Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis

Abstract

In spite of the ecological importance of protists, very little data is available on their distribution in soil. This investigation is the first of its kind on what could be the major components of the soil protistan community, the Myxomycetes, or plasmodial slime-moulds, a monophyletic class in the phylum Amoebozoa. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour, which can be found in every terrestrial biome. Despite their prevalence, they are paradoxically absent from environmental DNA sampling studies. We obtained myxomycete SSU rRNA gene sequences from soil-extracted RNAs using specific primers. Soil samples were collected in three mountain ranges (France, Scotland and Japan). Our study revealed an unexpectedly high diversity of dark-spored Myxomycetes, with the recovery of 74 phylotypes. Of these, 74% had < 98% identity with known sequences, showing a hidden diversity; there was little overlap between localities, implying biogeographical patterns. Few phylotypes were dominant and many were unique, consistent with the 'rare biosphere' phenomenon. Our study provides the first detailed insight into the community composition of this ecologically important group of protists, establishing means for future studies of their distribution, abundance and ecology.

Metacommunity analysis of amoeboid protists in grassland soils

“…Because they have been classified as fungi for a long time, Myxomycetes are excluded from amoebozoan treatises 26 and consequently from most soil inventories 5 . Providing that specific molecular probes are used, dark-spore Myxomycetes can be recovered from soils 27 28 29 , litter 30 and air 31 . This class benefits from a well-studied phylogeny 32 33 34 35 , with a major division between the dark spore and bright spore clades, the former being the better studied to date and the group targeted here.…”

Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa)

“…Myxomycetes probably spend most of their lifetime as amoebae or flagellates in the soil (Kamono et al. ) or dead wood (Clissmann et al. ), but they also occur in marine habitats where they cannot form fruiting bodies (Dyková et al.…”

Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes

“…New primers were designed to be able to successfully amplify the frag ment of COI (Table 2), based on a comparison among the partial/full length COI sequences of six myxogas trian species representing four orders available in GenBank ( Table 1). The primers S2 [9] and SP03r [17] were unable to amplify the 5' fragment of SSU rRNA (~600 bp) for Lycogala epidendrum. Thus, a new upstream primer, SF12, was designed to work with SP03r [17] to amplify the same region of SSU rRNA (~600 bp).…”

“…The primers S2 [9] and SP03r [17] were unable to amplify the 5' fragment of SSU rRNA (~600 bp) for Lycogala epidendrum. Thus, a new upstream primer, SF12, was designed to work with SP03r [17] to amplify the same region of SSU rRNA (~600 bp). All primers are listed in Table 2.…”