Differences in soil micro‐eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs

Abstract

Griffiths, R.I.; Bass, D. 2016. Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs. Environmental Microbiology, 18 (6). 10.1111/1462-2920.13220 Contact CEH NORA team at noraceh@ceh.ac.ukThe NERC and CEH trademarks and logos ('the Trademarks') are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner.This article is protected by copyright. All rights reserved. Running title: Soil pH and protistan diversity.This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1462-2920.13220 Accepted ArticleThis article is protected by copyright. All rights reserved. 2 INTRODUCTIONProtists are key components of microbial communities in both aquatic and terrestrial environments. They represent 10 4 -10 7 individuals per gram of dry soil (Adl and Coleman, 2005;Adl and Gupta, 2006;Bamforth, 2007) and over 50% of total aquatic biomass (Sherr and Sherr, 2002, 2007). The diversity of functional groups (trophic status, free-living vs symbiotic, etc.) makes them major participants of the microbial loop and regulators of biogeochemical flows (Calbet and Landry, 2004). With the continuing development and growing capability of molecular techniques, protist diversity is increasingly revealed as orders of magnitude greater than morphological or even earlier sequence-based assays suggested (Bates et al., 2012). The past ten years have seen extraordinary advances in our knowledge of microbial eukaryotic diversity, primarily through the adoption of molecular tools for phylogenetically-based classification which provides a coherent evolutionary framework to explore diversity.Additionally the routine use of environmental sequencing utilising next generation sequencing technologies has permitted the discovery of many new groups and novel eukaryotic lineages in many different biomes (e.g. Takishita et al., 2007;Jones et al., 2011; de Vargas et al., 2015). However, the challenge of overlaying ecological and biogeographical insight onto this diversity still remains, particularly in the complex and heterogeneous soil environment.Microscopy-based soil protist diversity studies far outnumber soil eDNA studies, and both lag far behind their marine and freshwater counterparts. Diversity assessments that rely on culturing and/or visual identification have revealed a large diversity of cell forms and taxa dominated by bacterivores, predators, and some autotrophs (inferred from e.g. Stout 1984;Bamforth, 2007; Domonell et al., 2013). These studies often rely on protists capable of growing in culture medium supplemented with bacteria and recognition of visually distinctive (and relatively large) forms, e.g. via liquid Accepted ArticleThis article is protected by copyright...

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

“…3). This pattern of dominating parasites contrasts with the prevailing view that soil protist communities are dominated by predators of bacteria 34 , although a considerable presence of protist predators of fungi and animals, as well as protist parasites, has been observed elsewhere [35][36][37][38][39][40][41] . These dominating protist parasites also potentially contribute to the high animal diversity in the rainforests by the same mechanisms that other parasites contribute to high tree diversity as hypothesized in the Janzen-Connell model 4,5 .…”

“…To put the 50,118,536 soil protist reads into a phylogenetic context, they were dereplicated into 10,567,804 strictly identical amplicons and placed onto a comprehensive eukaryotic reference tree. The corresponding multiple sequence alignment used to build this tree contained 512 full-length sequences from all major eukaryotic clades (see Supplementary Data 1 and 2 for GenBank accession numbers, sequences and clade assignments), based on the taxon sampling as summarized in a range of pan-eukaryotic phylogenomic studies reviewed in refs 61,62 , with a bias towards lineages known to occur in soils from environmental sequencing studies; for example, refs 35,37,38 . To reduce phylogenetic artefacts, only high quality, full-or near-full length 18S rRNA reads were selected, and reads that have previously been observed to form long branches were omitted.…”

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

“…farinacea [57] along with the high relative abundance of Trebouxia OTUs in this part, as pointed out in this study, supports the apical growth type of this species. The variation in photobiont localization could be partially explained by the different environmental conditions [58] along the laciniae, which could suggest a succession of Trebouxia species inside the thallus, with pioneer algal communities in the apical zone, where they are exposed to more changeable environmental conditions. This hypothesis should be further confirmed by more detailed quantitative analyses and fluorescent in situ hybridization.…”

Quest of Soil Protists in a New Era

“…The predominance of active heterolobosean amoeba under anoxic conditions was demonstrated by RNA-based molecular analysis (47). Soil pH, an important environmental factor to shape the soil bacterial community, is known to affect the emerging abundance of putatively parasitic protists (17). …”

“…Technical issues in molecular analyses of soil protists remain to be solved (56, 57). There are partly incompatible databases present (17). The HTS does not always give us a true picture of protistan community (22).…”