Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems

Singer, David; Seppey, Christophe V. W.; Lentendu, Guillaume; Dunthorn, Micah; Bass, David; Belbahri, Lassaâd; Blandenier, Quentin; Debroas, Didier; Groot, G.A. de; Vargas, Colomban de; Domaizon, Isabelle; Duckert, Clément; Izaguirre, Irina; Koenig, Isabelle; Mataloni, Gabriela; Schiaffino, M. Romina; Mitchell, Edward A. D.; Geisen, Stefan; Lara, Enrique

doi:10.1016/j.envint.2020.106262

Cited by 173 publications

(134 citation statements)

References 58 publications

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“…Our data confirm the existence of a substantial undescribed taxonomic diversity of Cercozoa, a dominant phylum of microbial eukaryotes in terrestrial ecosystems (Singer et al . 2021 ).…”

Section: Discussionmentioning

confidence: 99%

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies

Walden

Jauss

Feng

et al. 2021

FEMS Microbiology Ecology

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Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality, and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. In the canopy seasonality was largest among communities detected on the foliar surface: In spring, higher variance within alpha diversity of foliar samples indicated greater heterogeneity during initial colonization. However, communities underwent compositional changes during the aging of leaves in autumn, highly reflecting recurring phenological changes during protistan colonization. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn, demonstrating a potential role of the canopy surface as a physical filter for air-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species—representing dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.

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“…Our data confirm the existence of a substantial undescribed taxonomic diversity of Cercozoa, a dominant phylum of microbial eukaryotes in terrestrial ecosystems (Singer et al . 2021 ).…”

Section: Discussionmentioning

confidence: 99%

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies

Walden

Jauss

Feng

et al. 2021

FEMS Microbiology Ecology

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“…The clear differences in beta diversity between microhabitats indicate that well-adapted taxa accumulated and dominated over those that arrived as resting stages by passive dispersal. This leads to differences in traits, which only can be inferred from related taxa (Dumack et al 2020) as almost 80% of the OTUs showed a similarity of less than 97% to any sequence in the reference database, confirming the existence of a substantial undescribed taxonomic diversity within this dominant phylum of microbial eukaryotes in terrestrial ecosystems (Singer et al 2021).…”

Section: Discussionmentioning

confidence: 99%

On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies

Walden

Jauss

Feng

et al. 2021

Preprint

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Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the extreme microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study we investigated seasonality patterns of protists in tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. Seasonality was largest among communities detected on the foliar surface. Higher variance within alpha diversity of foliar communities in spring indicated greater heterogeneity during community assembly. However, communities underwent distinct changes during the aging of leaves in autumn, reflecting recurring phenological changes during microbial colonization of leaves. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn season, demonstrating a potential role of the canopy surface as an important reservoir for wind-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species - representing only a fraction of dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.

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“…This means that the presence of each taxon depends on the occurrence of associated organisms nearby, as illustrated by co-occurrence networks [89][90][91], thus likely reducing niche breadth to that of the whole consortium [92] or at least part of it. In contrast, most soil protists are heterotrophic [93] and depend mostly on the presence of prey, even though food specialization occurs to various degrees [94]. Furthermore, both bacteria and archaea have similar cell size ranges, on average 1-3 orders of magnitude lower than the size of protists [37,38], allowing more efficient passive wind dispersal [35].…”

Section: Discussionmentioning

confidence: 99%

The environmental niche of soil bacterial, archaeal, fungal and protist communities differ along edaphic and topoclimatic gradients in the Alps

Malard

Mod

Guex

et al. 2021

Preprint

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BackgroundThe niche concept describes the range of conditions supporting the establishment and persistence of species in the environment. Although widely used in ecology, it has not been often applied to microbes, for which comparative niche analyses are still lacking. Yet, quantifying the niche of microbial taxa is necessary to forecast how taxa and the communities they compose might respond to environmental changes. In this study, we identified important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta diversity of bacterial, archaeal, fungal and protist communities. Then, we established a method to calculate the niche breadth and position of each taxon along environmental gradients to determine whether microorganisms have distinct environmental niches. ResultsFor all microbial groups, edaphic properties were identified as the most important drivers of both community diversity and composition. Protists presented the largest niche breadths, followed by bacteria and archaea, with fungi displaying the smallest. Niche breadth generally decreased towards environmental extremes, especially along edaphic gradients, suggesting increased specialisation of all microbial taxa in highly selective environments. ConclusionIn this study, we showed that microorganisms have well defined niches, as do macro-organisms, and that these likely drive part of the observed spatial patterns of community variations, but with notable differences among taxonomic groups. Applying the niche concept more widely to microbial ecology should open many novel perspectives, especially to tackle global change challenges.

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Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems

Cited by 173 publications

References 58 publications

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies

On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies

The environmental niche of soil bacterial, archaeal, fungal and protist communities differ along edaphic and topoclimatic gradients in the Alps

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