Metatranscriptomic census of active protists in soils

Abstract

The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

Figure 1

Community composition of protist supergroups in the investigated soils. For detailed information on soil parameters, see Table 1.

Figure 2

Unweighted Pair Group Method (UPGMA) clustering analysis to evaluate differences between soil protist communities. For detailed information on soil characteristics and abbreviations, see Table 1.

Figure 3

Community composition within the SAR supergroup independently showing the community compositions within the individual clades of SAR, i.e., Rhizaria (a), Alveolata (b) and Stramenopiles (c). Shown are means of biological replicates. Labels and sites as described in Table 1 and Figures 1 and 2.

Figure 4

Community composition within the supergroup Amoebozoa in the investigated soils. Shown are means of biological replicates. Labels and sites as described in Table 1 and Figures 1 and 2.

Figure 5

SSU rRNA transcript abundance±s.d. of Foraminifera and Choanoflagellida in the soil metatranscriptomes. Labels and sites as described in Figure 2 and Table 1.

Figure 6

Maximum likelihood tree of Choanoflagellida placing assembled long SSU rRNA contigs (red) with sequences of described and uncultivated choanoflagellates. Seventy-one sequences with 1232 unambiguously aligned positions were used; the tree is unrooted; values higher than 50 for maximum likelihood analyses (left) and 0.50 for Bayesian analyses (right) shown. Black circles indicate full support.