Fungal communities in European alpine soils are not affected by short-term in situ simulated warming than bacterial communities

The impact of global warming on biological communities colonizing European alpine ecosystems was recently studied. Hexagonal open top chambers (OTCs) were used for simulating a short-term in situ warming (estimated around 1°C) in some alpine soils to predict the impact of ongoing climate change on resident microbial communities. Total microbial DNA was extracted from soils collected either inside or outside the OTCs over 3 years of study. Bacterial and fungal rRNA copies were quantified by qPCR. Metabarcoding sequencing of taxonomy target genes was performed (Illumina MiSeq) and processed by bioinformatic tools. Alpha- and beta-diversity were used to evaluate the structure of bacterial and fungal communities. qPCR suggests that, although fluctuations have been observed between soils collected either inside and outside the OTCs, the simulated warming induced a significant (p < 0.05) shift only for bacterial abundance. Likewise, significant (p < 0.05) changes in bacterial community structure were detected in soils collected inside the OTCs, with a clear increase of oligotrophic taxa. On the contrary, fungal diversity of soils collected either inside and outside the OTCs did not exhibit significant (p < 0.05) differences, suggesting that the temperature increase in OTCs compared to ambient conditions was not sufficient to change fungal communities.

Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17^T, SOSP1-1^T, 1-9^T, 1-30^T and 150040^T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15-40 °C (optimally at 30 °C) and pH 4.0-8.0 (optimally at pH 6.0-7.0), and had 7.21-12.67 Mb genomes with 49.7-53.7 mol% G+C content. They shared MK9(H₂) as the major menaquinone and C_16 : 1-2OH and iso-C_17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17^T and SOSP1-9^T were most closely related to members of the genus Dictyobacter, with 94.43-96.21 % 16S rRNA gene similarities and 72.16-81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1^T and SOSP1-30^T was Ktedonobacter racemifer SOSP1-21^T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040^T formed a distinct clade within the order Ktedonobacterales, showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040^T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040^T=CGMCC 1.17052^T=BCRC 81202^T) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales; strain SOSP1-1^T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1^T=CGMCC 1.17205^T=BCRC 81203^T) and strain SOSP1-30^T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30^T=CGMCC 1.17733^T=BCRC 81205^T) within the family Ktedonobacteraceae; strain Uno17^T as Dictyobacter arantiisoli sp. nov. (type strain Uno17^T=NBRC 113155^T=BCRC 81116^T); and strain SOSP1-9^T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9^T=CGMCC 1.17206^T=BCRC 81204^T) within the family Dictyobacteraceae.

Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria

Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H₂) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H₂ and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.

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

An aerobic, Gram-stain-positive, mesophilic Ktedonobacteria strain, W12T, was isolated from soil of the Mt Zao volcano in Miyagi, Japan. Cells were filamentous, non-motile, and grew at 20–37 °C (optimally at 30 °C), at pH 5.0–7.0 (optimally at pH 6.0) and with <2 % (w/v) NaCl on 10-fold diluted Reasoner’s 2A (R2A) medium. Oval-shaped spores were formed on aerial mycelia. Strain W12T hydrolysed microcrystalline cellulose and xylan very weakly, and used d-glucose as its sole carbon source. The major menaquinone was MK-9, and the major cellular fatty acids were C16 : 1 2-OH, iso-C17 : 0, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c) and anteiso-C17 : 0. Cell-wall sugars were mannose and xylose, and cell-wall amino acids were d-glutamic acid, glycine, l-serine, d-alanine, l-alanine, β-alanine and l-ornithine. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain W12T has a genome of 7.42 Mb with 49.7 mol% G+C content. Nine copies of 16S rRNA genes with a maximum dissimilarity of 1.02 % and 13 biosynthetic gene clusters mainly coding for peptide products were predicted in the genome. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that strain W12T represents a novel species in the genus Dictyobacter . The most closely related Dictyobacter type strain was Dictyobacter alpinus Uno16T, with 16S rRNA gene sequence similarity and genomic average nucleotide identity of 98.37 % and 80.00 %, respectively. Herein, we propose the name Dictyobacter vulcani sp. nov. for the type strain W12T (=NBRC 113551T=BCRC 81169T) in the bacterial class Ktedonobacteria .