International Journal of Systematic and Evolutionary Microbiology

A Gram-stain-negative, non-motile, rod-shaped and imazamox-resistant bacterium, designated as H34T, was isolated from soil obtained from a farmland. Strain H34T grew at pH 6.0–9.0 (optimum, 7.0), temperature 15–40 °C (optimum, 30 °C) and salinity of 0–3.0% NaCl (optimum 0.5% NaCl, w/v). Phylogenetic analysis of the 16S rRNA gene and genome sequences showed that strain H34T was affiliated to the family Chitinophagaceae but formed a distinct phyletic branch. The values of 16S rRNA gene sequence similarity, average nt identity (ANI), digital DNA–DNA hybridization (dDDH) and average aa identity (AAI) between strain H34T and closely related type strains of the genera Flavisolibacter, Paraflavisolibacter, Paracnuella, Flaviaesturariibacter and Cnuella were 90.9–92.6%, 68.4–72.1%, 18.7–20.5% and 60.5–65.9%, respectively. The genome size was 7.01 Mb with a G+C content of 56.5 mol%. The major fatty acids (≥10%) were iso-C15 : 0, iso-C15 : 1 G and C16 : 1  ω5c. The only isoprenoid quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminophosphoglycolipid, two unidentified phospholipids, three unidentified aminolipids and four unidentified lipids. The distinct phylogenetic relationships; low values of 16S rRNA gene sequence similarity, AAI, ANI and dDDH; and the differences in phenotypic and genotypic characteristics support that strain H34T represents a novel species in a novel genus in the family Chitinophagaceae, for which the name Huijunlia imazamoxiresistens gen. nov., sp. nov. is proposed (type strain H34T=MCCC 1K09117T=KCTC 102287T).

A Gram-positive, oval-shaped and non-motile strain, designated MMS21-DH1MA12T, was isolated from riverside soil and subjected to polyphasic taxonomic characterization. Strain MMS21-DH1MA12T grew optimally in tryptic soy agar, forming yellow-coloured, convex and smooth colonies. The optimal growth conditions of the strain were 30 °C, pH 7 and absence of NaCl. Strain MMS21-DH1MA12T shared the highest 16S rRNA gene sequence similarity with Agrococcus sediminis NS18T (97.3%), and then with Diaminobutyricimonas aerilata 6408 J-67T (97.1%) and Mycetocola miduiensis CGMCC 1.11101 T (96.9%), all belonging to the family Microbacteriaceae. Strain MMS21-DH1MA12T had a genome size of 2.4 Mbp and G+C content of 62.6%. The digital DNA–DNA hybridization (dDDH), orthologous average nucleotide identity (orthoANI) and average amino acid identity (AAI) values between strain MMS21-DH1MA12T and related type strains of the genera within the family Microbacteriaceae were no higher than 22.2%, 71.54% and 60.19%, respectively. The dDDH, orthoANI and AAI values of MMS21-DH1MA12T with related taxa were no higher than 22.2%, 71.54% and 61.96%, thus showing a distant relationship of the strain with other members of Microbacteriaceae. It was also notable that the species sharing the highest similarities were different for all three indices. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The main cellular fatty acids were anteiso-C15 : 1, antesio-C17 : 1 and iso-C15 : 0. The predominant menaquinones were MK-10 and MK-11. The combination of physiological and biochemical properties, as well as chemotaxonomic features, clearly separated strain MMS21-DH1MA12T from related taxa of Microbacteriaceae. It is, thus, evident that MMS21-DH1MA12T represents a novel species in a novel genus, for which the name Humidisolicoccus flavus gen. nov., sp. nov. is proposed (type strain=MMS21-DH1MA12T = KCTC 49751T = LMG 32525T=JCM 37009T).

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria. However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae. In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 families were significantly separated with p values < 2.2×10−16. Thus, it was speculated that the AAI and ED thresholds for distinguishing different families were <0.6 and >0.5, respectively. Additionally, we reclassified 163 species into new genera with their phylogenetic topologies, according to the previous genus AAI and ED boundaries of 0.7 and 0.4. Our study is the first genomic-based study of the order Sphingomonadales and will promote further insights into the evolution of this order.

A Gram-stain-negative coccobacillus, LMG 32992T, was isolated from water that had collected in a tyre in Pingtung, Donggang Township, Taiwan. Upon preliminary 16S rRNA gene sequence analysis, it was most closely related to members of the genus Ralstonia (16S rRNA gene sequence similarities of 96.7–97.5%). The present study aimed to elucidate its taxonomic position and to propose a formal classification. To this end, the complete genome sequence was determined, and taxonomic, phylogenomic, metabolic and physiological analyses were performed. Comparative genomic analyses demonstrated that strain LMG 32992T and another unclassified strain, Burkholderiaceae bacterium PBA, which was isolated earlier from textile wastewater in Malaysia, represented a single novel species within a novel genus of the family Burkholderiaceae. The G+C content of the LMG 32992T genomic DNA was 63.77 mol%. Genomic analyses and growth tests demonstrated that LMG 32992T had an asaccharolytic metabolism but that it was well-equipped to synthetize, if necessary autotrophically, and transform all required carbohydrates and that it used the Krebs and related cycles to generate reductive power for a heterotrophic energy metabolism. We propose the name Imbroritus primus gen. nov., sp. nov. with strain LMG 32992T (=CIP 112179T=BCRC 81361T=A30B1T) as the type strain, for this novel taxon.

Following Rule 51b(4) of the International Code of Nomenclature of Prokaryotes (2022 Revision) (ICNP), the prokaryotic generic name Moorella Collins et al. 1994 is illegitimate, as it is a later homonym of the fungal genus name Moorella P. Rag. Rao & D. Rao 1964 (Ascomycota: Pezizomycotina). Accordingly, as required by Rule 54 of the ICNP, we propose the replacement name Neomoorella and the replacement type species name Neomoorella thermoacetica. We also propose replacement names for the six other species with validly published and not rejected names belonging to the genus Moorella, for one species with effectively but not validly published name and for the family name Moorellaceae and the order name Moorellales.

A strictly anaerobic bacterial strain, designated as AMB_02T, was isolated from a propionate enrichment culture obtained from a high-ammonia biogas digester. The cells were anaerobic and coccoid (0.5 µm), often appearing as diplococci or in a short chain of three to four cells. Growth was observed between 20 and 45 °C (optimum at 37–39 °C), with an initial pH of 6.5–9.0 (optimum pH 8.0–8.5), and the species tolerated up to 0.8 M NH4Cl and 0.5 M NaCl. The major cellular fatty acids were C16 : 0 (31.6%), C14 : 0 (14.6%) and C18 : 0 (13.3%). AMB_02T grew with formate, carbohydrates and aa, including asparagine, histidine, tryptone and tryptophan. Acetate was the major product formed. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AMB_02T was most closely related to the species Citroniella saccharovorans (92.5%). The genome of strain AMB_02T was 2.5 Mb in length with a G+C content of 34.8 mol%, and 2,354 protein-coding genes were predicted. Furthermore, genes coding for the reductive glycine pathway potentially used for formate metabolism were identified. Comparative genomic analysis of AMB_02T revealed the closest similarity to C. saccharovorans [21.2% digital DNA–DNA hybridization (dDDH) and 77.4% average nt identity (ANI)] and to Parvimonas micra (24.4% dDDH and 76.9% ANI). Based on the phenotypic characteristics and phylogenetic analyses, AMB_02T is regarded as a novel genus, Microaceticoccus, within the family Peptoniphilaceae for which the species name Microaceticoccus formicicus is proposed. The type strain is AMB_02T=DSM 110248T=JCM 39108T.

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).