International Journal of Systematic and Evolutionary Microbiology

The genus Pseudalkalibacillus, created by the reclassification of specific deep-branching Alkalihalobacillus species, exhibits polyphyletic branching. The Genome Taxonomy Database (GTDB) also assigns Pseudalkalibacillus species into two families and three genera. To clarify the evolutionary relationships and classification of Pseudalkalibacillus species, we report detailed investigations using phylogenomic and molecular signature-based approaches. In phylogenomic trees, Pseudalkalibacillus species are distributed within two family-level lineages. One of these clades, containing the type species of Pseudalkalibacillus (viz. Pseudalkalibacillus decolorationis), represents the genus Pseudalkalibacillus, groups within the family Fictibacillaceae. Ten novel conserved signature indels (CSIs) identified in this study are specific for this clade, providing a robust means for the differentiation of the emended genus Pseudalkalibacillus. The remaining Pseudalkalibacillus species form a separate family-level clade, designated as f_HBI72195 in the GTDB. Within this clade, all species except Pseudalkalibacillus caeni form a robust clade designated as Pseudalkalibacillus clade −2 in our work and g_Anaerobacillus_A in the GTDB. We have also identified 15 novel CSIs specific to this clade. As the Pseudalkalibacillus clade −2 is distinct from Pseudalkalibacillus, we propose transferring species from this clade into a new genus, Guptibacillus gen. nov. The species P. caeni branches distinctly from other Pseudalkalibacillus species, and the GTDB considers it a novel genus (g_Bacillus_BR). Six newly identified CSIs are specific to this species, and we are proposing the transfer of this species into a new genus, Exobacillus gen. nov. Two additional identified CSIs are shared by members of the novel family-level taxon (f_HBI72195) comprising the proposed genera Guptibacillus and Exobacillus, for which we are proposing the name Guptibacillaceae fam. nov. Lastly, the results presented here also show that ‘Pseudalkalibacillus hemicentroti’ and ‘Pseudalkalibacillus macyae’ are later heterotypic synonyms of Guptibacillus hwajinpoensis. These changes, which reliably depict the evolutionary relationships among Pseudalkalibacillus species, should be helpful in future studies of these organisms.

A novel, strictly anaerobic, slightly alkaliphilic, halotolerant, peptide- and amino acid-utilizing bacterial strain, SD1T, was isolated from a hypersaline lake in Western Australia. The strain stained Gram-negative and was a motile, spore-forming rod. The strain grew between 15 and 50 °C (optimum 40 °C), 1–15% w/v sodium chloride (optimum 5%) and pH 6.0–10.0 (optimum 9.0). Major fatty acids included anteiso-C15 : 0 (24.9%), C14 : 0 dimethyl acetyl (13.2%), anteiso-C15 : 0 dimethyl acetyl (11.5%) and iso-C15 : 0 (10.4%). The DNA G+C content was 30.3 mol%. The isolate did not grow using any tested sugars but grew well on arginine and glycine. It is capable of using elemental sulfur and thiosulfate as alternate electron acceptors, but not sulfide, sulfate, nitrate or nitrite. 16S rRNA gene similarity indicates that the isolate is related to Sporosalibacterium tautonense MRo-4T (94.33% identity). SD1T showed 76.18%–76.31% average nucleotide identity with other strains within the family Thermohalobacteraceae. Phylogenetics, based on the 16S rRNA gene and whole-genome sequence, as well as phenotypic analysis, differentiates the isolate from close neighbors. We propose that SD1T represents a novel species in a new genus, which we have named Dethiothermospora halolimnae gen. nov., sp. nov., type strain SD1T (DSM 117405T = TSD-443T). From this work, we also propose repositioning of the genus Anaeromonas to the family Thermohalobacteraceae.

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, SYSU D60014T, was isolated from a sandy soil sample collected from the Gurbantunggut Desert in Xinjiang, PR China. Colonies of SYSU D60014T were pink-coloured, crystalline, irregular edge with a rough surface. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain SYSU D60014T belonged to the family Rhodospirillaceae, formed a distinct lineage and showed 92.5–91.0% similarity to closely related strains. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain SYSU D60014T and members of its related species were 17.2–19.6%, 70.8–74.4% and 48.9–64.5%, respectively. The complete genome of strain SYSU D60014T was 5,100,926 bp with a DNA G+C content of 65.1%. Cells were oxidase-positive and catalase-negative. The strain could grow at 28–40 °C (optimum, 37 °C), pH 5.0–8.0 (optimum, pH 7.0), and in the presence of up to 3% NaCl (optimum, 1–1.5%, w/v) on R2A. The predominant menaquinone was Q-10. The main polar lipids were phosphatidylethanolamine, phosphatidylmethyl ethanolamine, diphosphatidylglycerol, unidentified aminophospholipid, unidentified aminolipid, unidentified phospholipid, four unidentified polar lipids and two unidentified phosphoglycolipids. Major cellular fatty acids were C19 : 0 cyclo ω8c, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. Based on the results obtained through genotypic and phenotypic analyses, we propose that strain SYSU D60014T represents a novel species and genus within the family Rhodospirillaceae, for which we propose the name Virgifigura deserti gen. nov., sp. nov. (type strain SYSU D60014T=NBRC 112951T=CPCC 101030T).

A Gram-positive, aerobic, non-motile coccoid bacterium, designated strain ZF39T, was isolated from a farm in Quandian Village, Zhengzhou City, Henan Province, China, and subjected to taxonomic characterization. Optimal growth occurred at 32 ℃, pH 7.0 and 0–1% NaCl (w/v). Mannose and glucose were identified as the sugar components in the whole-cell hydrolysates. The strain’s peptidoglycan type was classified as A3γ (ll-Dpm-Gly), and MK-9(H4) was identified as the predominant respiratory quinone. Aminoglycolipid, aminophospholipid, glycolipids, phosphatidylglycerol and phospholipid were detected as the major polar lipids. The predominant cellular fatty acids were anteiso-C15 : 0 (48.7%) and iso-C15 : 0 (20.2%). Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZF39T within the family Propionibacteriaceae. The strain formed a distinct genetic lineage adjacent to the genus Desertihabitans, with 16S rRNA gene sequence similarities of 94.70% to Desertihabitans aurantiacus CPCC 204711T and 94.56% to Desertihabitans brevis KCTC 49116T. The genomic G+C content was 67.7 mol%. Genome comparisons revealed that the average nucleotide identity values between strain ZF39T and D. aurantiacus CPCC 204711T, D. brevis KCTC 49116T, Granulicoccus phenolivorans DSM 17626T were 72.50%, 71.98% and 72.36%, respectively. Moreover, phylogenetic analysis and phenotypic characterization supported the classification of strain ZF39T as a novel species of a new genus within the family Propionibacteriaceae. The name Ammonicoccus fulvus gen. nov., sp. nov. is proposed, with ZF39T (=CGMCC 1.60047T=KCTC 59250T=MCCC 1K08851T) as the type strain.

Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez’s frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0–7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.

The strain TOYAMA8T is a deep-sea alkaliphilic cellulolytic bacterium isolated from a slurry-adhered epiphytic site of Megalodicopia hians. Cells of this strain are Gram-negative, aerobic, curved rods or spirilla, motile with monopolar flagella, and grow on cellulose as the sole carbon source. Compared to other closely related species, this bacterium is characterized by a large number of cellulase genes. Strain TOYAMA8T showed alkaliphilic growth within the pH range 7.5–9.0. The major cellular fatty acids were C18 : 1 ω7, C14 : 0, C16 : 0 and C16 : 1 ω7. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids and aminolipids. A major respiratory lipoquinone was Q-9. Phylogenomic analysis using the 16S rRNA gene and whole-genome sequence data showed that the strain is related to the families Gynuellaceae, Saccharospirillaceae and Natronospirillaceae. The values of 16S rRNA gene sequence similarity, amino acid identity and percentage of conserved proteins between the strain TOYAMA8T and related species were low, with maximum values of 90.6, 48.1 and 34.6%, respectively. These results, together with differences in phenotypic and biochemical characteristics, indicate that the new isolate TOYAMA8T represents a novel genus and species, for which the name Marinicellulosiphila megalodicopiae gen. nov., sp. nov., is proposed. The type strain is TOYAMA8T (JCM 31119T=DSM 114864T).

Phylogenetic analysis of the genus Aureimonas, utilizing both 16S rRNA gene sequences and comprehensive whole-genome data, revealed its polyphyletic nature, necessitating a revision to accommodate phylogenetically distinct species. Based on established threshold values for genus demarcation – specifically, 16S rRNA gene similarity, Average Amino Acid Identity and Percentage of Conserved Proteins – a notably substantial divergence was observed within the genus Aureimonas, and the division of Aureimonas into four distinct genera is strongly supported. To address this, we propose the establishment of four new genera: Dennerimonas gen. nov., Mesocryomonas gen. nov., Rathsackimonas gen. nov. and Plantimonas gen. nov. These classifications accommodate species that are significantly divergent from the type species of Aureimonas, thereby more accurately reflecting their distinct evolutionary lineages. Additionally, Aureimonas glaciistagni is proposed to be reclassified within the genus Jiella as Jiella glaciistagni comb. nov. based on phylogenetic evidence indicating a closer evolutionary relationship to Jiella species than to other members of Aureimonas. Our analysis, which included assessments of 16S rRNA gene similarity, Average Nucleotide Identity, and digital DNA–DNA hybridization values exceeding species delineation thresholds, further supports the reclassification of Jeongeupella Jiang et al. 2024 as a later heterotypic synonym of Antarcticirhabdus Du et al. 2023.

An anaerobic isolate, designated me31T, was isolated from pit mud in Yibin, Sichuan Province, PR China. Phylogenetic results based on 16S rRNA gene sequence showed that strain me31T belongs to the family Dysgonomonadaceae, and the most closely related isolated relatives were Seramator thermalis SYSU GA16112T (93.65%) and Proteiniphilum propionicum JNU-WLY501T (93.22%). The DNA G+C content was 44.26 mol%. The ANI and AAI values between strain me31T and the closely related strains were 69.25–71.18% and 69.59–71.15%, respectively. Cells of strain me31T were Gram-stain-negative, rod-shaped and non-motile. Growth of strain me31T was observed at 25–37 °C, pH 6.0–8.0 and a salt tolerance range of 0–1.0% (w/v). The predominant respiratory quinone was MK-9. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C17 : 0 2OH. The polar lipids of strain me31T were found to consist of phosphatidylethanolamine, three unidentified phospholipids, three unidentified phosphoglycolipids, one unidentified phosphoglycolipid, one unidentified lipid, two unidentified glycolipids and one aminophosphoglycolipid. According to the results of morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic analysis, strain me31T represents a novel species of a novel genus of the family Dysgonomonadaceae, for which the name Limibacterium fermenti gen. nov., sp. nov. is proposed. The type strain is me31T (=GDMCC 1.4237T=KCTC 25756T=WMCC 10035T).

A taxonomic study was conducted on four bacterial strains isolated from the soil of a coking plant. Phylogenetic analysis showed that the four strains belonged to three families: Comamonadaceae, Micrococcaceae and Roseiarcaceae. Identification of the 16S rRNA gene exhibited that their sequence similarities were between 94.96 and 98.98% when compared to known and validly nominated species. Their genomes ranged from 3.4 to 7.2 Mb, with DNA G+C molar contents varying from 62.3 to 67.2%. The average nucleotide identities ranged from 71.4 to 92.3%, and digital DNA–DNA hybridization values were 19.7–47.0% when comparing them with closely related type species, supporting the classification of these four strains. Functional analysis demonstrated that strain H3Y2-7T was robustly resistant to chromate (VI) and arsenite (III) and was able to grow on aromatic compounds including naphthalene as carbon sources even in the presence of chromate (VI). These features reflect its ability to treat combined pollutants and adapt to a polluted environment. Based on the analysis of polyphasic taxonomy, we propose the four bacterial strains representing novel species, namely Curvibacter soli sp. nov. (type strain H39-3-26T=JCM 36178T=CGMCC 1.61344T), Extensimonas soli sp. nov. (type strain H3M7-6T=JCM 36176T=CGMCC 1.61336T), Pseudarthrobacter naphthalenicus sp. nov. (type strain H3Y2-7T=JCM 36482T=CGMCC 1.61323T) and Terripilifer ovatus gen. nov., sp. nov. (type strain H3SJ34-1T=JCM 36465T=CGMCC 1.61333T).