Distribution of polyamines in methanogenic bacteria

Ochrobactrum chromiisoli sp. nov., Isolated from Chromium-Contaminated Soil

A Gram-stain-negative, non-spore-forming, flagellated, motile, aerobic, rod-shaped bacteria strain, designated YY2XT, was isolated from chromium-contaminated soil. Phylogenetic analysis based on 16S rRNA gene, recA gene, and whole genome indicated that the strain represented a new member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. The phylogenetic trees based on 16 s rRNA gene, revealed that Falsochrobactrum ovis DSM26720T (96.7%), Ochrobactrum gallinifaecis DSM15295T (96.2%), and Pseudochrobactrum asaccharolyticum DSM25619T (96.2%) are the most closely related phylogenetic neighbors of strain YY2XT. The draft genome of YY2XT was approximately 4,650,646 bp in size with a G + C content of 53.0 mol%. Average nucleotide identity and digital DNA-DNA hybridization values among strain YY2XT and the selected Brucellaceae species were 71.4-83.1% and 13.5-42.7%, which are below the recommended cut-off values for species delineation. Growth of strain YY2XT occurred within pH 5-10 (optimum, pH 7-8), 4 ℃-42 °C (optimum, 30 °C), and NaCl concentrations of 0.0-6.0% (optimum, 1.0%). Major quinone system was ubiquinone 10, the major fatty acids were C16:0, C18:1ω7c, and C16:1ω7c and the major polyamines were spermidine and putrescine. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, and four undefined lipids. On the basis of the phenotypic, genotypic and chemotaxonomic traits, strain YY2XT was considered to represent a novel species of the genus Ochrobactrum, for which the name Ochrobactrum chromiisoli sp. nov. is proposed. The type strain is YY2XT (= CCTCC AB 2023035T = JCM 36000T).

Description of Flavobacterium agricola sp. nov., an auxin producing bacterium isolated from paddy field

An auxin-producing bacterial strain, CC-SYL302T, was isolated from paddy soil in Taiwan and identified using a polyphasic taxonomic approach. The cells were observed to be aerobic, non-motile, non-spore-forming rods, and tested positive for catalase and oxidase. Produced carotenoid but flexirubin-type pigments were absent. Optimal growth of strain CC-SYL302T was observed at 25 °C, pH 7.0, and with 2% (w/v) NaCl present. Based on analysis of 16S rRNA gene sequences, it was determined that strain CC-SYL302T belongs to the genus Flavobacterium of the Flavobacteriaceae family. The closest known relatives of this strain are F. tangerinum YIM 102701-2 T (with 93.3% similarity) and F. cucumis R2A45-3 T (with 93.1% similarity). Digital DNA-DNA hybridization (dDDH) values were calculated to assess the genetic distance between strain CC-SYL302T and its closest relatives, with mean values of 21.3% for F. tangerinum and 20.4% for F. cucumis. Strain CC-SYL302T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the Flavobacterium genus, ranging from 67.2 to 72.1% (n = 22). The dominating cellular fatty acids (> 5%) included iso-C14:0, iso-C15:0, iso-C16:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C16:1 ω6c/C16:1 ω7c and C16:0 10-methyl/iso-C17:1 ω9c. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and nine unidentified polar lipids. The genome (2.7 Mb) contained 33.6% GC content, and the major polyamines were putrescine and sym-homospermidine. Strain CC-SYL302T exhibits distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, dDDH, and phylogenomic placement. Therefore, it is proposed that this strain represents a new species of the Flavobacterium genus, for which the name Flavobacterium agricola sp. nov. is proposed. The type strain is CC-SYL302T (= BCRC 81320 T = JCM 34764 T).

Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667T, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667T was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C16 : 0, C17 : 0cyclo, C19 : 0cyclo ω8c and C14 : 0 3OH/iso-C16 : 1 I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with 'Neopusillimonas minor' (with 98.2 % similarity) and Paralcaligenes ureilyticus (with 97.3 % similarity) of the family Alcaligenaceae. The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667T shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera Neopusillimonas (72.4‒77.9 %, n=2), Pusillimonas (72.8‒73.0 %, n=2) and Pollutimonas (71.7‒73.0 %, n=5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA-DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667T is considered to represent a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aromaticivorans sp. nov. is proposed. The type strain is CC-YST667T (=BCRC 81321T =JCM 34761T).

Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G + C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and β chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n = 3), followed by Tabrizicola (72.3%‒73.7%, n = 5), and Gemmobacter(72.3%‒73.5%, n = 7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T = BCRC 81286T = JCM 34182T).

Niabella agricola sp. nov., isolated from paddy soil

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative, orange-coloured bacterium (designated strain CC-SYL272T) isolated from paddy soil. Cells were observed to be strictly aerobic, non-motile and non-spore-forming rods, exhibiting positive catalase and oxidase. Strain CC-SYL272T was found to grow optimally at 20–40 °C, pH 6.0–8.0 and NaCl 0–2 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CC-SYL272T belongs to the genus Niabella , family Chitinophagaceae , and is most closely related to Niabella pedocola (97.8 %) followed by Niabella drilacis (97.2 %) and established a distinct taxonomic lineage associated with these species. The highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-SYL272T versus Niabella species (69.1–83.5 %, n=8). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-SYL272T against N. pedocola was 27.3 %. The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The major polyamines were putrescine and sym-homospermidine. The dominating cellular fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3OH and C16 : 1  ω6c/C16 : 1  ω7c. The draft genome (6.25 Mb) of strain CC-SYL272T spanned three contigs having 47.1 mol% DNA G+C content, 5087 protein-encoding genes, 10 rRNA genes and 44 tRNA genes. The genome harboured genes involved in the depolymerization of both animal and plant polysaccharides. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH and the phylogenomic placement, strain CC-SYL272T is considered to represent a novel species of the genus Niabella , affiliated to the family Chitinophagaceae , for which the name Niabella agricola sp. nov. is proposed. The type strain is CC-SYL272T (=BCRC 81319T=JCM 34758T).

Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere

Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7T, RRHST34T and RHCKR47T, were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus Sphingomonas , among which both strains RHCKR7T and RRHST34T showed a close relationship with Sphingomonas yunnanensis YIM 003T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47T was most closely related to Sphingomonas palmae KACC 17591T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7T and RRHST34T were 90.43 and 40.80 %, respectively, and their most closely related type strain, S. yunnanensis YIM 003T, showed 90.43 % ANI and 40.7 % dDDH with RHCKR7T and 90.21 % and 42.9 % with RRHST34T, respectively, and the corresponding values between strain RHCKR47T and S. palmae KACC 17591T were 85.53 % and 29.30%, respectively. They all took C14 : 0 2-OH and summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym-Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus Sphingomonas , for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7T (=GDMCC 1.2663T=JCM 34794T), RRHST34T (=GDMCC 1.2665T=JCM 34796T) and RHCKR47T (=GDMCC 1.2664T=JCM 34795T) as the type strains, respectively.

Agrilactobacillus fermenti sp. nov. isolated from fermented vegetable residue

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive fermentative bacterium, designated strain CC-MHH1034T, isolated from a fermented vegetable residue. Cells of strain CC-MHH1034T were facultatively anaerobic, non-motile, and non-spore-forming rods, exhibiting positive catalase, oxidase and protease activities. Optimal growth occurred at 30 °С and pH 6.0. Strain CC-MHH1034T shared the highest 16S rRNA gene sequence similarities with Agrilactobacillus composti (95.9 %) followed by Agrilactobacillus yilanensis (95.1 %) and established a distinct taxonomic lineage associated with these species. Highest orthologous average nucleotide identity (OrthoANI) values were recorded for strain CC-MHH1034T versus Agrilactobacillus (71.1–71.6 %, n=2) followed by Ligilactobacillus (66.5–66.8 %, n=2), Lactobacillus (64.1–65.8 %, n=4). The mean digital DNA–DNA hybridization (dDDH) value obtained for strain CC-MHH1034T against Agrilactobacillus was 19.2–19.5 % (n=2). The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, four unidentified glycolipids, four unidentified phospholipids and one unidentified lipid. The major polyamine was sym-homospermidine and meso-diaminopimelic acid was detected as the cell-wall peptidoglycan. The dominating cellular fatty acids (>5 %) included C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 1  ω9c. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, dDDH, and the phylogenomic placement, strain CC-MHH1034T is considered to represent a novel species of the genus Agrilactobacillus , affiliated to the family Lactobacillaceae , for which the name Agrilactobacillus fermenti sp. nov. is proposed. The type strain is CC-MHH1034T (=BCRC 81220T=JCM 33476T).

Pusillimonas faecipullorum sp. nov., isolated from the poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST705^T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST705^T were aerobic, Gram-stain-negative, non-motile, non-spore-forming rods, displaying positive reactions for catalase, oxidase and β-glucosidase. Optimal growth occurred at 30 °C and pH 8. Strain CC-YST705^T shared the highest (> 96.0%) pair-wise 16S rRNA gene sequence similarity with Pusillimonas noertemannii (96.7%), followed by Pusillimonas caeni (96.6%), Eoetvoesia caeni (96.1%) and Paracandidimonas soli (96.0%), and formed a distinct phyletic lineage associate with the clade that accommodated Pusillimonas species. The draft genome (3.1 Mb) having 57.4 mol % G + C content contained genes involved in the catabolism of aromatic hydrocarbons. The orthologous average nucleotide identity (OrthoANI) values were 62.8-73.1% (n = 8), 72.6 (n = 1), 71.5% (n = 1) compared within the type strains of the genera Pusillimonas, Eoetvoesia and Paracandidimonas, respectively. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid, two unidentified phospholipids and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C_12:0, C_16:0, C_17:0 cyclo, C_19:0 cyclo ω8c and 2 C_14:0 3OH/iso-C_16:1 I. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST705^T is considered to represent a novel species of the genus Pusillimonas, for which the name Pusillimonas faecipullorum sp. nov. is proposed. The type strain is CC-YST705^T (= BCRC 81285 ^T = JCM 34168 ^T).

Vineibacter terrae gen. nov., sp. nov., an ammonium-assimilating and nitrate-reducing bacterium isolated from vineyard soil

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640^T, isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640^T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640^T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n=1) followed by Hypericibacter (89.4-90.0 %, n=2), Reyranella (88.8-89.8 %, n=5) and Nitrospirillum (89.2-89.4 %, n=2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % (n=1), 74.0-74.6 % (n=2), 67.5-68.3 % (n=2) when compared within the type strains of the genera Enhydrobacter, Reyranella and Niveispirillum, respectively. The dominant cellular fatty acids (>5 %) included C_16 : 0, iso-C_17 : 1  ω10c, C_19 : 0 cyclo ω8c, C_18 : 1 2-OH and C_18 : 1  ω7c/C_18 : 1  ω6c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640^T is considered to represent a novel genus and species of the family Rhodospirillaceae, for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640^T (=BCRC 81219^T=JCM 33507^T).

Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT501^T, harboring xenobiotic- and allelochemical-metabolizing genes, isolated from a long-term ecological research field in Taiwan. Cells of strain CC-CFT501^T were catalase- and oxidase-positive, non-motile and short rods. Optimal growth occurred at 30 °C, pH 8 and 1% NaCl. Strain CC-CFT501^T was found to share high 16S rRNA gene sequence similarity with the members of genera Quisquiliibacterium (94.3%, n = 1), Pandoraea (93.4-94.0%, n = 23) and Paraburkholderia (93.3-94.0%, n = 9), affiliated to the family Burkholderiaceae. Strain CC-CFT501^T shared 76.4% orthologous average nucleotide identity (OrthoANI) and 20.9% digital DNA-DNA hybridization (dDDH) values with Quisquiliibacterium transsilvanicum DSM 29781^T. Draft genome sequence (3.83 Mb) of strain CC-CFT501^T revealed several genes encoding the proteins involved in biphenyl and phenolic acid metabolism. Fatty acid profile contained C_16:0, C_18:0, C_10:0 3-OH, C_16:1 ω7c/C_16:1 ω6c and C_18:1 ω7c/C_18:1 ω6c in predominant amounts. The polar lipid profile consisted of phosphatidylethanolamine, thirteen unidentified amino lipids, two unidentified phospholipids and two unidentified glycolipids. The major polyamine was spermidine and ubiquinone Q-8 was the sole respiratory quinone. The DNA G + C content was 70.0 mol%. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT501^T is considered to represent a novel genus and species of the family Burkholderiaceae, for which the name Zeimonas arvi gen. nov., sp. nov. is proposed. The type strain of the type species is CC-CFT501^T (= BCRC 81218^T = JCM 33506^T).

Novel Glutamate-Putrescine Ligase Activity in Haloferax mediterranei: A New Function for glnA-2 Gene

The genome of the halophilic archaea Haloferax mediterranei contains three ORFs that show homology with glutamine synthetase (GS) (glnA-1, glnA-2, and glnA-3). Previous studies have focused on the role of GlnA-1, suggesting that proteins GlnA-2 and GlnA-3 could play a different role to that of GS. Glutamine synthetase (EC 6.3.1.2) belongs to the class of ligases, including 20 subclasses of other different enzymes, such as aspartate–ammonia ligase (EC 6.3.1.1), glutamate–ethylamine ligase (EC 6.3.1.6), and glutamate–putrescine ligase (EC 6.3.1.11). The reaction catalyzed by glutamate–putrescine ligase is comparable to the reaction catalyzed by glutamine synthetase (GS). Both enzymes can bind a glutamate molecule to an amino group: ammonium (GS) or putrescine (glutamate–putrescine ligase). In addition, they present the characteristic catalytic domain of GS, showing significant similarities in their structure. Although these proteins are annotated as GS, the bioinformatics and experimental results obtained in this work indicate that the GlnA-2 protein (HFX_1688) is a glutamate–putrescine ligase, involved in polyamine catabolism. The most significant results are those related to glutamate–putrescine ligase’s activity and the analysis of the transcriptional and translational expression of the glnA-2 gene in the presence of different nitrogen sources. This work confirms a new metabolic pathway in the Archaea domain which extends the knowledge regarding the utilization of alternative nitrogen sources in this domain.

Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696^T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696^T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696^T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696^T contained C_16:0, C_18:0, C_18:1ω7c 11-methyl and C_18:1ω6c/ C_18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696^T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696^T=BCRC 81284^T=JCM 34167^T) is proposed.

Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin

It is known that the physiology of Methanosarcina species can differ significantly, but the ecological impact of these differences is unclear. We recovered two strains of Methanosarcina from two different ecosystems with a similar enrichment and isolation method. Both strains had the same ability to metabolize organic substrates and participate in direct interspecies electron transfer but also had major physiological differences. Strain DH-1, which was isolated from an anaerobic digester, used H₂ as an electron donor. Genome analysis indicated that it lacks an Rnf complex and conserves energy from acetate metabolism via intracellular H₂ cycling. In contrast, strain DH-2, a subsurface isolate, lacks hydrogenases required for H₂ uptake and cycling and has an Rnf complex for energy conservation when growing on acetate. Further analysis of the genomes of previously described isolates, as well as phylogenetic and metagenomic data on uncultured Methanosarcina in anaerobic digesters and diverse soils and sediments, revealed a physiological dichotomy that corresponded with environment of origin. The physiology of type I Methanosarcina revolves around H₂ production and consumption. In contrast, type II Methanosarcina species eschew H₂ and have genes for an Rnf complex and the multiheme, membrane-bound c-type cytochrome MmcA, shown to be essential for extracellular electron transfer. The distribution of Methanosarcina species in diverse environments suggests that the type I H₂-based physiology is well suited for high-energy environments, like anaerobic digesters, whereas type II Rnf/cytochrome-based physiology is an adaptation to the slower, steady-state carbon and electron fluxes common in organic-poor anaerobic soils and sediments. IMPORTANCE Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process. Methanosarcina species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus Methanosarcina is composed of two physiologically distinct groups. This is important to recognize when interpreting the role of Methanosarcina in methanogenic environments, especially regarding H₂ metabolism. Furthermore, the finding that type I Methanosarcina species predominate in environments with high rates of carbon and electron flux and that type II Methanosarcina species predominate in lower-energy environments suggests that evaluating the relative abundance of type I and type II Methanosarcina may provide further insights into rates of carbon and electron flux in methanogenic environments.

Maritimibacter harenae sp. nov. and Sneathiella litorea sp. nov.: members of Alphaproteobacteria isolated from sea sand

Two Gram-negative, rod bacteria, strains DP07^T and DP05^T, showing catalase- and oxidase-positive activities, were isolated from sea sand in South Korea. Strain DP07^T was strictly aerobic and had a yellow colony colour. Contrastingly, strain DP05^T was facultatively aerobic and had a creamy colony colour. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain DP07^T contained cyclo-C_19:0 ω8c, C_16:0, summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c), and C_16:0 2-OH as the major fatty acids and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, and an unidentified polar lipid as the major polar lipids. Strain DP05^T contained C_16:0, cyclo-C_19:0, and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c) as the major fatty acids and phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, and two unidentified polar lipids as the major polar lipids. Cadaverine was detected as the predominant polyamine in both strains. The DNA G + C contents of strains DP07^T and DP05^T were 66.1 mol% and 51.8 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains DP07^T and DP05^T formed close phylogenetic lineages with Maritimibacter alkaliphilus HTCC2654^T (similarity, 98.1%) and Sneathiella chungangensis CAU 1294 ^T (similarity, 98.5%), respectively. The average nucleotide identity and DNA-DNA hybridisation values between strain DP07^T and M. alkaliphilus were 80.0% and 23.0%, respectively, and those between strain DP05^T and S. chungangensis were 77.1% and 19.9%, respectively. Based on the results of phenotypic, chemotaxonomic, and molecular analyses, strains DP07^T and DP05^T represent two novel species of the genera Maritimibacter and Sneathiella, respectively, for which we propose the following names: Maritimibacter harenae sp. nov. and Sneathiella litorea sp. nov. The type strains of M. harenae and S. litorea were DP07^T (= KACC 21429 ^T = JCM 33811 ^T) and DP05^T (= KACC 21431 ^T = JCM 33810 ^T), respectively.

Aeromicrobium terrae sp. nov., isolated from a maize field

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486^T, isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486^T were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486^T associated with Aeromicrobium panacisoli (97.0 % sequence identity), Aeromicrobium lacus (97.0 %), Aeromicrobium erythreum (96.8 %) and Aeromicrobium alkaliterrae (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % (n=11) compared within the type strains of the genus Aeromicrobium. Strain CC-CFT486^T contained C_16 : 0, C_17 : 0, C_17 : 1  ω8c and C_18 : 1  ω9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486^T contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486^T is proposed to represent a novel Aeromicrobium species, for which the name Aeromicrobium terrae sp. nov. (type strain CC-CFT486^T=BCRC 81217^T=JCM 33499^T).

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

Luteimonas weifangensis sp. nov., Isolated from Bensulfuron-Methyl Contaminated Watermelon Soil

A Gram-stain-negative bacterium, designated WF-2^T, was isolated from bensulfuron-methyl contaminated watermelon soil in Weifang, Shandong province, China. Cells of strain WF-2^T were strictly aerobic, non-motile and rod-shaped. Strain WF-2^T grew optimally at 30 °C, pH 7.0. Strain WF-2^T possessed ubiquinone-8 (Q-8) as the predominant respiratory quinone. The major cellular fatty acids of the strain WF-2^T (> 5.0%) were iso-C_15:0, anteiso-C_15:0, iso-C_16:0, C_16:0, iso-C_17:0, and summed feature 9 (iso-C_17:1 ω9c/C_16:0 10-methyl). The polar lipids consisted of two unidentified lipids, three unidentified phospholipids, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidyl glycolipid. Phylogenetic analysis based on 16S rRNA g^Tne sequences revealed that WF-2^T was a member of the genus Luteimonas and showed the highest sequence similarity to Luteimonas lumbrici 1.1416^T (98.6%) and Lysobacter pocheonensis Gsoil 193^T (97.9%), lower sequence similarity (< 97.0%) to other known species. The genomic DNA G + C content of WF-2^T was 69.2 mol%. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (DDH) between strains WF-2^T and L. lumbrici 1.1416^T were 81.9% and 24.7%, respectively. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, a new species with the name Luteimonas weifangensis sp. nov. is proposed. The type strain is WF-2^T (= KCTC 62441^T = CGMCC 1.13633^T).

Cerasibacillus terrae sp. nov., isolated from maize field, and emended description of Cerasibacillus quisquiliarum Nakamura et al. 2004

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480^T, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480^T were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480^T associated with Cerasibacillus quisquiliarum (97.2 % sequence identity), Virgibacillus soli (95.7 %), Virgibacillus carmonensis (95.4 %) and Virgibacillus byunsanensis (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480^T and C. quisquiliarum were 74.2 and 20.1 %, respectively. Strain CC-CFT480^T contained iso-C_15:0, C_16:1 ω7c alcohol and iso-C_17:1 ω10c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480^T is proposed to represent a novel Cerasibacillus species, for which the name Cerasibacillus terrae sp. nov. (type strain CC-CFT480^T=BCRC 81216^T=JCM 33498^T).

Flaviaesturariibacter flavus sp. nov., isolated from soil in Jeju Island

A Gram-stain-negative, non-motile and yellow-colored bacterium, designated 17J68-12^T, was isolated from soil in Jeju Island, Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 17J68-12^T formed a distinct lineage within the family Chitinophagaceae and was mostly related to members of Flaviaesturariibacter luteus (97.5%), Flaviaesturariibacter amylovorans (96.8%) and Flaviaesturariibacter terrae (96.8%). Growth was observed at 18-42 °C (optimum 30 °C) in R2A broth at pH 7.0. The major cellular fatty acids of the strain 17J68-12 ^T were summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), summed feature 1 (C_15:1 iso-H and/or C_13:0 3-OH), and iso-C_15:0. The predominant respiratory quinones are MK-7 and MK-6. The major polar lipid was identified as phosphatidylethanolamine. Based on biochemical, chemotaxonomic and phylogenetic characteristics, the strain 17J68-12^T represents a novel bacterial species within the family Chitinophagaceae, for which the name Flaviaesturariibacter flavus sp. nov. is proposed. The type strain of Flaviaesturariibacter flavus is 17J68-12^T (= KCTC 62219^T = JCM 33179^T).

Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

A Gram-stain-negative, short rod-shaped, yellow bacterium (strain LMO-1^T) was isolated from deep-sea sediment of the Mariana Trench, Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1^T belonged to genus Sphingomonas, with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2^T (96.3 %), followed by Sphingomonas prati W18RD^T (96.1 %), Sphingomonas arantia 6P^T (96.0 %) and Sphingomonas montana W16RD^T (95.9 %). The predominant polar lipids were phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c), C_16 : 0 and C_14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1^T was 69.2 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LMO-1^T and CC-Nfb-2^T were 75.9 and 20.5 %, respectively. Based on these data, LMO-1^T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1^T (=MCCC 1K04066^T=JCM 33666^T).

Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C17 : 1  ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).

Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber

A bacterial strain CC-CTC003^T was isolated from a synthetic wooden board. Cells of strain CC-CTC003^T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003^T belonged to the genus Flavobacterium and was most closely related to Flavobacterium cerinum (95.3 % sequence identity), Flavobacterium maris (94.9 % sequence identity), Flavobacterium qiangtangense (94.8 %) and Flavobacterium subsaxonicum (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003^T and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with F. cerinum was 19.4 %. Strain CC-CTC003^T contained C_15 : 0, iso-C_15 : 0, iso-C_15 : 0 3-OH, iso-C_17 : 0 3-OH, summed feature 3 (C_16 : 1  ω6c / C_16 : 1  ω7c) and summed feature 9 (C_16 : 0 10-methyl / iso-C_17 : 1  ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003^T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003^T (=BCRC 81146^T=JCM 32838^T).

Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae, we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus, is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae, for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae.

Description of Azoarcus nasutitermitis sp. nov. and Azoarcus rhizosphaerae sp. nov., two nitrogen-fixing species isolated from termite nest and rhizosphere of Ficus religiosa

A polyphasic taxonomic approach was used to characterise two presumably novel bacteria, designated strains CC-YHH838^T and CC-YHH848^T isolated from termite nest and rhizosphere of Ficus religiosa, respectively. These two nitrogen-fixing strains were observed to be Gram-staining-negative, aerobic rod, and colonies were yellowish in color. Growth of strains was observed at 20-37 °C, pH 7-8, and in the presence of 1-2% NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YHH838^T and CC-YHH848^T associated with Thauera hydrothermalis (97.1% sequence identity), and formed a separate branch with Azoarcus indigens (95.4%), Aromatoleum aromaticum (96.2%), and lower sequence similarity to other species. The calculation of OrthoANI values pointed out strains CC-YHH838^T and CC-YHH848^T gave 78.9% and 79.8% compared to Thauera hydrothermalis, respectively. The major fatty acids (> 5%) were C_16:0, C_17:0 cyclo, C_10:0 3-OH, C_16:1ω7c/C_16:1ω6c and C_18:1ω7c/C_18:1ω6c. The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminophospholipid and phospholipids; the predominant polyamines were putrescine and spermidine. The predominant respiratory system was ubiquinone (Q-8) and the DNA G + C contents were 61.4 ± 0.1 mol% and 60.2 ± 1.3 mol%, respectively. Based on the phylogenetic and polyphasic comparisons, strains CC-YHH838^T and CC-YHH848^T are proposed to represent two novel species within the genus Azoarcus in the family Rhodocyclaceae, for which the name Azoarcus nasutitermitis sp. nov. (type strain CC-YHH838^T = BCRC 81059^T = JCM 32001^T) and Azoarcus rhizosphaerae sp. nov. (type strain CC-YHH848^T = BCRC 81060^T = JCM 32002^T) were proposed.

Haemophilus seminalis sp. nov., isolated from human semen

Two Haemophilus-like isolates with similar biochemical characteristics, designated strains SZY H1^T and SZY H2, were isolated from human semen specimens. Cells were Gram-negative, non-motile, non-acid-fast, pleomorphic rods or coccobacilli. The major fatty acids (>10 %) were C_{16 : 0}, C_{14 : 0}, iso-C_{16 : 0} and/or C_{14 : 0} 3-OH and C_{16 : 1} ω6c and/or C_{16 : 1} ω7c. The polar lipids were determined to be phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminophospholipid, two unidentified polar lipids and four unidentified aminolipids. The major polyamine was found to be cadaverine. The near-full-length (1462 nt) 16S rRNA gene sequences analysis showed the two isolates were nearly identical (>99.8 %), and closely matched Haemophilus haemolyticus ATCC 33390^T with 98.9-99.1 % sequence similarities. Phylogenetic analysis based on 16S rRNA gene sequences and concatenation of 30 protein markers also revealed that the isolates clustered together with H. haemolyticus ATCC 33390^T, and formed a distinct lineage well separated from the other members of the genus Haemophilus. Further, the average nucleotide identity values between the two isolates and their related species were below the established cut-off values for species delineation (95 %). Based on these findings, the two isolates are considered to represent a new species of the genus Haemophilus, for which name Haemophilus seminalis sp. nov. is proposed. The type strain is SZY H1^T (=NBRC 113782^T=CGMCC 1.17137^T).

Cohnella fermenti sp. nov., isolated from a fermentation process

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044^T, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044^T occurred at 15-50 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044^T consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044^T belonged to the genus Cohnella and showed a close relationship with the type strains of Cohnella damuensis (96.2 %) and Cohnella panacarvi (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044^T represents a distinct Cohnella species. The dominant cellular fatty acids (>5 %) included iso-C_14 : 0(7.4 %), iso-C_15 : 0 (6.4 %), anteiso-C_15 : 0(40.3 %), C_16 : 0 (6.6 %) and iso-C_16 : 0 (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA-DNA hybridization analyses, we conclude that strain CC-MHH1044^T represents a novel member of the genus Cohnella, for which the name Cohnella fermenti sp. nov. is proposed. The type strain is CC-MHH1044^T (=BCRC 81147^T=JCM 32834^T).

Ochrobactrum teleogrylli sp. nov., a pesticide-degrading bacterium isolated from the insect Teleogryllus occipitalis living in deserted cropland

A Gram-stain-negative, non-spore-forming, motile, aerobic, rod-shaped bacteria strain, designated LCB8^T, was isolated from the insect Teleogryllus occipitalis captured from a deserted cropland in Shuangliu district, Chengdu, PR China. Phylogenetic analysis on the basis of 16S rRNA gene sequence indicated that the strain represented a member of the genus Ochrobactrum, family Brucellaceae, class Alphaproteobacteria. Ochrobactrum pecoris CCUG 60088^T (97.9 %) and Ochrobactrum haematophilum CCUG 38531^T (98.8 %) were identified as the most closely related phylogenetic neighbours of strain LCB8^T. The novel strain was able to grow at salt concentrations of 0-4.5 % (w/v), pH 5-9 and temperatures of 20-42 °C. The major quinone system was ubiquinone Q-10, the major fatty acids were C_18 : 1ω7c, C_16 : 0 and C_18 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and four undefined aminolipids. The major polyamines were putrescine and spermidine. Genome sequencing revealed a genome size of 4.76 Mbp and a DNA G+C content of 57.1 mol%. These phenotypic, genotypic and chemotaxonomic traits excellently supported the affiliation of LCB8^T to the genus Ochrobactrum. Pairwise determined whole-genome average nucleotide identity (ANI) values indicated that strain LCB8^T represents a novel species, for which we propose the name Ochrobactrum teleogrylli sp. nov. with the type strain LCB8^T (=KCTC 72031^T=CGMCC 1.13984^T).

Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov

A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110^T, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110^T were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110^T associated with Rhizobium oryziradicis (98.4 % sequence identity), Allorhizobium vitis (97.8 %), Allorhizobium taibaishanense (97.7 %) and Allorhizobium undicola (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110^T and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110^T contained C_16 : 0 3-OH, C_14 : 0 3-OH/iso C_16 : 1 I and C_18 : 1 ω7c/C_{18  : 1} ω6c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110^T is proposed to represent a novel Allorhizobium species, for which the name Allorhizobium terrae sp. nov. (type strain CC-HIH110^T=BCRC 80932^T=JCM 31228^T). In addition, Rhizobium oryziradicis is reclassified as Allorhizobium oryziradicis (type strain N19^T=ACCC 19962^T=KCTC 52413^T) comb. nov.

Deminuibacter soli gen. nov., sp. nov., isolated from forest soil, and reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov

A novel strain, designated K23C18032701^T, was isolated from a sample of forest soil collected from Dinghushan Biosphere Reserve, Guangdong Province, PR China. The strain was Gram-stain-negative, aerobic, motile and showed a shape change from a filamentous cell to coccobacilli. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain belongs to the family Chitinophagaceae, and showed the highest similarities to Arvibacter flaviflagrans JCM 31293^T (95.0 %) and Filimonas aurantiibacter LMG 29039^T (94.4 %). The major cellular fatty acids included iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The predominant polar lipid was phosphatidylethanolamine (PE). The predominant respiratory quinone was menaquinone-7. The major polyamine was sym-homospermidine. The draft genome size of strain K23C18032701^T was 5.84 Mb with a DNA G+C content of 47.2 mol%. Based on phenotypic, genotypic and phylogenetic analysis, strain K23C18032701^T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Deminuibacter soli is proposed. The type strain is K23C18032701^T (=GDMCC 1.1403^T=KCTC 62913^T). We also propose the reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. (type strain 1458^T=NRRL B-65305^T=LMG 29039^T).

Polyamine function in archaea and bacteria

Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNA^Ile As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.

Castellaniella fermenti sp. nov., isolated from a fermented meal

A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH191^T, isolated from a fermented meal in Taiwan. Cells of strain CC-YTH191^T were Gram-stain-negative aerobic rods, which grew at 15-40 °C (optimal 25-30 °C), pH 6.0-9.0 (optimal 7.0) and 1-2 % (w/v) NaCl (optimal 1 %). On the basis of 16S rRNA gene sequence analysis, strain CC-YTH191^T appeared to belong to the genus Castellaniella, and was closely related to Castellaniella hirudinis (96.7 % similarity), Castellaniella ginsengisoli (96.7 %) and Castellaniella caeni (96.0 %), while with other related species it shared <96.0 % similarity. The major cellular fatty acids of the isolate were C16 : 0, C17 : 0cyclo, C14 : 0 3OH/C16 : 1iso I and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholpid. Putrescine was the predominant polyamine followed by spermidine. The DNA G+C content was 62.2 mol% and the predominant quinone system was ubiquinone 8 (Q-8). All these features confirmed the placement of the strain CC-YTH191^T as a novel species within the genus Castellaniella, for which the name Castellaniella fermenti sp. nov. is proposed. The type strain is CC-YTH191^T (=BCRC 81023^T=JCM 31755^T).

Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta)

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539^T) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539^T was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539^T showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2^T (96.8 %), Sphingobium boeckii 469^T (96.5 %), Sphingomonas faucium E62-3^T (96.4 %) and Sphingosinicella vermicomposti YC7378^T (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539^T was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539^T. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539^T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539^T (=BCRC 80933^T=JCM 31229^T).

Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine

A difficult to cultivate bacterial strain, designated 1PNM-26^T, isolated from a lead-zinc mine, was investigated using a polyphasic taxonomic approach. The strain was able to grow on solid medium but not in liquid medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped. It showed positive reactions for catalase and oxidase and hydrolysis of aesculin. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 1PNM-26^T represents a member of the genus Sphingomonas and forms a stable cluster with Sphingomonas morindae KCTC 42183^T, Sphingomonas polyaromaticivorans JCM 16711^T and Sphingomonas oligoaromativorans NBRC 105508^T. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. C14 : 0 2-OH was present as the major hydroxyl fatty acid. The major polyamine was sym-homospermidine, and ubiquinone 10 (Q-10) was the predominant respiratory quinone. The genomic DNA G+C content of strain 1PNM-26^T was determined to be 66.3±0.3 mol%, and the polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycolipid, three unidentified aminolipids and three unidentified lipids. The phenotypic, phylogenetic and chemotaxonomic results strongly supported the hypothesis that strain 1PNM-26^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdifficilis sp. nov. is proposed. The type strain is 1PNM-26^T (=GDMCC 1.664^T=KCTC 42758^T=DSM 27573^T).

Lacihabitans lacunae sp. nov., isolated from a lagoon

A non-motile, orange-pigmented bacterium, designated strain HME7103T, was isolated from lagoon water in the Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7103T formed a lineage within the genus Lacihabitans and family Cytophagaceae. Strain HME7103T was closely related to Lacihabitans soyangensis HME6675T (95.7 % 16S rRNA gene sequence similarity). The major fatty acids of strain HME7103T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0. The major respiratory quinone was MK-7. The major polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content of strain HME7103T was 40.6 mol%. On the basis of the evidence presented in this study, strain HME7103T represents a novel species within the genus Lacihabitans, for which the name Lacihabitans lacunae sp. nov. is proposed. The type strain is HME7103T (=KCTC 23619T=CECT 7956T).

Novosphingobium guangzhouense sp. nov., with the ability to degrade 1-methylphenanthrene

A novel Gram-stain-negative, flagellated, rod-shaped, yellow-pigmented aerobic bacterium, strain SA925T, that is capable of degrading 1-methylphenanthrene was isolated from oil-polluted soil collected from a refinery located in Guangzhou, China. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain SA925T belongs to the genus Novosphingobium and is evolutionarily close to the type strains of Novosphingobium gossypii (98.5 % similarity), Novosphingobium panipatense (98.2 %), Novosphingobium mathurense (98.0 %) and Novosphingobium pentaromativorans (96.5 %). The G+C content of the genomic DNA was 60.2 mol%. DNA-DNA hybridization experiments between strain SA925T and the closest strain, Novosphingobium gossypii JM-1396T, revealed a low level of relatedness (35.5 %). Strain SA925T grew at 10-35 °C, at pH 6.0-8.0 and in the presence of 0-4 % (w/v) NaCl. The major fatty acids were C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profiles mainly consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylethanolamine and sphingoglycolipid (the characteristic polar lipid). The predominant ubiquinone was Q-10. The major polyamine was spermidine. Based on the phylogenetic, phenotypic and physiological characteristics, strain SA925T was considered to represent a novel species of the genus Novosphingobium, for which the name Novosphingobium guangzhouense sp. nov. is proposed. The type strain is SA925T (=DSM 32207T=GDMCC 1.1110T).

Olivibacter composti sp. nov., isolated from compost collected at a greenhouse

A polyphasic approach was used to characterize a presumably novel bacterium, designated strain CC-KYC063T, isolated from a compost sample collected at a greenhouse facility within Taiwan. Strain CC-KYC063T was Gram-stain-negative and aerobic, able to grow at 15-37 °C (optimal 30 °C), at pH 7.0-9.0 (optimal pH 7.0) and with 0-2 % (w/v) NaCl. The 16S rRNA gene sequence of strain CC-KYC063T showed highest similarity to Olivibacter ginsengisoli Gsoil 060T (96.2 %) and Olivibacter terrae Jip13T (95.5 %). The DNA G+C content was 43.0 mol% and the predominant quinone system was menaquinone-7 (MK-7). The polyamine pattern showed a predominance of sym-homospermidine. The major fatty acids found in strain CC-KYC063T were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-KYC063T is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter composti sp. nov. is proposed. The type strain is CC-KYC063T (=BCRC 80939T=JCM 31198T).

Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea

Translation initiation factor 5A (IF5A) is essential and highly conserved in Eukarya (eIF5A) and Archaea (aIF5A). The activity of IF5A requires hypusine, a posttranslational modification synthesized in Eukarya from the polyamine precursor spermidine. Intracellular polyamine analyses revealed that agmatine and cadaverine were the main polyamines produced in Haloferax volcanii in minimal medium, raising the question of how hypusine is synthesized in this halophilic Archaea. Metabolic reconstruction led to a tentative picture of polyamine metabolism and aIF5A modification in Hfx. volcanii that was experimentally tested. Analysis of aIF5A from Hfx. volcanii by LC-MS/MS revealed it was exclusively deoxyhypusinylated. Genetic studies confirmed the role of the predicted arginine decarboxylase gene (HVO_1958) in agmatine synthesis. The agmatinase-like gene (HVO_2299) was found to be essential, consistent with a role in aIF5A modification predicted by physical clustering evidence. Recombinant deoxyhypusine synthase (DHS) from S. cerevisiae was shown to transfer 4-aminobutyl moiety from spermidine to aIF5A from Hfx. volcanii in vitro. However, at least under conditions tested, this transfer was not observed with the Hfx. volcanii DHS. Furthermore, the growth of Hfx. volcanii was not inhibited by the classical DHS inhibitor GC7. We propose a model of deoxyhypusine synthesis in Hfx. volcanii that differs from the canonical eukaryotic pathway, paving the way for further studies.

Chryseobacterium endophyticum sp. nov., isolated from a maize leaf

A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-producing, rod-shaped and endophytic bacterium, designated strain CC-YTH209^T, was isolated from a maize leaf and subjected to a taxonomic study. Strain CC-YTH209^T was found to grow at 15-40 °C (optimal 30 °C), at pH 6.0-8.0 (optimal pH 7.0) and in the presence of 0-2 % (optimal 1 %) (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain CC-YTH209^T appeared to belong to the genus Chryseobacterium within the class Flavobacteriia, and was closely related to Chryseobacterium rigui CJ16^T (97.5 % similarity) and Chryseobacterium taeanense PHA3-4^T (96.9 %). The level of DNA-DNA relatedness between strain CC-YTH209^T and Chryseobacterium rigui CJ16^T was 14.4 % (reciprocal, 13.0 %). Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YTH209^T within the clade that accommodated Chryseobacterium species. The DNA G+C content was 37.2 mol%. Strain CC-YTH209^T contained menaquinone MK-6 as the predominant respiratory quinone and sym-homospermidine as the major polyamine. The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. The polar lipid profile comprised phosphatidylethanolamine and five aminolipids, three lipids, one glycolipid, one aminophospholipid and one phospholipid, which are presently uncharacterized. On the basis of evidence presented in this study, strain CC-YTH209^T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium endophyticum sp. nov. is proposed. The type strain is CC-YTH209^T (=BCRC 80938^T=JCM 31226^T).