- Volume 72, Issue 10, 2022

A Gram-stain-negative, motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strain, Adcm-6AT, was isolated from a seawater sample collected from the deep chlorophyll maximum layer in the West Pacific Ocean. Strain Adcm-6AT grew at 20–37 °C (optimum, 28–32 °C), at pH 6–11 (pH 7) and in the presence of 0–6 % (1–2 %) NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it belonged to the genus Zavarzinia and had 97.7 and 96.9 % sequence similarity to Zavarzinia compransoris DSM 1231T and Zavarzinia aquatilis JCM 32263T, respectively. Digital DNA–DNA hybridization and average nucleotide identity values between strain Adcm-6AT and the two type strains were 22.2–22.9 % and 79.7–80.4 %, respectively. The principal fatty acids were C19:0 cyclo ω8c, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and C16:0. The predominant respiratory quinone was Q-10. The polar lipids were diphosphatidylglycerol, two phosphatidylethanolamines, two phosphatidyglycerols and an unidentified lipid. The genomic DNA G+C content of strain Adcm-6AT was 67.7 %. Based on phylogenetic analysis and genomic-based relatedness indices, as well as phenotypic and genotypic characteristics, strain Adcm-6AT represents a novel species within the genus Zavarzinia , for which the name Zavarzinia marina sp. nov. is proposed. The type strain is Adcm-6AT (=MCCC M24951T=KCTC 82849T).

A novel Gram-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, designated J26T, was isolated from the sediment of a river in Ronggui, Foshan city, China. Strain J26T grew optimally at 0 % (w/v) NaCl, pH 6.5–7.5, and 30 °C, and it formed milky white irregular colonies on Reasoner's 2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J26T had the highest similarity to Tabrizicola aquatica RCRI19T (97.1 %) and formed a distinct clade in the genus Tabrizicola . Cellular components of J26T supported this strain as a member of the genus Tabrizicola . The predominant fatty acids were C18 : 1  ω7c, C18 : 1  ω7c-11 methyl and C16 : 0. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphorylethanolamine. Ubiquinone Q-10 was the major respiratory quinone, and the DNA G+C content was 64.2 mol%. However, low 16S rRNA gene sequence similarity and average nucleotide identity (73.56 % for ANIb between strain J26T with RCRI19T) demonstrated that strain J26T should be assigned to a novel species. Moreover, the differences between J26T and RCRI19T in terms of physiological and biochemical properties, such as carbon, nitrogen and sulphur metabolism, further supported that J26T represents a novel species, for which the name Tabrizicola rongguiensis sp. nov. is proposed. The type strain is J26T (=GDMCC 1.2843T=KCTC 92112T).

Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter , Anaeromyxobacter dehalogenans 2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.

Two novel strains, Z083T and Z084, were isolated from the viscera of abalone, Haliotis discus hannai, sampled in Weihai, PR China. The phenotypic, chemotaxonomic and genomic characteristics of the two strains were studied. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the two strains were 99.8 and 98.9 %, respectively, suggesting that the two strains belonged to the same species. The 16S rRNA gene sequence analysis showed 99.8 % similarity between the two strains, while the genome analysis indicated that they were not from one clonal origin. Phylogenetic analysis of 16S rRNA gene sequences showed the two strains belonged to the genus Aestuariirhabdus and Aestuariirhabdus litorea JCM 32043T was the closest strain (97.5 %). Genomic analysis, including calculations of ANI, dDDH, amino acid identity (AAI) and percentage of conserved proteins (POCP), between Z083T, Z084 and A. litorea JCM 32043T clearly separated those two strains from A. litorea JCM 32043T as the values were below the thresholds for species delineation. The genome size of strains Z083T and Z084 were approximately 4.16 and 4.23 Mbp, respectively, and the DNA G+C contents of both strains were 51.8 mol%. According to the phenotypic, chemotaxonomic and phylogenetic characterizations and the results of genome analysis, Z083T and Z084 could be identified as belonging to a novel species of the genus Aestuariirhabdus , for which the name Aestuariirhabdus haliotis sp. nov., is proposed, with Z083T (=MCCC 1H00501T=KCTC 92006T) as the type strain.

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel   Bradyrhizobium   lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit (rps) gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named   Bradyrhizobium   species with   B. japonicum   USDA 6T as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome blast distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4T, 323S2, 1S5 and 38S5T have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4T and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5T (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names Bradyrhizobium barranii sp. nov. subsp. barranii subsp. nov. (sv. glycinearum) and Bradyrhizobium barranii sp. nov. subsp. apii subsp. nov. (sv. septentrionale) are proposed with strain 144S4T (=LMG 31552T=HAMBI 3722T) as the species type strain and type strain of subsp. barranii subsp. nov., and strain 38S5T (=LMG 31556T=HAMBI 3721T) as the type strain of subsp. apii subsp. nov.

A Gram-stain-negative, yellow-pigmented, motile, flagellated and rod-shaped bacterium, designated as 13AT, was isolated from a river sediment sample of Fuyang River in Hengshui City, Hebei Province, PR China. Strain 13AT grew at 10–37 °C (optimum, 30 °C), at pH 5.0–11.0 (optimum, pH 7.0) and at 0–7 % (w/v) NaCl concentration (optimum, 0 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 13AT belongs to the genus Lysobacter , and was most closely related to Lysobacter spongiicola DSM 21749T (97.8 %), Lysobacter concretionis DSM 16239T (97.5 %), Lysobacter daejeonensis GIM 1.690T (97.3 %) and Lysobacter arseniciresistens CGMCC 1.10752T (96.9 %). Meanwhile, the type species Lysobacter enzymogenes ATCC 29487T was selected as a reference strain (95.2 %). The genomic size of strain 13AT was 3.0 Mb and the DNA G+C content was 69.0 %. The average nucleotide identity values between strain 13AT and each of the reference type strains L. spongiicola DSM 21749T, L. concretionis DSM 16239T, L. daejeonensis GIM 1.690T, L. arseniciresistens CGMCC 1.10752T and L. enzymogenes ATCC 29487T were 75.9, 76.1, 77.7, 78.0 and 73.2 %, respectively. The digital DNA–DNA hybridization values between strain 13AT and each of the reference type strains were 21.7, 22.2, 21.9, 22.7 and 23.2 %, respectively. The average amino acid identity values between strain 13AT and each of the reference type strains were 72.5, 72.9, 72.3, 75.0 and 69.2 %, respectively. The major fatty acids were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl). The sole respiratory quinone was identified as ubiquinone-8. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified lipid, four unidentified phospholipids and two unidentified glycolipids. Based on the phenotypic, physiological, phylogenetic and chemotaxonomic data, strain 13AT represents a novel species of the genus Lysobacter , for which the name Lysobacter selenitireducens sp. nov. is proposed. The type strain is 13AT (=JCM 34786T=GDMCC 1.2722T).

In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus Pseudomonas , and multilocus sequence analysis revealed that Pseudomonas gozinkensis IzPS32dT, Pseudomonas glycinae MS586T, Pseudomonas allokribbensis IzPS23T, 'Pseudomonas kribbensis' 46–2 and Pseudomonas koreensis PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain P. gozinkensis IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).

A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4T was isolated from Cannabis sativa L. ‘Cheungsam’ in Andong, Republic of Korea. The strain DM2-R-LB4T grew at temperatures of 15–45 °C (optimum, 30–37 °C), pH of 5.5–9 (optimum, 8.0), and 0–2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4T is related to species of the genus Sphingomonas , and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244T and Sphingomonas leidyi DSM 4733T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4T and S. kyenggiensis KCTC 42244T, and S. leidyi DSM 4733T was 76.8 and 76.7 %, respectively, while the values of digital DNA–DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C14 : 0 2-OH, C16 : 0, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4T (=KCTC 92075T = GDMCC 1.3018T).

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated CMS5P-6T, was isolated from a surface-sterilized bark of Aegiceras corniculatum collected from Guangxi Zhuang Autonomous Region, PR China, and investigated by a polyphasic approach to determine its taxonomic position. Strain CMS5P-6T was found to grow optimally with 0–1 % (w/v) NaCl, at 30 °C and pH 6.0–7.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis showed that strain CMS5P-6T showed high 16S rRNA gene sequence similarity of 96.7 % to Hephaestia caeni DSM 25527T and Sphingomonas colocasiea CC-MHH0539T. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between strain CMS5P-6T and H. caeni DSM 25527T were 78.0, 21.7 and 70.8 %, respectively. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between strain CMS5P-6T and S. colocasiea JCM 31229T were 74.0, 19.9 and 61.4 %, respectively. Phylogenomic analyses based on genome sequences showed that strain CMS5P-6T and H. caeni DSM 25527T formed a distinct cluster within the family Sphingomonadaceae and far away from S. colocasiea JCM 31229T. The DNA G+C content of strain CMS5P-6T was determined to be 65.6 mol%. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid and ubiquinone Q-10 was identified as the respiratory lipoquinone. The polar lipids were found to comprise diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingoglycolipid and two unidentified aminolipids, and the major fatty acids were identified as C18 : 1  ω7c, C19 : 0 cycloω8c and C16 : 0. On the basis of phylogenetic, genomic, chemotaxonomic and phenotypic data, strain CMS5P-6T can be concluded to represent a novel species of the genus Hephaestia , for which the name Hephaestia mangrovi sp. nov. is proposed. The type strain is CMS5P-6T (=JCM 33125T=CGMCC 1.13868T).

A Gram-stain-negative, non-motile, ovoid or short rod shaped and aerobic marine bacterium, designated as strain LXJ103T, was isolated from a coastal phytoplankton bloom in Xiamen, PR China. Cells were oxidase- and catalase-positive. Strain LXJ103T grew at 4–40 °C (optimum, 28–37 °C), at pH 6–10 (optimum, pH 8.5) and with 1–15 % (w/v) NaCl (optimum, 3 %). The major cellular fatty acids (>10 %) were iso-C18 : 1  ω7c/iso-C18 : 1  ω6c (70.2 %) and C16 : 0 (10.3 %). The following polar lipids were found to be present: phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five unknown glycolipids. The predominant respiratory quinone was ubiquinone-10. Strain LXJ103T exhibited the highest 16S rRNA gene sequence similarity to Roseovarius litorisediminis D1-W8T (96.97 %). The phylogenetic trees based on 16S rRNA gene sequences showed that strain LXJ103T was a member of the genus Roseovarius . The draft genome size of strain LXJ103T is 3.05 Mb with a genomic G+C content of 61.22 mol%. The digital DNA–DNA genome hybridization value of strain LXJ103T compared with the most similar type strain R. litorisediminis CECT 8287T was 18.80 %. The average nucleotide identity value between strain LXJ103T and R. litorisediminis CECT 8287T was 72.60 %. On the basis of polyphasic data, strain LXJ103T represents a novel species of the genus Roseovarius , for which the name Roseovarius carneus sp. nov. is proposed. The type strain is LXJ103T (=CGMCC 1.19168T=MCCC 1K06527T=JCM 34778T).

The three novel bacterial strains designated as 3Y2T, 4Y16 and 4Y11T were isolated from an aquaculture farm and characterized using a polyphasic taxonomic approach. These strains were determined to be catalase- and oxidase-positive and to hydrolyze gelatin and aesculin. The results of 16S rRNA gene-based phylogenetic analysis indicated that the three strains were related to members of the genus Ideonella . The phylogenomic results further indicated that the three strains formed two independent branches distinct from reference type strains within this genus. The digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) values between the three strains and their relatives were far below the thresholds of 70 % dDDH, 95–96 % ANI and 95 % AAI for species definition, respectively, indicating that the three strains represent two novel genospecies. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of the three strains were summed feature 3 (C16 : 1ω6c and/or C16 : 1 ω7c) and C16 : 0; the common main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol; the respiratory quinone was ubiquinone-8. The genomic DNA G+C contents of the three strains were 70.2, 70.1 and 69.7%, respectively. On the basis of the different genotypes and distinctive phenotypes such as the phosphatidylcholine and glycolipid only in 3Y2T and the utilization of malic acid and trisodium citrate only in 4Y11T, strains 3Y2T and 4Y11T are concluded to represent two novel species of the genus Ideonella , for which the names Ideonella alba sp. nov. (type strain 3Y2T = GDMCC 1.2584T = KCTC 82813T) and Ideonella aquatica sp. nov. (type strain 4Y11T = GDMCC 1.1935T = JCM 34285T) are proposed.

A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325T grew optimally at 37–40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325T was most similarly related to Limibaculum halophilum CAU 1123T (96.2 %), Phaeovulum vinaykumarii DSM 18714T (93.9%) and Amaricoccus solimangrovi HB 172011T (93.7 %). The major fatty acids (>10 %) were C18 : 1  ω7c (60.0 %) and 11-methyl C18 : 1  ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325T represents a novel species of the genus Limibaculum , for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397T=KCTC 92313T).

Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate–formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus . Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).

On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus , for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.

A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10–45 °C (optimum, 35 °C), pH 4.5–9.0 (optimum, pH 7.0) and in the presence of 1.0–8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus Sulfurimonas , with the highest similarity to the 16S rRNA gene sequences of Sulfurimonas indica NW8NT (95.9 %), Sulfurimonas crateris SN118T (95.7 %), Sulfurimonas xiamenensis 1-1NT (95.6 %) and Sulfurimonas paralvinellae GO25T (95.4 %). Sequence similarities to other members of the genus Sulfurimonas were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA–DNA hybridization (dDDH) estimate between B2T and S. indica NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus Sulfurimonas , for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).

A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic motile bacterium, designated strain OG9-811T, was isolated from the gut of an oyster collected in the Yellow Sea, Republic of Korea. The strain grew at 10–37 °C, pH 6.0–9.0 and with 0.5–10% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain OG9-811T affiliated with the genus Vibrio , with the highest sequence similarity of 98.2% to Vibrio coralliilyticus ATCC BAA-450T followed by Vibrio variabilis R-40492T (98.0 %), Vibrio hepatarius LMG 20362T (97.7 %) and Vibrio neptunius LMG 20536T (97.6 %); other relatives were Vibrio tritonius JCM 16456T (97.4 %), Vibrio fluvialis NBRC 103150T (97.0 %) and Vibrio furnissii CIP 102972T (97.0 %). The complete genome of strain OG9-811T comprised two chromosomes of a total 4 807 684 bp and the G+C content was 50.2 %. Results of analysis based on the whole genome sequence showed the distinctiveness of strain OG9-811T. The average nucleotide identity (ANI) values between strain OG9-811T and the closest strains V. coralliilyticus ATCC BAA-450T, V. variabilis R-40492T, V. hepatarius LMG 20362T, V. neptunius KCTC 12702T , V. tritonius JCM 16456T, V. fluvialis ATCC 33809T and V. furnissi CIP 102972T were 73.0, 72.6, 73.3, 73.0, 72.7, 78.5 and 77.8 %, respectively, while the digital DNA–DNA hybridization values between strain OG9-811T and the above closely related strains were 20.8, 21.2, 20.8, 21.7, 20.7, 23.2 and 22.4 %, respectively. The major fatty acids of strain OG9-811T were summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and C16:0. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain OG9-811T contained Q-8 as a quinone. On the basis of polyphasic taxonomic characteristics, strain OG9-811T is considered to represent a novel species, for which the name Vibrio ostreae sp. nov. is proposed. The type strain is OG9-811T (=KCTC 72623T=GDMCC 1.2610T).

Three Gram-stain-negative, motile, with amphilophotrichous flagella, and rod-shaped bacteria (LJ1, LJ2T and LJ3) were isolated from lower leaves with black spots on flue-cured tobacco in Yunnan, PR China. The results of phylogenetic analysis based on 16S rRNA gene sequences indicate that all the strains from tobacco were closely related to the type strains of the Pseudomonas syringae group within the P. fluorescens lineage and LJ2T has the highest sequence identities with P. cichorii DSM 50259T (99.92 %), P. capsici Pc19-1T (99.67 %) and P. ovata F51T (98.94 %) . The 16S rRNA gene sequence identities between LJ2T and other members of the genus Pseudomonas were below 98.50%. The average nucleotide identity by blast (ANIb) values between LJ2T and P. cichorii DSM 50259T, P. capsici Pc19-1T and P. ovata F51T were less than 95 %, and the in silico DNA–DNA hybridization (isDDH) values (yielded by formula 2) were less than 70 %. The major fatty acids were C16  :  1ω7c and/or C16  :  1ω6c (summed feature 3), C16  :  0 and C18  :  1ω7c and/or C18  :  1ω6c (summed feature 8). The polar lipids profile of LJ2T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and one unidentified glycolipid. The predominant respiratory quinone was Q-9. The DNA G+C content of LJ2T was 58.4 mol%. On the basis of these data, we concluded that LJ2T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas lijiangensis sp. nov. is proposed. The type strain of Pseudomonas lijiangensis sp. nov. is LJ2T (=CCTCC AB 2021465T=GDMCC 1.2884T=JCM 35177T).

We studied a novel taxon of the genus Acinetobacter , which comprised six strains collected in Czechia, Germany, Indonesia and Turkey between 2015 and 2021. The organisms were isolated from environmental soil, water samples and cow faeces. Their genome sizes varied between 3.3 and 3.5 Mb, with a G+C content of 40.4–40.8 mol%. Based on genus-wide core genome analysis, the taxon formed a distinct clade, with Acinetobacter gandensis being the phylogenetically closest related species. The intrataxon genomic average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values reached 95.3–97.4% and 62.5–77.8 %, respectively, whereas its ANIb/dDDH values against the known Acinetobacter type strains were ≤82.7 %/≤25.7 %. Cluster analysis of whole-cell MALDI-TOF mass spectra corroborated the distinctness and cohesiveness of the taxon. The novel strains were non-glucose-oxidizing, non-haemolytic and non-proteolytic, growing at up to 37–41 °C but not at 44 °C and utilizing 8–10 of the 36 carbon sources tested. Growth on glutarate, tricarballylate and at 37 °C combined with the inability to assimilate 4-aminobutyrate and d-malate differentiated them from all validly named Acinetobacter species. The inspection of genome sequences in the NCBI database revealed the existence of numerous strains conspecific with this group, which were collected from pig faeces and environmental samples in China. We conclude that the taxon represents an ecologically and geographically widespread species, for which we propose the name Acinetobacter amyesii sp. nov., with ANC 5579T (= CCM 9242T=CCUG 76274T=CNCTC 8134T) as the type strain.

Six strains of black meristematic fungi were isolated from Antarctic soils, gasoline car tanks and from the marine alga Flabellia petiolata. These fungi were characterized by morphological, physiological and phylogenetic analyses. According to the maximum-likelihood analysis reconstructed with ITS and LSU sequences, these strains belonged to the genus Knufia. Knufia obscura sp. nov. (holotype CBS 148926) and Knufia victoriae sp. nov. (holotype CBS 149015) are proposed as two novel species and descriptions of their morphological, physiological and phylogenetic features are presented. Based on the maximum-likelihood analyses, K. obscura was closely related to Knufia hypolithi (99 % bootstrap support), while K. victoriae clustered in the clade of Knufia cryptophialidica and Knufia perfecta (93 % bootstrap support). Knufia victoriae, recorded in Antarctic soil samples, had a psychrophilic behaviour, with optimal growth between 10 and 15 °C and no growth recorded at 20 °C. Knufia obscura, from a gasoline car tank and algae, displayed optimal growth between 20 and 25 °C and was more tolerant to salinity than K. victoriae.

As currently circumscribed, Acrogenospora (Acrogenosporaceae, Minutisphaerales, Dothideomycetes) is a genus of saprobic hyphomycetes with distinctive conidia. Although considered common and cosmopolitan, the genus is poorly represented by sequence data, and no neotropical representatives are present in public sequence databases. Consequently, Acrogenospora has been largely invisible to ecological studies that rely on sequence-based identification. As part of an effort to identify fungi collected during ecological studies, we identified strains of Acrogenospora isolated in culture from seeds in the soil seed bank of a lowland tropical forest in Panama. Here we describe Acrogenospora terricola sp. nov. based on morphological and phylogenetic analyses. We confirm that the genus has a pantropical distribution. The observation of Acrogenospora infecting seeds in a terrestrial environment contrasts with previously described species in the genus, most of which occur on decaying wood in freshwater environments. This work highlights the often hidden taxonomic value of collections derived from ecological studies of fungal communities and the ways in which rich sequence databases can shed light on the identity, distributions and diversity of cryptic microfungi.