Diversity of <i>Ktedonobacteria</i> with Actinomycetes-Like Morphology in Terrestrial Environments

Abstract

Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181–2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503–5613; Shannon index, 4.21–6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas.

Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems

“…However, this pattern did not hold in PC2 and PC3, as CcrShv-favored OTUs were more abundant under no-till instead of chisel tillage. Considering that OTUs in PC2 and PC3 were either aerobic or facultatively anaerobic [70,71,75,80,88], the CT-favored OTUs in these PCs might have been responding positively to the soil aeration from tillage. The two Ktedonobacteria OTUs that responded positively to no-till somewhat contradicted a past report, where this class increased with conventional tillage over reduced tillage [89].…”

Dictyobacter vulcani sp. nov., belonging to the class Ktedonobacteria, isolated from soil of the Mt Zao volcano

“…The class Ktedonobacteria was initially established in 2006 for the Gram-positive, aerobic, mycelia-and spore-forming branching lineage in the phylum Chloroflexi [1] and, at the time or writing, contains six genera and 13 formally proposed mesophilic and thermophilic species [1][2][3][4][5][6][7][8][9]. Strains belonging to this class were characterized with actinomycete-like morphologies [1][2][3][4][5][6][7][8][9], relatively large genomes (5.54-13.66 Mb) [10][11][12], ubiquity in various terrestrial environments [13][14][15][16][17][18] and having potential for secondary metabolism [12,[19][20][21].…”

Temperature-dependent expression of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula strains of the class Halobacteria

“…Prokaryotes harbour 16S rRNA genes encoding rRNA in the small subunit of the prokaryotic ribosome, and the sequences are highly conserved. Therefore, the 16S rRNA gene sequence is generally used for the identification of prokaryotes and for the assessment of prokaryotic diversity in various environments (Narihiro and Kamagata 2017 ; Yabe et al 2017 ). A high percentage of prokaryotic genomes (83%) contain two or more copies of 16S rRNA genes, and the sequences are nearly identical among the copies of 16S rRNA genes (Sun et al 2013 ).…”