Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage

Abstract

Forest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.

Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties

“…To our knowledge, this striking pattern was not observed to date, although Ferreira de Araujo et al (2018) noted that grass-dominated ecosystems hosted more plant parasites than tree-dominated ones. The absence of Phytomyxea in temperate forests is corroborated by a recent metatranscriptomics study on leaf litter of 18 Biodiversity Exploratories forest sites (Voss et al, 2019), but they were detected in low abundance in tropical forest soils (Mahé et al, 2017). The dominant endomyxan OTUs in grasslands were identified as Polymyxa graminis, Spongospora nasturtii and Woronina pythii (Table S2).…”

Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties

“…To our knowledge, this striking pattern was not observed to date, although Ferreira de Araujo et al (2018) noted that grass-dominated ecosystems hosted more plant parasites than tree-dominated ones. The absence of Phytomyxea in temperate forests is corroborated by a recent metatranscriptomics study on leaf litter of 18 Biodiversity Exploratories forest sites ( Voss et al, 2019 ), however, they were detected in low abundance in tropical forest soils ( Mahé et al, 2017 ). The dominant endomyxan OTUs in grasslands were identified as Polymyxa graminis , Spongospora nasturtii , and Woronina pythii ( Supplementary Table S5 ).…”

To the canopy and beyond: Air samples reveal wind dispersal as a driver of ubiquitous protistan pathogen assembly in tree canopies

“…Within the paraphyletic taxon of protists, the group of Cercozoa (Rhizaria) are highly diverse in morphology and physiology and show a high functional and ecological variety (Bass et al, 2009;Harder et al, 2016). They dominate terrestrial habitats (Urich et al, 2008;Voss et al, 2019) and harbor important plant pathogens, such as the Endomyxa, which have recently been elevated from the Cercozoa into a separate phylum (Cavalier-Smith et al, 2018). Another protistan taxon, the Oomycetes (Stramenopiles), contain important parasites of forest trees, and many lineages produce caducous sporangia for dissemination (Goheen & Frankel, 2009;Robideau et al, 2011;Lang-Yona et al, 2018).…”