International Journal of Systematic and Evolutionary Microbiology

An anaerobic, salt-tolerant, rod-shaped bacterium, strain JL216-2 T , was isolated from the shell of the hydrothermal gastropod Alviniconcha marisindica in the Tianxiu hydrothermal field on the Carlsberg Ridge, Indian Ocean. Cells of strain JL216-2 T were motile and 0.5×3–6 µm in size. Strain JL216-2 T grew at 10–32 °C (optimal 28 °C), pH 6.0–9.0 (optimal pH 7.0) and 0.5–12.0% (w/v) sodium chloride(NaCl, optimal 2.5%). Strain JL216-2 T exhibited metabolic versatility, being capable of heterotrophic growth on complex organic compounds. It also performed autotrophic growth by utilizing carbon dioxide (CO₂) fixation or sodium bicarbonate (NaHCO 3 ) as the sole carbon source, driven by hydrogen oxidation coupled with Fe(III) reduction. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to Helicovermis profundi S502 T (90.43% sequence similarity). The genome size of strain JL216-2 T was 4.91 Mb, with a G+C content of 39.54 mol%. Phylogenomic analysis and overall genome relatedness indices values indicated a close relatedness of strain JL216-2 T to H. profundi S502 T and Fusibacter spp. The combined genotypic and phenotypic data showed that strain JL216-2 T represents a novel genus within the order Eubacteriales . The type strain is JL216-2 T (=MCCC M30262 T =KACC 23553 T ).

Bacteria involved in the anaerobic degradation of lignocellulosic waste in landfill sites play crucial roles in carbon turnover and biogas generation. In this study, we isolated and characterized a novel anaerobic bacterium, strain meth-B3ᵀ, from a laboratory-scale methanogenic bioreactor fed with maize-based biomass. Cells were Gram-stain-negative, non-spore-forming, motile rods with optimal growth at 35 °C, pH 7.0 and 0.7% sodium chloride (NaCl). Strain meth-B3ᵀ utilized a broad spectrum of carbohydrates, amino acids and organic acids, including glucose, cellobiose, glycerol, sucrose, maltose and various nitrogenous compounds. It fermented glucose into acetate, butyrate, lactate, propionate, valerate and ethanol. Whole-genome sequencing revealed a 3.8 Mbp genome with a G+C content of 62.65 mol%. Phylogenomic analyses based on 16S rRNA and conserved marker genes placed strain meth-B3ᵀ within the order Eubacteriales , forming a distinct clade from other known families. Comparative genomic metrics (average nucleotide identity, ≤69.4%; average amino acid identity, ≤54.2%; percentage of conserved protein, ≤35.2%) confirmed that strain meth-B3ᵀ represents a novel genus and family. Notably, carbohydrate-active enzyme and Clusters of Orthologous Groups (COG) functional profiling revealed an extensive suite of enzymes with potential activities against cellulose, xylan, starch and other maize-derived polymers, underscoring its ecological and biotechnological relevance in biomass degradation and biogas production. On the basis of genotypic and phenotypic distinctions, we propose the name Anaerozeibacter quisquiliarum gen. nov., sp. nov., with strain meth-B3ᵀ (=DSM 112769ᵀ=ATCC TSD-269ᵀ) being the type strain, and designate Anaerozeibacteraceae fam. nov. within the order Eubacteriales to accommodate this lineage.

‘ Candidatus Ferrigenium straubiae’ strain KS (KCTC 25982, DSM 118991) is a neutrophilic, Fe(II)-oxidizing bacterium representing up to 98% of the community in culture KS, the most extensively studied mixed culture known for autotrophic nitrate-reducing Fe(II) oxidation. The phylogeny and genome of this bacterium were previously analysed and identified as ‘ Candidatus Ferrigenium straubiae’. In this study, we report the first-time successful isolation of ‘ Candidatus Ferrigenium straubiae’ strain KS and its experimental physiological characterization. The bacterium was identified as a non-stalk-forming, rod-shaped and non-halophilic strain with a Gram-negative classification. We characterized its physiology when grown in agarose-stabilized Fe(II)-O 2 gradient tubes where Fe(II) stemming from FeS functions as the electron donor and O 2 as the electron acceptor. It showed growth at temperatures of 20–30 °C (optimal at 25°C) and at pH levels of 6.0–7.5 (optimal at pH 6.5–7.0). The doubling time at 20 °C and pH 6.5 was 16 h. We further optimized the gradient tubes for sustainable culture maintenance using modified Wolfe’s mineral medium (MWMM; 1 g l −1 NH 4 Cl) supplemented with 7-vitamin solution, SL-10 trace elements, selenite-tungstate solution and selenite-molybdate-nickel-copper-arsenic-vanadium solution (final concentrations of 10 µM Se, 10 µM Mo, 0.1 µM Ni, 0.1 µM Cu, 0.1 µM As and 5 nM V). We also evaluated several Fe(II) sources (with O 2 as electron acceptor), as well as both inorganic and organic substrates for their influence on growth. Although a known member of the denitrifying community in culture KS, the isolated strain ‘ Candidatus Ferrigenium straubiae’ KS exhibited exclusively microaerobic and autotrophic growth in agarose-stabilized Fe(II)-O 2 gradients, utilizing Fe(II) from FeS as the electron donor.

The prokaryotic generic names Bogoriella Groth et al. 1997 and Stella Vasilyeva 1985 are illegitimate because they are later homonyms of the genus names Bogoriella Zahlbr. 1928 (Ascomycota) and Stella Massee 1889 (Basidiomycota) (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement names Allobogoriella gen. nov., Allobogoriella caseilytica comb. nov., Allobogoriellaceae fam. nov., Allobogoriellales ord. nov., Allostella gen. nov., Allostella humosa comb. nov. and Allostellaceae fam. nov. as replacement names for the illegitimate prokaryotic names Bogoriella, Bogoriella caseilytica, Bogoriellaceae, Bogoriellales, Stella, Stella humosa, Stella vacuolata and Stellaceae, respectively.

A novel bacterial strain UR115T belonging to the class Alphaproteobacteria was isolated from tomato rhizosphere soil. Strain UR115T was Gram-stain-negative, motile, facultative anaerobic, catalase positive, oxidase positive and rod shaped. Strain UR115T showed growth at 15–37 °C, pH 5.5–9.5 and up to 4.0% NaCl. Strain UR115T exhibited 16S rRNA gene sequence similarities of <90.40% with members of the class Alphaproteobacteria. Based on the phylogenetic analysis inferred from both 16S rRNA gene and whole-genome sequences, strain UR115T formed a separate and distinct clade, leading to its classification as a member of a novel order within the class Alphaproteobacteria. The genome size and G+C content of strain UR115T were 5,059,753 bp and 63.9%, respectively. Average amino acid identity values between strain UR115ᵀ and reference genomes ranged from 47.85% to 59.96%, and pairwise Percentage of Conserved Protein values ranged from 4.12% to 46.63%. The major cellular fatty acids of strain UR115T were C19 : 0 cyclo ω8c, C16 : 0 and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipids of strain UR115T were phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipid, two unidentified aminolipids and two unidentified lipids. The predominant quinone was ubiquinone-10. Based on its distinct phylogenetic position, unique genomic characteristics and chemotaxonomic profiles, we proposed the novel species Radicibacter daui gen. nov., sp. nov., the novel family Radicibacteraceae fam. nov. and the novel order Radicibacterales ord. nov. The type strain is strain UR115T (=KACC 23674T=JCM 36738T).

A Gram-stain-negative, aerobic, non-motile and short rod-shaped bacterium, designated strain SCSIO 64248T, was isolated from the stony coral Fungia sp. collected from South China Sea. Phylogenetic analysis indicated that strain SCSIO 64248T belonged to the family Geminicoccaceae and showed the highest 16S rRNA gene similarities with the types of Marinimicrococcus flavescens (90.5%), Arboricoccus pini (90.2%) and Benzoalithermus flavus (89.8%). The whole genome of strain SCSIO 64248T was 4.9 Mbp with a 68.8mol% G+C content. It shared average amino acid identity (AAI) values of 52–56.2%, which is below the proposed AAI threshold at the genus level and when compared to the known species of Geminicoccaceae. Colonies of strain SCSIO 64248T are circular, pink and convex. It was able to grow in the range of 4–37 °C, at pH 6.0–10.0 and in the presence of up to 8.0% (w/v) NaCl concentration. The major cellular fatty acid (>9%) was summed feature 8, C19 : 0 cyclo ω8c and C16 : 0, and the sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified phospholipid. Data of polyphasic characteristics revealed that strain SCSIO 64248T represented a novel species of a new genus within the family Geminicoccaceae, for which the name Marinivivus gen. nov. is proposed with the type strain of the type species Marinivivus vitaminiproducens SCSIO 64248T (=MCCC 1K08013T=KCTC 92503T).