Abstract
Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands.
Highlights
The Rokubacteria is one of the deeply branching lineages of prokaryotes, which are often addressed as members of the rare biosphere [1,2,3]
The pool of 16S rRNA gene reads examined in this study included 1,024,783 sequences, which were retrieved from the peat samples and retained after quality filtration, denoising and removing chimeras
Archaeal populations in raised bogs were represented by members of the Euryarchaeota and Taumarchaeota, while fens were colonized by the Euryarchaeota, Crenarchaeota and Nanoarchaeaeota
Summary
The Rokubacteria is one of the deeply branching lineages of prokaryotes, which are often addressed as members of the rare biosphere [1,2,3]. The existence of this bacterial group was first recognized by Lipson and Schmidt [4], who retrieved the corresponding. 16S rRNA gene sequences (GenBank accession numbers AY192281 and AY192282) from an alpine meadow of the Colorado Rocky Mountains These sequences clustered together with two other environmental 16S rRNA gene sequences (AF234132 and AF428647), which were earlier obtained from an Australian arid soil and a lake sediment in China, and formed a deeply rooting, phylum-level bacterial lineage, which was originally referred to as the Candidate phylum SPAM (for Spring Alpine Meadow) [4].
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