Papers citing PR2

2025

Adyari, B., L. Zhang, A. Maravić, et al. (2025). “Urbanization enhances consumer protist-driven ARGs dissemination in riverine ecosystems”. In: Environment International 195. DOI: 10.1016/j.envint.2024.109238.

Alacid, E., A. Reñé, N. Timoneda, et al. (2025). “Macroalgal biofilm harbours a wide diversity of parasitic protists with distinct temporal dynamics”. In: Molecular Ecology 34.5. DOI: 10.1111/mec.17666.

Amacker, N., Z. Gao, A. L. Jousset, et al. (2025). “Identity and timing of protist inoculation affect plant performance largely irrespective of changes in the rhizosphere microbial community”. In: Applied and Environmental Microbiology 91.4. DOI: 10.1128/aem.00240-25.

Badra, M., J. Freudenthal, and K. Dumack (2025). “Sludge retention time in anaerobic digestion affects Archaea by a cascade through microeukaryotes”. In: Water Research 278. DOI: 10.1016/j.watres.2025.123371.

Bao, Y., B. Li, R. Jia, et al. (2025). “Effects of different river crab eriocheir sinensis polyculture practices on bacterial, fungal and protist communities in pond water”. In: Biomolecules 15.1. DOI: 10.3390/biom15010031.

Bashenkhaeva, M., Y. R. Zakharova, Y. P. Galachyants, et al. (2025). “Under-ice bacterial and microeukaryotic communities of the maloe more strait (lake baikal)”. In: Microbiology (Russian Federation) 94.2, pp. 172 - 180. DOI: 10.1134/S002626172460890X.

Bludau, D., G. Sieber, M. Shah, et al. (2025). “Breaking the standard: Can oxford nanopore technologies sequencing compete with illumina in protistan amplicon studies?” In: Environmental DNA 7.2. DOI: 10.1002/edn3.70084.

Böttner, L., F. Dudenhausen, S. Nouere, et al. (2025). “Herbivory can increase plant fitness via reduced interspecific competition - evidence from models and mesocosms”. In: Proceedings of the Royal Society B: Biological Sciences 292.2039. DOI: 10.1098/rspb.2024.1149.

Cao, Y., Y. Lei, J. Shi, et al. (2025). “Indications of a benthic foraminifer Cribrononion gnythosuturatum to salinities revealed by eDNA metabarcoding and morphological methods”. In: Marine Pollution Bulletin 211. DOI: 10.1016/j.marpolbul.2024.117428.

Casabianca, S., M. Basili, S. Capellacci, et al. (2025). “Temporal dynamics of communities on plastic debris in a polluted marine habitat”. In: Marine Pollution Bulletin 214. DOI: 10.1016/j.marpolbul.2025.117763.

Chang, C., E. Hu, X. Tang, et al. (2025). “Assembly of soil multitrophic community regulates multifunctionality via multifaceted biotic factors in subtropical ecosystems”. In: Environment International 195. DOI: 10.1016/j.envint.2025.109272.

Chen, Y., J. Ning, D. Su, et al. (2025). “Molecular diversity and potential ecological risks of toxic HAB species in the coastal waters off Qinhuangdao, China”. In: Environmental Pollution 373. DOI: 10.1016/j.envpol.2025.126121.

Connors, E., K. L. Gallagher, A. Dutta, et al. (2025). “Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot”. In: Polar Biology 48.2. DOI: 10.1007/s00300-025-03380-y.

Dai, R., Z. Wen, H. Hong, et al. (2025). “Eukaryotic phytoplankton drive a decrease in primary production in response to elevated CO2 in the tropical and subtropical oceans”. In: Proceedings of the National Academy of Sciences of the United States of America 122.11. DOI: 10.1073/pnas.2423680122.

Daraghmeh, N., K. Exter, J. Pagnier, et al. (2025). “A long-term ecological research data set from the marine genetic monitoring program ARMS-MBON 2018–2020”. In: Molecular Ecology Resources 25.4. DOI: 10.1111/1755-0998.14073.

Debnath, S. C., D. L. Chaput, J. McMurtrie, et al. (2025). “Seasonal dynamics and factors shaping microbiomes in freshwater finfish earthen aquaculture ponds in Bangladesh”. In: Environmental Microbiome 20.1. DOI: 10.1186/s40793-025-00687-5.

Du, S., D. Lin, T. Zhang, et al. (2025). “Earthworm gut’s potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size”. In: Fundamental Research. DOI: 10.1016/j.fmre.2025.03.018.

Echenique-Subiabre, I., S. L. Jackrel, J. McCarren, et al. (2025). “Traits determine dispersal and colonization abilities of microbes”. In: Applied and Environmental Microbiology 91.3. DOI: 10.1128/aem.02055-24.

Egge, E., D. Vaulot, A. Larsen, et al. (2025). “The community of marine alveolate parasites in the Atlantic inflow to the Arctic Ocean is structured by season, depth, and water mass”. In: Arctic Science 11. DOI: 10.1139/as-2024-0016.

Fagín, E., M. Felip, A. Brancelj, et al. (2025). “Parasite sedimentary DNA reveals fish introduction into a European high-mountain lake by the seventh century”. In: Nature Communications 16.1. DOI: 10.1038/s41467-025-57801-x.

Frigaard, N. and S. E. Seemann (2025). “Methane and CO2 consumption from a synthetic waste gas by microbial communities in enriched seawater”. In: Carbon Capture Science and Technology 14. DOI: 10.1016/j.ccst.2024.100324.

Fukai, Y., A. Fujiwara, S. Nishino, et al. (2025). “Characteristics of autumn phytoplankton communities in the Chukchi Sea: resuspension of settled diatoms to the surface during strong wind events”. In: Marine Ecology Progress Series 752, pp. 35 - 50. DOI: 10.3354/meps14753.

Fuß, T., L. Thuile Bistarelli, R. Ptacnik, et al. (2025). “Niche partitioning in a periphyton metacommunity peaks at intermediate species richness in midsized rivers”. In: Ecology 106.1. DOI: 10.1002/ecy.4524.

Gerasimova, E. A., A. S. Balkin, V. Y. Kataev, et al. (2025). “Taxonomic and functional diversity of protists in saline and hypersaline lakes in southern Western Siberia, a region strongly affected by climate change”. In: Water Biology and Security 4.1. DOI: 10.1016/j.watbs.2024.100316.

Gleich, S. J., L. Y. Mesrop, J. A. Cram, et al. (2025). “With a little help from my friends: importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel”. In: mSystems 10.2. DOI: 10.1128/msystems.01045-24.

Guo, P., C. Li, J. Liu, et al. (2025). “Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake”. In: Marine Life Science and Technology 7.1, pp. 176 - 186. DOI: 10.1007/s42995-024-00256-8.

Hamard, S., S. Planchenault, R. Walcker, et al. (2025). “Microbial photosynthesis mitigates carbon loss from northern peatlands under warming”. In: Nature Climate Change 15.4, pp. 436 - 443. DOI: 10.1038/s41558-025-02271-8.

Hao, S., Z. Hei, J. Ma, et al. (2025). “Soil microbial diversity-function relationships are changed by human activity at a landscape scale”. In: Plant and Soil. DOI: 10.1007/s11104-024-07174-9.

Hayden, H. L., R. Ghaderi, C. Trollip, et al. (2025). “Advancing the use of metabarcoding derived nematode-based indices as soil health bioindicators in agricultural and natural environments”. In: Soil Biology and Biochemistry 205. DOI: 10.1016/j.soilbio.2025.109772.

Hernández-Becerril, D. U., R. Rodríguez-Martínez, F. Varona-Cordero, et al. (2025). “Diversity and distribution of the eukaryotic picoplankton in the oxygen minimum zone of the tropical Mexican Pacific”. In: Journal of Plankton Research 47.2. DOI: 10.1093/plankt/fbae083.

Hervé, V., J. Morelle, J. Lambourdière, et al. (2025). “Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary”. In: Environmental Microbiome 20.1. DOI: 10.1186/s40793-025-00664-y.

Holman, L. E., G. Zampirolo, R. Gyllencreutz, et al. (2025). “Navigating past oceans: Comparing metabarcoding and metagenomics of marine ancient sediment environmental DNA”. In: Molecular Ecology Resources. DOI: 10.1111/1755-0998.14086.

Hu, Y., K. Jiang, S. Xia, et al. (2025). “Amoeba community dynamics and assembly mechanisms in full-scale drinking water distribution networks under various disinfectant regimens”. In: Water Research 271. DOI: 10.1016/j.watres.2024.122861.

Huang, J., J. Zhang, T. Huang, et al. (2025). “Unraveling assembly processes shaping soil protist community dynamics across successional stages of temperate forests on the Chinese Loess Plateau”. In: Catena 255. DOI: 10.1016/j.catena.2025.109030.

Huber, L., E. Malfatti, C. S. R. Huber, et al. (2025). “Is the composition of communities in bromeliad water and adjacent soil similar?” In: Journal of Eukaryotic Microbiology 72.3. DOI: 10.1111/jeu.70009.

Jeevannavar, A., J. Florenza, A. Divne, et al. (2025). “Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate”. In: ISME Journal 19.1. DOI: 10.1093/ismejo/wraf046.

Jiang, J., L. Zhou, D. Lin, et al. (2025). “Effects of multispecies management on the soil protist community in Pinus massoniana plantations in subtropical China”. In: Pedobiologia 109. DOI: 10.1016/j.pedobi.2025.151035.

Kaiser, P., W. Hagen, A. Schukat, et al. (2025). “Phytoplankton diversity and zooplankton diet across Fram Strait: Spatial patterns with implications for the future Arctic Ocean”. In: Progress in Oceanography 234. DOI: 10.1016/j.pocean.2025.103423.

Kalra, I., B. P. Stewart, K. M. Florea, et al. (2025). “Temporal and spatial dynamics of harmful algal bloom-associated microbial communities in eutrophic Clear Lake, California”. In: Applied and Environmental Microbiology 91.4. DOI: 10.1128/aem.00011-25.

Kassim, N. S., L. K. Lee, K. S. Hii, et al. (2025). “Molecular diversity of benthic harmful dinoflagellates on a tropical reef: Comparing natural and artificial substrate sampling methods using DNA metabarcoding and morphological analysis”. In: Harmful Algae 142. DOI: 10.1016/j.hal.2024.102795.

Kaushik, T., V. Dixit, and R. Mohan (2025). “Spatial distribution of picoeukaryotic community from the hydrographic fronts of the indian sector of the southern ocean as revealed by metabarcoding”. In: Polar Biology 48.1. DOI: 10.1007/s00300-024-03319-9.

Klein, S. G., L. Frühe, A. J. Parry, et al. (2025). “Deep oxygen-depleted depressions in a Red Sea coral reef sustain resistant ecosystems”. In: PNAS Nexus 4.3. DOI: 10.1093/pnasnexus/pgaf049.

Krabberød, A. K., E. Stokke, E. Thoen, et al. (2025). “The ribosomal operon database: a full-length rDNA operon database derived from genome assemblies”. In: Molecular Ecology Resources 25.1. DOI: 10.1111/1755-0998.14031.

Lazrak, K., Z. Tazart, M. Nothof, et al. (2025). “Assessment of the short-term salinity effect on algal biofilm through field transfer in the Drâa river (Southeastern Morocco) using metabarcoding and morphological analyses”. In: Environmental Monitoring and Assessment 197.4. DOI: 10.1007/s10661-025-13842-9.

Lentendu, G., D. Singer, S. Agatha, et al. (2025). “EukFunc: a holistic eukaryotic functional reference for automated profiling of soil eukaryotes”. In: Molecular Ecology Resources. DOI: 10.1111/1755-0998.14118.

Li, D., C. Ma, C. Yue, et al. (2025). “Windfarm construction alters soil multinutrient cycling by destabilizing microfauna community in a mountain ecosystem”. In: Journal of Environmental Management 373. DOI: 10.1016/j.jenvman.2024.123758.

Li, J., L. Chen, C. Zhang, et al. (2025). “Organic amendments with low C/N ratios enhanced the deposition of crop root exudates into stable soil organic carbon in a sodic soil”. In: Plant and Soil. DOI: 10.1007/s11104-024-07170-z.

Li, X., Y. Wang, M. Dunthorn, et al. (2025). “Distinct ecological processes shape micro-eukaryotic generalists and specialists in a canal-disturbed wetland, Lake Weishan, China”. In: Water Biology and Security 4.1. DOI: 10.1016/j.watbs.2024.100320.

Li, Y. and N. Chen (2025). “Optimization and evaluation of 18S rDNA V4-based metabarcoding analysis of tripos species”. In: Journal of Applied Phycology 37.2, pp. 1089 - 1103. DOI: 10.1007/s10811-024-03428-2.

Li, Y., Y. Sun, Y. Li, et al. (2025). “Small-sized soil organisms drive the legacy of soil addition in a degraded grassland”. In: Functional Ecology 39.4, pp. 1031 - 1045. DOI: 10.1111/1365-2435.70019.

Lian, W., W. Zhao, J. Han, et al. (2025). “Impacts of forest expansion on microbial diversity and community assembly in fragmented mountain ecosystems”. In: Environmental Research 270. DOI: 10.1016/j.envres.2025.120956.

Lian, W., W. Zhao, P. Wang, et al. (2025). “Habitat island biogeography of mountaintop plant and soil microbiomes: Similar patterns driven by different mechanisms”. In: Global Ecology and Conservation 59. DOI: 10.1016/j.gecco.2025.e03574.

Liao, X., H. Wang, D. Wu, et al. (2025). “Geographical and environmental factors differentially shape planktonic microbial community assembly and resistomes composition in urban rivers”. In: Global Change Biology 31.4. DOI: 10.1111/gcb.70211.

Liu, H., F. Ren, S. Wan, et al. (2025). “Nitrogen and water additions with or without mowing altered soil microbial community characteristics in a semi-arid steppe”. In: Ecological Processes 14.1. DOI: 10.1186/s13717-024-00568-8.

Luo, B., H. Hu, H. Zheng, et al. (2025). “Fertilization regulates maize nutrient use efficiency through soil rhizosphere biological network and root transcriptome”. In: Applied Soil Ecology 207. DOI: 10.1016/j.apsoil.2025.105912.

Mei, Z., C. Wu, S. Shi, et al. (2025). “Loss of protistan diversity weakens soil phosphorus availability”. In: Applied Soil Ecology 208. DOI: 10.1016/j.apsoil.2025.105976.

Mikhailov, I. S., Y. S. Bukin, A. D. Firsova, et al. (2025). “Comparison of relative and absolute abundance and biomass of freshwater phytoplankton taxa using metabarcoding and microscopy”. In: Ecology and Evolution 15.3. DOI: 10.1002/ece3.70856.

Mills, D. B., A. Vuillemin, K. Muschler, et al. (2025). “The Rise of Algae promoted eukaryote predation in the Neoproterozoic benthos”. In: Science Advances 11.8. DOI: 10.1126/sciadv.adt2147.

Mitrović, M., A. Čačković, L. Selak, et al. (2025). “A preliminary study on the eukaryotic microbial diversity in croatian geothermal waters”. In: Water (Switzerland) 17.4. DOI: 10.3390/w17040541.

Neri, F., M. Ubaldi, S. Accoroni, et al. (2025). “Comparative analysis of phytoplankton diversity using microscopy and metabarcoding: insights from an eLTER station in the Northern Adriatic Sea”. In: Hydrobiologia 852.1, pp. 169 - 183. DOI: 10.1007/s10750-024-05692-2.

Neupane, S., T. Davis, C. Olds, et al. (2025). “Unraveling the relationships between midge abundance and incidence, microbial communities, and soil and water properties in a protected natural tallgrass prairie”. In: Parasites and Vectors 18.1. DOI: 10.1186/s13071-025-06780-5.

Ong, D. R. Y., A. Gutiérrez-Rodríguez, K. A. Safi, et al. (2025). “Consistent cell-specific carbon fixation rates by small eukaryotic phytoplankton in contrasting nutrient-limited conditions”. In: Limnology and Oceanography 70.1, pp. 162 - 177. DOI: 10.1002/lno.12751.

Pagnier, J., N. Daraghmeh, and M. Obst (2025). “Using the long-term genetic monitoring network ARMS-MBON to detect marine non-indigenous species along the European coasts”. In: Biological Invasions 27.2. DOI: 10.1007/s10530-024-03503-2.

Park, J., B. L. Muhammad, T. Kim, et al. (2025). “Assessment of ship hull-attached marine diatoms: species composition and reattachment”. In: Marine Pollution Bulletin 216. DOI: 10.1016/j.marpolbul.2025.117962.

Pelusi, A., M. L. R. Martínez, A. Mule, et al. (2025). “Diatom distribution and long-term survival in a heavily polluted sediment core from the Bay of Bagnoli (Tyrrhenian Sea, Italy)”. In: Mediterranean Marine Science 26.1, pp. 40 - 54. DOI: 10.12681/mms.37946.

Pérez-Barrancos, C., E. Fraile-Nuez, J. P. Martín-Díaz, et al. (2025). “Shallow hydrothermal fluids shape microbial dynamics at the tagoro submarine volcano (canary islands, spain)”. In: Environmental Microbiology 27.2. DOI: 10.1111/1462-2920.70052.

Piwosz, K., A. Ameryk, K. Wdówka, et al. (2025). “Vertical distribution of heterotrophic nanoflagellates in the Baltic Proper”. In: Oceanologia 67.1. DOI: 10.5697/JMZS3739.

Ren, P., A. Sun, X. Jiao, et al. (2025). “The relationship between protist consumers and soil functional genes under long-term fertilization”. In: Science of the Total Environment 966. DOI: 10.1016/j.scitotenv.2025.178658.

Ren, X., C. Liu, Y. Yue, et al. (2025). “Exploring the potential role of soil protists in predicting banana health”. In: Microbiological Research 295. DOI: 10.1016/j.micres.2025.128109.

Salis, R. and L. Hansson (2025). “Comparative analysis of environmental DNA metabarcoding and spectro-fluorescence for phytoplankton community assessments”. In: Environmental DNA 7.2. DOI: 10.1002/edn3.70097.

Schalch-Schuler, M., B. Bassin, A. Andrei, et al. (2025). “The planktonic freshwater ciliate Balanion planctonicum (Ciliophora, Prostomatea): A cryptic species complex or a “complex species”?” In: Journal of Eukaryotic Microbiology 72.1. DOI: 10.1111/jeu.13084.

Shimonaka, T., T. Kodama, S. Otosaka, et al. (2025). “Differences in sinking processes and biological pump contribution among phytoplankton groups in the mesopelagic layer”. In: Global Biogeochemical Cycles 39.4. DOI: 10.1029/2024GB008476.

Sidón-Ceseña, K., M. A. Martínez-Mercado, J. Chong-Robles, et al. (2025). “The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season”. In: FEMS Microbiology Ecology 101.2. DOI: 10.1093/femsec/fiaf009.

Sow, S. L. S., W. H. van de Poll, R. Eveleth, et al. (2025). “Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula”. In: Environmental Microbiome 20.1. DOI: 10.1186/s40793-025-00663-z.

Stewart, J., N. M. de Lima, D. J. Eldridge, et al. (2025). “Restoring aboveground trophic diversity contributes to belowground microbial diversity in drylands”. In: Biological Conservation 305. DOI: 10.1016/j.biocon.2025.111056.

Stock, W., C. Rousseau, G. Dierickx, et al. (2025). “Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data”. In: Briefings in Bioinformatics 26.1. DOI: 10.1093/bib/bbae642.

Sun, Y., L. Tang, Y. Cui, et al. (2025). “Inoculation of plant growth-promoting rhizobacteria and rhizobia changes the protist community of alfalfa rhizosphere soil under saline-alkali environment”. In: Applied Soil Ecology 206. DOI: 10.1016/j.apsoil.2024.105775.

Sweetlove, M., B. Tytgat, E. Van de Vyver, et al. (2025). “Differences in community structuring among planktonic bacterial and micro-eukaryotic phyla in Chilean freshwater lakes”. In: Limnologica (Online) 111. DOI: 10.1016/j.limno.2025.126233.

Tapolczai, K., F. Rimet, M. Ćirić, et al. (2025). “A novel framework for phytoplankton biomonitoring: Trait assignment of 23S rRNA sequences”. In: Ecological Indicators 173. DOI: 10.1016/j.ecolind.2025.113361.

Tian, M., Z. Zhao, Q. Li, et al. (2025). “Nanoscale phosphorus-based agrochemicals enhance tomato and rice growth via positively modulating the growth-associated gene expression and endophytic microbial community”. In: Environmental Science: Nano. DOI: 10.1039/d5en00140d.

TONG, Y., L. WANG, C. WU, et al. (2025). “Promotion of symbiotic interaction between phagotrophic protists and beneficial bacteria, mediated via a balancing of soil nutrients, reduces the incidence of watermelon Fusarium wilt”. In: Pedosphere 35.2, pp. 352 - 363. DOI: 10.1016/j.pedsph.2023.12.014.

Tong, Y., X. Zheng, H. Liu, et al. (2025). “Bio-organic fertilizer enhances soil mineral solubilization, microbial community stability, and fruit quality in an 8-year watermelon continuous cropping system”. In: Biology and Fertility of Soils 61.4, pp. 747 - 760. DOI: 10.1007/s00374-025-01892-7.

Tucker, S. J., Y. M. Rii, K. C. Freel, et al. (2025). “Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific”. In: Limnology and Oceanography. DOI: 10.1002/lno.70075.

Vader, A., E. Handler, R. Skogseth, et al. (2025). “Seasonality and interannual variability of an Arctic marine time series, IsA”. In: Arctic Science 11, pp. 1 - 17. DOI: 10.1139/as-2024-0044.

Varrella, S., S. Livi, C. Corinaldesi, et al. (2025). “A comprehensive assessment of non-indigenous species requires the combination of multi-marker eDNA metabarcoding with classical taxonomic identification”. In: Environment International 199. DOI: 10.1016/j.envint.2025.109489.

Verdon, V., L. Malard, F. Collart, et al. (2025). “Can we accurately predict the distribution of soil microorganism presence and relative abundance?” In: Ecography 2025.3. DOI: 10.1111/ecog.07086.

Wang, H., K. Liu, Z. He, et al. (2025). “Rich molecular diversity of ribosomal RNA genes in Pseudo-nitzschia species (Bacillariophyceae) revealed through single-strain high throughput sequencing”. In: Algal Research 85. DOI: 10.1016/j.algal.2024.103869.

Wang, H., J. Yang, D. R. Finn, et al. (2025). “Distinct seasonal and annual variability of prokaryotes, fungi and protists in cropland soil under different tillage systems and soil texture”. In: Soil Biology and Biochemistry 203. DOI: 10.1016/j.soilbio.2025.109732.

Wang, L., X. Du, W. Shen, et al. (2025). “Inter-trophic networks reveal the central role of methanogens in deposited estuarine soils”. In: Soil Ecology Letters 7.2. DOI: 10.1007/s42832-025-0295-1.

Wang, X., F. Chen, J. Zeng, et al. (2025). “Divergent responses of soil glomalin and microbial necromass to precipitation reduction: New perspectives from soil aggregates and multi-trophic networks”. In: Soil Biology and Biochemistry 200. DOI: 10.1016/j.soilbio.2024.109638.

Wieber, C., L. Z. Jensen, L. Vergeynst, et al. (2025). “Terrestrial runoff is an important source of biological ice-nucleating particles in Arctic marine systems”. In: Atmospheric Chemistry and Physics 25.6, pp. 3327 - 3346. DOI: 10.5194/acp-25-3327-2025.

Willemsen, A., A. Manzano-Marín, and M. Horn (2025). “Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts”. In: Genome Biology and Evolution 17.1. DOI: 10.1093/gbe/evae271.

Wittmers, F., C. Poirier, C. Bachy, et al. (2025). “Symbionts of predatory protists are widespread in the oceans and related to animal pathogens”. In: Cell Host and Microbe 33.2, pp. 182 - 199.e7. DOI: 10.1016/j.chom.2025.01.009.

Wu, F., F. Li, Y. Zou, et al. (2025). “Environmental DNA reveals multitrophic insight into the mechanism of community stability changes in shallow eutrophic lakes”. In: ACS ES and T Water. DOI: 10.1021/acsestwater.4c01064.

Xu, H., X. He, J. Chen, et al. (2025). “Soil nutrient limitation controls trophic cascade effects of micro-food web-derived ecological functions in degraded agroecosystems”. In: Journal of Advanced Research. DOI: 10.1016/j.jare.2025.01.018.

Xu, M., X. Liu, T. Chen, et al. (2025). “Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages”. In: Science of the Total Environment 964. DOI: 10.1016/j.scitotenv.2025.178524.

Xu, Q., M. Feng, B. He, et al. (2025). “Soil micro-structure drives trophic interactions within micro-food webs via bottom-up regulation under different planting patterns”. In: Agriculture, Ecosystems and Environment 383. DOI: 10.1016/j.agee.2025.109539.

Xu, W., C. Lam, Y. Wang, et al. (2025). “Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters”. In: Environmental Pollution 367. DOI: 10.1016/j.envpol.2024.125572.

Yu, Y., M. Shangguan, P. Sun, et al. (2025). “Light-mediated population dynamics of picocyanobacteria shaping the diurnal patterns of microbial communities in an atoll lagoon”. In: Microorganisms 13.4. DOI: 10.3390/microorganisms13040727.

Záhonová, K., H. Kaur, C. C. Furgason, et al. (2025). “Comparative analysis of protist communities in oilsands tailings using amplicon sequencing and metagenomics”. In: Environmental Microbiology 27.1. DOI: 10.1111/1462-2920.70029.

Zhang, A., A. M. Potapov, R. Luo, et al. (2025). “Protist communities are correlated with abiotic soil factors, but not resources, prey, or predators along a subalpine secondary succession”. In: Geoderma 458. DOI: 10.1016/j.geoderma.2025.117310.

Zhang, W., Y. Zhang, Z. Shao, et al. (2025). “Differences in biogeographic patterns and mechanisms of assembly in estuarine bacterial and protist communities”. In: Microorganisms 13.1. DOI: 10.3390/microorganisms13010214.

Zhao, R., Y. Shi, L. Huang, et al. (2025). “Dynamics of protist and bacterial communities during the nitrogen removal by ecological floating beds of Sesuvium portulacastrum”. In: Ecological Processes 14.1. DOI: 10.1186/s13717-025-00602-3.

Zhu, H., K. Fazliddin, Q. Li, et al. (2025). “Contrasting adaptations of soil prokaryotes and arbuscular mycorrhizal fungi in saline wildland and non-saline farmland”. In: Fundamental Research. DOI: 10.1016/j.fmre.2025.02.009.

Zuo, J., S. Yang, H. Grossart, et al. (2025). “Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu”. In: Water Research 269. DOI: 10.1016/j.watres.2024.122784.

2024

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2023

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2021

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2020

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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. 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.

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Obiol, A., C. R. 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.

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Pearman, J. K., 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.

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Pinseel, E., S. B. 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. M. 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. M., C. A. Durkin, and K. M. 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.

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Ribeiro, C. G., A. L. 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.

Rodríguez-Martínez, R., G. Leonard, D. S. 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. E. Pérez-Jaramillo, V. N. 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. Martínez-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. and G. B. McManus (2020). Diversity and biogeography as revealed by morphologies and DNA sequences: Tintinnid ciliates as an example.

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.

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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.

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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. L. S., T. W. 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. A., K. S. 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 mass–driven 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. G. 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.

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Thompson, A. R., S. Geisen, and B. J. 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.

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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.

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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. D., J. M. Questel, K. R. 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. A. 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.

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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.

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.

2019

Ahmed, M., M. A. 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., G. A. Ellis, H. W. 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.

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. R. Edwards, J. M. 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. J. Syberg-Olsen, N. A. T. 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. A., 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. A. and S. K. 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. F. R. (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.

Degrune, F., K. Dumack, A. M. 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.

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. N., F. J. Coelho, D. F. 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. A. 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. M., 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.

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. J. 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. R., V. Balagué, A. K. 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.

Gołębiewski, 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.

Gómez-Consarnau, L., D. M. Needham, P. K. 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.

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. R. 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. K. 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. K. A. Suleiman, S. J. J. 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. F. 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 (2019a). “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 (2019b). “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. H. 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. R. B. Buosi, A. F. Cabral, et al. (2019). “Protist biodiversity and biogeography in lakes from four brazilian river–floodplain systems”. In: Journal of Eukaryotic Microbiology 66.4, pp. 592 - 599. DOI: 10.1111/jeu.12703.

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Pasulka, A., S. K. Hu, P. D. 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.

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2018

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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.

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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. K., P. E. Connell, L. Y. 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.

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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. V. W. 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. 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., H. D. Laughinghouse, 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. C. 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. C., 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. C., 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. S., 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. M., 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 river–south china 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. P. 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. B., M. B. 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. S. Benevides, J. B. O. Santos, et al. (2017). “Does environmental heterogeneity explain temporal β 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. M. 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.

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. M., 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. S. L., T. J. Sharpton, and N. J. 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. R. 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. H., B. Scholz, T. G. Jephcott, et al. (2017). Key ecological roles for zoosporic true fungi in aquatic habitats. DOI: 10.1128/9781555819583.ch18.

Gołębiewski, M., J. Całkiewicz, S. Creer, et al. (2017). “Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary”. In: Environmental Microbiology Reports 9.2, pp. 129 - 143. DOI: 10.1111/1758-2229.12509.

Gran-Stadniczeñko, S., L. Šupraha, E. D. 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. G. H., P. R. S. Zanoni, R. 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. W. and A. F. 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. T. Melachio, G. R. 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. 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. A. Wood, L. A. 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. H., L. S. Ab Samad, P. M. 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. J., 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. R., 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. F. 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.

Pan, J., J. del Campo, and P. J. 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. K., 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. F. 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. B. 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. M. 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. A. 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. S., I. Nunes, T. K. 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. N. Shchepin, N. H. A. 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. V., 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. F., G. S. Kohli, S. A. 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-García (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. C., 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. P. 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. R., J. L. Metcalf, S. J. 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. DOI: 10.1017/CBO9781139236355.010.

Bass, D., J. D. Silberman, M. W. 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.

Cleary, A. C. and E. G. 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. J. R. C., A. Louvado, P. M. 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. K., D. N. Phalen, S. L. 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. M., A. M. 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. R. 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. R., 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.

Guardiola, M., O. S. 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. O., 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. L. 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. M., 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.

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. I. 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. P. and H. J. 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. A. 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.

Needham, D. M. and J. A. Fuhrman (2016). “Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom”. In: Nature Microbiology 1.4. DOI: 10.1038/NMICROBIOL.2016.5.

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.

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. K., 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., C. R. 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.

Ramírez-Sánchez, O., P. Pérez-Rodríguez, 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. R., E. Lara, L. D. 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. V. 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. U. A., P. Vďačný, J. H. 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-García, 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. 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. A. 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. C. 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. D. 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.

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.

Decelle, J., S. Romac, R. F. 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. S., 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. S. A., L. R. Comolli, B. C. 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 α- and β-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. J. 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. C., M. Ostrowski, R. B. 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.

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 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. 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. F. 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.

Pánek, T., P. Táborskỳ, M. G. Pachiadaki, et al. (2015). “Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage”. In: Frontiers in Microbiology 6.NOV. DOI: 10.3389/fmicb.2015.01288.

Pochon, X., A. Zaiko, G. A. 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. A., 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.

Rodríguez-Marconi, S., R. De La Iglesia, B. Díez, et al. (2015). “Characterization of bacterial, archaeal and eukaryote symbionts from antarctic sponges reveals a high diversity at a three-domain level and a particular signature for this ecosystem”. In: PLoS ONE 10.9. DOI: 10.1371/journal.pone.0138837.

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-García, 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. A. 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. J., V. P. 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. V. W. Seppey, G. 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. A. Y., Z. Liu, S. K. 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. E. 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., W. A. Walters, C. L. 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. J., S. Ganesh, V. P. 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. J. (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. D. 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. W. 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. M., 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.

Cheung, M. K., W. Nong, H. S. 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.

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. M. and M. Y. 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. N., X. Bailly, D. R. 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.