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- PublicationAccès libreSoil protistology rebooted: 30 fundamental questions to start with
;Geisen, Stefan ; ;Wilkinson, David M ;Adl, Sina ;Bonkowski, Michael ;Brown, Matthew W ;Fiore-Donno, Anna Maria ; ;Jassey, Vincent E.J ;Krashevska, Valentyna ;Lahr, Daniel J.G ;Marcisz, Katarzyna ; ;Payne, Richard ; ;Anderson, Roger O ;Charman, Dan J ;Ekelund, Flemming ;Griffiths, Bryan S ;Rønn, Regin ;Smirnov, Alexey ;Bass, David ; ;Berney, Cédric ; ;Blandenier, Quentin ;Chatzinotas, Antonis ;Clarholm, Marianne ;Dunthorn, Micah ;Feest, Alan ;Fernández, Leonardo D ;Foissner, Wilhelm ; ;Gentekaki, Eleni ;Hájek, Michal ;Helder, Johannes ;Jousset, Alexandre ;Koller, Robert ;Kumar, Santosh ;La Terza, Antonietta ;Lamentowicz, Mariusz ;Mazei, Yuri ;Santos, Susana S ;Seppey, Christophe V.W ;Spiegel, Frederick W ;Walochnik, Julia ;Winding, AnneProtists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology.
- PublicationAccès libreEnvironmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa;Arcellinida; Hyalospheniidae)Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community com-position estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.
- PublicationAccès libreEukaryotic plankton diversity in the sunlit ocean
;de Vargas, Colomban ;Audic, Stéphane ;Henry, Nicolas ;Decelle, Johan ;Mahé, Frédéric ;Logares, Ramiro ; ;Berney, Cédric ;Le Bescot, Noan ;Probert, Ian ;Carmichael, Margaux ;Poulain, Julie ;Romac, Sarah ;Colin, Sébastien ;Aury, Jean-Marc ;Bittner, Lucie ;Chaffron, Samuel ;Dunthorn, Micah ;Engelen, Stefan ;Flegontova, Olga ;Guidi, Lionel ;Horák, Aleš ;Jaillon, Olivier ;Lima-Mendez, Gipsi ;Lukeš, Julius ;Malviya, Shruti ;Morard, Raphael ; ;Scalco, Eleonora ;Siano, Raffaele ;Vincent, Flora ;Zingone, Adriana ;Dimier, Céline ;Picheral, Marc ;Searson, Sarah ;Kandels-Lewis, Stefanie ;Acinas, Silvia G ;Bork, Peer ;Bowler, Chris ;Gorsky, Gabriel ;Grimsley, Nigel ;Hingamp, Pascal ;Iudicone, Daniele ;Not, Fabrice ;Ogata, Hiroyuki ;Pesant, Stephane ;Raes, Jeroen ;Sieracki, Michael E ;Speich, Sabrina ;Stemmann, Lars ;Sunagawa, Shinichi ;Weissenbach, Jean ;Wincker, PatrickKarsenti, EricMarine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size.We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition.We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ∼150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ∼11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.
- PublicationAccès libreAssessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencingCurrent projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.