Environmental filtering and phylogenetic clustering correlate with the distribution patterns of cryptic protist species

Abstract

The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast-growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within Sphagnum-dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species-level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen-poor samples, supporting phylogenetic inheritance of adaptations in the group of N. guttata. This study showed that the studied free-living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.

Phylogenetic and compositional diversity are governed by different rules: a study of fleas parasitic on small mammals in four biogeographic realms

“…The diversity and structure of any biological community results from a complex interaction of assembly processes acting on both ecological and evolutionary time scales (Ricklefs 1987, Wiens and Donoghue 2004, Graham and Fine 2008, Singer et al 2018. Ecological processes affecting biological diversity and/or community structure include, for example, environmental filtering, which causes a community to only contain species that possess certain traits allowing persistence in a certain environment (Ingram and Shurin 2009), or species interactions that may cause either loss (e.g.…”

“…Among evolutionary processes influencing biodiversity and community structure, the most prominent are diversifications and extinctions (Melián et al 2015) as well as biogeographic processes such as dispersal (Cadotte 2006) and taxon pulses (Halas et al 2005). Despite common recognition of the multiple processes affecting biodiversity, there are substantial debates on the relative importance of ecological versus evolutionary processes in their effect on assembly rules, community structure and, consequently, biodiversity (Stevens 2006, Singer et al 2018.…”

Soil protist diversity in the Swiss western Alps is better predicted by topo‐climatic than by edaphic variables

“…Our data are in accordance with previous studies related to the impact of edaphic variables on protist communities (Dupont et al, ; Ekelund, ; Foissner, , ; Nesbitt & Adl, ; Singer et al, ) but we also show that topo‐climatic predictors explain equally well soil protists distributions. Therefore, the method of measurement of the predictors (in situ for edaphic variables or remote sensing/modelling for topo‐climatic) did not seem to affect our capacity to explain protist community distribution.…”

“…As a whole, soil protist communities have been shown to respond to edaphic conditions, such as gradients of pH (Dupont, Griffiths, Bell, & Bass, 2016), nutrients and moisture (Singer et al, 2018), as well as pesticide amounts (Ekelund, 1999;Foissner, 1999;Nesbitt & Adl, 2014) and other perturbations (Foissner, 1997). These variables are rarely integrated in spatial modelling of biodiversity in general (Mod, Scherrer, Luoto, and Guisan, (2016) for plant communities), especially at broad spatial scales, because they are most often not available at the sites of species observations and not easily generalizable in a spatially explicit way (Buri et al, 2017;Cianfrani, Buri, Verrecchia, & Guisan, 2018; Dubuis et al, 2013).…”

Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments

“…These processes can be balanced by densitydependent negative biotic interactions, like competitive exclusion when functionally similar species are after the same resource and co-exclude themselves. Environmental filtering and dispersal limitation have been identified as the main drivers shaping the assembly of most protists in the environment (Boenigk et al, 2018;del Campo et al, 2015;Lentendu et al, 2018;Mahé et al, 2017;Singer et al, 2018;Wetzel et al, 2012), while competition have been only formally tested in laboratory conditions (Saleem, Fetzer, Dormann, Harms, & Chatzinotas, 2012;Violle, Nemergut, Pu, & Jiang, 2011). These mechanisms have been largely evaluated for macroorganisms in different environments (Cavender-Bares, Kozak, Fine, & Kembel, 2009;Kraft et al, 2015), but have not yet been broadly evaluated for microbes in natural environments, for which community ecological analyses have rarely integrated phylogenetic information.…”