High‐throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity

Abstract

Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high-throughput environmental sequencing was used to characterize the diversity and community structure of litter- and moss-associated protists along a gradient of soil drainage and forest primary productivity in a temperate rainforest in British Columbia. We identified 3262 distinct protist OTUs from 36 sites. Protists were strongly structured along the landscape gradient, with a significant increase in alpha diversity from the blanket bog ecosystem to the zonal forest ecosystem. Among all investigated environmental variables, calcium content was the most strongly associated with the community composition of protists, but substrate composition, plant cover and other edaphic factors were also significantly correlated with these communities. Furthermore, a detailed phylogenetic analysis of unicellular opisthokonts identified OTUs covering most lineages, including novel OTUs branching with Discicristoidea, the sister group of Fungi, and with Filasterea, one of the closest unicellular relatives to animals. Altogether, this study provides unprecedented insight into the community composition of moss- and litter-associated protists.

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

“…Sequencing of environmental DNA (eDNA), here encompassing DNA contained in cells as well as cell-free DNA, is a popular approach to study the diversity and ecology of microbial eukaryotes, including small animals, fungi and protists. eDNA has catalysed the discoveries of novel lineages at all taxonomic ranks from abundant to rare taxa, and revealed that most, if not all, known groups of microbes are genetically much more diverse than anticipated (Heger et al, 2018;Massana et al, 2015;Pawlowski et al, 2012;de Vargas et al, 2015). For protists, recent global molecular surveys revealed that they can account for up to 80% of the total diversity of eukaryotes in the environment (Logares et al, 2014;Massana et al, 2015;Pawlowski et al, 2012;de Vargas et al, 2015).…”

A new framework for the study of apicomplexan diversity across environments

“…The library was 300bp paired-end sequenced at the Genotyping Core Facility of the University California Los Angeles (Los Angeles, CA, USA). Further details on sampling and sequence generation can be found at Heger et al 2018 [54]. Amplicon data are available on NCBI Sequence Read Archive (SRA) under project number: PRJNA396681.…”

What Drives the Diversity of the Most Abundant Terrestrial Cercozoan Family (Rhogostomidae, Cercozoa, Rhizaria)?

“…(ii) We measured morphological traits in these strains, which were subjected to ordination techniques to identify the best suited morphological characters for species delimitation of Rhogostomidae. (iii) We extracted all sequences that could be assigned to the Rhogostomidae from the NCBI database and five publicly available environmental sequencing datasets [5,6,9,24,25] to explore genetic diversity on a large scale. (iv) Finally, we delimit edaphic factors that shape the community composition of Rhogostomidae, based on three of the previously mentioned datasets that come with extensive environmental data [6,24,25].…”

“…(iii) We extracted all sequences that could be assigned to the Rhogostomidae from the NCBI database and five publicly available environmental sequencing datasets [5,6,9,24,25] to explore genetic diversity on a large scale. (iv) Finally, we delimit edaphic factors that shape the community composition of Rhogostomidae, based on three of the previously mentioned datasets that come with extensive environmental data [6,24,25]. Based on the consensus of morphological, genetic, and ecological data, we describe eleven novel species grouped into four newly defined Rhogostomidae morphotypes and shed light on the large diversity of Rhogostomidae that yet awaits exploration.…”