Patterns of Rare and Abundant Marine Microbial Eukaryotes

Logares, Ramiro; Audic, Stéphane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean‐Michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angélique; Kooistra, Wiebe H. C. F.; Mahé, Frédéric; Not, Fabrice; Ogata, Hiroyuki; Pawłowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-Tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sébastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A.; Vargas, Colomban de; Massana, Ramón

doi:10.1016/j.cub.2014.02.050

Cited by 448 publications

(478 citation statements)

References 51 publications

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“…For example, while the broadly targeted V4 primers used here amplify a wide variety of eukaryotic lineages 13,[25][26][27][28][29] , other primers could have amplified additional taxa [30][31][32] (Supplementary Table 1). The resolution power of metabarcoding also has its limits.…”

Section: Discussionmentioning

confidence: 99%

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Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

et al. 2017

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High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.S ince the works of early naturalists such as von Humboldt and Bonpland 1 , we have known that animal and plant communities in tropical rainforests are exceedingly species rich. For example, one hectare can contain more than 400 tree species 2 and one tree can harbour more than 40 ant species 3 . This hyperdiversity of trees has been partially explained by the Janzen-Connell model 4,5 , which hypothesizes that host-specific predators and parasites reduce plant population growth in a density-dependent manner 6,7 . Sampling up in the tree canopies and below on the ground has further led to the view that arthropods are the most diverse eukaryotes in tropical rainforests 8,9 .The focus on eukaryotic macroorganisms in these studies is primarily because they are familiar and readily observable to us. We do not know whether the less familiar and less readily observable protists-microbial eukaryotes that are not animals, plants or fungi 10 -inhabiting these same ecosystems exhibit similar diversity patterns. To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador. This metabarcoding approach has the power to uncover known and new taxa on a massive scale 11 . By amplifying DNA extracted from the soils with broadly targeted primers for the V4 region of 18S rRNA and sequencing it using the Illumina MiSeq platform, we were able to detect most eukaryotic lineages, and assess the diversity and relative dominance of free-living and parasitic lineages.

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Section: Discussionmentioning

confidence: 99%

“…Samples from European near-shore marine sites (see Supplementary Code 1 for coordinates of each sample) came from the BioMarKs consortium 28,56 . We re-sequenced the samples here to obtain deeper sequencing.…”

Section: Marine Samplesmentioning

confidence: 99%

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

et al. 2017

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“…In studies targeting particular groups of protists, this should guide the marker choice. For instance, the v4 and v9 regions of the 18S gene have been extensively used for protist metabarcoding in the marine realm (e.g., Pawlowski et al, 2011;Logares et al, 2014;Malviya et al, 2016), with different advantages and pitfalls (Stoeck et al, 2010;Pawlowski et al, 2011). The nature of the target group, marker variability, and completeness of databases should be carefully considered before undertaking any metabarcoding study.…”

Section: Discussionmentioning

confidence: 99%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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“…Some plankton groups, such as phytoplankton and zooplankton, have been studied extensively for decades, with earlier research founded on microscope-based assessments of diversity and abundance (Russell et al, 1971;Southward, 1974). More recently, through the application of DNA-based tools that incorporate previously poorly described plankton groups, such as bacterioplankton and protists, marine plankton diversity has been shown to be vast, complex and influenced by a wide range of environmental drivers Logares et al, 2014;de Vargas et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

2016

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Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services.

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Patterns of Rare and Abundant Marine Microbial Eukaryotes

Abstract: We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.

Cited by 448 publications

References 51 publications

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

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