Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite

Elucidation of cold adaptation in Glaciimonas sp. PAMC28666 with special focus on trehalose biosynthesis

Glaciimonas sp. PAMC28666, an extremophilic bacterium thriving in Antarctic soil and belonging to the Oxalobacteraceae family, represents the only complete genome of its genus available in the NCBI database. Its genome measures 5.2 Mb and comprises 4,476 genes (4,350 protein-coding and 72 non-coding). Phylogenetic analysis shows the strain PAMC28666 in a unique branch within the genus Glaciimonas, closely related to Glaciimonas alpine Cr9-12, supported by robust bootstrap values. In addition, strain PAMC28666 showed 77.08 and 23.3% ANI and DDH, respectively, with Glaciimonas sp. PCH181.This study focuses on how polar strain PAMC28666 responds to freeze-thaw conditions, Experimental results revealed a notable survival rate of 47.28% when subjected to a temperature of 15°C for a period of 10 days. Notably, two genes known to be responsive to cold stress, Trehalose 6-phosphate synthase (otsA) and Trehalose 6-phosphate phosphatase (otsB), exhibited increased expression levels as the temperature shifted from 25°C to 15°C. The upregulation of otsAB and the consequent synthesis of trehalose play pivotal roles in enhancing the cold resistance of strain PAMC28666, offering valuable insights into the correlation between trehalose production and adaptation to cold stress. Furthermore, research into this neglected cold-adapted variation, like Glaciimonas sp. PAMC28666, has the potential to shed light on how trehalose is produced in cold-adapted environments Additionally, there is potential to extract trehalose compounds from this strain for diverse biotechnological applications, including food and cosmetics, with ongoing research exploring its unique properties.

Marinigracilibium pacificum gen. nov., sp. nov., a starch-degrading bacterium isolated from tropical western Pacific

The Gram-stain-negative, golden-yellow-colored, non-spore-forming, strictly aerobic, slender rod-shaped bacterial strain, designated KN852^T, was isolated from a seamount in the tropical western Pacific. The predominant respiratory quinone was MK-7 and the polar lipid profiles contained phosphatidylethanolamine, one unidentified phospholipid and six unidentified polar lipids. The predominant cellular fatty acids were iso-C_15:0, summed feature 3(C_16:1ω7c and/or iso-C_15:0 2OH), iso-C_17:0 3OH and iso-C_15:1 G. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain KN852^T was affiliated with the family Flammeovirgaceae of the phylum Bacteroidota and formed a distinct lineage. The genomic DNA G + C content of strain KN852^T was 34.8%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence presented, strain KN852^T represents a novel species of a novel genus of the family Flammeovirgaceae, for which the name Marinigracilibium pacificum gen. nov., sp. nov. is proposed. The type strain is KN852^T (= CGMCC 1.17119^T = KCTC 72433^T).

The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads

Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here, we release a high-quality complete genome sequence for the X. theicola type strain, CFBP 4691^T. Single-molecule real-time sequencing with a mean coverage of 264× revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.

Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments

Life in environments devoid of photosynthesis, such as on early Earth or in contemporary dark subsurface ecosystems, is supported by chemical energy. How, when, and where chemical nutrients released from the geosphere fuel chemosynthetic biospheres is fundamental to understanding the distribution and diversity of life, both today and in the geologic past. Hydrogen (H₂) is a potent reductant that can be generated when water interacts with reactive components of mineral surfaces such as silicate radicals and ferrous iron. Such reactive mineral surfaces are continually generated by physical comminution of bedrock by glaciers. Here, we show that dissolved H₂ concentrations in meltwaters from an iron and silicate mineral-rich basaltic glacial catchment were an order of magnitude higher than those from a carbonate-dominated catchment. Consistent with higher H₂ abundance, sediment microbial communities from the basaltic catchment exhibited significantly shorter lag times and faster rates of net H₂ oxidation and dark carbon dioxide (CO₂) fixation than those from the carbonate catchment, indicating adaptation to use H₂ as a reductant in basaltic catchments. An enrichment culture of basaltic sediments provided with H₂, CO₂, and ferric iron produced a chemolithoautotrophic population related to Rhodoferax ferrireducens with a metabolism previously thought to be restricted to (hyper)thermophiles and acidophiles. These findings point to the importance of physical and chemical weathering processes in generating nutrients that support chemosynthetic primary production. Furthermore, they show that differences in bedrock mineral composition can influence the supplies of nutrients like H₂ and, in turn, the diversity, abundance, and activity of microbial inhabitants.

Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold-Dry Limits of Life on Earth

Soils on the world's highest volcanoes in the Atacama region represent some of the harshest ecosystems yet discovered on Earth. Life in these environments must cope with high UV flux, extreme diurnal freeze-thaw cycles, low atmospheric pressure and extremely low nutrient and water availability. Only a limited spectrum of bacterial and fungal lineages seems to have overcome the harshness of this environment and may have evolved the ability to function in situ. However, these communities may lay dormant for most of the time and spring to life only when enough water and nutrients become available during occasional snowfalls and aeolian depositions. We applied water and nutrients to high-elevation soils (5100 meters above sea level) from Volcán Llullaillaco, both in lab microcosms and in the field, to investigate how microbial communities respond when resource limitations are alleviated. The dominant taxon in these soils, the extremophilic yeast Naganishia sp., increased in relative sequence abundance and colony-forming unit counts after water + nutrient additions in microcosms, and marginally in the field after only 6 days. Among bacteria, only a Noviherbaspirillum sp. (Oxalobacteraceae) significantly increased in relative abundance both in the lab and field in response to water addition but not in response to water and nutrients together, indicating that it might be an oligotroph uniquely suited to this extreme environment. The community structure of both bacteria and eukaryotes changed significantly with water and water + nutrient additions in the microcosms and taxonomic richness declined with amendments to water and nutrients. These results indicate that only a fraction of the detected community is able to become active when water and nutrients limitations are alleviated in lab microcosms, and that water alone can dramatically change community structure. Our study sheds light on which extremophilic organisms are likely to respond when favorable conditions occur in extreme earthly environments and perhaps in extraterrestrial environments as well.

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, facultative anaerobic, motile bacterial strain, designated TP390^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP390^T was related to the genus Flavobacterium and had highest 16S rRNA gene sequence identity with the type strain of Flavobacterium jejuense EC11^T (97.8 %). Sequence similarities to all other type strains of current species of the genus Flavobacterium were below 97 %. The predominant cellular fatty acids were iso-C_15 : 0 and iso-C_15 : 1G. The quinone system for strain TP390^T comprised predominantly menaquinone MK-6 and the polar lipid profile contained phosphatidylethanolamine, four unknown aminolipids, one glycolipid and six unknown polar lipids. The genomic DNA G+C content of strain TP390^T was 31.2 mol%. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain TP390^T with F. jejuense KCTC 42149^T were 22.60 and 80.01% respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI data demonstrated that the strain TP390^T is representative of a novel species of the genus Flavobacterium, for which we propose the name Flavobacterium profundi sp. nov. (type strain TP390^T=KACC 18559^T=CGMCC 1.15398^T).

Glaciimonas soli sp. nov., a soil bacterium isolated from the forest of a high elevation mountain

A Gram-negative, psychrophilic bacterium, designated strain GS1^T, was isolated from a forest soil sample collected from the West Peak of Mt. Yushan, Yushan National Park, Taiwan. Cells grown in broth cultures were mostly non-motile and non-flagellated, whereas motile cells with monotrichous, subpolar flagella were also observed. The novel strain grew over a temperature range of 4-25 °C with optimum growth at 10-15 °C. It grew aerobically and was not capable of anaerobic growth by fermentation of D-glucose or other carbohydrates. Ubiquinone 8 was the predominant isoprenoid quinone. The major polar lipids comprised phosphatidylethanolamine, diphosphatidylglycerol and dimethylaminoethanol. Cellular fatty acids were dominated by C_16:1ω7c (35.2%), C_16:0 (19.5%), C_18:1ω7c (18.8%) and C_17:0ω7c cyclo (15.5%). The DNA G + C content was 49.2 mol% evaluated according to the genomic sequencing data. Strain GS1^T shared more than 96.5% 16S rRNA gene sequence similarities with type strains of four Collimonas species (97.2-97.5%), three Glaciimonas species (97.3% for each of the three) and Oxalicibacterium solurbis (96.5%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GS1^T formed a stable genus-level clade with type strains of species in the genus Glaciimonas in the family Oxalobacteraceae and GS1^T was an outgroup with respect to these Glaciimonas species. Characteristically, strain GS1^T could be easily distinguished from the recognised Glaciimonas species by exhibition of swimming motility with monotrichous, subpolar flagellum in some of the cells, ability to grow in NaCl at 2% but not at 3% and the distinguishable fatty acid profiles. On the basis of the polyphasic taxonomic data from this study, strain GS1^T is considered to represent a novel species of the genus Glaciimonas, for which the name Glaciimonas soli sp. nov. is proposed. The type strain is GS1^T (= JCM 33275^T = BCRC 81091^T).

Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10^T, was isolated from marine sediment. Strain S1-10^T grew at 4-42 °C (optimally at 30-35 °C), at pH 7.0-10 (optimally at pH 9) and in the presence of 0.5-8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10^T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1b^T (97.7%). The predominant cellular fatty acids were iso-C_15 : 0 and anteiso-C_15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10^T was 34.6 mol%. The polar lipid profile of strain S1-10^T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10^T and A. viscosa CGMCC 1.11023^T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10^T is the representative of a novel species of the genus Aequorivita, for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10^T=CGMCC 1.12579^T=JCM 19789^T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2^T (= KCTC 62141^T= NBRC 113025^T) and the type strain of Aequorivita aquimaris comb. nov. is D-24^T (=KCTC 42708^T=DSM 101732^T).

Algibacter pacificus sp. nov., isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, yellow-pigmented and facultative anaerobic bacterial strain, designated H164T, was isolated from seawater collected from the Caroline Seamounts in the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H164T was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity to Algibacter wandonensis WS-MY22T (97.4 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The genomic DNA G+C content of strain H164T was 33.2 mol%. The values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain H164T and A. wandonensis KCTC 32381T were 26.10 and 81.88 %. The isDDH and ANI values between strain H164T and Algibacter lectus DSM 15365T were 25.40 and 81.79 %. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain H164T represents a novel species of the genus Algibacter , for which we propose the name Algibacter pacificus sp. nov. (type strain H164T=KCTC 72432T=CGMCC 1.17117T).

Mesoflavibacter profundi sp. nov. Isolated from a Deep-Sea Seamount

The Gram-stain-negative, rod-shaped, aerobic strain, designated YC1039^T, was isolated from a seamount northern Mariana Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC1039^T was related to the genus Mesoflavibacter and had highest 16S rRNA gene sequence similarities to Mesoflavibacter sabulilitoris GJMS-9^T (98.3%) and Mesoflavibacter zeaxanthinifaciens TD-ZX30^T (98.2%). The predominant cellular fatty acids were iso-C_15:1 G and iso-C_15:0. The polar lipid profile contained phosphatidylethanolamine, two unidentified phospholipids, and 13 unidentified lipids. The respiratory quinone was MK-6. The genomic DNA G+C content of strain YC1039^T was 29.8 mol%. On the basis of the evidence presented in this study, strain YC1039^T represents a novel species of the genus Mesoflavibacter, for which we propose the name Mesoflavibacter profundi sp. nov. (type strain YC1039^T = KACC 19026^T = CGMCC 1.16329^T).

Parvibium lacunae gen. nov., sp. nov., a new member of the family Alcaligenaceae isolated from a freshwater pond

A bacterial strain designated KMB9^T was isolated from a freshwater pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain KMB9^T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming and rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 20-40 °C (optimum, 25-37 °C), at pH 6.5-7.5 (optimum, pH 7.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene and four housekeeping gene sequences (recA, rpoA, rpoB and atpD) showed that strain KMB9^T forms a distinct phyletic line within the family Alcaligenaceae, and the levels of 16S rRNA gene sequence similarity to its closest relatives with validly published names were less than 93.3 %. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The major polyamine was putrescine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and several uncharacterized aminophospholipids, aminolipids, phospholipids and lipids. The genomic DNA G+C content of strain KMB9^T was 54.5 mol%. On the basis of the genotypic and phenotypic data, strain KMB9^T represents a novel species of a new genus in the family Alcaligenaceae, for which the name Parvibium lacunae gen. nov., sp. nov. is proposed. The type strain is KMB9^T (=BCRC 81053^T=LMG 30055^T=KCTC 52814^T).

Ponticaulis profundi sp. nov. isolated from a deep-sea seamount

A Gram-stain negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YC239^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC239^T is related to the genus Ponticaulis and has high 16S rRNA gene sequence similarity with the type strain of Ponticaulis koreensis GSW-23^T (97.9%). The predominant cellular fatty acids were C_18:1ω7c, C_16:0, C_17:0 and C_17:1ω6c. Strain YC239^T had Q-10 as the predominant ubiquinone. The polar lipid profile contained phosphatidylglycerol, two unidentified aminolipids and six unidentified polar lipids. The genomic DNA G+C content of strain YC239^T was 52.8 mol%. Strain YC239^T shared DNA relatedness of 38% with Ponticaulis koreensis KCTC 22146^T. On the basis of the evidence presented in this study, strain YC239^T represents a novel species of the genus Ponticaulis, for which we propose the name Ponticaulis profundi sp. nov. (type strain YC239^T = KACC 19027^T = CGMCC 1.15741^T).

Rheinheimera marina sp. nov., isolated from a deep-sea seamount

A bacterial strain designated TP462^T, isolated from a seamount near the Yap Trench in the tropical western Pacific, was characterized using a polyphasic taxonomic approach. Strain TP462^T was found to be Gram-stain-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 4-37 °C (optimum, 25-30 °C) and with 0-4.0 % NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP462^T was related to the genus Rheinheimera and had the highest 16S rRNA gene sequence similarity with the type strain Rheinheimera tangshanensis JA3-B52^T (96.8 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and C16 : 0. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The genomic DNA G+C content of strain TP462^T was 48.7 mol%. On the basis of the evidence presented in this study, strain TP462^T represents a novel species of the genus Rheinheimera, for which we propose the name Rheinheimera marina sp. nov. (type strain TP462^T=KACC 18560^T=CGMCC 1.15399^T).

Maribacter marinus sp. nov. isolated from a deep-sea seamount

A Gram-stain negative, rod-shaped, aerobic strain, designated YC973^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain YC973^T is related to the genus Maribacter and has high 16S rRNA gene sequence similarity to Maribacter orientalis KMM 3947^T (97.6%). The predominant cellular fatty acids were iso-C_15:0, iso-C_15:1 G and an unidentified fatty acid of equivalent chain-length 13.565. The polar lipid profile contained phosphatidylethanolamine and five unidentified lipids. The genomic DNA G+C content of strain YC973^T was 36.1 mol%. On the basis of the evidence presented in this study, strain YC973^T represents a novel species of the genus Maribacter, for which we propose the name Maribacter marinus sp. nov. (type strain YC973^T = KACC 19025^T = CGMCC 1.16328^T).

Thalassotaleaprofundi sp. nov. isolated from a deep-sea seamount

The Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM155^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM155^T was related to the genus Thalassotalea and had highest 16S rRNA gene sequence similarities with the type strains of Thalassotalea piscium T202^T (97.2 %) and Thalassotalea agariperforans M-M1^T (97.2 %). The predominant cellular fatty acids were C17 : 1ω8c, summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C16 : 0. Ubiquinone 8 (Q-8) was the respiratory quinone. The polar lipid profile contained phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified lipid. The genomic DNA G+C content of strain YM155^T was 36.1 mol%. On the basis of the evidence presented in this study, strain YM155^T represents a novel species of the genus Thalassotalea, for which we propose the name Thalassotalea profundi sp. nov. (type strain YM155^T=KACC 18563^T=CGMCC 1.15922^T).

Lysobacter zhanggongensis sp. nov. Isolated from a Pit Mud

The Gram-stain-negative, rod-shaped and non-motile bacterial strain, designated ZGLJ7-1^T, was isolated from a pit mud. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain ZGLJ7-1^T was related to the genus Lysobacter and had the highest 16S rRNA gene sequence similarity with the type strain of Lysobacter arseniciresistens ZS79^T (97.4%). The predominant cellular fatty acids were iso-C_15:0, iso-C_17:1ω9c, iso-C_11:0 and iso-C_11:03-OH. Strain ZGLJ7-1^T had Q-8 as the predominant ubiquinone. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain ZGLJ7-1^T was 69.5 mol%. Strain ZGLJ7-1^T shared DNA relatedness with 35% Lysobacter arseniciresistens CGMCC 1.10752^T. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that the strain ZGLJ7-1^T is a representative of a novel species of the genus Lysobacter, for which we propose the name Lysobacter zhanggongensis sp. nov. (type strain ZGLJ7-1^T = KACC 18547^T = CGMCC 1.15404^T).

Microbial Community Analysis of Colored Snow from an Alpine Snowfield in Northern Japan Reveals the Prevalence of Betaproteobacteria with Snow Algae

Psychrophilic algae blooms can be observed coloring the snow during the melt season in alpine snowfields. These algae are important primary producers on the snow surface environment, supporting the microbial community that coexists with algae, which includes heterotrophic bacteria and fungi. In this study, we analyzed the microbial community of green and red-colored snow containing algae from Mount Asahi, Japan. We found that Chloromonas spp. are the dominant algae in all samples analyzed, and Chlamydomonas is the second-most abundant genus in the red snow. For the bacterial community profile, species belonging to the subphylum Betaproteobacteria were frequently detected in both green and red snow, while members of the phylum Bacteroidetes were also prominent in red snow. Furthermore, multiple independently obtained strains of Chloromonas sp. from inoculates of red snow resulted in the growth of Betaproteobacteria with the alga and the presence of bacteria appears to support growth of the xenic algal cultures under laboratory conditions. The dominance of Betaproteobacteria in algae-containing snow in combination with the detection of Chloromonas sp. with Betaproteobacteria strains suggest that these bacteria can utilize the available carbon source in algae-rich environments and may in turn promote algal growth.

Piscinibacterium candidicorallinum gen. nov., sp. nov., a member of the order Burkholderiales isolated from a fish pond

A bacterial strain designated LYH-15T was isolated from a freshwater fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of LYH-15T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, non-spore forming, straight rods and formed light-coral-colored colonies. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that LYH-15T forms a distinct phyletic line within the order Burkholderiales, with less than 94 % sequence similarity to its closest relatives with validly published names. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 63.8 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized lipids. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of the genotypic and phenotypic data, LYH-15T represents a novel species of a new genus in the order Burkholderiales, for which the name Piscinibacterium candidicorallinum gen. nov., sp. nov. is proposed. The type strain is LYH-15T (=BCRC 80969T=LMG 29480T=KCTC 52168T).

Novosphingobium profundi sp. nov. isolated from a deep-sea seamount

A marine bacterial strain, F72^T, was isolated from a solitary scleractinian coral, collected in Yap seamounts in the Pacific Ocean. Strain F72^T is a Gram-negative, light-yellow-pigmented, motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F72^T is related to the genus Novosphingobium and has high 16S rRNA gene sequence similarities with the type strains of Novosphingobium pentaromativorans US6-1^T (97.7 %), Novosphingobium panipatense SM16^T (97.6 %), Novosphingobium mathurense SM117^T (97.2 %) and Novosphingobium barchaimii LL02^T (97.1 %). Ubiquinone Q-10 was detected as the dominant quinone. The predominant cellular fatty acids were C_18:1ω7c and C_17:1ω6c. The genomic DNA G+C content of strain F72^T was 63.4 mol %. The polar lipids profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, sphingoglycolipid and one uncharacterized lipid. Strain F72^T shared DNA relatedness of 25 % with N. pentaromativorans JCM 12182^T, 31 % with N. panipatense DSM 22890^T, 21 % with N. mathurense DSM 23374^T and 26 % with N. barchaimii DSM 25411^T. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that the strain F72^T is a representative of a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium profundi sp. nov. (type strain F72^T = KACC 18566^T = CGMCC 1.15390^T).

Pseudoalteromonas profundi sp. nov., isolated from a deep-sea seamount

A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated TP162T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain TP162T was related to the genus Pseudoalteromonas and had highest 16S rRNA gene sequence similarities with the type strains Pseudoalteromonas shioyasakiensis SE3T (98.2 %), Pseudoalteromonas lipolytica LMEB 39T (97.7 %), Pseudoalteromonas arabiensis k53T (97.4 %) and Pseudoalteromonas aliena KMM 3562T (97.2 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1ω7c), C17 : 1ω8c and C16 : 0. The quinone system for strain TP162T comprised predominantly ubiquinone-8, and the polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, one unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content of strain TP162T was 46.7 mol%. Strain TP162T shared 28 % DNA-DNA relatedness with P.shioyasakiensis JCM 18891T, 21 % with P. lipolytica JCM 15903T, 35 % with P.arabiensis JCM 17292T and 18 % with P.aliena LMG 22059T. Combined data from phenotypic, chemotaxonomic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain TP162T is a representative of a novel species of the genus Pseudoalteromonas, for which we propose the name Pseudoalteromonas profundi sp. nov. (type strain TP162T=KACC 18554T=CGMCC 1.15394T).

Glaciimonas frigoris sp. nov., a psychrophilic bacterium isolated from ancient Siberian permafrost sediment, and emended description of the genus Glaciimonas

The bacterial strain N1-38^T was isolated from ancient Siberian permafrost sediment. The strain was Gram-reaction-negative, motile by gliding, rod-shaped and psychrophilic, and showed good growth over a temperature range of - 5 to 25 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain N1-38^T was most closely related to members of the genus Glaciimonas and shared the highest 16S rRNA gene sequence similarities with the type strains of Glaciimonas alpina (99.3 %), Glaciimonas immobilis (98.9 %) and Glaciimonas singularis (96.5 %). The predominant cellular fatty acids of strain N1-38^T were summed feature 3 (C_16 : 1ω7c and/or iso-C_15 : 0 2-OH), C_16 : 0 and C_18 : 1ω7c. The major respiratory quinone was ubiquinone 8 and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genomic DNA G+C content was 53.0 mol%. Combined data of phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain N1-38^T represents a novel species of the genus Glaciimonas, for which the name Glaciimonas frigoris sp. nov. is proposed. The type strain is N1-38^T ( = LMG 28868^T = CCOS 838^T). An emended description of the genus Glaciimonas is also provided.

Glaciimonas alpina sp. nov. isolated from alpine glaciers and reclassification of Glaciimonas immobilis Cr9-12 as the type strain of Glaciimonas alpina sp. nov

Psychrophilic bacterial strains were isolated from alpine glaciers in Switzerland and characterized taxonomically. On the basis of phylogenetic analysis of partial 16S rRNA and rpoB genes, three of those strains, strain 79 ( = CCOS 247), strain 4/58 ( = CCOS 250) and strain 4/56 ( = CCOS 258) clustered together with strain Cr9-12T and separately from the type strains Glaciimonas immobilis Cr9-30T and Glaciimonas singularis LMG 27070T. Strain Cr9-12T has been previously described as a strain of G. immobilis. The three newly isolated strains were compared phenotypically with strain Cr9-12T and with the type strains of the species G. immobilis and G. singularis. Cr9-12T and the three novel strains from an alpine glacier in Switzerland were Gram-stain-negative, non-motile, rod-shaped and psychrophilic and showed good growth throughout a temperature range of 1-20 °C and characteristically oxidized d-mannitol, l-fucose and bromosuccinic acid. The predominant cellular fatty acids of strain Cr9-12T and the three novel strains were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The respiratory quinone of these strains was ubiquinone 8 (UQ-8). The genomic DNA G+C content of Cr9-12T was 49.2 mol%. The combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies strongly support the reclassification of strain Cr9-12T as representing a novel species. This strain and the isolates 79 ( = CCOS 247), 4/58 ( = CCOS 250) and 4/56 ( = CCOS 258) are representatives of a novel species of the genus Glaciimonas, for which the name Glaciimonas alpina sp. nov. is proposed. The type strain of Glaciimonas alpina is Cr9-12T ( = CCOS 761T = DSM 22814T).

Noviherbaspirillum suwonense sp. nov., isolated from an air sample

A Gram-stain-negative bacterium, strain 5410S-62T, was isolated from an air sample collected in Suwon, Republic of Korea. It was aerobic, motile, mesophilic and formed rod-shaped cells. Colonies on R2A agar were convex, circular and pale orange with entire margins. Growth occurred at pH 5-9 (optimally at pH 7) and at 10-40 °C (optimally at 28 °C). It did not grow in the presence of 1% NaCl. Comparative analyses of 16S rRNA gene sequences demonstrated that the novel strain was closely related to members of the genus Noviherbaspirillum. Strain 5410S-62T showed the highest sequence similarity (98.2%) to Glaciimonas singularis A2-57T. It also showed high 16S rRNA gene sequence similarity (98.1-95.6%) to members of the genus Noviherbaspirillum (98.1% to Noviherbaspirillum aurantiacum SUEMI08T, 97.8% to Noviherbaspirillum soli SUEMI10T and Noviherbaspirillum canariense SUEMI03T, 97.6% to Noviherbaspirillum psychrotolerans PB1T and 95.6% to Noviherbaspirillum malthae CC-AFH3T). The strain contained summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as major fatty acids, Q-8 as the only ubiquinone and large amounts of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. Strain 5410S-62T revealed less than 70% DNA-DNA relatedness with the type strains of closely related species of the genera Noviherbaspirillum and Herbaspirillum and Glaciimonas singularis. Based on the physiological, biochemical and chemotaxonomic data obtained in this study, it is proposed that strain 5410S-62T represents a novel species, Noviherbaspirillum suwonense sp. nov., with 5410S-62T (=KACC 16657T= NBRC 108944T) as the type strain.

Isolation and characterization of bacteria from ancient siberian permafrost sediment

In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of phospolipid fatty acids (PLFA) demonstrated the dominance of bacteria over fungi; the analysis of fatty acids specific for Gram-positive and Gram-negative bacteria revealed an approximately twofold higher amount of Gram-negative bacteria compared to Gram-positive bacteria. Direct microbial counts after natural permafrost enrichment showed the presence of (4.7 ± 1.5) × 108 cells g-1 sediment dry mass. Viable heterotrophic bacteria were found at 0 °C, 10 °C and 25 °C, but not at 37 °C. Spore-forming bacteria were not detected. Numbers of viable fungi were low and were only detected at 0 °C and 10 °C. Selected culturable bacterial isolates were identified as representatives of Arthrobacter phenanthrenivorans, Subtercola frigoramans and Glaciimonas immobilis. Representatives of each of these species were characterized with regard to their growth temperature range, their ability to grow on different media, to produce enzymes, to grow in the presence of NaCl, antibiotics, and heavy metals, and to degrade hydrocarbons. All strains could grow at -5 °C; the upper temperature limit for growth in liquid culture was 25 °C or 30 °C. Sensitivity to rich media, antibiotics, heavy metals, and salt increased when temperature decreased (20 °C > 10 °C > 1 °C). In spite of the ligninolytic activity of some strains, no biodegradation activity was detected.

Glaciimonas singularis sp. nov., isolated from a uranium mine wastewater treatment plant

A bacterial strain, A2-57(T), recovered from a water sample collected in a uranium mine was taxonomically studied in detail. This strain was a Gram-reaction-negative, rod-shaped bacterium that grew optimally at 25 °C and at pH 6.0-7.0 and had a DNA G+C content of 55.0 mol%. Ubiquinone 8 (UQ-8) was the predominant respiratory quinone and the major fatty acids were C16:0, C17:0 cyclo, summed feature 3 (C16:1ω6c and/or ω7c and/or C15:0 iso 2-OH) and C18:1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A2-57(T) belonged to the family Oxalobacteraceae and formed a distinct branch with Glaciimonas immobilis Cr9-30(T). Strain A2-57(T) shared approximately 97.3% 16S rRNA sequence similarity with G. immobilis Cr9-30(T) and also showed high sequence similarity with members of the genera Herbaspirillum (96.3-97.0%) and Collimonas (96.2-97.0%). Although phylogenetically closely related to the type strain of G. immobilis, the low level of DNA-DNA hybridization between the two strains (21.6%) and several physiological and biochemical properties indicated that the novel strain could be clearly distinguished from G. immobilis LMG 25547(T). Therefore, it is concluded that strain A2-57(T) represents a novel species of the genus Glaciimonas, for which the name Glaciimonas singularis sp. nov. is proposed. The type strain is A2-57(T) (=CIP 110539(T)=LMG 27070(T)).

Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite

A Gram-positive, non-motile, rod-shaped, psychrophilic actinomycete, designated strain Cr7-14T, was isolated from alpine glacier cryoconite. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cr7-14T was related to members of the genus Nocardioides and shared highest 16S rRNA gene sequence similarities with the type strains of Nocardioides furvisabuli (98.6 %), Nocardioides ganghwensis (98.2 %), Nocardioides oleivorans (98.1 %) and Nocardioides exalbidus (97.6 %). The predominant cellular fatty acids of strain Cr7-14T were C17 : 1ω8c (39.5 %) and iso-C16 : 0 (32.4 %). The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were galactose and rhamnose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, four unknown glycolipids and two unknown polar lipids. The genomic DNA G+C content was 71.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species, Nocardioides alpinus sp. nov., is proposed, with Cr7-14T ( = DSM 23325T = LMG 26053T = CGMCC 1.10697T) as the type strain.

Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.)

Two Gram-reaction-negative, yellow–orange-pigmented, rod-shaped bacterial strains, designated YC6722T and YC6723T, were isolated from rhizosphere soil samples collected from rice fields in Jinju, Korea. Strains YC6722T and YC6723T grew optimally at 25–30 °C and at pH 7.0–8.5. Phylogenetic analyses of 16S rRNA gene sequences showed that strain YC6722T was most closely related to Sphingomonas jaspsi TDMA-16T (96.6 % sequence similarity) and strain YC6723T was related most closely to Sphingomonas aquatilis JSS7T (96.9 %). The two strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system and sym-homospermidine as the major polyamine. The G+C contents of the genomic DNA of strains YC6722T and YC6723T were 63.3 and 61.0 mol%, respectively. The major fatty acid was C18 : 1ω7c. The polar lipids detected in the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and other unknown lipids. On the basis of their phylogenetic positions, and their biochemical and phenotypic characteristics, strains YC6722T and YC6723T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas oryziterrae sp. nov. ( = KCTC 22476T  = DSM 21455T) and Sphingomonas jinjuensis sp. nov. (KCTC 22477T  = DSM 21457T) are proposed.