DOI: 10.1016/j.envpol.2020.115472.

Clarke, L. and B. Deagle (2020). “Eukaryote plankton assemblages in the southern Kerguelen Axis region: Ecological drivers differ between size fractions”. In: Deep-Sea Research Part II: Topical Studies in Oceanography 174, p. 104538. DOI: 10.1016/j.dsr2.2018.12.003.

Clerissi, C., L. Guillou, J. Escoubas, et al. (2020). “Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers”. In: BMC Microbiology 20.1. DOI: 10.1186/s12866-020-01860-1.

Cruaud, P., A. Vigneron, C. Dorea, et al. (2020). “Rapid changes in microbial community structures along a meandering river”. In: Microorganisms 8.11, pp. 1-21. DOI: 10.3390/microorganisms8111631.

De La Iglesia, R., I. Echenique-Subiabre, S. Rodr'iguez-Marconi, et al. (2020). “Distinct oxygen environments shape picoeukaryote assemblages thriving oxygen minimum zone waters off central Chile”. In: Journal of Plankton Research 42.5, pp. 514-529. DOI: 10.1093/plankt/fbaa036.

Delgado-Baquerizo, M., P. Reich, C. Trivedi, et al. (2020). “Multiple elements of soil biodiversity drive ecosystem functions across biomes”. In: Nature Ecology and Evolution 4.2, pp. 210-220. DOI: 10.1038/s41559-019-1084-y.

Deng, L., D. Bölsterli, E. Kristensen, et al. (2020). “Macrofaunal control of microbial community structure in continental margin sediments”. In: Proceedings of the National Academy of Sciences of the United States of America 117.27, pp. 15911-15922. DOI: 10.1073/pnas.1917494117.

der Reis, A. van, A. Jeffs, and S. Lavery (2020). “From feeding habits to food webs: Exploring the diet of an opportunistic benthic generalist”. In: Marine Ecology Progress Series, pp. 107-121. DOI: 10.3354/meps13511.

Djemiel, C., D. Plassard, S. Terrat, et al. (2020). “µgreen-db: A reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-62555-1.

Dudek, K., B. Cruz, B. Polidoro, et al. (2020). “Microbial colonization of microplastics in the Caribbean Sea”. In: Limnology And Oceanography Letters 5.1, pp. 5-17. DOI: 10.1002/lol2.10141.

Duret, M., R. Lampitt, and P. Lam (2020). “Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles”. In: Limnology and Oceanography 65.S1, pp. S49-S70. DOI: 10.1002/lno.11319.

Fawley, M. and K. Fawley (2020). “Identification of eukaryotic microalgal strains”. In: Journal of Applied Phycology 32.5, pp. 2699-2709. DOI: 10.1007/s10811-020-02190-5.

Finkel, Z., Y. Liang, D. Nanjappa, et al. (2020). “A ribosomal sequence-based oil sensitivity index for phytoplankton groups”. In: Marine Pollution Bulletin 151. DOI: 10.1016/j.marpolbul.2019.110798.

Fiore-Donno, A., T. Richter-Heitmann, and M. Bonkowski (2020). “Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.01823.

Flegontova, O., P. Flegontov, P. Londoño, et al. (2020). “Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans”. In: Environmental Microbiology 22.9, pp. 4014-4031. DOI: 10.1111/1462-2920.15190.

Fu, Y., P. Zheng, X. Zhang, et al. (2020). “Protist interactions and seasonal dynamics in the coast of yantai, northern yellow sea of china as revealed by metabarcoding”. In: Journal of Ocean University of China 19.4, pp. 961-974. DOI: 10.1007/s11802-020-4461-x.

Gad, M., L. Hou, J. Li, et al. (2020). “Distinct mechanisms underlying the assembly of microeukaryotic generalists and specialists in an anthropogenically impacted river”. In: Science of the Total Environment 748. DOI: 10.1016/j.scitotenv.2020.141434.

Gaonkar, C., R. Piredda, D. Sarno, et al. (2020). “Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity”. In: Environmental Microbiology 22.5, pp. 1917-1929. DOI: 10.1111/1462-2920.14984.

Garc'ia-Gómez, C., L. Yebra, D. Cortés, et al. (2020). “Shifts in the protist community associated with an anticyclonic gyre in the Alboran Sea (Mediterranean Sea)”. In: FEMS Microbiology Ecology 96.11. DOI: 10.1093/femsec/fiaa197.

Genitsaris, S., N. Stefanidou, M. Moustaka-Gouni, et al. (2020). “Variability and community composition of marine unicellular eukaryote assemblages in a eutrophic mediterranean urban coastal area with marked plankton blooms and red tides”. In: Diversity 12.3. DOI: 10.3390/d12030114.

Giner, C., M. Pernice, V. Balagué, et al. (2020). “Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean”. In: ISME Journal 14.2, pp. 437-449. DOI: 10.1038/s41396-019-0506-9.

Gu, R., P. Sun, Y. Wang, et al. (2020). “Genetic diversity, community assembly, and shaping factors of benthic microbial eukaryotes in dongshan bay, southeast china”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.592489.

Guo, X., L. Wu, and L. Huang (2020). “Spatiotemporal patterns in diversity and assembly process of marine protist communities of the changjiang (yangtze river) plume and its adjacent waters”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.579290.

Harakeh, S., E. Angelakis, T. Karamitros, et al. (2020). “Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study”. In: PLoS ONE 15.4. DOI: 10.1371/journal.pone.0230895.

Harkes, P., J. van Steenbrugge, S. van den Elsen, et al. (2020). “Shifts in the active rhizobiome paralleling low meloidogyne chitwoodi densities in fields under prolonged organic soil management”. In: Frontiers in Plant Science 10. DOI: 10.3389/fpls.2019.01697.

Helfer, V. and C. Hassenrück (2020). Microbial communities in mangrove sediments , pp. 141-175. DOI: 10.1016/B978-0-12-816437-2.00003-3.

Hernández-Ruiz, M., E. Barber-Lluch, A. Prieto, et al. (2020). “Response of pico-nano-eukaryotes to inorganic and organic nutrient additions”. In: Estuarine, Coastal and Shelf Science 235. DOI: 10.1016/j.ecss.2019.106565.

Hervé, V. and P. Lopez (2020). “Analysis of interdomain taxonomic patterns in urban street mats”. In: Environmental Microbiology 22.4, pp. 1280-1293. DOI: 10.1111/1462-2920.14933.

Hirose, Y., T. Shiozaki, I. Hamano, et al. (2020). “A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform”. In: DNA Research 27.4. DOI: 10.1093/dnares/dsaa017.

Hirose, Y., T. Shiozaki, M. Otani, et al. (2020). “Investigating algal communities in lacustrine and hydro-terrestrial environments of East Antarctica using deep amplicon sequencing”. In: Microorganisms 8.4. DOI: 10.3390/microorganisms8040497.

Hupfauf, S., M. Etemadi, M. Juárez, et al. (2020). “CoMA an intuitive and user-friendly pipeline for amplicon-sequencing data analysis”. In: PLoS ONE 15.12 December. DOI: 10.1371/journal.pone.0243241.

Irion, S., L. Jardillier, I. Sassenhagen, et al. (2020). “Marked spatiotemporal variations in small phytoplankton structure in contrasted waters of the Southern Ocean (Kerguelen area)”. In: Limnology and Oceanography 65.11, pp. 2835-2852. DOI: 10.1002/lno.11555.

Jauss, R., S. Walden, A. Fiore-Donno, et al. (2020). “From forest soil to the canopy: Increased habitat diversity does not increase species richness of cercozoa and oomycota in tree canopies”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.592189.

Jiang, Y., L. Luan, K. Hu, et al. (2020). “Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences”. In: Microbiome 8.1. DOI: 10.1186/s40168-020-00918-6.

Jin, S., K. Kim, M. Kim, et al. (2020). “An assessment of the taxonomic reliability of dna barcode sequences in publicly available databases”. In: Algae (Korean Phycological Society) 35.3, pp. 293-301. DOI: 10.4490/algae.2020.35.9.4.

Joglar, V., A. Prieto, E. Barber-Lluch, et al. (2020). “Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system”. In: Biogeosciences (Online) 17.10, pp. 2807-2823. DOI: 10.5194/bg-17-2807-2020.

Kase, L., A. Kraberg, K. Metfies, et al. (2020). “Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea”. In: Journal of Plankton Research 42.3, pp. 305-319. DOI: 10.1093/plankt/fbaa017.

Keck, F., L. Millet, D. Debroas, et al. (2020). “Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA”. In: Nature Communications 11.1. DOI: 10.1038/s41467-020-17682-8.

Klimek, B., M. Jazwa, M. Golebiewski, et al. (2020). “No apparent effect of invasive alien goldenrod on soil microbial communities or soil fauna feeding activity”. In: Acta Oecologica 109. DOI: 10.1016/j.actao.2020.103669.

Kling, J., M. Lee, F. Fu, et al. (2020). “Transient exposure to novel high temperatures reshapes coastal phytoplankton communities”. In: ISME Journal 14.2, pp. 413-424. DOI: 10.1038/s41396-019-0525-6.

Kolisko, M., O. Flegontova, A. Karnkowska, et al. (2020). “EukRef-excavates: Seven curated SSU ribosomal RNA gene databases”. In: Database-the Magazine of Electronic Database Reviews 2020. DOI: 10.1093/database/baaa080.

Labarre, A., A. Obiol, S. Wilken, et al. (2020). “Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates”. In: Limnology and Oceanography 65.S1, pp. S149-S160. DOI: 10.1002/lno.11379.

Leconte, J., L. Benites, T. Vannier, et al. (2020). “Genome resolved biogeography of mamiellales”. In: Genes 11.1. DOI: 10.3390/genes11010066.

Li, F., F. Altermatt, J. Yang, et al. (2020). “Human activities’ fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China”. In: Global Change Biology 26.12, pp. 6867-6879. DOI: 10.1111/gcb.15357.

Li, Q., Y. Lei, R. Morard, et al. (2020). “Diversity hotspot and unique community structure of foraminifera in the world’s deepest marine blue hole Sansha Yongle Blue Hole”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-67221-0.

Logares, R., I. Deutschmann, P. Junger, et al. (2020). “Disentangling the mechanisms shaping the surface ocean microbiota”. In: Microbiome 8.1. DOI: 10.1186/s40168-020-00827-8.

Lohan, K., R. DiMaria, D. Martin, et al. (2020). “Diversity and microhabitat associations of labyrinthula spp. In the indian river lagoon system”. In: Diseases of Aquatic Organisms 137.2, pp. 145-157. DOI: 10.3354/dao03431.

Luan, L., Y. Jiang, M. Cheng, et al. (2020). “Organism body size structures the soil microbial and nematode community assembly at a continental and global scale”. In: Nature Communications 11.1. DOI: 10.1038/s41467-020-20271-4.

Mars Brisbin, M., O. Brunner, M. Grossmann, et al. (2020). “Paired high-throughput, in situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution”. In: Limnology and Oceanography 65.12, pp. 2953-2965. DOI: 10.1002/lno.11567.

Mars Brisbin, M., A. Conover, and S. Mitarai (2020). “Influence of regional oceanography and hydrothermal activity on protist diversity and community structure in the okinawa trough”. In: Microbial Ecology 80.4, pp. 746-761. DOI: 10.1007/s00248-020-01583-w.

Metegnier, G., S. Paulino, P. Ramond, et al. (2020). “Species specific gene expression dynamics during harmful algal blooms”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-63326-8.

Michaud, C., V. Hervé, S. Dupont, et al. (2020). “Efficient but occasionally imperfect vertical transmission of gut mutualistic protists in a wood-feeding termite”. In: Molecular Ecology 29.2, pp. 308-324. DOI: 10.1111/mec.15322.

Minerovic, A., M. Potapova, C. Sales, et al. (2020). “18S-V9 DNA metabarcoding detects the effect of water-quality impairment on stream biofilm eukaryotic assemblages”. In: Ecological Indicators 113. DOI: 10.1016/j.ecolind.2020.106225.

Moccia, K., S. Papoulis, A. Willems, et al. (2020). “Using the Microbiome Amplification Preference Tool (MAPT) to reveal medicago sativa-associated eukaryotic microbes”. In: Phytobiomes Journal 4.4, pp. 340-350. DOI: 10.1094/PBIOMES-02-20-0022-R.

Mukherjee, I., M. Salcher, A. Andrei, et al. (2020). “A freshwater radiation of diplonemids”. In: Environmental Microbiology 22.11, pp. 4658-4668. DOI: 10.1111/1462-2920.15209.

Nguyen, B., Q. Chen, J. He, et al. (2020). “Oxytetracycline and ciprofloxacin exposure altered the composition of protistan consumers in an agricultural soil”. In: Environmental Science and Technology 54.15, pp. 9556-9563. DOI: 10.1021/acs.est.0c02531.

Obiol, A., C. Giner, P. Sánchez, et al. (2020). “A metagenomic assessment of microbial eukaryotic diversity in the global ocean”. In: Molecular Ecology Resources 20.3, pp. 718-731. DOI: 10.1111/1755-0998.13147.

Oliverio, A., S. Geisen, M. Delgado-Baquerizo, et al. (2020). “The global-scale distributions of soil protists and their contributions to belowground systems”. In: Science Advances 6.4. DOI: 10.1126/sciadv.aax8787.

Pan, Y., J. Yang, G. McManus, et al. (2020). “Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales”. In: Limnology and Oceanography 65.5, pp. 1103-1115. DOI: 10.1002/lno.11375.

Pearman, J., L. Biessy, G. Thomson-Laing, et al. (2020). “Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient”. In: FEMS Microbiology Ecology 96.6. DOI: 10.1093/femsec/fiaa070.

Pereira, T., A. De Santiago, T. Schuelke, et al. (2020). “The impact of intragenomic rRNA variation on metabarcoding-derived diversity estimates: A case study from marine nematodes”. In: Environmental DNA 2.4, pp. 519-534. DOI: 10.1002/edn3.77.

Pinseel, E., S. Janssens, E. Verleyen, et al. (2020). “Global radiation in a rare biosphere soil diatom”. In: Nature Communications 11.1. DOI: 10.1038/s41467-020-16181-0.

Piwosz, K., T. Shabarova, J. Pernthaler, et al. (2020). “Bacterial and eukaryotic small-subunit amplicon data do not provide a quantitative picture of microbial communities, but they are reliable in the context of ecological interpretations”. In: mSphere 5.2. DOI: 10.1128/MSPHERE.00052-20.

Porter, T. and M. Hajibabaei (2020). “Putting COI metabarcoding in context: The utility of exact sequence variants (ESVs) in biodiversity analysis”. In: Frontiers in Ecology and Evolution 8. DOI: 10.3389/fevo.2020.00248.

Preston, C., C. Durkin, and K. Yamahara (2020). “DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean”. In: Deep-Sea Research Part II: Topical Studies in Oceanography 173. DOI: 10.1016/j.dsr2.2019.104708.

Qingxia, L., L. Yanli, and L. Tiegang (2020). “A preliminary study on the dna molecular diversity and community composition of deep-sea benthic foraminifera from the northwest pacific ocean”. In: Quaternary Sciences 40.3, pp. 825-836. DOI: 10.11928/j.issn.1001-7410.2020.03.19.

Reczuga, M., C. Seppey, M. Mulot, et al. (2020). “Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing”. In: PeerJ 8. DOI: 10.7717/peerj.9821.

Ribeiro, C., A. dos Santos, I. Probert, et al. (2020). “Taxonomic reassignment of Pseudohaptolina birgeri comb. nov. (Haptophyta)”. In: Phycologia 59.6, pp. 606-615. DOI: 10.1080/00318884.2020.1830255.

Rodr'iguez-Mart'inez, R., G. Leonard, D. Milner, et al. (2020). “Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink”. In: ISME Journal 14.4, pp. 984-998. DOI: 10.1038/s41396-019-0581-y.

Rossmann, M., J. Pérez-Jaramillo, V. Kavamura, et al. (2020). “Multitrophic interactions in the rhizosphere microbiome of wheat: From bacteria and fungi to protists”. In: FEMS Microbiology Ecology 96.4. DOI: 10.1093/femsec/fiaa032.

Rusiñol, M., S. Mart'inez-Puchol, N. Timoneda, et al. (2020). “Metagenomic analysis of viruses, bacteria and protozoa in irrigation water”. In: International Journal of Hygiene and Environmental Health 224. DOI: 10.1016/j.ijheh.2019.113440.

Sachs, M., R. Schluckebier, K. Poll, et al. (2020). “Evidence of batrachochytrium dendrobatidis and other amphibian parasites in the green toad (Bufotes viridis), syntopic amphibians and environment in the Cologne Bay, Germany”. In: Salamandra 56.3, pp. 275-284.

Salmaso, N., A. Boscaini, and M. Pindo (2020). “Unraveling the diversity of eukaryotic microplankton in a large and deep perialpine lake using a high throughput sequencing approach”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.00789.

Santoferrara, L., F. Burki, S. Filker, et al. (2020). “Perspectives from ten years of protist studies by high-throughput metabarcoding”. In: Journal of Eukaryotic Microbiology 67.5, pp. 612-622. DOI: 10.1111/jeu.12813.

Santos, S., A. Schöler, T. Nielsen, et al. (2020). “Land use as a driver for protist community structure in soils under agricultural use across Europe”. In: Science of the Total Environment 717. DOI: 10.1016/j.scitotenv.2020.137228.

Sassenhagen, I., S. Irion, L. Jardillier, et al. (2020). “Protist interactions and community structure during early autumn in the kerguelen region (southern ocean)”. In: Protist 171.1. DOI: 10.1016/j.protis.2019.125709.

Schoenle, A., M. Hohlfeld, M. Rosse, et al. (2020). “Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae”. In: European Journal of Protistology 73. DOI: 10.1016/j.ejop.2019.125665.

Seppey, C., O. Broennimann, A. Buri, et al. (2020). “Soil protist diversity in the Swiss western Alps is better predicted by topo-climatic than by edaphic variables”. In: Journal of Biogeography 47.4, pp. 866-878. DOI: 10.1111/jbi.13755.

Shi, J., Y. Lei, Q. Li, et al. (2020). “Molecular diversity and spatial distribution of benthic foraminifera of the seamounts and adjacent abyssal plains in the tropical Western Pacific Ocean”. In: Marine Micropaleontology 156. DOI: 10.1016/j.marmicro.2020.101850.

Simonin, M., C. Dasilva, V. Terzi, et al. (2020). “Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils”. In: FEMS Microbiology Ecology 96.6. DOI: 10.1093/femsec/fiaa067.

Sow, S., T. Trull, and L. Bodrossy (2020). “Oceanographic fronts shape phaeocystis assemblages: A high-resolution 18S rRNA gene survey from the ice-edge to the equator of the south pacific”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.01847.

Sprong, P., V. Fofonova, K. Wiltshire, et al. (2020). “Spatial dynamics of eukaryotic microbial communities in the German Bight”. In: Journal of Sea Research 163. DOI: 10.1016/j.seares.2020.101914.

Suleiman, A., K. Lourenço, C. Clark, et al. (2020). “From toilet to agriculture: Fertilization with microalgal biomass from wastewater impacts the soil and rhizosphere active microbiomes, greenhouse gas emissions and plant growth”. In: Resources, Conservation and Recycling 161. DOI: 10.1016/j.resconrec.2020.104924.

Sun, P., Y. Wang, E. Laws, et al. (2020). “Water massdriven spatial effects and environmental heterogeneity shape microeukaryote biogeography in a subtropical, hydrographically complex ocean system - A case study of ciliates”. In: Science of the Total Environment 706. DOI: 10.1016/j.scitotenv.2019.135753.

Sunagawa, S., S. Acinas, P. Bork, et al. (2020). “Tara Oceans: towards global ocean ecosystems biology”. In: Nature Reviews Microbiology 18.8, pp. 428-445. DOI: 10.1038/s41579-020-0364-5.

Taerum, S., B. Steven, D. Gage, et al. (2020). “Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies”. In: Phytobiomes Journal 4.4, pp. 291-302. DOI: 10.1094/PBIOMES-05-20-0040-TA.

Thompson, A., S. Geisen, and B. Adams (2020). “Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem”. In: Environmental Microbiology 22.11, pp. 4620-4632. DOI: 10.1111/1462-2920.15198.

Tian, H., J. Feng, L. Zhang, et al. (2020). “Ecological drivers of methanotrophic communities in paddy soils around mercury mining areas”. In: Science of the Total Environment 721. DOI: 10.1016/j.scitotenv.2020.137760.

Tkacz, A., E. Bestion, Z. Bo, et al. (2020). “Influence of plant fraction, soil, and plant species on microbiota: A multikingdom comparison”. In: mBio 11.1. DOI: 10.1128/mBio.02785-19.

Velasco-González, I., A. Sanchez-Jimenez, D. Singer, et al. (2020). “Rain-fed granite rock basins accumulate a high diversity of dormant microbial eukaryotes”. In: Microbial Ecology 79.4, pp. 882-897. DOI: 10.1007/s00248-019-01463-y.

Wang, W., K. Ren, H. Chen, et al. (2020). “Seven-year dynamics of testate amoeba communities driven more by stochastic than deterministic processes in two subtropical reservoirs”. In: Water Research 185. DOI: 10.1016/j.watres.2020.116232.

Wang, X., J. Long, J. Li, et al. (2020). “Diversity of soil eukaryotic microbes in different succession stages in maolan karst forest of guizhou [贵州茂兰喀斯特森林不同演替下土壤真核微生物多样性]”. In: Huanjing Kexue/Environmental Science 41.9, pp. 4314-4321. DOI: 10.13227/j.hjkx.202001010.

Wang, Y., X. Hu, Y. Sun, et al. (2020). “Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer”. In: Science of the Total Environment. DOI: 10.1016/j.scitotenv.2020.143496.

Wang, Y., G. Li, F. Shi, et al. (2020). “Taxonomic diversity of pico-/nanoeukaryotes is related to dissolved oxygen and productivity, but functional composition is shaped by limiting nutrients in eutrophic coastal oceans”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.601037.

Wang, Z., X. Gong, Y. Zheng, et al. (2020). “Soil protist communities in burrowing and casting hotspots of different earthworm species”. In: Soil Biology and Biochemistry 144. DOI: 10.1016/j.soilbio.2020.107774.

Wideman, J., A. Monier, R. Rodr'iguez-Mart'inez, et al. (2020). “Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists”. In: Nature Microbiology 5.1, pp. 154-165. DOI: 10.1038/s41564-019-0605-4.

Xiong, W., X. Huang, Y. Chen, et al. (2020). “Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review”. In: Environmental Science and Ecotechnology 1. DOI: 10.1016/j.ese.2019.100008.

Xiong, W., Y. Song, K. Yang, et al. (2020). “Rhizosphere protists are key determinants of plant health”. In: Microbiome 8.1. DOI: 10.1186/s40168-020-00799-9.

Xu, D., H. Kong, E. Yang, et al. (2020). “Contrasting community composition of active microbial eukaryotes in melt ponds and sea water of the arctic ocean revealed by high throughput sequencing”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.01170.

Xu, Z., Y. Li, Y. Lu, et al. (2020). “Impacts of the Zhe-Min Coastal Current on the biogeographic pattern of microbial eukaryotic communities”. In: Progress in Oceanography 183. DOI: 10.1016/j.pocean.2020.102309.

Yeh, H., J. Questel, K. Maas, et al. (2020). “Metabarcoding analysis of regional variation in gut contents of the copepod Calanus finmarchicus in the North Atlantic Ocean”. In: Deep-Sea Research Part II: Topical Studies in Oceanography 180. DOI: 10.1016/j.dsr2.2020.104738.

Zaiko, A., S. Wood, X. Pochon, et al. (2020). “Elucidating biodiversity shifts in ballast water tanks during a cross-latitudinal transfer: Complementary insights from molecular analyses”. In: Environmental Science and Technology 54.13, pp. 8443-8454. DOI: 10.1021/acs.est.0c01931.

Zamora-Terol, S., A. Novotny, and M. Winder (2020). “Reconstructing marine plankton food web interactions using DNA metabarcoding”. In: Molecular Ecology 29.17, pp. 3380-3395. DOI: 10.1111/mec.15555.

Zhao, F., S. Filker, K. Xu, et al. (2020). “Microeukaryote communities exhibit phyla-specific distance-decay patterns and an intimate link between seawater and sediment habitats in the Western Pacific Ocean”. In: Deep-Sea Research Part I: Oceanographic Research Papers 160. DOI: 10.1016/j.dsr.2020.103279.

Zhao, F., C. Wang, K. Xu, et al. (2020). “Diversity and connectivity of microeukaryote communities across multiple habitats from intertidal zone to deep-sea floor in the Western Pacific Ocean”. In: Deep-Sea Research Part I: Oceanographic Research Papers 165. DOI: 10.1016/j.dsr.2020.103395.

Zhao, Z., J. He, Z. Quan, et al. (2020). “Fertilization changes soil microbiome functioning, especially phagotrophic protists”. In: Soil Biology and Biochemistry 148. DOI: 10.1016/j.soilbio.2020.107863.

2019

Ahmed, M., M. Back, T. Prior, et al. (2019). “Metabarcoding of soil nematodes: The importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s)”. In: Metabarcoding and Metagenomics 3, pp. 37-99. DOI: 10.3897/mbmg.3.36408.

Angelakis, E., D. Bachar, M. Yasir, et al. (2019). “Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals”. In: New Microbes and New Infections 27, pp. 14-21. DOI: 10.1016/j.nmni.2018.10.009.

Angelakis, E., D. Bachar, M. Yasir, et al. (2019). “Comparison of the gut microbiota of obese individuals from different geographic origins”. In: New Microbes and New Infections 27, pp. 40-47. DOI: 10.1016/j.nmni.2018.11.005.

Angelova, A., G. Ellis, H. Wijesekera, et al. (2019). “Microbial composition and variability of natural marine planktonic and biofouling communities from the bay of bengal”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02738.

Armeli Minicante, S., R. Piredda, G. Quero, et al. (2019). “Habitat heterogeneity and connectivity: Effects on the planktonic protist community structure at two adjacent coastal sites (the lagoon and the gulf of venice, northern adriatic sea, italy) revealed by metabarcoding”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02736.

Belilla, J., D. Moreira, L. Jardillier, et al. (2019). “Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area”. In: Nature Ecology and Evolution 3.11, pp. 1552-1561. DOI: 10.1038/s41559-019-1005-0.

Boeuf, D., B. Edwards, J. Eppley, et al. (2019). “Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean”. In: Proceedings of the National Academy of Sciences of the United States of America 116.24, pp. 11824-11832. DOI: 10.1073/pnas.1903080116.

Boscaro, V., M. Syberg-Olsen, N. Irwin, et al. (2019). “What can environmental sequences tell us about the distribution of low-rank taxa? The case of euplotes (ciliophora, spirotrichea), including a description of euplotes enigma sp. nov.” In: Journal of Eukaryotic Microbiology 66.2, pp. 281-293. DOI: 10.1111/jeu.12669.

Buccheri, M., E. Salvo, M. Coci, et al. (2019). “Investigating microbial indicators of anthropogenic marine pollution by 16S and 18S High-Throughput Sequencing (HTS) library analysis”. In: FEMS Microbiology Letters 366.14. DOI: 10.1093/femsle/fnz179.

Caron, D. and S. Hu (2019). “Are we overestimating protistan diversity in nature?” In: Trends in Microbiology 27.3, pp. 197-205. DOI: 10.1016/j.tim.2018.10.009.

Chambouvet, A., A. Monier, F. Maguire, et al. (2019). “Intracellular infection of diverse diatoms by an evolutionary distinct relative of the fungi”. In: Current Biology 29.23, pp. 4093-4101.e4. DOI: 10.1016/j.cub.2019.09.074.

Chénard, C., W. Wijaya, D. Vaulot, et al. (2019). “Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-52648-x.

Cleary, D. (2019). “A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system”. In: Annals of Microbiology 69.8, pp. 861-866. DOI: 10.1007/s13213-019-01476-5.

Cleary, D. and N. Gomes (2019). “Baseline information on prokaryotic and microeukaryotic plankton communities inside and outside of Indonesian marine lakes”. In: Journal of Sea Research 148-149, pp. 23-32. DOI: 10.1016/j.seares.2019.04.001.

Cordier, T., A. Lanzén, L. Apothéloz-Perret-Gentil, et al. (2019). “Embracing environmental genomics and machine learning for routine biomonitoring”. In: Trends in Microbiology 27.5, pp. 387-397. DOI: 10.1016/j.tim.2018.10.012.

Couton, M., T. Comtet, S. Le Cam, et al. (2019). “Metabarcoding on planktonic larval stages: An efficient approach for detecting and investigating life cycle dynamics of benthic aliens”. In: Management of Biological Invasions 10.4, pp. 657-689. DOI: 10.3391/mbi.2019.10.4.06.

Cruaud, P., A. Vigneron, M. Fradette, et al. (2019). “Annual protist community dynamics in a freshwater ecosystem undergoing contrasted climatic conditions: The saint-charles river (canada)”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02359.

Czech, L., P. Barbera, and A. Stamatakis (2019). “Methods for automatic reference trees and multilevel phylogenetic placement”. In: Bioinformatics (Oxford, England) 35.7, pp. 1151-1158. DOI: 10.1093/bioinformatics/bty767.

De Gruyter, J., J. Weedon, S. Bazot, et al. (2019). “Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities”. In: FEMS Microbiology Ecology 96.3. DOI: 10.1093/femsec/fiaa018.

De Schepper, S., J. Ray, K. Skaar, et al. (2019). “The potential of sedimentary ancient DNA for reconstructing past sea ice evolution”. In: ISME Journal 13.10, pp. 2566-2577. DOI: 10.1038/s41396-019-0457-1.

Degrune, F., K. Dumack, A. Fiore-Donno, et al. (2019). “Distinct communities of Cercozoa at different soil depths in a temperate agricultural field”. In: FEMS Microbiology Ecology 95.4. DOI: 10.1093/femsec/fiz041.

Del Campo, J., T. Heger, R. Rodr'iguez-Mart'inez, et al. (2019). “Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework”. In: Frontiers in Microbiology 10.OCT. DOI: 10.3389/fmicb.2019.02373.

Demory, D., A. Baudoux, A. Monier, et al. (2019). “Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean”. In: ISME Journal 13.1, pp. 132-146. DOI: 10.1038/s41396-018-0248-0.

Duarte, L., F. Coelho, D. Cleary, et al. (2019). “Bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture system of sea bass (Dicentrarchus labrax): A seasonal survey”. In: Aquaculture (Amsterdam, Netherlands) 503, pp. 59-69. DOI: 10.1016/j.aquaculture.2018.12.066.

Dufresne, Y., F. Lejzerowicz, L. Perret-Gentil, et al. (2019). “SLIM: A flexible web application for the reproducible processing of environmental DNA metabarcoding data”. In: BMC Bioinformatics 20.1. DOI: 10.1186/s12859-019-2663-2.

Faure, E., F. Not, A. Benoiston, et al. (2019). “Mixotrophic protists display contrasted biogeographies in the global ocean”. In: ISME Journal 13.4, pp. 1072-1083. DOI: 10.1038/s41396-018-0340-5.

Fiore-Donno, A., T. Richter-Heitmann, F. Degrune, et al. (2019). “Functional traits and spatio-temporal structure of a major group of soil protists (rhizaria: Cercozoa) in a temperate grassland”. In: Frontiers in Microbiology 10.JUN. DOI: 10.3389/fmicb.2019.01332.

Forster, D., S. Filker, R. Kochems, et al. (2019). “A comparison of different ciliate metabarcode genes as bioindicators for environmental impact assessments of salmon aquaculture”. In: Journal of Eukaryotic Microbiology 66.2, pp. 294-308. DOI: 10.1111/jeu.12670.

Gómez-Consarnau, L., D. Needham, P. Weber, et al. (2019). “Influence of light on particulate organic matter utilization by attached and free-living marine bacteria”. In: Frontiers in Microbiology 10.JUN. DOI: 10.3389/fmicb.2019.01204.

Gao, Y., Y. Chen, W. Xiong, et al. (2019). “Distribution patterns of dinoflagellate communities along the songhua river”. In: PeerJ 2019.4. DOI: 10.7717/peerj.6733.

Geisen, S., M. Briones, H. Gan, et al. (2019). “A methodological framework to embrace soil biodiversity”. In: Soil Biology and Biochemistry 136. DOI: 10.1016/j.soilbio.2019.107536.

Giner, C., V. Balagué, A. Krabberød, et al. (2019). “Quantifying long-term recurrence in planktonic microbial eukaryotes”. In: Molecular Ecology 28.5, pp. 923-935. DOI: 10.1111/mec.14929.

Golebiewski, M., A. Tarasek, M. Sikora, et al. (2019). “Rapid microbial community changes during initial stages of pine litter decomposition”. In: Microbial Ecology 77.1, pp. 56-75. DOI: 10.1007/s00248-018-1209-x.

Gran-Stadniczeñko, S., E. Egge, V. Hostyeva, et al. (2019). “Protist diversity and seasonal dynamics in skagerrak plankton communities as revealed by metabarcoding and microscopy”. In: Journal of Eukaryotic Microbiology 66.3, pp. 494-513. DOI: 10.1111/jeu.12700.

Gutierrez-Rodriguez, A., M. Stukel, A. Lopes dos Santos, et al. (2019). “High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding”. In: ISME Journal 13.4, pp. 964-976. DOI: 10.1038/s41396-018-0322-7.

Haas, S., D. Desai, J. LaRoche, et al. (2019). “Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater”. In: Environmental Microbiology 21.10, pp. 3927-3952. DOI: 10.1111/1462-2920.14743.

Harkes, P., A. Suleiman, S. van den Elsen, et al. (2019). “Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-49854-y.

He, X., T. Sutherland, J. Pawlowski, et al. (2019). “Responses of foraminifera communities to aquaculture-derived organic enrichment as revealed by environmental DNA metabarcoding”. In: Molecular Ecology 28.5, pp. 1138-1153. DOI: 10.1111/mec.15007.

Isabwe, A., K. Ren, Y. Wang, et al. (2019). “Community assembly mechanisms underlying the core and random bacterioplankton and microeukaryotes in a river-reservoir system”. In: Water (Switzerland) 11.6. DOI: 10.3390/w11061127.

Kataoka, T. and R. Kondo (2019b). “Data on taxonomic annotation and diversity of 18S rRNA gene amplicon libraries derived from high throughput sequencing”. In: Data in Brief 25. DOI: 10.1016/j.dib.2019.104213.

Kataoka, T. and R. Kondo (2019a). “Protistan community composition in anoxic sediments from three salinity-disparate Japanese lakes”. In: Estuarine, Coastal and Shelf Science 224, pp. 34-42. DOI: 10.1016/j.ecss.2019.04.046.

Kong, J., Y. Wang, A. Warren, et al. (2019). “Diversity distribution and assembly mechanisms of planktonic and benthic microeukaryote communities in intertidal zones of southeast fujian, china”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02640.

Kulk, G., A. Buist, W. van de Poll, et al. (2019). “Size scaling of photophysiology and growth in four freshly isolated diatom species from Ryder Bay, western Antarctic peninsula”. In: Journal of Phycology 55.2, pp. 314-328. DOI: 10.1111/jpy.12813.

Lambert, S., M. Tragin, J. Lozano, et al. (2019). “Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations”. In: ISME Journal 13.2, pp. 388-401. DOI: 10.1038/s41396-018-0281-z.

Lentendu, G., P. Buosi, A. Cabral, et al. (2019). “Protist biodiversity and biogeography in lakes from four brazilian Riversystems”. In: Journal of Eukaryotic Microbiology 66.4, pp. 592-599. DOI: 10.1111/jeu.12703.

Leray, M., N. Knowlton, S. Ho, et al. (2019). “GenBank is a reliable resource for 21st century biodiversity research”. In: Proceedings of the National Academy of Sciences of the United States of America 116.45, pp. 22651-22656. DOI: 10.1073/pnas.1911714116.

Li, F., X. Zhang, Y. Xie, et al. (2019). “Sedimentary DNA reveals over 150 years of ecosystem change by human activities in Lake Chao, China”. In: Environment International 133. DOI: 10.1016/j.envint.2019.105214.

Liu, F., X. Zhang, S. Tang, et al. (2019). “Effects of acid mine drainage on eukaryotic community in river sediments [酸性矿山废水对沉积物真核微生物群落的影响]”. In: Zhongguo Huanjing Kexue/China Environmental Science 39.12, pp. 5285-5292.

Liu, L., H. Chen, M. Liu, et al. (2019). “Response of the eukaryotic plankton community to the cyanobacterial biomass cycle over 6 years in two subtropical reservoirs”. In: ISME Journal 13.9, pp. 2196-2208. DOI: 10.1038/s41396-019-0417-9.

Liu, M., Y. Xue, and J. Yang (2019). “Rare plankton subcommunities are far more affected by DNA extraction kits than abundant plankton”. In: Frontiers in Microbiology 10.MAR. DOI: 10.3389/fmicb.2019.00454.

Lupatini, M., G. Korthals, L. Roesch, et al. (2019). “Long-term farming systems modulate multi-trophic responses”. In: Science of the Total Environment 646, pp. 480-490. DOI: 10.1016/j.scitotenv.2018.07.323.

Lutz, S., L. Procházková, L. Benning, et al. (2019). “Evaluating amplicon high throughput sequencing data of microalgae living in melting snow: Improvements and limitations”. In: Fottea 19.2, pp. 115-131. DOI: 10.5507/fot.2019.003.

Macingo, S., K. Kormas, A. Oikonomou, et al. (2019). “Taxa-area and distance-decay relationships of unicellular eukaryotes along an elevation gradient of mountainous freshwater ecosystems”. In: Journal of Plankton Research 41.6, pp. 821-834. DOI: 10.1093/plankt/fbz066.

Marquardt, M., R. Skogseth, I. Wiedmann, et al. (2019). “Vertical export of marine pelagic protists in an ice-free high-Arctic fjord (Adventfjorden, West Spitsbergen) throughout 2011-2012”. In: Aquatic Microbial Ecology 83.1, pp. 65-82. DOI: 10.3354/ame01904.

Metz, S., A. Dos Santos, M. Berman, et al. (2019). “Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing”. In: FEMS Microbiology Ecology 95.5. DOI: 10.1093/femsec/fiz038.

Metz, S., D. Singer, I. Domaizon, et al. (2019). “Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches”. In: Environmental Microbiology 21.10, pp. 3885-3895. DOI: 10.1111/1462-2920.14738.

Moore, L., T. Huang, M. Ostrowski, et al. (2019). “Unicellular cyanobacteria are important components of phytoplankton communities in Australia’s northern oceanic ecoregions”. In: Frontiers in Microbiology 10.JAN. DOI: 10.3389/fmicb.2018.03356.

Mukherjee, I., Y. Hodoki, Y. Okazaki, et al. (2019). “Widespread dominance of kinetoplastids and unexpected presence of diplonemids in deep freshwater lakes”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02375.

Murdock, S. and S. Juniper (2019). “Hydrothermal vent protistan distribution along the Mariana arc suggests vent endemics may be rare and novel”. In: Environmental Microbiology 21.10, pp. 3796-3815. DOI: 10.1111/1462-2920.14729.

Nagler, M., K. Kozjek, M. Etemadi, et al. (2019). “Simple yet effective: Microbial and biotechnological benefits of rumen liquid addition to lignocellulose-degrading biogas plants”. In: Journal of Biotechnology 300, pp. 1-10. DOI: 10.1016/j.jbiotec.2019.05.004.

Panagiota-Chronopoulou, M., I. Salonen, C. Bird, et al. (2019). “Metabarcoding insights into the trophic behavior and identity of intertidal benthic foraminifera”. In: Frontiers in Microbiology 10.MAY. DOI: 10.3389/fmicb.2019.01169.

Pasulka, A., S. Hu, P. Countway, et al. (2019). “SSU-rRNA gene sequencing survey of benthic microbial eukaryotes from guaymas basin hydrothermal vent”. In: Journal of Eukaryotic Microbiology 66.4, pp. 637-653. DOI: 10.1111/jeu.12711.

Piwosz, K. (2019). “Weekly dynamics of abundance and size structure of specific nanophytoplankton lineages in coastal waters (Baltic Sea)”. In: Limnology and Oceanography 64.5, pp. 2172-2186. DOI: 10.1002/lno.11177.

Polinski, J., J. Bucci, M. Gasser, et al. (2019). “Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-51341-3.

Ramond, P., M. Sourisseau, N. Simon, et al. (2019). “Coupling between taxonomic and functional diversity in protistan coastal communities”. In: Environmental Microbiology 21.2, pp. 730-749. DOI: 10.1111/1462-2920.14537.

Reboul, G., D. Moreira, P. Bertolino, et al. (2019). “Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania”. In: Environmental Microbiology Reports 11.3, pp. 464-473. DOI: 10.1111/1758-2229.12756.

Rey, A., K. Carney, L. Quinones, et al. (2019). “Environmental DNA metabarcoding: A promising tool for ballast water monitoring”. In: Environmental Science and Technology 53.20, pp. 11849-11859. DOI: 10.1021/acs.est.9b01855.

Ribeiro, H., A. Martins, M. Gonçalves, et al. (2019). “Development of an autonomous biosampler to capture in situ aquatic microbiomes”. In: PLoS ONE 14.5. DOI: 10.1371/journal.pone.0216882.

Rimet, F., E. Gusev, M. Kahlert, et al. (2019). “Diat.barcode, an open-access curated barcode library for diatoms”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-51500-6.

Rudolph, K., C. Fichtel, D. Schneider, et al. (2019). “One size fits all? Relationships among group size, health, and ecology indicate a lack of an optimal group size in a wild lemur population”. In: Behavioral Ecology and Sociobiology 73.9. DOI: 10.1007/s00265-019-2746-0.

Santoferrara, L. (2019). “Current practice in plankton metabarcoding: Optimization and error management”. In: Journal of Plankton Research 41.5, pp. 571-582. DOI: 10.1093/plankt/fbz041.

Shiozaki, T., Y. Hirose, K. Hamasaki, et al. (2019). “Eukaryotic phytoplankton contributing to a seasonal bloom and carbon export revealed by tracking sequence variants in the western north pacific”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02722.

Singer, D., S. Metz, F. Unrein, et al. (2019). “Contrasted micro-eukaryotic diversity associated with sphagnum mosses in tropical, subtropical and temperate climatic zones”. In: Microbial Ecology 78.3, pp. 714-724. DOI: 10.1007/s00248-019-01325-7.

Sousa, A. de, M. Tomasino, P. Duarte, et al. (2019). “Diversity and composition of pelagic prokaryotic and protist communities in a thin arctic sea-ice regime”. In: Microbial Ecology 78.2, pp. 388-408. DOI: 10.1007/s00248-018-01314-2.

Suleiman, A., P. Harkes, S. van den Elsen, et al. (2019). “Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare)”. In: Science of the Total Environment 695. DOI: 10.1016/j.scitotenv.2019.133885.

Sun, P., L. Huang, D. Xu, et al. (2019). “Integrated space-time dataset reveals high diversity and distinct community structure of ciliates in mesopelagic waters of the northern south china sea”. In: Frontiers in Microbiology 10. DOI: 10.3389/fmicb.2019.02178.

Swalethorp, R., J. Dinasquet, R. Logares, et al. (2019). “Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom”. In: Progress in Oceanography 170, pp. 1-10. DOI: 10.1016/j.pocean.2018.10.008.

Tito, R., S. Chaffron, C. Caenepeel, et al. (2019). “Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota”. In: Gut 68.7, pp. 1180-1189. DOI: 10.1136/gutjnl-2018-316106.

Tragin, M. and D. Vaulot (2019). “Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-41680-6.

Tsao, H., U. Scheikl, C. Herbold, et al. (2019). “The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes”. In: Water Research 159, pp. 464-479. DOI: 10.1016/j.watres.2019.04.028.

Voss, C., A. Fiore-Donno, M. Guerreiro, et al. (2019). “Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage”. In: FEMS Microbiology Ecology 95.10. DOI: 10.1093/femsec/fiz142.

Whalen, K., J. Becker, A. Schrecengost, et al. (2019). “Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean”. In: Microbiome 7.1. DOI: 10.1186/s40168-019-0711-9.

Wilschut, R., W. van der Putten, P. Garbeva, et al. (2019). “Root traits and belowground herbivores relate to plantsoil feedback variation among congeners”. In: Nature Communications 10.1. DOI: 10.1038/s41467-019-09615-x.

Wilschut, R., S. Geisen, H. Martens, et al. (2019). “Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants”. In: Global Change Biology 25.8, pp. 2714-2726. DOI: 10.1111/gcb.14657.

Wood, S., X. Pochon, O. Laroche, et al. (2019). “A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species-specific detection in environmental DNA”. In: Molecular Ecology Resources 19.6, pp. 1407-1419. DOI: 10.1111/1755-0998.13055.

Wu, W., C. Guo, P. Pitta, et al. (2019). “Response of active picoeukaryotes to the deposition of Saharan dust and European aerosols in the eastern Mediterranean Sea”. In: Aquatic Microbial Ecology 82.1, pp. 31-42. DOI: 10.3354/ame01881.

Wu, W. and B. Huang (2019). “Protist diversity and community assembly in surface sediments of the South China Sea”. In: MicrobiologyOpen 8.10. DOI: 10.1002/mbo3.891.

Yu, Z. and N. Chen (2019). “Emerging trends in red tide and major research progresses [国内外赤潮的叒展趋势与研究热点]”. In: Oceanologia et Limnologia Sinica 50.3, pp. 474-486. DOI: 10.11693/hyhz20190200041.

Zhao, Z., J. He, S. Geisen, et al. (2019). “Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils”. In: Microbiome 7.1. DOI: 10.1186/s40168-019-0647-0.

2018

Ali, S., M. Isa, S. Safari, et al. (2018). “Eukaryotic biodiversity in mixed peat ecosystems in Sarawak, Malaysia”. In: Journal of Oil Palm Research 30.3, pp. 429-450. DOI: 10.21894/jopr.2018.0023.

Ammon, U. von, S. Wood, O. Laroche, et al. (2018). “The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis”. In: Marine Environmental Research 133, pp. 57-66. DOI: 10.1016/j.marenvres.2017.12.003.

Ammon, U., S. Wood, O. Laroche, et al. (2018). “Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-34541-1.

Araujo, A. de, L. Mendes, L. Lemos, et al. (2018). “Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado”. In: Communications Biology 1.1. DOI: 10.1038/s42003-018-0129-0.

Arroyo, A., D. López-Escardó, E. Kim, et al. (2018). “Novel diversity of deeply branching holomycota and unicellular holozoans revealed by metabarcoding in Middle Paraná River, Argentina”. In: Frontiers in Ecology and Evolution 6.JUL. DOI: 10.3389/fevo.2018.00099.

Bahram, M., F. Hildebrand, S. Forslund, et al. (2018). “Structure and function of the global topsoil microbiome”. In: Nature 560.7717, pp. 233-237. DOI: 10.1038/s41586-018-0386-6.

Balzano, S., J. Lattaud, L. Villanueva, et al. (2018). “A quest for the biological sources of long chain alkyl diols in the western tropical North Atlantic Ocean”. In: Biogeosciences (Online) 15.19, pp. 5951-5968. DOI: 10.5194/bg-15-5951-2018.

Bass, D., L. Czech, B. Williams, et al. (2018). “Clarifying the relationships between microsporidia and cryptomycota”. In: Journal of Eukaryotic Microbiology 65.6, pp. 773-782. DOI: 10.1111/jeu.12519.

Bensaoud, C., J. Nishiyama M.Y., C. Ben Hamda, et al. (2018). “De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression”. In: Parasites and Vectors 11.1. DOI: 10.1186/s13071-018-2874-9.

Berdjeb, L., A. Parada, D. Needham, et al. (2018). “Short-term dynamics and interactions of marine protist communities during the spring-summer transition”. In: ISME Journal 12.8, pp. 1907-1917. DOI: 10.1038/s41396-018-0097-x.

Boast, A., L. Weyrich, J. Wood, et al. (2018). “Coprolites reveal ecological interactions lost with the extinction of New Zealand birds”. In: Proceedings of the National Academy of Sciences of the United States of America 115.7, pp. 1546-1551. DOI: 10.1073/pnas.1712337115.

Boaventura, C., F. Coelho, P. Martins, et al. (2018). “Micro-eukaryotic plankton diversity in an intensive aquaculture system for production of Scophthalmus maximus and Solea senegalensis”. In: Aquaculture (Amsterdam, Netherlands) 490, pp. 321-328. DOI: 10.1016/j.aquaculture.2018.02.033.

Bock, C., M. Salcher, M. Jensen, et al. (2018). “Synchrony of eukaryotic and prokaryotic planktonic communities in three seasonally sampled Austrian lakes”. In: Frontiers in Microbiology 9.JUN. DOI: 10.3389/fmicb.2018.01290.

Boscaro, V., L. Santoferrara, Q. Zhang, et al. (2018). “EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates”. In: Environmental Microbiology 20.6, pp. 2218-2230. DOI: 10.1111/1462-2920.14264.

Briand, J., X. Pochon, S. Wood, et al. (2018). “Metabarcoding and metabolomics offer complementarity in deciphering marine eukaryotic biofouling community shifts”. In: Biofouling 34.6, pp. 657-672. DOI: 10.1080/08927014.2018.1480757.

Brown, M., J. Van De Kamp, M. Ostrowski, et al. (2018). “Data Descriptor: Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative”. In: Scientific Data 5. DOI: 10.1038/sdata.2018.130.

Bruce Cahoon, A., A. Huffman, M. Krager, et al. (2018). “A meta-barcoding census of freshwater planktonic protists in appalachia - natural tunnel state park, virginia, USA”. In: Metabarcoding and Metagenomics 2. DOI: 10.3897/mbmg.2.26939.

Cai, J., C. Bai, X. Tang, et al. (2018). “Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake”. In: Environmental Science and Pollution Research 25.31, pp. 31543-31557. DOI: 10.1007/s11356-018-2987-x.

Campo, J. del, M. Kolisko, V. Boscaro, et al. (2018). “EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution”. In: PLoS Biology 16.9. DOI: 10.1371/journal.pbio.2005849.

Celussi, M., G. Quero, L. Zoccarato, et al. (2018). “Planktonic prokaryote and protist communities in a submarine canyon system in the Ligurian Sea (NW Mediterranean)”. In: Progress in Oceanography 168, pp. 210-221. DOI: 10.1016/j.pocean.2018.10.002.

Clerissi, C., S. Brunet, J. Vidal-Dupiol, et al. (2018). “Protists within corals: The hidden diversity”. In: Frontiers in Microbiology 9.AUG. DOI: 10.3389/fmicb.2018.02043.

Decelle, J., Q. Carradec, X. Pochon, et al. (2018). “Worldwide occurrence and activity of the reef-building coral symbiont symbiodinium in the open ocean”. In: Current Biology 28.22, pp. 3625-3633.e3. DOI: 10.1016/j.cub.2018.09.024.

der Reis, A. van, O. Laroche, A. Jeffs, et al. (2018). “Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding”. In: PeerJ 2018.9. DOI: 10.7717/peerj.5641.

Douglas, G., A. Comeau, and M. Langille (2018). “Processing a 16S rRNA sequencing dataset with the microbiome helper workflow”. In: Methods in Molecular Biology 1849, pp. 131-141. DOI: 10.1007/978-1-4939-8728-3_9.

Duarte, S., L. Nunes, P. Borges, et al. (2018). “A bridge too far? An integrative framework linking classical protist taxonomy and metabarcoding in lower termites”. In: Frontiers in Microbiology 9.NOV. DOI: 10.3389/fmicb.2018.02620.

Enberg, S., M. Majaneva, R. Autio, et al. (2018). “Phases of microalgal succession in sea ice and the water column in the baltic sea from autumn to spring”. In: Marine Ecology Progress Series 599, pp. 19-34. DOI: 10.3354/meps12645.

Engesmo, A., D. Strand, S. Gran-Stadniczeñko, et al. (2018). “Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae)”. In: Harmful Algae 75, pp. 105-117. DOI: 10.1016/j.hal.2018.04.007.

Fiore-Donno, A., C. Rixen, M. Rippin, et al. (2018). “New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts”. In: Molecular Ecology Resources 18.2, pp. 229-239. DOI: 10.1111/1755-0998.12729.

Flegontova, O., P. Flegontov, S. Malviya, et al. (2018). “Neobodonids are dominant kinetoplastids in the global ocean”. In: Environmental Microbiology 20.2, pp. 878-889. DOI: 10.1111/1462-2920.14034.

Gaonkar, C., R. Piredda, C. Minucci, et al. (2018). “Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae”. In: PLoS ONE 13.12. DOI: 10.1371/journal.pone.0208929.

Garvetto, A., E. Nézan, Y. Badis, et al. (2018). “Novel widespread marine oomycetes parasitising diatoms, including the toxic genus pseudo-nitzschia: Genetic, morphological, and ecological characterisation”. In: Frontiers in Microbiology 9. DOI: 10.3389/fmicb.2018.02918.

Gebert, M., M. Delgado-Baquerizo, A. Oliverio, et al. (2018). “Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health”. In: mBio 9.5, pp. 1-15. DOI: 10.1128/mbio.01614-18.

Geisen, S., E. Mitchell, S. Adl, et al. (2018). “Soil protists: A fertile frontier in soil biology research”. In: FEMS Microbiology Reviews 42.3, pp. 293-323. DOI: 10.1093/femsre/fuy006.

Geisen, S., L. Snoek, F. ten Hooven, et al. (2018). “Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion”. In: Methods in Ecology and Evolution 9.6, pp. 1366-1378. DOI: 10.1111/2041-210X.12999.

Gérikas Ribeiro, C., A. Dos Santos, D. Marie, et al. (2018). “Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria”. In: ISME Journal 12.5, pp. 1360-1374. DOI: 10.1038/s41396-018-0050-z.

Guo, S., W. Xiong, H. Xu, et al. (2018). “Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities”. In: European Journal of Soil Biology 88, pp. 8-14. DOI: 10.1016/j.ejsobi.2018.05.007.

Hernández-Ruiz, M., E. Barber-Lluch, A. Prieto, et al. (2018). “Seasonal succession of small planktonic eukaryotes inhabiting surface waters of a coastal upwelling system”. In: Environmental Microbiology 20.8, pp. 2955-2973. DOI: 10.1111/1462-2920.14313.

Hervé, V., B. Leroy, A. Da Silva Pires, et al. (2018). “Aquatic urban ecology at the scale of a capital: Community structure and interactions in street gutters”. In: ISME Journal 12.1, pp. 253-266. DOI: 10.1038/ismej.2017.166.

Hu, S., P. Connell, L. Mesrop, et al. (2018). “A hard day’s night: Diel shifts in microbial eukaryotic activity in the north pacific subtropical gyre”. In: Frontiers in Marine Science 5.OCT. DOI: 10.3389/fmars.2018.00351.

Hunsucker, K., G. Vora, J. Hunsucker, et al. (2018). “Biofilm community structure and the associated drag penalties of a groomed fouling release ship hull coating”. In: Biofouling 34.2, pp. 162-172. DOI: 10.1080/08927014.2017.1417395.

Jing, H., Y. Zhang, Y. Li, et al. (2018). “Spatial variability of picoeukaryotic communities in the mariana trench”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-33790-4.

Kamp, A., C. Petro, H. Røy, et al. (2018). “Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms”. In: FEMS Microbiology Ecology 94.8. DOI: 10.1093/FEMSEC/FIY122.

Kisand, V., L. Talas, A. Kisand, et al. (2018). “From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last 14,500 years”. In: Geobiology 16.6, pp. 628-639. DOI: 10.1111/gbi.12307.

Kuwata, A., K. Yamada, M. Ichinomiya, et al. (2018). “Bolidophyceae, a sister picoplanktonic group of diatoms - A review”. In: Frontiers in Marine Science 5.OCT. DOI: 10.3389/fmars.2018.00370.

López-Escardó, D., J. Paps, C. De Vargas, et al. (2018). “Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-27509-8.

Laroche, O., S. Wood, L. Tremblay, et al. (2018). “A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations”. In: Marine Pollution Bulletin 127, pp. 97-107. DOI: 10.1016/j.marpolbul.2017.11.042.

Leblanc, K., B. Quéguiner, F. Diaz, et al. (2018). “Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export”. In: Nature Communications 9.1. DOI: 10.1038/s41467-018-03376-9.

Leff, J., R. Bardgett, A. Wilkinson, et al. (2018). “Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits”. In: ISME Journal 12.7, pp. 1794-1805. DOI: 10.1038/s41396-018-0089-x.

Lentendu, G., F. Mahé, D. Bass, et al. (2018). “Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists”. In: Molecular Ecology 27.13, pp. 2846-2857. DOI: 10.1111/mec.14731.

Leray, M., S. Ho, I. Lin, et al. (2018). “MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database”. In: Bioinformatics (Oxford, England) 34.21, pp. 3753-3754. DOI: 10.1093/bioinformatics/bty454.

Lewitus, E., L. Bittner, S. Malviya, et al. (2018). “Clade-specific diversification dynamics of marine diatoms since the Jurassic”. In: Nature Ecology and Evolution 2.11, pp. 1715-1723. DOI: 10.1038/s41559-018-0691-3.

Li, F., Y. Peng, W. Fang, et al. (2018). “Application of environmental DNA metabarcoding for predicting anthropogenic pollution in rivers”. In: Environmental Science and Technology 52.20, pp. 11708-11719. DOI: 10.1021/acs.est.8b03869.

Li, R., N. Jiao, A. Warren, et al. (2018). “Changes in community structure of active protistan assemblages from the lower Pearl River to coastal Waters of the South China Sea”. In: European Journal of Protistology 63, pp. 72-82. DOI: 10.1016/j.ejop.2018.01.004.

Morard, R., M. Garet-Delmas, F. Mahé, et al. (2018). “Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-20833-z.

Mordret, S., R. Piredda, D. Vaulot, et al. (2018). “dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene”. In: Molecular Ecology Resources 18.5, pp. 974-987. DOI: 10.1111/1755-0998.12781.

Moreno-Pino, M., B. Krock, R. De la Iglesia, et al. (2018). “Next Generation Sequencing and mass spectrometry reveal high taxonomic diversity and complex phytoplankton-phycotoxins patterns in Southeastern Pacific fjords”. In: Toxicon : official journal of the International Society on Toxinology 151, pp. 5-14. DOI: 10.1016/j.toxicon.2018.06.078.

Mucko, M., S. Bosak, R. Casotti, et al. (2018). “Winter picoplankton diversity in an oligotrophic marginal sea”. In: Marine Genomics 42, pp. 14-24. DOI: 10.1016/j.margen.2018.09.002.

Oliverio, A., J. Power, A. Washburne, et al. (2018). “The ecology and diversity of microbial eukaryotes in geothermal springs”. In: ISME Journal 12.8, pp. 1918-1928. DOI: 10.1038/s41396-018-0104-2.

Pearman, J., F. Afandi, P. Hong, et al. (2018). “Plankton community assessment in anthropogenic-impacted oligotrophic coastal regions”. In: Environmental Science and Pollution Research 25.31, pp. 31017-31030. DOI: 10.1007/s11356-018-3072-1.

Pearman, J., M. Leray, R. Villalobos, et al. (2018). “Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-26332-5.

Piwosz, K., J. Calkiewicz, M. Golebiewski, et al. (2018). “Diversity and community composition of pico- and nanoplanktonic protists in the Vistula River estuary (Gulf of Gdansk, Baltic Sea)”. In: Estuarine, Coastal and Shelf Science 207, pp. 242-249. DOI: 10.1016/j.ecss.2018.04.013.

Rachik, S., U. Christaki, L. Li, et al. (2018). “Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel)”. In: PLoS ONE 13.5. DOI: 10.1371/journal.pone.0196987.

Ren, K., Y. Xue, R. Rønn, et al. (2018). “Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers”. In: Water Research 146, pp. 177-186. DOI: 10.1016/j.watres.2018.09.011.

Ser-Giacomi, E., L. Zinger, S. Malviya, et al. (2018). “Ubiquitous abundance distribution of non-dominant plankton across the global ocean”. In: Nature Ecology and Evolution 2.8, pp. 1243-1249. DOI: 10.1038/s41559-018-0587-2.

Stefanidou, N., S. Genitsaris, J. Lopez-Bautista, et al. (2018). “Unicellular eukaryotic community response to temperature and salinity variation in mesocosm experiments”. In: Frontiers in Microbiology 9.OCT. DOI: 10.3389/fmicb.2018.02444.

Stern, R., A. Kraberg, E. Bresnan, et al. (2018). “Molecular analyses of protists in long-term observation programmes - Current status and future perspectives”. In: Journal of Plankton Research 40.5, pp. 519-536. DOI: 10.1093/plankt/fby035.

Stoeck, T., R. Kochems, D. Forster, et al. (2018). “Metabarcoding of benthic ciliate communities shows high potential for environmental monitoring in salmon aquaculture”. In: Ecological Indicators 85, pp. 153-164. DOI: 10.1016/j.ecolind.2017.10.041.

Stoeck, T., H. Pan, V. Dully, et al. (2018). “Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants”. In: Water Research 144, pp. 322-331. DOI: 10.1016/j.watres.2018.07.051.

Szelecz, I., S. Lösch, C. Seppey, et al. (2018). “Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-017-18179-z.

Taberlet, P., A. Bonin, L. Zinger, et al. (2018). Environmental DNA: For biodiversity research and monitoring , pp. 1-253. DOI: 10.1093/oso/9780198767220.001.0001.

Tan, S. and H. Liu (2018). “Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA”. In: Applied Microbiology and Biotechnology 102.1, pp. 389-401. DOI: 10.1007/s00253-017-8565-1.

Tragin, M. and D. Vaulot (2018). “Green microalgae in marine coastal waters: The ocean sampling day (OSD) dataset”. In: Scientific Reports 8.1. DOI: 10.1038/s41598-018-32338-w.

Tragin, M., A. Zingone, and D. Vaulot (2018). “Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta”. In: Environmental Microbiology 20.2, pp. 506-520. DOI: 10.1111/1462-2920.13952.

Vader, A., I. Laughinghouse H.D., C. Griffiths, et al. (2018). “Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord”. In: Environmental Microbiology 20.2, pp. 890-902. DOI: 10.1111/1462-2920.14035.

Varkey, D., S. Mazard, T. Jeffries, et al. (2018). “Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary”. In: PLoS ONE 13.12. DOI: 10.1371/journal.pone.0209857.

Venter, P., F. Nitsche, and H. Arndt (2018). “The hidden diversity of flagellated protists in soil”. In: Protist 169.3, pp. 432-449. DOI: 10.1016/j.protis.2018.04.007.

Venter, P., F. Nitsche, A. Scherwass, et al. (2018). “Discrepancies between molecular and morphological databases of soil ciliates studied for temperate grasslands of central europe”. In: Protist 169.4, pp. 521-538. DOI: 10.1016/j.protis.2018.04.001.

Wang, Y., T. Shi, G. Huang, et al. (2018). “Molecular detection of eukaryotic diets and gut mycobiomes in two marine sediment-dwelling worms, sipunculus nudus and urechis unicinctus”. In: Microbes and Environments 33.3, pp. 290-300. DOI: 10.1264/jsme2.ME18065.

Wangensteen, O., E. Cebrian, and C. Palacín (2018). “Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding”. In: Marine Pollution Bulletin 127, pp. 54-66. DOI: 10.1016/j.marpolbul.2017.11.033.

Ward, G., S. Neuhauser, R. Groben, et al. (2018). “Environmental sequencing fills the gap between parasitic haplosporidians and free-living giant amoebae”. In: Journal of Eukaryotic Microbiology 65.5, pp. 574-586. DOI: 10.1111/jeu.12501.

Wu, W. and H. Liu (2018). “Disentangling protist communities identified from DNA and RNA surveys in the Pearl RiverChina Sea Continuum during the wet and dry seasons”. In: Molecular Ecology 27.22, pp. 4627-4640. DOI: 10.1111/mec.14867.

Wu, W., H. Lu, A. Sastri, et al. (2018). “Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities”. In: ISME Journal 12.2, pp. 485-494. DOI: 10.1038/ismej.2017.183.

Wylezich, C., D. Herlemann, and K. Jürgens (2018). “Improved 18S rDNA amplification protocol for assessing protist diversity in oxygen-deficient marine systems”. In: Aquatic Microbial Ecology 81.1, pp. 83-94. DOI: 10.3354/ame01864.

Xie, Y., T. Floehr, X. Zhang, et al. (2018). “In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments”. In: Environmental Pollution 239, pp. 189-197. DOI: 10.1016/j.envpol.2018.03.099.

Xie, Y., X. Zhang, J. Yang, et al. (2018). “eDNA-based bioassessment of coastal sediments impacted by an oil spill”. In: Environmental Pollution 238, pp. 739-748. DOI: 10.1016/j.envpol.2018.02.081.

Zaiko, A., X. Pochon, E. Garcia-Vazquez, et al. (2018). “Advantages and limitations of environmental DNA/RNA tools for marine biosecurity: Management and surveillance of non-indigenous species”. In: Frontiers in Marine Science 5.SEP. DOI: 10.3389/fmars.2018.00322.

Zhao, H., X. Li, Z. Zhang, et al. (2018). “Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China”. In: PeerJ 2018.12. DOI: 10.7717/peerj.6042.

Zhu, P., Y. Wang, T. Shi, et al. (2018). “Genetic diversity of benthic microbial eukaryotes in response to spatial heterogeneity of sediment geochemistry in a mangrove ecosystem”. In: Estuaries and Coasts 41.3, pp. 751-764. DOI: 10.1007/s12237-017-0317-z.

Zouari, A., M. Hassen, V. Balagué, et al. (2018). “Picoeukaryotic diversity in the Gulf of Gabès: Variability patterns and relationships to nutrients and water masses”. In: Aquatic Microbial Ecology 81.1, pp. 37-53. DOI: 10.3354/ame01857.

2017

Alves-De-Souza, C., T. Benevides, J. Santos, et al. (2017). “Does environmental heterogeneity explain temporal \(\beta\) diversity of small eukaryotic phytoplankton? Example from a tropical eutrophic coastal lagoon”. In: Journal of Plankton Research 39.4, pp. 698-714. DOI: 10.1093/plankt/fbx026.

Berney, C., A. Ciuprina, S. Bender, et al. (2017). “UniEuk: Time to speak a common language in protistology!” In: Journal of Eukaryotic Microbiology 64.3, pp. 407-411. DOI: 10.1111/jeu.12414.

Biard, T., E. Bigeard, S. Audic, et al. (2017). “Biogeography and diversity of Collodaria (Radiolaria) in the global ocean”. In: ISME Journal 11.6, pp. 1331-1344. DOI: 10.1038/ismej.2017.12.

Christaki, U., S. Genitsaris, S. Monchy, et al. (2017). “Parasitic eukaryotes in a meso-eutrophic coastal system with marked Phaeocystis globosa blooms”. In: Frontiers in Marine Science 4.DEC. DOI: 10.3389/fmars.2017.00416.

Deiner, K., H. Bik, E. Mächler, et al. (2017). “Environmental DNA metabarcoding: Transforming how we survey animal and plant communities”. In: Molecular Ecology 26.21, pp. 5872-5895. DOI: 10.1111/mec.14350.

Domaizon, I., A. Winegardner, E. Capo, et al. (2017). “DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity”. In: Journal of Paleolimnology 58.1. DOI: 10.1007/s10933-017-9958-y.

Dos Santos, A., P. Gourvil, M. Tragin, et al. (2017). “Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters”. In: ISME Journal 11.2, pp. 512-528. DOI: 10.1038/ismej.2016.120.

Dunthorn, M., H. Kauserud, D. Bass, et al. (2017). “Yeasts dominate soil fungal communities in three lowland Neotropical rainforests”. In: Environmental Microbiology Reports 9.5, pp. 668-675. DOI: 10.1111/1758-2229.12575.

Filker, S., D. Forster, L. Weinisch, et al. (2017). “Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions”. In: Environmental Microbiology 19.8, pp. 3186-3200. DOI: 10.1111/1462-2920.13805.

Fletcher, L., A. Zaiko, J. Atalah, et al. (2017). “Bilge water as a vector for the spread of marine pests: a morphological, metabarcoding and experimental assessment”. In: Biological Invasions 19.10, pp. 2851-2867. DOI: 10.1007/s10530-017-1489-y.

Foster, Z., T. Sharpton, and N. Grünwald (2017). “Metacoder: An R package for visualization and manipulation of community taxonomic diversity data”. In: PLoS Computational Biology 13.2. DOI: 10.1371/journal.pcbi.1005404.

Frank, N., T. Helge Abuldhauge, and J. Daniel (2017). “Bridging the gap between morphological species and molecular barcodes Exemplified by loricate choanoflagellates”. In: European Journal of Protistology 57, pp. 26-37. DOI: 10.1016/j.ejop.2016.10.006.

Gleason, F., B. Scholz, T. Jephcott, et al. (2017). Key ecological roles for zoosporic true fungi in aquatic habitats , pp. 399-416. DOI: 10.1128/9781555819583.ch18.

Gran-Stadniczeñko, S., L. Å upraha, E. Egge, et al. (2017). “Haptophyte diversity and vertical distribution explored by 18S and 28S ribosomal RNA gene metabarcoding and scanning electron microscopy”. In: Journal of Eukaryotic Microbiology 64.4, pp. 514-532. DOI: 10.1111/jeu.12388.

Groendahl, S., M. Kahlert, and P. Fink (2017). “The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods”. In: PLoS ONE 12.2. DOI: 10.1371/journal.pone.0172808.

Heinz, K., P. Zanoni, R. Oliveira, et al. (2017). “Recycled paper sludge microbial community as a potential source of cellulase and xylanase enzymes”. In: Waste and Biomass Valorization 8.6, pp. 1907-1917. DOI: 10.1007/s12649-016-9792-x.

Hugerth, L. and A. Andersson (2017). “Analysing microbial community composition through amplicon sequencing: From sampling to hypothesis testing”. In: Frontiers in Microbiology 8.SEP. DOI: 10.3389/fmicb.2017.01561.

Jacob, F., T. Melachio, G. Njitchouang, et al. (2017). “Intestinal bacterial communities of trypanosome-infected and uninfected Glossina palpalis palpalis from three human African trypanomiasis foci in Cameroon”. In: Frontiers in Microbiology 8.AUG. DOI: 10.3389/fmicb.2017.01464.

Kataoka, T., H. Yamaguchi, M. Sato, et al. (2017). “Seasonal and geographical distribution of near-surface small photosynthetic eukaryotes in the western north pacific determined by pyrosequencing of 18S rDNA”. In: FEMS Microbiology Ecology 93.2. DOI: 10.1093/femsec/fiw229.

Kaysen, A., A. Heintz-Buschart, E. Muller, et al. (2017). “Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation”. In: Translational Research 186, pp. 79-94.e1. DOI: 10.1016/j.trsl.2017.06.008.

Khomich, M., H. Kauserud, R. Logares, et al. (2017). “Planktonic protistan communities in lakes along a large-scale environmental gradient”. In: FEMS Microbiology Ecology 93.4. DOI: 10.1093/femsec/fiw231.

Laroche, O., S. Wood, L. Tremblay, et al. (2017). “Metabarcoding monitoring analysis: The pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities”. In: PeerJ 2017.5. DOI: 10.7717/peerj.3347.

Lee, K., L. Ab Samad, P. Lwin, et al. (2017). “On the rocks: Microbiological quality and microbial diversity of packaged ice in southern California”. In: Journal of Food Protection 80.6, pp. 1041-1049. DOI: 10.4315/0362-028X.JFP-16-295.

Leray, M. and N. Knowlton (2017). “Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding”. In: PeerJ 2017.3. DOI: 10.7717/peerj.3006.

Machida, R., M. Leray, S. Ho, et al. (2017). “Data Descriptor: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples”. In: Scientific Data 4. DOI: 10.1038/sdata.2017.27.

Mahé, F., C. De Vargas, D. Bass, et al. (2017). “Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests”. In: Nature Ecology and Evolution 1.4. DOI: 10.1038/s41559-017-0091.

Marie, D., F. Le Gall, R. Edern, et al. (2017). “Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry”. In: Journal of Phycology 53.2, pp. 271-282. DOI: 10.1111/jpy.12495.

Meshram, A., A. Vader, S. Kristiansen, et al. (2017). “Microbial eukaryotes in an arctic under-ice spring bloom north of Svalbard”. In: Frontiers in Microbiology 8.JUN. DOI: 10.3389/fmicb.2017.01099.

Morard, R., F. Lejzerowicz, K. Darling, et al. (2017). “Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology”. In: Biogeosciences (Online) 14.11, pp. 2741-2754. DOI: 10.5194/bg-14-2741-2017.

Mukherjee, I., Y. Hodoki, and S. Nakano (2017). “Seasonal dynamics of heterotrophic and plastidic protists in the water column of Lake Biwa, Japan”. In: Aquatic Microbial Ecology 80.2, pp. 123-137. DOI: 10.3354/ame01843.

Pagenkopp Lohan, K., R. Fleischer, K. Carney, et al. (2017). “Molecular characterisation of protistan species and communities in ships’ ballast water across three U.S. coasts”. In: Diversity and Distributions 23.6, pp. 680-691. DOI: 10.1111/ddi.12550.

Pagenkopp Lohan, K., R. Fleischer, M. Torchin, et al. (2017). “Protistan biogeography: A snapshot across a major shipping corridor spanning two oceans”. In: Protist 168.2, pp. 183-196. DOI: 10.1016/j.protis.2016.12.003.

Pan, J., J. del Campo, and P. Keeling (2017). “Reference tree and environmental sequence diversity of labyrinthulomycetes”. In: Journal of Eukaryotic Microbiology 64.1, pp. 88-96. DOI: 10.1111/jeu.12342.

Pearman, J., J. Ellis, X. Irigoien, et al. (2017). “Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence”. In: Scientific Reports 7.1. DOI: 10.1038/s41598-017-06928-z.

Penna, A., S. Casabianca, A. Guerra, et al. (2017). “Analysis of phytoplankton assemblage structure in the Mediterranean Sea based on high-throughput sequencing of partial 18S rRNA sequences”. In: Marine Genomics 36, pp. 49-55. DOI: 10.1016/j.margen.2017.06.001.

Piredda, R., D. Sarno, C. Lange, et al. (2017). “Diatom resting stages in surface sediments: A pilot study comparing next generation sequencing and serial dilution cultures”. In: Cryptogamie, Algologie 38.1, pp. 31-46. DOI: 10.7872/crya/v38.iss1.2017.31.

Piredda, R., M. Tomasino, A. D’Erchia, et al. (2017). “Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site”. In: FEMS Microbiology Ecology 93.1. DOI: 10.1093/femsec/fiw200.

Pochon, X., A. Zaiko, L. Fletcher, et al. (2017). “Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications”. In: PLoS ONE 12.11. DOI: 10.1371/journal.pone.0187636.

Reich, M. and A. Labes (2017). “How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry”. In: Marine Genomics 36, pp. 57-75. DOI: 10.1016/j.margen.2017.09.007.

Saghaï, A., A. Gutiérrez-Preciado, P. Deschamps, et al. (2017). “Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond”. In: Environmental Microbiology 19.6, pp. 2405-2421. DOI: 10.1111/1462-2920.13754.

Salvitti, L., S. Wood, R. Fairweather, et al. (2017). “In situ accumulation of tetrodotoxin in non-toxic Pleurobranchaea maculata (Opisthobranchia)”. In: Aquatic Sciences 79.2, pp. 335-344. DOI: 10.1007/s00027-016-0500-5.

Santos, S., I. Nunes, T. Nielsen, et al. (2017). “Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome”. In: Protist 168.3, pp. 283-293. DOI: 10.1016/j.protis.2017.03.002.

Schnittler, M., O. Shchepin, N. Dagamac, et al. (2017). “Barcoding myxomycetes with molecular markers: Challenges and opportunities”. In: Nova Hedwigia 104.1-3, pp. 323-341. DOI: 10.1127/nova_hedwigia/2017/0397.

Seppey, C., D. Singer, K. Dumack, et al. (2017). “Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling”. In: Soil Biology and Biochemistry 112, pp. 68-76. DOI: 10.1016/j.soilbio.2017.05.002.

Simon, N., E. Foulon, D. Grulois, et al. (2017). “Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species M. pusilla (butcher) manton & parke and of the species M. commoda van baren, bachy and worden and description of two new species based on the genetic and phenotypic characterization of cultured isolates”. In: Protist 168.5, pp. 612-635. DOI: 10.1016/j.protis.2017.09.002.

Smith, K., G. Kohli, S. Murray, et al. (2017). “Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities”. In: New Zealand Journal of Marine and Freshwater Research 51.4, pp. 555-576. DOI: 10.1080/00288330.2017.1298632.

Sun, P., L. Huang, D. Xu, et al. (2017). “Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the ‘abundant’ and ‘intermediate’ biospheres”. In: Scientific Reports 7.1. DOI: 10.1038/s41598-017-10308-y.

Tirichine, L., A. Rastogi, and C. Bowler (2017). “Recent progress in diatom genomics and epigenomics”. In: Current Opinion in Plant Biology 36, pp. 46-55. DOI: 10.1016/j.pbi.2017.02.001.

Torruella, G., D. Moreira, and P. López-Garc'ia (2017). “Phylogenetic and ecological diversity of apusomonads, a lineage of deep-branching eukaryotes”. In: Environmental Microbiology Reports 9.2, pp. 113-119. DOI: 10.1111/1758-2229.12507.

Venter, P., F. Nitsche, A. Domonell, et al. (2017). “The protistan microbiome of grassland soil: Diversity in the mesoscale”. In: Protist 168.5, pp. 546-564. DOI: 10.1016/j.protis.2017.03.005.

Wampach, L., A. Heintz-Buschart, A. Hogan, et al. (2017). “Colonization and succession within the human gut microbiome by archaea, bacteria, and microeukaryotes during the first year of life”. In: Frontiers in Microbiology 8.MAY. DOI: 10.3389/fmicb.2017.00738.

Wang, Y., X. Guo, P. Zheng, et al. (2017). “Distinct seasonality of chytrid-dominated benthic fungal communities in the neritic oceans (Bohai Sea and North Yellow Sea)”. In: Fungal Ecology 30, pp. 55-66. DOI: 10.1016/j.funeco.2017.08.008.

Weber, F., A. Mylnikov, K. Jürgens, et al. (2017). “Culturing heterotrophic protists from the baltic sea: Mostly the ``Usual suspects’’ but a few novelties as well”. In: Journal of Eukaryotic Microbiology 64.2, pp. 153-163. DOI: 10.1111/jeu.12347.

Wu, W., R. Logares, B. Huang, et al. (2017). “Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean”. In: Environmental Microbiology 19.1, pp. 287-300. DOI: 10.1111/1462-2920.13606.

Xie, Y., S. Hong, S. Kim, et al. (2017). “Ecogenomic responses of benthic communities under multiple stressors along the marine and adjacent riverine areas of northern Bohai Sea, China”. In: Chemosphere 172, pp. 166-174. DOI: 10.1016/j.chemosphere.2016.12.121.

Xie, Y., J. Wang, J. Yang, et al. (2017). “Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types”. In: Chemosphere 172, pp. 201-209. DOI: 10.1016/j.chemosphere.2016.12.117.

Xu, D., N. Jiao, R. Ren, et al. (2017). “Distribution and diversity of microbial eukaryotes in bathypelagic waters of the south china sea”. In: Journal of Eukaryotic Microbiology 64.3, pp. 370-382. DOI: 10.1111/jeu.12372.

2016

Aguilar, M., E. Richardson, B. Tan, et al. (2016). “Next-generation sequencing assessment of eukaryotic diversity in oil sands tailings ponds sediments and surface water”. In: Journal of Eukaryotic Microbiology 63.6, pp. 732-743. DOI: 10.1111/jeu.12320.

Amato, K., J. Metcalf, S. Song, et al. (2016). “Using the gut microbiota as a novel tool for examining colobine primate GI health”. In: Global Ecology and Conservation 7, pp. 225-237. DOI: 10.1016/j.gecco.2016.06.004.

Angelakis, E., M. Yasir, D. Bachar, et al. (2016). “Gut microbiome and dietary patterns in different Saudi populations and monkeys”. In: Scientific Reports 6. DOI: 10.1038/srep32191.

Bass, D. and T. Bell (2016). Protist systematics, ecology and next generation sequencing , pp. 195-216. DOI: 10.1017/CBO9781139236355.010.

Bass, D., J. Silberman, M. Brown, et al. (2016). “Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists”. In: Environmental Microbiology 18.5, pp. 1604-1619. DOI: 10.1111/1462-2920.13235.

Boyer, F., C. Mercier, A. Bonin, et al. (2016). “obitools: A unix-inspired software package for DNA metabarcoding”. In: Molecular Ecology Resources 16.1, pp. 176-182. DOI: 10.1111/1755-0998.12428.

Campo, J. del, L. Guillou, E. Hehenberger, et al. (2016). “Ecological and evolutionary significance of novel protist lineages”. In: European Journal of Protistology 55, pp. 4-11. DOI: 10.1016/j.ejop.2016.02.002.

Cleary, A. and E. Durbin (2016). “Unexpected prevalence of parasite 18S rDNA sequences in winter among Antarctic marine protists”. In: Journal of Plankton Research 38.3, pp. 401-417. DOI: 10.1093/plankt/fbw005.

Coelho, F., A. Louvado, P. Domingues, et al. (2016). “Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz”. In: Scientific Reports 6. DOI: 10.1038/srep35272.

Cooper, M., D. Phalen, S. Donahoe, et al. (2016). “The utility of diversity profiling using Illumina 18S rRNA gene amplicon deep sequencing to detect and discriminate Toxoplasma gondii among the cyst-forming coccidia”. In: Veterinary Parasitology 216, pp. 38-45. DOI: 10.1016/j.vetpar.2015.12.011.

Cornejo-Castillo, F., A. Cabello, G. Salazar, et al. (2016). “Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton”. In: Nature Communications 7. DOI: 10.1038/ncomms11071.

Dubourg, G., J. Lagier, S. Hüe, et al. (2016). “Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen”. In: BMJ Open Gastroenterology 3.1. DOI: 10.1136/bmjgast-2016-000080.

Ferrera, I., C. Giner, A. Reñé, et al. (2016). “Evaluation of alternative high-throughput sequencing methodologies for the monitoring of marine picoplanktonic biodiversity based on rRNA gene amplicons”. In: Frontiers in Marine Science 3.AUG. DOI: 10.3389/fmars.2016.00147.

Forster, D., M. Dunthorn, F. Mahé, et al. (2016). “Benthic protists: The under-charted majority”. In: FEMS Microbiology Ecology 92.8. DOI: 10.1093/femsec/fiw120.

Forster, D., M. Dunthorn, T. Stoeck, et al. (2016). “Comparison of three clustering approaches for detecting novel environmental microbial diversity”. In: PeerJ 2016.2. DOI: 10.7717/peerj.1692.

Genitsaris, S., S. Monchy, E. Breton, et al. (2016). “Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations”. In: Marine Ecology Progress Series 548, pp. 61-75. DOI: 10.3354/meps11647.

Genitsaris, S., S. Monchy, J. Denonfoux, et al. (2016). “Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing”. In: Marine Biology Research 12.1, pp. 30-42. DOI: 10.1080/17451000.2015.1084425.

Gimmler, A., R. Korn, C. De Vargas, et al. (2016). “The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates”. In: Scientific Reports 6. DOI: 10.1038/srep33555.

Giner, C., I. Forn, S. Romac, et al. (2016). “Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes”. In: Applied and Environmental Microbiology 82.15, pp. 4757-4766. DOI: 10.1128/AEM.00560-16.

Groot, G. de, I. Laros, and S. Geisen (2016). “Molecular identification of soil eukaryotes and focused approaches targeting protist and faunal groups using high-throughput metabarcoding”. In: Methods in Molecular Biology 1399, pp. 125-140. DOI: 10.1007/978-1-4939-3369-3_7.

Guardiola, M., O. Wangensteen, P. Taberlet, et al. (2016). “Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA”. In: PeerJ 2016.12. DOI: 10.7717/peerj.2807.

Hu, Y., B. Karlson, S. Charvet, et al. (2016). “Diversity of pico- to mesoplankton along the 2000 km salinity gradient of the baltic sea”. In: Frontiers in Microbiology 7.MAY. DOI: 10.3389/fmicb.2016.00679.

Ichinomiya, M., A. Dos Santos, P. Gourvil, et al. (2016). “Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms”. In: ISME Journal 10.10, pp. 2419-2434. DOI: 10.1038/ismej.2016.38.

Kozlov, A., J. Zhang, P. Yilmaz, et al. (2016). “Phylogeny-aware identification and correction of taxonomically mislabeled sequences”. In: Nucleic Acids Research 44.11, pp. 5022-5033. DOI: 10.1093/nar/gkw396.

Le Bescot, N., F. Mahé, S. Audic, et al. (2016). “Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding”. In: Environmental Microbiology 18.2, pp. 609-626. DOI: 10.1111/1462-2920.13039.

Leray, M. and N. Knowlton (2016). “Censusing marine eukaryotic diversity in the twenty-first century”. In: Philosophical Transactions of the Royal Society B: Biological Sciences 371.1702. DOI: 10.1098/rstb.2015.0331.

Malviya, S., E. Scalco, S. Audic, et al. (2016). “Insights into global diatom distribution and diversity in the world’s ocean”. In: Proceedings of the National Academy of Sciences of the United States of America 113.11, pp. E1516-E1525. DOI: 10.1073/pnas.1509523113.

Marquardt, M., A. Vader, E. Stübner, et al. (2016). “Strong seasonality of marine microbial eukaryotes in a high-Arctic fjord (Isfjorden, in West Spitsbergen, Norway)”. In: Applied and Environmental Microbiology 82.6, pp. 1868-1880. DOI: 10.1128/AEM.03208-15.

More, R. and H. Purohit (2016). “The identification of discriminating patterns from 16S rRNA gene to generate signature for bacillus genus”. In: Journal of Computational Biology 23.8, pp. 651-661. DOI: 10.1089/cmb.2016.0002.

Moustaka-Gouni, M., K. Kormas, M. Scotti, et al. (2016). “Warming and acidification effects on planktonic heterotrophic pico- and nanoflagellates in a mesocosm experiment”. In: Protist 167.4, pp. 389-410. DOI: 10.1016/j.protis.2016.06.004.

Nitsche, F. (2016). “A phylogenetic and morphological re-investigation of Diaphanoeca spiralifurca, Didymoeca elongata and Polyoeca dichotoma (Acanthoecida/Choanomonadida) from the Caribbean Sea”. In: European Journal of Protistology 52, pp. 58-64. DOI: 10.1016/j.ejop.2015.11.001.

Obbels, D., E. Verleyen, M. Mano, et al. (2016). “Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the sør rondane mountains, dronning maud land, east antarctica”. In: FEMS Microbiology Ecology 92.6, pp. 1-13. DOI: 10.1093/femsec/fiw041.

Pagenkopp Lohan, K., R. Fleischer, K. Carney, et al. (2016). “Amplicon-based pyrosequencing reveals high diversity of protistan parasites in ships’ ballast water: Implications for biogeography and infectious diseases”. In: Microbial Ecology 71.3, pp. 530-542. DOI: 10.1007/s00248-015-0684-6.

Pawlowski, J., F. Lejzerowicz, L. Apotheloz-Perret-Gentil, et al. (2016). “Protist metabarcoding and environmental biomonitoring: Time for change”. In: European Journal of Protistology 55, pp. 12-25. DOI: 10.1016/j.ejop.2016.02.003.

Pearman, J., H. Anlauf, X. Irigoien, et al. (2016). “Please mind the gap - Visual census and cryptic biodiversity assessment at central Red Sea coral reefs”. In: Marine Environmental Research 118, pp. 20-30. DOI: 10.1016/j.marenvres.2016.04.011.

Pearman, J., S. Kürten, Y. Sarma, et al. (2016). “Biodiversity patterns of plankton assemblages at the extremes of the Red Sea”. In: FEMS Microbiology Ecology 92.3. DOI: 10.1093/femsec/fiw002.

Pernice, M., C. Giner, R. Logares, et al. (2016). “Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans”. In: ISME Journal 10.4, pp. 945-958. DOI: 10.1038/ismej.2015.170.

Ram'irez-Sánchez, O., P. Pérez-Rodr'iguez, L. Delaye, et al. (2016). “Plant proteins are smaller because they are encoded by fewer exons than animal proteins”. In: Genomics, Proteomics and Bioinformatics 14.6, pp. 357-370. DOI: 10.1016/j.gpb.2016.06.003.

Rimet, F., P. Chaumeil, F. Keck, et al. (2016). “R-Syst::diatom: An open-access and curated barcode database for diatoms and freshwater monitoring”. In: Database-the Magazine of Electronic Database Reviews 2016. DOI: 10.1093/database/baw016.

Rocke, E., H. Jing, X. Xia, et al. (2016). “Effects of hypoxia on the phylogenetic composition and species distribution of protists in a subtropical harbor”. In: Microbial Ecology 72.1, pp. 96-105. DOI: 10.1007/s00248-016-0751-7.

Schiaffino, M., E. Lara, L. Fernández, et al. (2016). “Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes”. In: Environmental Microbiology 18.12, pp. 5249-5264. DOI: 10.1111/1462-2920.13566.

Scholz, B., L. Guillou, A. Marano, et al. (2016). “Zoosporic parasites infecting marine diatoms-A black box that needs to be opened”. In: Fungal Ecology 19, pp. 59-76. DOI: 10.1016/j.funeco.2015.09.002.

Shazib, S., P. Vdacn'y, J. Kim, et al. (2016). “Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region”. In: Molecular Phylogenetics and Evolution 102, pp. 128-144. DOI: 10.1016/j.ympev.2016.05.041.

Simon, M., P. López-Garc'ia, P. Deschamps, et al. (2016). “Resilience of freshwater communities of small microbial eukaryotes undergoing severe drought events”. In: Frontiers in Microbiology 7.MAY. DOI: 10.3389/fmicb.2016.00812.

Singer, D., E. Lara, M. Steciow, et al. (2016). “High-throughput sequencing reveals diverse oomycete communities in oligotrophic peat bog micro-habitat”. In: Fungal Ecology 23, pp. 42-47. DOI: 10.1016/j.funeco.2016.05.009.

Sun, P., J. Clamp, D. Xu, et al. (2016). “An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates”. In: Scientific Reports 6. DOI: 10.1038/srep21695.

Volant, A., M. Héry, A. Desoeuvre, et al. (2016). “Spatial distribution of eukaryotic communities using high-throughput sequencing along a pollution gradient in the arsenic-rich creek sediments of carnoulès mine, france”. In: Microbial Ecology 72.3, pp. 608-620. DOI: 10.1007/s00248-016-0826-5.

Voudanta, E., K. Kormas, S. Monchy, et al. (2016). “Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater”. In: PeerJ 2016.3. DOI: 10.7717/peerj.1829.

Zaiko, A., K. Schimanski, X. Pochon, et al. (2016). “Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management”. In: Biofouling 32.6, pp. 671-684. DOI: 10.1080/08927014.2016.1186165.

Zoccarato, L., A. Pallavicini, F. Cerino, et al. (2016). “Water mass dynamics shape Ross Sea protist communities in mesopelagic and bathypelagic layers”. In: Progress in Oceanography 149, pp. 16-26. DOI: 10.1016/j.pocean.2016.10.003.

2015

Balzano, S., E. Abs, and S. Leterme (2015). “Protist diversity along a salinity gradient in a coastal lagoon”. In: Aquatic Microbial Ecology 74.3, pp. 263-277. DOI: 10.3354/ame01740.

Bass, D., G. Stentiford, D. Littlewood, et al. (2015). “Diverse applications of environmental DNA methods in parasitology”. In: Trends in Parasitology 31.10, pp. 499-513. DOI: 10.1016/j.pt.2015.06.013.

Campo, J. del, D. Mallo, R. Massana, et al. (2015). “Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing”. In: Environmental Microbiology 17.9, pp. 3195-3207. DOI: 10.1111/1462-2920.12759.

Christaki, U., C. Georges, S. Genitsaris, et al. (2015). “Microzooplankton community associated with phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)”. In: FEMS Microbiology Ecology 91.7. DOI: 10.1093/femsec/fiv068.

De Vargas, C., S. Audic, N. Henry, et al. (2015). “Eukaryotic plankton diversity in the sunlit ocean”. In: Science (New York, N.Y.) 348.6237. DOI: 10.1126/science.1261605.

Decelle, J., S. Romac, R. Stern, et al. (2015). “PhytoREF: A reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy”. In: Molecular Ecology Resources 15.6, pp. 1435-1445. DOI: 10.1111/1755-0998.12401.

Egge, E., W. Eikrem, and B. Edvardsen (2015). “Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing”. In: Journal of Eukaryotic Microbiology 62.1, pp. 121-140. DOI: 10.1111/jeu.12157.

Esling, P., F. Lejzerowicz, and J. Pawlowski (2015). “Accurate multiplexing and filtering for high-throughput amplicon-sequencing”. In: Nucleic Acids Research 43.5, pp. 2513-2524. DOI: 10.1093/nar/gkv107.

Geisen, S., I. Laros, A. Vizcaíno, et al. (2015). “Not all are free-living: High-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa”. In: Molecular Ecology 24.17, pp. 4556-4569. DOI: 10.1111/mec.13238.

Genitsaris, S., S. Monchy, E. Viscogliosi, et al. (2015). “Seasonal variations of marine protist community structure based on taxon-specific traits using the eastern English Channel as a model coastal system”. In: FEMS Microbiology Ecology 91.5. DOI: 10.1093/femsec/fiv034.

Goltsman, D., L. Comolli, B. Thomas, et al. (2015). “Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities”. In: ISME Journal 9, pp. 1014-1023. DOI: 10.1038/ismej.2014.200.

Gong, J., F. Shi, B. Ma, et al. (2015). “Depth shapes \(\alpha\)- and \(\beta\)-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems”. In: Environmental Microbiology 17.10, pp. 3722-3737. DOI: 10.1111/1462-2920.12763.

Guardiola, M., M. Uriz, P. Taberlet, et al. (2015). “Deep-sea, deep-sequencing: Metabarcoding extracellular DNA from sediments of marine canyons”. In: PLoS ONE 10.10. DOI: 10.1371/journal.pone.0139633.

Jeffries, T., M. Ostrowski, R. Williams, et al. (2015). “Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll”. In: Scientific Reports 5. DOI: 10.1038/srep15383.

Jing, H., E. Rocke, L. Kong, et al. (2015). “Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing”. In: Biogeosciences Discussions 12.16, pp. 13483-13509. DOI: 10.5194/bgd-12-13483-2015.

Lejzerowicz, F., P. Esling, L. Pillet, et al. (2015). “High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems”. In: Scientific Reports 5. DOI: 10.1038/srep13932.

Lima-Mendez, G., K. Faust, N. Henry, et al. (2015). “Determinants of community structure in the global plankton interactome”. In: Science (New York, N.Y.) 348.6237. DOI: 10.1126/science.1262073.

Mahé, F., J. Mayor, J. Bunge, et al. (2015). “Comparing high-throughput platforms for sequencing the V4 region of SSU-rDNA in environmental microbial eukaryotic diversity surveys”. In: Journal of Eukaryotic Microbiology 62.3, pp. 338-345. DOI: 10.1111/jeu.12187.

Mahé, F., T. Rognes, C. Quince, et al. (2015). “Swarmv2: Highly-scalable and high-resolution amplicon clustering”. In: PeerJ 2015.12. DOI: 10.7717/peerj.1420.

Massana, R. (2015). Protistan diversity in environmental molecular surveys , pp. 3-21. DOI: 10.1007/978-4-431-55130-0_1.

Massana, R., A. Gobet, S. Audic, et al. (2015). “Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing”. In: Environmental Microbiology 17.10, pp. 4035-4049. DOI: 10.1111/1462-2920.12955.

Morard, R., K. Darling, F. Mahé, et al. (2015). “PFR2: A curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution”. In: Molecular Ecology Resources 15.6, pp. 1472-1485. DOI: 10.1111/1755-0998.12410.

Pochon, X., A. Zaiko, G. Hopkins, et al. (2015). “Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices”. In: Biofouling 31.3, pp. 241-251. DOI: 10.1080/08927014.2015.1028923.

Pringault, O., J. Aube, O. Bouchez, et al. (2015). “Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat”. In: Chemosphere 135, pp. 189-201. DOI: 10.1016/j.chemosphere.2015.04.037.

Richards, T., G. Leonard, F. Mahé, et al. (2015). “Molecular diversity and distribution of marine fungi across 130 european environmental samples”. In: Proceedings of the Royal Society B: Biological Sciences 282.1819. DOI: 10.1098/rspb.2015.2243.

Saghaï, A., Y. Zivanovic, N. Zeyen, et al. (2015). “Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites”. In: Frontiers in Microbiology 6.AUG. DOI: 10.3389/fmicb.2015.00797.

Simon, M., P. López-Garc'ia, P. Deschamps, et al. (2015). “Marked seasonality and high spatial variability of protist communities in shallow freshwater systems”. In: ISME Journal 9.9, pp. 1941-1953. DOI: 10.1038/ismej.2015.6.

Wu, W., L. Wang, Y. Liao, et al. (2015). “Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea”. In: MicrobiologyOpen 4.5, pp. 826-840. DOI: 10.1002/mbo3.282.

2014

Chambouvet, A., C. Berney, S. Romac, et al. (2014). “Diverse molecular signatures for ribosomally ‘active’ Perkinsea in marine sediments”. In: BMC Microbiology 14.1. DOI: 10.1186/1471-2180-14-110.

Christaki, U., K. Kormas, S. Genitsaris, et al. (2014). “Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system”. In: Microbial Ecology 67.1, pp. 13-23. DOI: 10.1007/s00248-013-0290-4.

Decelle, J., S. Romac, E. Sasaki, et al. (2014). “Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing”. In: PLoS ONE 9.8. DOI: 10.1371/journal.pone.0104297.

Georges, C., S. Monchy, S. Genitsaris, et al. (2014). “Protist community composition during early phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean)”. In: Biogeosciences (Online) 11.20, pp. 5847-5863. DOI: 10.5194/bg-11-5847-2014.

Heger, T., V. Edgcomb, E. Kim, et al. (2014). “A resurgence in field research is essential to better understand the diversity, ecology, and evolution of microbial eukaryotes”. In: Journal of Eukaryotic Microbiology 61.2, pp. 214-223. DOI: 10.1111/jeu.12095.

Lara, E., C. Seppey, G. Garraza, et al. (2014). “Planktonic eukaryote molecular diversity: Discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina)”. In: Journal of Plankton Research 37.3, pp. 645-655. DOI: 10.1093/plankt/fbv016.

Lejzerowicz, F., P. Esling, and J. Pawlowski (2014). “Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing”. In: Deep-Sea Research Part II: Topical Studies in Oceanography 108, pp. 17-26. DOI: 10.1016/j.dsr2.2014.07.018.

Lentendu, G., T. Wubet, A. Chatzinotas, et al. (2014). “Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach”. In: Molecular Ecology 23.13, pp. 3341-3355. DOI: 10.1111/mec.12819.

Lie, A., Z. Liu, S. Hu, et al. (2014). “Investigating microbial eukaryotic diversity from a global census: Insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes”. In: Applied and Environmental Microbiology 80.14, pp. 4363-4373. DOI: 10.1128/AEM.00057-14.

Logares, R., S. Audic, D. Bass, et al. (2014). “Patterns of rare and abundant marine microbial eukaryotes”. In: Current Biology 24.8, pp. 813-821. DOI: 10.1016/j.cub.2014.02.050.

Massana, R., J. Del Campo, M. Sieracki, et al. (2014). “Exploring the uncultured microeukaryote majority in the oceans: Reevaluation of ribogroups within stramenopiles”. In: ISME Journal 8.4, pp. 854-866. DOI: 10.1038/ismej.2013.204.

Nanjappa, D., S. Audic, S. Romac, et al. (2014). “Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach”. In: PLoS ONE 9.8. DOI: 10.1371/journal.pone.0103810.

Parfrey, L., W. Walters, C. Lauber, et al. (2014). “Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity”. In: Frontiers in Microbiology 5.JUN. DOI: 10.3389/fmicb.2014.00298.

Parris, D., S. Ganesh, V. Edgcomb, et al. (2014). “Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile”. In: Frontiers in Microbiology 5.OCT. DOI: 10.3389/fmicb.2014.00543.

Patterson, D. (2014). “Helping Protists to find their place in a big data world”. In: Acta Protozoologica 53.1, pp. 115-128. DOI: 10.4467/16890027AP.14.011.1448.

Taylor, J. and M. Cunliffe (2014). “High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters”. In: Journal of Phycology 50.5, pp. 960-965. DOI: 10.1111/jpy.12228.

Wu, W., B. Huang, Y. Liao, et al. (2014). “Picoeukaryotic diversity and distribution in the subtropical-tropical South China Sea”. In: FEMS Microbiology Ecology 89.3, pp. 563-579. DOI: 10.1111/1574-6941.12357.

Xiuhai, L. (2014). “An OpenFlow switch model using kepler GPU”. In: Journal of Software Engineering 8.4, pp. 304-313. DOI: 10.3923/jse.2014.304.313.

Xu, Y., T. Vick-Majors, R. Morgan-Kiss, et al. (2014). “Ciliate diversity, community structure, and Novel Taxa in lakes of the McMurdo Dry Valleys, Antarctica”. In: Biological Bulletin 227.2, pp. 175-190. DOI: 10.1086/BBLv227n2p175.

Yilmaz, P., L. Parfrey, P. Yarza, et al. (2014). “The SILVA and”all-species Living Tree Project (LTP)” taxonomic frameworks”. In: Nucleic Acids Research 42.D1, pp. D643-D648. DOI: 10.1093/nar/gkt1209.

2013

Adl, S., A. Habura, and Y. Eglit (2013). “Amplification primers of SSU rDNA for soil protists”. In: Soil Biology and Biochemistry 69, pp. 328-342. DOI: 10.1016/j.soilbio.2013.10.024.

Campo, J. del, V. Balagué, I. Forn, et al. (2013). “Culturing bias in marine heterotrophic flagellates analyzed through seawater enrichment incubations”. In: Microbial Ecology 66.3, pp. 489-499. DOI: 10.1007/s00248-013-0251-y.

Cheung, M., W. Nong, H. Kwan, et al. (2013). “Composition of heterotrophic flagellates in coastal waters of different trophic status”. In: Current Microbiology 67.3, pp. 351-355. DOI: 10.1007/s00284-013-0374-x.

Decelle, J., P. Martin, K. Paborstava, et al. (2013). “Diversity, ecology and biogeochemistry of cyst-forming acantharia (radiolaria) in the oceans”. In: PLoS ONE 8.1. DOI: 10.1371/journal.pone.0053598.

Del Campo, J. and I. Ruiz-Trillo (2013). “Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts”. In: Molecular Biology and Evolution 30.4, pp. 802-805. DOI: 10.1093/molbev/mst006.

Egge, E., L. Bittner, T. Andersen, et al. (2013). “454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: A test for marine haptophytes”. In: PLoS ONE 8.9. DOI: 10.1371/journal.pone.0074371.

Fernández-Suárez, X. and M. Galperin (2013). “The 2013 nucleic acids research database issue and the online molecular biology database collection”. In: Nucleic Acids Research 41.D1, pp. D1-D7. DOI: 10.1093/nar/gks1297.

Risse-Buhl, U., M. Herrmann, P. Lange, et al. (2013). “Phagotrophic protist diversity in the groundwater of a karstified aquifer - Morphological and molecular analysis”. In: Journal of Eukaryotic Microbiology 60.5, pp. 467-479. DOI: 10.1111/jeu.12054.

Thaler, M. and C. Lovejoy (2013). “Environmental selection of marine stramenopile clades in the Arctic Ocean and coastal waters”. In: Polar Biology 37.3, pp. 347-357. DOI: 10.1007/s00300-013-1435-0.

Vinogradov, S., X. Bailly, D. Smith, et al. (2013). “Microbial eukaryote globins”. In: Advances in Microbial Physiology 63, pp. 391-446. DOI: 10.1016/B978-0-12-407693-8.00009-1.