Baekduia alba sp. nov., a novel representative of the order Solirubrobacterales isolated from temperate grassland soil.

Strain 0141_2T was isolated from a temperate grassland soil in Germany and was found to be affiliated with the order Solirubrobacterales. It is most closely related to Baekduia soli BR7-21T, with 98.1 % 16S rRNA gene sequence similarity. Cells are rod-shaped, non-motile, stain Gram-positive and can have multiple vesicles in the cell surface. Polyhydroxybutyrate is accumulated within the cells. Catalase- and oxidase-positive. It is a mesophilic aerobe and grows best around neutral to slightly acidic pH in R2A medium. The major fatty acids are C18 : 1 ω9c, iso-C16 : 0, C18 : 0, C16 : 0, C16 : 1 ω7c and C17 : 1 ω8c. Diphosphatidylglycerol is present. The predominant respiratory quinone is MK-7(H4). Meso-diaminopimelic acid is the diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content of genomic DNA is 72.9 mol%. Based on the results of phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the novel species Baekduia alba sp. nov. with the type strain 0141_2T (=DSM 104299T=LMG 30000T=CECT 9239T).

Aurantibacillus circumpalustris gen. nov., sp. nov., the first characterized representative of the Bacteroidota candidate family env.OPS 17 and proposal of Aurantibacillaceae fam. nov.

16S rRNA sequence types associated with the candidate family env.OPS 17 have been reported from various environments, but no representatives have been characterized and validly named. Bacteria of env.OPS 17 are affiliated with the order Sphingobacteriales and were first detected more than two decades ago in the vicinity of a thermal spring in Yellowstone National Park. Strain Swamp196T, isolated from the soil surrounding a swamp in Northern Germany, is the first characterized representative of candidate family env.OPS 17. Cells of strain Swamp196T are rod-shaped, non-motile, non-spore-forming, non-capsulated and stain Gram-negative. Colonies are small and orange-coloured. The strain is mesophilic and grows under aerobic or microaerophilic conditions. It grows chemo-organotrophically over a narrow range of pH and exclusively on proteinaceous substrates. The major cellular fatty acids are iso-C15 : 0, iso-C15 : 1 ω10c, C18 : 1 ω9c and C16 : 1 ω7c and the major polar lipids are two unidentified aminophospholipids, one unidentified aminolipid and one unidentified lipid. The predominant respiratory quinone is MK-7. The DNA G+C content of genomic DNA is 35.5 mol%. Strain Swamp196T is related to Pedobacter cryophilus AR-3-17T, Arcticibacter pallidicorallinus Hh36T and Pedobacter daechungensis Dae 13T with 16S rRNA gene sequence similarity of 84.1, 83.8 and 83.5 %, respectively. Based on our phenotypic, genomic and phylogenetic analysis, we propose the novel species Aurantibacillus circumpalustris sp. nov (type strain Swamp196T=DSM 105849T=CECT 30420T) of the novel genus Aurantibacillus gen. nov. and the novel family Aurantibacillaceae fam. nov.

Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil.

The order Solirubrobacterales is a deep-branching lineage within the phylum Actinomycetota. Most representatives have been isolated from terrestrial environments. A strain isolated from a grassland soil was found to be affiliated with this order and therefore characterized by a polyphasic approach. Cells of strain 0166_1T are Gram-positive, short rods, non-motile, non-spore-forming and divide by binary fission. A surface layer with protrusions covers the majority of the cells. Strain 0166_1T grows optimally around neutral to slightly alkaline pH (pH 7.1-7.9) and at temperatures between 24-36 °C in SSE/HD 1 : 10 medium. It grows optimally with 0-0.5% NaCl (w/v) but can withstand concentrations up to 5 %. The major fatty acids are C18 : 1 ω9c, C16 : 1 ω7c, C17 : 0 cyclo ω7c, C18 : 1 ω7c methyl and C19 : 0 cyclo ω9c. The major polar lipids are diphosphatidylglycerol, two unidentified phospholipids and one unidentified glycolipid. MK-7(H4) and MK-7(H2) are the predominant respiratory quinones. meso-2,6-Diaminopimelic acid is the diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content for strain 0166_1T is 72.8 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Conexibacter arvalis KV-962T and Conexibacter stalactiti YC2-25T with 95.5 and 95.2 % sequence similarity, respectively. Based on the phenotypic, genomic and phylogenetic data, we propose the novel species Capillimicrobium parvum sp. nov. (type strain 0166_1T=DSM 104329T=LMG 29999T=CECT 9240T) of the novel genus Capillimicrobium gen. nov. within the novel family Capillimicrobiaceae fam. nov.

Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil.

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1 ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.

Bacterial colonization of minerals in grassland soils is selective and highly dynamic.

Bacteria colonize reactive minerals in soils where they contribute to mineral weathering and transformation. So far, the specificity, patterns and dynamics of mineral colonization have rarely been assessed under natural conditions. High throughput Illumina sequencing was employed to investigate the bacterial communities assembling on illite and goethite during exposure to natural grassland soils. Two different types of organic carbon sources, simple carbon compounds representing root exudates and detritus of two dominant grassland plant species were applied, and their effects on the temporal dynamics of bacterial communities were investigated. The observed temporal patterns suggest that the surfaces of de novo exposed minerals in soils drive the establishment of bacterial communities and override the effect of the type of carbon sources and of other environmental properties. Mineral colonization was selective and specific bacterial sequence variants exhibited distinct colonization patterns, among which early, intermittent, and late colonizers could be distinguished. Based on our results, soil minerals are not only colonized by specific bacterial communities but enable a succession of different bacterial communities. Our results thereby expand the concept of the mineralosphere and provide novel insights into mechanisms of community assembly in the soil ecosystem.

Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil.

The family Caulobacteraceae comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4T was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family Caulobacteraceae which divided by budding. Cells of strain 0127_4T were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to Aquidulcibacter paucihalophilus TH1-2T and Asprobacter aquaticus DRW22-8T with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family Caulobacteraceae, phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c/C16 : 0 10-methyl), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4T represents a novel species of a new genus, Terricaulis silvestris gen. nov., sp. nov. The type strain of Terricaulis silvestris is 0127_4T (=DSM 104635T=CECT 9243T).

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum.

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913T and R5959T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C19 : 0 cyclo ω8c and C16 : 0; in addition, C18 : 1ω7c was also found as a predominant fatty acid in strain R5913T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913T and R5959T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656T, Dongia mobilis CGMCC 1.7660T, Dongia soli D78T and Dongia rigui 04SU4-PT. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913T=DSM 109816T=CECT 9472T) and Hypericibacter adhaerens sp. nov. (type strain R5959T=DSM 109817T=CECT 9620T).

Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil.

Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3-8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_-6_39T (=DSM 100886T=KCTC 52215T).

Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils.

Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the ß-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands.

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.

N-terminal acetylation modulates Bax targeting to mitochondria.

The pro-apoptotic Bax protein is the main effector of mitochondrial permeabilization during apoptosis. Bax is controlled at several levels, including post-translational modifications such as phosphorylation and S-palmitoylation. However, little is known about the contribution of other protein modifications to Bax activity. Here, we used heterologous expression of human Bax in yeast to study the involvement of N-terminal acetylation by yNaa20p (yNatB) on Bax function. We found that human Bax is N-terminal (Nt-)acetylated by yNaa20p and that Nt-acetylation of Bax is essential to maintain Bax in an inactive conformation in the cytosol of yeast and Mouse Embryonic Fibroblast (MEF) cells. Bax accumulates in the mitochondria of yeast naa20Δ and Naa25-/- MEF cells, but does not promote cytochrome c release, suggesting that an additional step is required for full activation of Bax. Altogether, our results show that Bax N-terminal acetylation by NatB is involved in its mitochondrial targeting.

First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain.

Although ubiquitous and abundant in soils, acidobacteria have mostly escaped isolation and remain poorly investigated. Only a few cultured representatives and just eight genomes of subdivisions 1, 3, and 4 are available to date. Here, we determined the complete genome sequence of strain HEG_-6_39, the first genome of Acidobacterium subdivision 6.