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

David Singer,Leonardo D Fernández,Christophe V W Seppey,Edward A D Mitchell,Enrique Lara,Anush Kosakyan,Amandine Pillonel,Diego Fontaneto

doi:10.1002/ecy.2161

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.

Highlights

Understanding the rules that determine the composition of communities is critical to the assessment and conservation of biodiversity (Colwell and Coddington 1994)
Organismal diversity and the theoretical concepts to understand the drivers of biodiversity have historically been based on macroscopic organisms (Wilkinson 1998) but microorganism models are increasingly used in ecology (Fukami and Morin 2003, Altermatt et al 2015)
High throughput sequencing (HTS) studies of aquatic and terrestrial habitats have revealed the existence of hundreds of thousands of previously unknown phylotypes within known clades as well as revealing highly diverse novel “environmental” clades

Summary

Introduction

Understanding the rules that determine the composition of communities is critical to the assessment and conservation of biodiversity (Colwell and Coddington 1994). Organismal diversity and the theoretical concepts to understand the drivers of biodiversity have historically been based on macroscopic organisms (Wilkinson 1998) but microorganism models are increasingly used in ecology (Fukami and Morin 2003, Altermatt et al 2015). High throughput sequencing (HTS) studies of aquatic and terrestrial habitats have revealed the existence of hundreds of thousands of previously unknown phylotypes (or operational taxonomic units OTUs) within known clades as well as revealing highly diverse novel “environmental” clades (de Vargas et al 2015, Grossmann et al 2016, Mahe et al 2017) These new molecular tools challenge our vision of Manuscript received 8 September 2017; revised 27 December 2017; accepted 8 January 2018.

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Conclusion