First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs

Abstract

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution.

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

“…However, the analysis on the deposited data packages in the associated study 5 focused solely on fungi and bacteria despite the presence of other groups of organisms in the studied deadwood. The present deposition of the metagenome assembly and total RNA sequencing data opens the opportunity for biologists interested in virus ecology 46 , bacterial metagenomics 47 , 48 and ecology of eukaryota 49 , 50 to explore the functional potential of the deadwood-associated biota through the analysis of the metagenome as well as to obtain taxonomic overview of all deadwood-associated organisms using total RNA that allows reliable taxonomic classification of taxa across the whole tree of life 51 , 52 . Amplicon data described here for the first time offer intra-comparison with metagenomes and metatranscriptomes as well as inter-comparison with further deadwood studies 16 , 53 , 54 and analysis of cross-domain interactions 6 , 55 .…”

Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa)

“…) or dead wood (Clissmann et al. ), but they also occur in marine habitats where they cannot form fruiting bodies (Dyková et al. ).…”

Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing

“…To evaluate the taxonomical resolution of SSU-based DNA barcoding at the intramorphospecies level, SSU sequences of Ph. albescens were clustered with two similarity thresholds that were applied for species determination or clustering of the operational taxonomic units (OTUs) in previous studies: (1) 99.1% (Borg Dahl et al, 2019;Borg Dahl, Brejnrod, et al, 2018;Borg Dahl, Shchepin, et al, 2018;Shchepin et al, 2017Shchepin et al, , 2019 and ( 2) 98% (Clissmann et al, 2015;Gao et al, 2019;Kamono et al, 2013;Shchepin et al, 2019). SSU sequences were trimmed to match ca.…”

“…However, since other mountains in North America are sampled poorly or not sampled at all, the real centre of diversity can be somewhere else on this continent. Borg Dahl, Brejnrod, et al, 2018;Borg Dahl, Shchepin, et al, 2018;Shchepin et al, 2017Shchepin et al, , 2019, (2) 98% (Clissmann et al, 2015;Gao et al, 2019;Kamono et al, 2013;Shchepin et al, 2019),…”