Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA

Ruicaihuangia caeni gen. nov., sp. nov., a novel taxon within the family Microbacteriaceae isolated from sludge

A Gram-stain-positive bacterium, designated YN-L-19T, was isolated from a sludge sample collected from a pesticide-manufacturing plant. Cells of YN-L-19T were strictly aerobic, non-spore-forming, non-motile and ovoid-shaped. Colonies were small, smooth and yellow. Growth occurred at 10-37 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, 7.0) and 0-3.0 % (w/v) NaCl (optimum 0.5 %). Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that YN-L-19T was affiliated to the family Microbacteriaceae and most closely related to Diaminobutyricimonas aenilata, Terrimesophilobacter mesophilus, Planctomonas deserti and Curtobacterium luteum. The major cellular fatty acids of YN-L-19T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unidentified lipid. The average amino acid identity values between strain YN-L-19T and the related strains were 57.9-61.9 %, which were below the genus boundary (70 %). On the basis of the evidence presented in this study, strain YN-L-19T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Ruicaihuangia caeni gen. nov., sp. nov. (type strain YN-L-19T=CCTCC AB 2022401T= KCTC 49935T) is proposed.

Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants

Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763T, CPCC 203386T, CPCC 205716T, CPCC 203406T, and CPCC 203407 were obtained from different ecosystems associated with four kinds of Chinese traditional medicinal plants. The 16S rRNA gene sequences of these five strains showed closely related to members of the genus Herbiconiux of the family Microbacteriaceae, with the highest similarities of 97.4-99.7% to the four validly named species of Herbiconiux. In the phylogenetic trees based on 16S rRNA gene sequences and the core genome, these isolates clustered into the clade of the genus Herbiconiux within the lineage of the family Microbacteriaceae. The overall genome relatedness indexes (values of ANI and dDDH) and the phenotypic properties (morphological, physiological and chemotaxonomic characteristics) of these isolates, readily supported to affiliate them to the genus Herbiconiux, representing four novel species, with the isolates CPCC 203406T and CPCC 203407 being classified in the same species. For which the names Herbiconiux aconitum sp. nov. (type strain CPCC 205763T = I19A-01430T = CGMCC 1.60067T), Herbiconiux daphne sp. nov. (type strain CPCC 203386T = I10A-01569T = DSM 24546T = KCTC 19839T), Herbiconiux gentiana sp. nov. (type strain CPCC 205716T = I21A-01427T = CGMCC 1.60064T), and Herbiconiux oxytropis sp. nov. (type strain CPCC 203406T = I10A-02268T = DSM 24549T = KCTC 19840T) were proposed, respectively. In the genomes of these five strains, the putative encoding genes for amidase, endoglucanase, phosphatase, and superoxidative dismutase were retrieved, which were classified as biosynthetic genes/gene-clusters regarding plant growth-promotion (PGP) functions. The positive results from IAA-producing, cellulose-degrading and anti-oxidation experiments further approved their potential PGP bio-functions. Pangenome analysis of the genus Herbiconiux supported the polyphasic taxonomy results and confirmed their bio-function potential.

Nutrients, temperature, and oxygen mediate microbial antibiotic resistance in sea bass (Lateolabrax maculatus) ponds

Antibiotic resistance genes (ARGs) have drawn increasing attention as novel environmental pollutants because of the threat they impose on human and animal health. The sea bass (Lateolabrax maculatus) is the third most cultured marine fish in China. Therefore, a study of ARG pollution in the sea bass culture environment is of great significance for the healthy and sustainable development of the sea bass industry. Here, we systematic investigated the contents of 23 antibiotic resistance-related genes (ARRGs), including 19 ARGs and four mobile genetic elements, and analyzed bacterial community composition and environmental parameters in sea bass ponds. The relative abundance (ARRG copies/16S ribosomal RNA gene copies) of ARRGs was up to 3.83 × 10^-2. Sul1 was the most abundant ARRG, followed by ereA, intI-1, sul2, dfrA1, and aadA. Both the ARRG changes and aquatic microbiota succession were mainly driven by water temperature (WT), dissolved oxygen (DO), and NO₃^-. WT is positively correlated with the most ARGs and some of the top 38 Operational Taxonomic Units (OTUs) belonging to the orders of Frankiales, Micrococcales, Chitinophagales, and Sphingomonadales. Furthermore, WT is negatively related with some other OTUs of the orders Frankiales, Xanthomonadales, Micrococcales, and Rhizobiales. However, DO and NO₃^- have the opposite function with WT on specific taxa and ARGs. These results indicate that sea bass ponds are reservoirs of ARGs, and are driven mainly by the nutrient, temperature, and oxygen with inducing specific microbial taxa. The regulation of environmental factors (increasing DO and NO₃^-) can be conducted to reduce drug resistance risk in aquaculture ponds. Therefore, environmental factors and specific taxa could be the indicators of ARG contamination and can be used to establish an antibiotic elimination system and consequently realize a sustainable aquaculture industry.

Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata

A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus Agromyces . The type strain with the highest pairwise similarity was Agromyces marinus H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus Agromyces , and only Agromyces atrinae P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus Agromyces indicated that G127ATT represented a previously undescribed species of the genus Agromyces . Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus Agromyces . The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus Agromyces , for which we propose the name Agromyces archimandritae sp. nov.

Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov

A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83^T, was isolated from a marine sediment of Indian Ocean. Strain WY83^T grew optimally at 30-35 °C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C_19:1 ω9c/C19:1 ω11c, anteiso-C_15:0, C_17:0 3OH, and iso-C_16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83^T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730^T, Chryseoglobus indicus CTD02-10-2^T, Yonghaparkia alkaliphila JCM 15138^T, Microcella alkaliphila DSM 18851^T and Microcella putealis DSM 19627^T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83^T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83^T, Y. alkaliphila JCM 15138^T, C. frigidaquae JCM 14730^T, M. alkaliphila DSM 18851^T and M. putealis DSM 19627^T should belong to different species of the same genus. Strain WY83^T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83^T (= KCTC 39637^T = MCCC 1A07099^T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov., respectively.

Aquiluna borgnonia gen. nov., sp. nov., a member of a Microbacteriaceae lineage of freshwater bacteria with small genome sizes

The actinobacterial strain 15G-AUS-rot^T was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rot^T to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rot^T were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C_16 : 0, antiso-C_15 : 0 and iso-C_14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rot^T (=DSM 107803^T=JCM 32974^T).

Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov., isolated from the gut of larvae of Protaetia brevitarsis seulensis, reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and emended description of the genus Pseudolysinimonas

Two bacterial strains, FWR-8^T and CFWR-9^T, were isolated from the gut of larvae of Protaetia brevitarsis seulensis that were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. Both strains were strictly aerobic, Gram-stain-positive and non-motile. Strain FWR-8^T possessed the highest sequence similarity (98.7 %) to that of Protaetiibacter intestinalis 2DFWR-13^T and the phylogenetic tree revealed that strain FWR-8^T formed a cluster with Ptb. intestinalis 2DFWR-13^T. Pseudolysinimonas kribbensis MSL-13^T and Lysinimonas yzui N7XX-4^T shared a high 16S rRNA gene sequence similarity (97.8 %) and formed a cluster adjacent to the cluster that included Ptb. intestinalis 2DFWR-13^T. The 16S rRNA gene sequence of strain CFWR-9^T exhibited the highest similarity (97.7 %) to that of Agromyces binzhouensis OAct353^T and the phylogenetic tree indicated that strain CFWR-9^T formed one independent cluster with A. binzhouensis OAct353^T that was within the radius of the genus Agromyces. The peptidoglycan type, major fatty acids, major menaquinones and total polar lipids of strain FWR-8^T were characterized as type B1, iso-C_16 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 0, MK-15, MK-16 and MK-14, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Those from strain CFWR-9^T were type B1, iso-C_16 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 0, MK-11, MK-12 and MK-10, and diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid, respectively. Based on the phenotypic and genotypic data, strains FWR-8^T and CFWR-9^T each represent a novel species within the genera Protaetiibacter and Agromyces, respectively. For these species, the names Protaetiibacter larvae sp. nov. and Agromyces intestinalis sp. nov. have been proposed, with the type strains FWR-8^T (=KACC 19322^T=NBRC 113051^T) and CFWR-9^T (=KACC 19306^T=NBRC 113046^T), respectively. Our results also justify a reclassification of Lysinimonas yzui as Pseudolysinimonas yzui comb. nov. and an emended description of the genus Pseudolysinimonas isprovided.

Marinisubtilis pacificus gen. nov., sp. nov., a Member of the Family Microbacteriaceae Isolated From a Deep-Sea Seamount

A Gram-stain-positive, yellow, aerobic, slender rod-shaped bacterial strain, designated KN1116^T, was isolated from a deep-sea seamount. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KN1116^T was related to the genus Chryseoglobus and had highest 16S rRNA gene sequence identity with Chryseoglobus frigidaquae CW1^T (98.5%). The predominant cellular fatty acids were anteiso-C_15:0 and iso-C_16:0. The quinone system for strain KN1116^T comprised menaquinone MK-12, MK-11, MK-10 and MK-13. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, six unknown glycolipids, two unidentified phospholipids and one unknown polar lipid. The cell-wall peptidoglycan of strain KN1116^T was of the type B1β, containing 2,4-diaminobutyric acid as the diamino acid. Genome sequencing revealed the strain KN1116^T has a genome size of 2.7 Mbp and a G+C content of 69.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strain KN1116^T represents a novel species of a novel genus of the family Microbacteriaceae, for which the name Marinisubtilis pacificus gen. nov., sp. nov. is proposed. The type strain of Marinisubtilis pacificus is KN1116^T (=CGMCC 1.17143^T =KCTC 49299^T).

Marisediminicola senii sp. nov. isolated from Queen Maud Land, Antarctica

A Gram-stain-variable, aerobic, orange pigmented, catalase-positive and oxidase-negative, cocci-shaped bacterium, designated SM7_A14^T, isolated from glacier fed sediment sample collected from the Queen Maud Land, near India's Maitri station in Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity with Marisediminicola antarctica DSM 22350^T (97.3 %), demonstrated distinct phylogenetic positioning of strain SM7_A14^T within the genus Marisediminicola. Growth of strain SM7_A14^T occurs at 5-25 °C (optimum, 20 °C), pH 7.0-10 (optimum, pH 8.0) with 0-5 % NaCl (optimum 1-4 %, w/v). C_15 : 0 anteiso, C_17 : 0 anteiso, C_16 : 0 iso and C_15 : 1 anteiso A are the major fatty acids (>5 % of the total fatty acids). The polar lipid profile consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values between SM7_A14^T and DSM 22350^T were 80.3 and 21.3 %, respectively. The genomic DNA G+C content of the strain SM7_A14^T was 68.5 %. Distinguishing characteristics based on the polyphasic analysis indicates strain SM7_A14^T as a novel species of genus Marisediminicola for which the name Marisediminicola senii sp. nov., is proposed. The type strain is SM7_A14^T (=MCC 4327^T=JCM 33936^T=LMG 31795^T).

Planctomonas psychrotolerans sp. nov., isolated from rhizosphere soil of Suaeda salsa

A psychrotolerant actinobacterium, designated strain J5903^T, was isolated from an alkaline soil sample from the rhizosphere of Suaeda salsa collected in desertification land surrounding Jiuliancheng Nur in Hebei Province, PR China. Cells of the isolate were Gram-stain-positive, aerobic, non-motile and non-spore-forming cocci. Strain J5903^T grew optimally at 20‒25 °C, at pH 7.0‒7.5 and with <1 % (w/v) NaCl. The cell-wall peptidoglycan type was B2γ with d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid as diagnostic amino acids. The muramyl residue was acetyl type. The menaquinones were MK-11, MK-12, MK-10 and MK-13. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major whole-cell fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The genomic DNA G+C content was 69.1 mol%. It shared the highest average nucleotide identity and digital DNA-DNA hybridization values with Planctomonas deserti 13S1-3^T. Phylogenies based on genome sequence showed that strain J5903^T and P. deserti 13S1-3^T formed a robust cluster with high bootstrap support. Strain J5903^T shared typical chemotaxonomic characteristics with P. deserti 13S1-3^T. Combining the polyphasic taxonomic evidence, strain J5903^T represents a novel species of the genus Planctomonas, for which the name Planctomonas psychrotolerans sp. nov. is proposed. The type strain is J5903^T (=DSM 101894^T=CGMCC 1.15523^T).

Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment

A novel Gram-stain-positive bacterial strain, CHu50b-6-2^T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2^T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148^T, Frigoribacterium faeni KACC 20509^T and Lysinibacter cavernae DSM 27960^T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2^T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2^T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2^T (= KCTC 49081^T = JCM 32673^T).

Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella

Two novel strains, designated 11W25H-1^T and 8H24J-4-2^T, were isolated from surface-sterilized plant tissues collected from the Taklamakan Desert in the Xinjiang Uygur Autonomous Region, China. The strains were characterized by a polyphasic approach in order to clarify their taxonomic positions. They were Gram-stain positive, aerobic, non-motile, non-spore-forming and rod-shaped. The 16S rRNA gene sequences of the strains showed highest similarities with Labedella gwakjiensis KCTC 19176^T (99.2% and 98.9%, respectively) and Labedella endophytica CPCC 203961^T (98.9% and 99.0%, respectively). The sequence similarity between strains 11W25H-1^T and 8H24J-4-2^T was 99.4%. Phylogenetic analyses based on 16S rRNA gene sequences and single-copy phylogenetic marker genes (pMGs) showed that the two strains belonged to the genus Labedella and formed a separate cluster from the closest species L. gwakjiensis KCTC 19176^T and L. endophytica CPCC 203961^T. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly separated the strains from each other and from the other species of the genus Labedella with values below the thresholds for species delineation. The two strains showed chemotaxonomic characteristics and phenotypic properties in agreement with the description of the genus Labedella and also confirmed the differentiation from the closest species. The data demonstrated that strains 11W25H-1^T and 8H24J-4-2^T represented two novel species of the genus Labedella, for which the names Labedella phragmitis sp. nov. (type strain 11W25H-1^T=JCM 33144^T=CGMCC 1.16700^T) and Labedella populi sp. nov. (type strain 8H24J-4-2^T=JCM 33143^T=CGMCC 1.16697^T) are proposed.

Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel aerobic, Gram-staining-positive and non-spore-forming bacterial strains, 194^T and S1194, were isolated from faeces of Tibetan antelopes sampled at the Qinghai-Tibet Plateau of China. The strains were able to grow in medium up to 10 % NaCl, similar to the NaCl-resistant property of the genus Salinibacterium members. The 16S rRNA gene sequences of the strains showed the highest similarity to Salinibacterium xinjiangense(98.1-98.2 %), and phylogenetic analysis based on 16S rRNA gene sequences indicated that strains 194^T and S1194 represent a new lineage. The DNA G+C contents of strain 194^T and S1194 are 64.1 and 64.2 mol%. Their genomes exhibit less than 96 % average nucleotide identity and 70 % DNA-DNA relatedness to known species of Salinibacterium. Strains 194^T and S1194 are unable to utilize d-mannose or produce naphthol-AS-BI-phosphohydrolase. The two strains had anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids, and their cell walls contained lysine, alanine, glycine and glutamic acid. The predominant menaquinones identified were MK-11 and MK-10, with diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. Overall, the major cellular content profiles of 194^T agreed with those of Salinibacterium xinjiangense and Salinibacterium amurskyense, though the proportions were distinct. Based on genotypic, phenotypic and biochemical analyses, the novel species Salinibacterium hongtaonis sp. nov. is proposed. The type strain is 194^T (=CGMCC 1.16371^T=DSM 106171^T).

Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert

A Gram-staining-positive, aerobic, irregular coccoid- to ovoid-shaped, non-spore-forming and motile bacterium, designated strain 13S1-3^T, was isolated from a soil sample from the rhizosphere of Tamarix collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Strain 13S1-3^T grew optimally at 28-30 °C, pH 7.0 and with 0-1 % (w/v) NaCl. The cell-wall peptidoglycan was of the B2γ type and contained d-alanine, d-glutamic acid, glycine, d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid. Ribose, xylose, glucose and galactose were detected as cell-wall sugars. The acyl type of the muramic acid was acetyl. The predominant menaquinones were MK-12, MK-11, MK-13 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified phospholipid. The major whole-cell fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 13S1-3^T represented a member of the family Microbacteriaceae and showed the highest level of 16S rRNA gene sequence similarity with Frondihabitans australicus E1HC-02^T (97.11 %). Phylogenetic trees revealed that 13S1-3^T formed a distinct lineage with respect to closely related genera within the family Microbacteriaceae. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, 13S1-3^T is distinguishable from phylogenetically related genera in the family Microbacteriaceae, and represents a novel species of a new genus, for which the name Planctomonas deserti gen. nov., sp. nov. is proposed. The type strain is 13S1-3^T (=KCTC 49115^T=CGMCC 1.16554^T).

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3^T, was isolated from a piece of surface-sterilized branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao, China. Comparative 16S rRNA gene sequence analysis showed that strain 1T4Z-3^T was clearly affiliated to the genus Amnibacterium and exhibited 97.9 % gene sequence similarity to Amnibacterium kyonggiense JCM 16463^T, 97.3 % gene sequence similarity to Amnibacterium soli JCM 19015^T and less than 96.4 % gene sequence similarities to other genera of the family Microbacteriaceae. Strain 1T4Z-3^T had L-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid. The major fatty acids (>10 % of total fatty acids) were iso-C16 : 0 (46.6 %) and anteiso-C15 : 0 (27.3 %). The predominant menaquinones of strain 1T4Z-3^T were MK-11 (81.4 %) and MK-12 (14.1 %). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids. The DNA G+C content of strain 1T4Z-3^T was 71.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 1T4Z-3^T is considered to represent a novel species of the genus Amnibacterium, for which the name Amnibacterium endophyticum sp. nov. is proposed. The type strain of Amnibacterium endophyticum is 1T4Z-3^T (=KCTC 39983^T=CGMCC 1.16066^T).

Arenivirga flava gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a mangrove tidal flat

A novel Gram-stain-positive actinobacterium, designated HIs16-32T, was isolated from a sand sample collected from a mangrove tidal flat in Japan and its taxonomic position was investigated by a polyphasic approach. The cells of strain HIs16-32T were Gram-stain-positive, rod-shaped, non-motile and non-endospore-forming. Strain HIs16-32T contained glutamic acid, glycine and lysine in the peptidoglycan; however, alanine was absent. Galactose and mannose were detected as cell-wall sugars. The isoprenoid quinones were identified as MK-11, MK-12 and MK-10, and the major fatty acids as anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was determined to be 72.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIs16-32T was related to members of the family Microbacteriaceae but did not form a reliable cluster with any known members of the family. The highest 16S rRNA gene sequence similarity values were obtained with species of the genera Herbiconiux(96.1-96.8 %), Plantibacter(96.5-96.7 %) and Schumannella (96.7 %). However, strain HIs16-32T was distinguishable from the phylogenetically related genera in terms of chemotaxonomic characteristics and phylogenetic relationship. Therefore, strain HIs16-32T is concluded to represent a novel genus and species of the family Microbacteriaceae, for which the name Arenivirga flava gen. nov., sp. nov. is proposed. The type strain of A. flava is HIs16-32T (=NBRC 112289T=TBRC 7038T).

Puzihella rosea gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from freshwater

Two Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93-95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria, which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized glycolipid and an uncharacterized aminophospholipid. The major polyamine was putrescine. The major isoprenoid quinone was MK-10. The G+C content of DNA was between 62.6 and 62.9 mol%. On the basis of the genotypic and phenotypic data, strains MI-28T and SKY-11 represent a novel genus and species of the family Microbacteriaceae, for which the name Puzihella rosea gen. nov., sp. nov. is proposed. The type strain of the type species is MI-28T (=BCRC 80688T=LMG 27848T=KCTC 29239T).

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.

Luethyella okanaganae gen. nov., sp. nov., a Novel Genus and Species of the Family Microbacteriaceae Isolated from the Insect Okanagana rimosa

The entomopathogen "Corynebacterium okanaganae" was described by Lüthy in 1974 but the name was never validly published. Phylogenetic analysis employing 16S rRNA gene sequences demonstrate that "Corynebacterium okanaganae" is not a member of the genus Corynebacterium but related to members of the Microbacteriaceae being most closely related to, but distinct from, members of the genera Rathayibacter, Mycetocola and Curtobacterium. The bacterium is an aerobic, Gram-positive staining, rod-shaped actinobacterium with the cell-wall peptidoglycan based on 2,4, diaminobutyric acid as the diagnostic diamino acid. The predominant menaquinones are MK-10, MK-11 and MK-12, and the principle polar lipids are phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids consist of anteiso-C_15:0 and anteiso-C_17:0. Therefore, based upon the phylogenetic, biochemical, and chemotaxonomic information, the organism merits recognition as a novel species and genus in the family Microbacteriaceae, for which the name Luethyella okanaganae gen. nov. sp. nov. is proposed. The type strain is LBG B4405^T = CCUG 43304^T = NCIMB 702272^T.

Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72

We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment.

Lysinibacter cavernae gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a karst cave

A Gram-stain-positive, aerobic, straight or slightly bent rod-shaped, non-motile, non-spore-forming bacterium, designated strain CC5-806T, was isolated from a soil sample collected from a wild karst cave in the Wulong region, Chongqing, PR China and examined using a polyphasic approach to clarify its taxonomic position. This bacterium did not produce substrate mycelium or aerial hyphae, and no diffusible pigments were observed on the media tested. Strain CC5-806T grew optimally without NaCl at 20 °C and at pH 7.0. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain CC5-806T belonged to the family Microbacteriaceae and showed the highest levels of 16S rRNA gene sequence similarities with Frigoribacterium endophyticum EGI 6500707T (97.56 %), Frigoribacterium faeni 801T (97.53 %) and Glaciihabitans tibetensis MP203T (97.42 %). Phylogenetic trees revealed that strain CC5-806T did not show a clear affiliation to any genus within the family Microbacteriaceae. The DNA G+C content of strain CC5-806T was 62.6 mol%. The cell-wall peptidoglycan contained l-lysine as a diagnostic diamino acid. The predominant menaquinones were MK-11, MK-10 and MK-9. Phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid, four unidentified phospholipids and other polar lipids were detected in the polar lipid extracts. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. On the basis of the phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, strain CC5-806T was distinguishable from phylogenetically related genera in the family Microbacteriaceae. It represents a novel species of a novel genus, for which the name Lysinibacter cavernae gen. nov., sp. nov. is proposed. The type strain is CC5-806T ( = DSM 27960T = CGMCC 1.14983T).

Allohumibacter endophyticus gen. nov., sp. nov., isolated from the root of wild Artemisia princeps (mugwort)

A novel actinobacterium designated strain MWE-A11T was isolated from the root of wild Artemisia princeps (mugwort). The isolate was aerobic, Gram-stain-positive and short rod-shaped, and the colonies were yellow and circular with entire margin. Strain MWE-A11T grew at 15-37 °C and pH 6.0-8.0. The predominant isoprenoid quinones were MK-11 and MK-10. The predominant fatty acids were anteiso-C15:0 and iso-C16:0, and the DNA G+C content was 68.8 mol%. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The peptidoglycan contained 2,4-diaminobutyric acid as the diagnostic diamino acid, and the acyl type was glycolyl. Phylogenetic analyses based on 16S rRNA gene sequence comparisons indicated that strain MWE-A11T was affiliated with the family Microbacteriaceae, and was most closely related to the type strains of Humibacter antri (96.4% 16S rRNA gene sequence similarity), Herbiconiux moechotypicola (96.3%), Leifsonia soli (96.3%), Leifsonia lichenia (96.2%), Leifsonia xyli subsp. cynodontis (96.1%), Microbacterium testaceum (96.0%) and Humibacter albus (96.0%). However, the combination of chemotaxonomic properties clearly distinguished strain MWE-A11T from the related taxa at genus level. Accordingly, Allohumibacter endophyticus gen. nov., sp. nov. is proposed to accommodate a new member of the family Microbacteriaceae. The type strain of the type species is MWE-A11T (=JCM 19371T=KCTC 29232T).

High-quality complete genome sequence of Microbacterium sp. SUBG005, a plant pathogen

Microbacterium sp. SUBG005 is a Gram positive bacterium, isolated from infected leaf of Mangifera indica L. in Rajkot (22.30°N, 70.78°E), Gujarat, India. The genome sequencing of Microbacterium sp. SUBG005 is having type I secretion system genes of pathogenicity as well as heavy metal resistance unique genes. The genome size is 7.01 Mb with G + C content of 64.80% and contains rRNA sequences. Genome sequencing analysis provides information about the microbe role in host–pathogen interaction. The whole genome sequencing has been deposited in DDBJ/EMBL/GenBank under the accession number JNNT00000000.

Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water

A Gram-stain-positive, aerobic, non-motile, curved (selenoid), rod-shaped actinobacterium, designated KNCT, was isolated from the 0.2 μm-filtrate of river water in western Japan. Cells of strain KNCT were ultramicrosized (0.04-0.05 μm3). The strain grew at 15-37 °C, with no observable growth at 10 °C or 40 °C. The pH range for growth was 7-9, with weaker growth at pH 10. Growth was impeded by the presence of NaCl at concentrations greater than 1 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KNCT showed relatively high sequence similarity (97.2 %) to Alpinimonas psychrophila Cr8-25T in the family Microbacteriaceae. However, strain KNCT formed an independent cluster with cultured, but as-yet-unidentified, species and environmental clones on the phylogenetic tree. The major cellular fatty acids were anteiso-C15 : 0 (41.0 %), iso-C16 : 0 (21.8 %), C16 : 0 (18.0 %) and anteiso-C17 : 0 (12.9 %), and the major menaquinones were MK-11 (71.3 %) and MK-12 (13.6 %). The major polar lipids were phosphatidylglycerol and two unknown glycolipids. The cell-wall muramic acid acyl type was acetyl. The peptidoglycan was B-type, and contained 3-hydroxyglutamic acid, glutamic acid, aspartic acid, glycine, alanine and lysine, with the latter being the diagnostic diamino acid. The G+C content of the genome was unusually low for actinobacteria (52.1 mol%), compared with other genera in the family Microbacteriaceae. Based on the phenotypic characteristics and phylogenetic evidence, strain KNCT represents a novel species of a new genus within the family Microbacteriaceae, for which the name Aurantimicrobium minutum gen. nov., sp. nov. is proposed. The type strain of the type species is KNCT ( = NBRC 105389T = NCIMB 14875T).

High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass

Leucobacter chironomi strain MM2LB^T (Halpern et al., Int J Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile, aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family Microbacteriaceae, a family within the class Actinobacteria. Strain MM2LB^T was isolated from a chironomid (Diptera; Chironomidae) egg mass that was sampled from a waste stabilization pond in northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain MM2LB^T formed a distinct branch within the radiation encompassing the genus Leucobacter. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 69.90%. The chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L. chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Gryllotalpicola reticulitermitis sp. nov., isolated from a termite gut

Strain TS-56(T) was isolated from the gut of a wood-feeding termite, Reticulitermes chinensis Snyder. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain represented a member of the genus Gryllotalpicola of the family Microbacteriaceae, with sequence similarities to other species of the genus ranging from 96.6 % to 97.8 %. The isolate was Gram-stain-positive, non-motile, with light yellow colonies and irregular short rod-shaped cells (0.4-0.6 µm in diameter, 0.6-1.0 µm in length). Growth of TS-56(T) occurred at 20-35 °C (optimum, 30 °C) and at pH 4.0-8.0 (optimum, pH 5.0). The peptidoglycan of TS-56(T) contained ornithine, glutamic acid, alanine, homoserine and glycine. The acyl type was acetyl. The most abundant cellular fatty acid of TS-56(T) was cyclohexyl-C17 : 0 (88.79 %). The respiratory menaquinone was MK-11. The polar lipid profile contained disphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and two unknown glycolipids. DNA of the type strain had a G+C content of 67.4 mol%. On the basis of the phylogenetic properties and phenotypic distinctiveness, TS-56(T) represents a novel species of the genus Gryllotalpicola, for which the name Gryllotalpicola reticulitermitis sp. nov. is proposed. The type strain is TS-56(T) ( = CGMCC 1.10363(T) = NBRC 109838(T)).

Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.)

Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.

Conyzicola lurida gen. nov., sp. nov., isolated from the root of Conyza canadensis

A novel Gram-stain-positive, non-spore-forming, pale yellow, irregular rod-shaped bacterium designated strain HWE2-01(T) was isolated from the surface-sterilized root of horseweed (Conyza canadensis). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HWE2-01(T) belongs to the family Microbacteriaceae and showed sequence similarity levels of 97.1-97.7% with species of the genus Salinibacterium, 95.9-97.6% with species of the genus Leifsonia and 97.1% with Homoserinimonas aerilata. The highest sequence similarity (97.7%) was with Salinibacterium xinjiangense 0543(T). The genomic DNA G+C content of the novel strain was 68.1 mol%. The predominant cellular fatty acid of strain HWE2-01(T) was anteiso-C15 : 0, major menaquinones were MK-10, MK-9 and MK-11, and diagnostic polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The peptidoglycan of the novel strain contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The cell-wall sugars of strain HWE2-01(T) were galactose, mannose and rhamnose. The murein was of the acetyl type. Based on the results of the phenotypic and phylogenetic analysis, strain HWE2-01(T) differed in some respects from other members of the family Microbacteriaceae. Therefore, strain HWE2-01(T) is proposed to represent a novel species of a new genus in the family Microbacteriaceae with the name Conyzicola lurida gen. nov., sp. nov. (type strain = HWE2-01(T) = KCTC 29231(T) = JCM 19257(T)).

Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae

Two bacterial strains, KIS66-7(T) and 5GH26-15(T), were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7(T) had the highest similarities with those of Labedella gwakjiensis KSW2-17(T) (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb(T) (97.2%), Leifsonia naganoensis JCM 10592(T) (97.0%), and Cryobacterium mesophilum MSL-15(T) (97.0%). Strain 5GH26-15(T) showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7(T) exhibited 96.4% similarity with that from 5GH26-15(T). Strain KIS66-7(T) contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C15:0, ai-C17:0, and i-C16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C15:0, i-C16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7(T) and 5GH26-15(T) represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7(T)=KACC 15515(T)=NBRC 108724(T)) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15(T)=KACC 15524(T)=NBRC 108755(T)) within the family Microbacteriaceae.

Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water

A Gram-stain-positive, aerobic, non-spore-forming, short-rod-shaped bacterium, designated strain MP203T, was isolated from ice water of Midui Glacier in Tibet Autonomous Region, China. The strain was psychrotolerant, growing at 0–25 °C. 16S rRNA gene sequence analysis showed that strain MP203T was most similar to Frigoribacterium faeni NBRC 103066T, Compostimonas suwonensis KACC 13354T, Frigoribacterium mesophilum KCTC 19311T, Marisediminicola antarctica CCTCC AB 209077T and Alpinimonas psychrophila JCM 18951T, with similarities of 97.4, 97.2, 97.2, 97.1 and 97.1 %, respectively. The maximum-likelihood phylogenetic tree indicated that strain MP203T clustered with nine genera of the family Microbacteriaceae , namely Frigoribacterium , Compostimonas , Marisediminicola , Alpinimonas , Frondihabitans , Clavibacter , Subtercola , Klugiella and Agreia . However, bootstrap analysis showed that there was no significance in the branching pattern of the linage comprising strain MP203T and any existing generic lineage of the family Microbacteriaceae . DNA–DNA hybridization results indicated levels of relatedness between strain MP203T and Marisediminicola antarctica CCTCC AB 209077T, Frigoribacterium faeni NBRC 103066T, Frigoribacterium mesophilum KCTC 19311T, Compostimonas suwonensis KACC 13354T and Alpinimonas psychrophila JCM 18951T were 25.8±7.3, 29.6±7.6, 19.7±6.7, 16.0±4.2 and 12.4±5.1 % (mean±sd), respectively. The G+C content of the genomic DNA was 64.1 mol%. Analysis of the cell-wall peptidoglycan revealed that the peptidoglycan structure of strain MP203T was B10 type with Gly[l-Hse]–d-Glu–d-DAB, containing 2, 4-diaminobutyric acid (DAB) as a diagnostic amino acid. The cell-wall sugars were rhamnose, ribose, mannose and glucose. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso A-C15 : 1. An unusual compound identified as anteiso-C15 : 0-DMA (1, 1-dimethoxy-anteiso-pentadecane) was also present in strain MP203T. The predominant menaquinone was MK-10. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unknown glycolipid and four unknown lipids were detected in the polar lipid extracts. As strain MP203T was distinguishable from phylogenetically related genera in the family Microbacteriaceae in terms of its physiological and chemotaxonomic characteristics and phylogenetic position, it was considered to represent a novel species of a new genus. Thus, the name Glaciihabitans tibetensis gen. nov., sp. nov. is proposed. The type strain of Glaciihabitans tibetensis is MP203T ( = CGMCC 1.12484T = KCTC 29148T).

Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov

Bacterial strains KIS82-1(T) and GRS42(T) were isolated from soil and from sap of Acer mono, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS82-1(T) showed the highest similarity to those of Frondihabitans peucedani RS-15(T) (97.6%), Frigoribacterium mesophilum MSL-08(T) (97.2%) and Labedella gwakjiensis KSW2-17(T) (97.0%), while strain GRS42(T) showed the highest 16S rRNA gene sequence similarity to Frondihabitans peucedani RS-15(T) (98.7%), Frondihabitans cladoniiphilus CafT13(T) (98.4%), Frondihabitans australicus E1HC-02(T) (98.2%) and Frigoribacterium faeni 801(T) (97.3%). The 16S rRNA gene sequence similarity between GRS42(T) and KIS82-1(T) was 97.0%. Phylogenetic trees indicated that strain GRS42(T) was firmly grouped into the genus Frondihabitans, while strain KIS82-1(T) did not show a clear affiliation to any genus within the family Microbacteriaceae. Strain KIS82-1(T) showed type B1β peptidoglycan with 2,4-diamino-L-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C(15 : 0), iso-C(16: 0) and iso-C(14 : 0) as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42(T) was of type B2β with D-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42(T) revealed low DNA-DNA hybridization (<50% relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1(T) represents a novel genus and species and that strain GRS42(T) represents a novel species in the family Microbacteriaceae. The genus Galbitalea gen. nov. is proposed, with strain KIS82-1(T) ( = KACC 15520(T) = NBRC 108727(T)) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42(T) ( = KACC 15521(T) = NBRC 108728(T)) is proposed as the type strain of Frondihabitans sucicola sp. nov.

Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil

A novel Gram-stain-positive, non-motile, rod-shaped bacterium, designated 5GHs34-4(T), was isolated from greenhouse soil in Yongin, Republic of Korea. Growth occurred in the temperature range of 10-37 °C (optimum 28-30 °C) and at pH 5.0-9.0 (optimum pH 7.0). It can tolerate up to 3 % (w/v) NaCl. The strain showed 16S rRNA gene sequence similarity levels of 95.1-97.0 % with species of the genus Leifsonia, 95.7-96.7 % with species of the genus Herbiconiux, 95.1-96.4 % with species of the genus Salinibacterium and 96.1 % with Labedella gwakjiensis and Homoserinimonas aerilata. The highest sequence similarities (97.0 %) were with Leifsonia aquatica JCM 1368(T), Leifsonia poae VKM Ac-1401(T) and Leifsonia psychrotolerans LI1(T). The peptidoglycan type determined for strain 5GHs34-4(T) was B2γ with dl-2,4-diaminobutyric acid at position 3. The murein was of the acetyl type. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The menaquinones detected were MK-13, MK-12 and MK-14, and the major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The phenotypic and phylogenetic traits of strain 5GHs34-4(T) differed in some respects from those of members of the family Microbacteriaceae. Therefore, strain 5GHs34-4(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Rudaibacter terrae gen. nov., sp. nov. is proposed. The type strain is 5GHs34-4(T) ( = KACC 15523(T) = NBRC 108754(T)).

Phenotypic and genotypic properties of Microbacterium yannicii, a recently described multidrug resistant bacterium isolated from a lung transplanted patient with cystic fibrosis in France

BACKGROUND

Cystic fibrosis (CF) lung microbiota consists of diverse species which are pathogens or opportunists or have unknown pathogenicity. Here we report the full characterization of a recently described multidrug resistant bacterium, Microbacterium yannicii, isolated from a CF patient who previously underwent lung transplantation.

RESULTS

Our strain PS01 (CSUR-P191) is an aerobic, rod shaped, non-motile, yellow pigmented, gram positive, oxidase negative and catalase positive bacterial isolate. Full length 16S rRNA gene sequence showed 98.8% similarity with Microbacterium yannicii G72T type strain, which was previously isolated from Arabidopsis thaliana. The genome size is 3.95Mb, with an average G+C content of 69.5%. In silico DNA-DNA hybridization analysis between our Microbacterium yannicii PS01isolate in comparison with Microbacterium testaceum StLB037 and Microbacterium laevaniformans OR221 genomes revealed very weak relationship with only 28% and 25% genome coverage, respectively. Our strain, as compared to the type strain, was resistant to erythromycin because of the presence of a new erm 43 gene encoding a 23S rRNA N-6-methyltransferase in its genome which was not detected in the reference strain. Interestingly, our patient received azithromycin 250 mg daily for bronchiolitis obliterans syndrome for more than one year before the isolation of this bacterium.

CONCLUSIONS

Although significance of isolating this bacterium remains uncertain in terms of clinical evolution, this bacterium could be considered as an opportunistic human pathogen as previously reported for other species in this genus, especially in immunocompromised patients.

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae . The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae . Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).

Genome sequence of Microbacterium yannicii, a bacterium isolated from a cystic fibrosis patient

Microbacterium yannicii is a Gram-positive, aerobic, yellow-pigmented, rod-shaped, nonmotile, oxidase-negative, and catalase-positive bacterium isolated on Columbia colistin-nalidixic acid (CNA) agar with 5% sheep blood from the sputum of a cystic fibrosis patient. The present study reports the draft genome of a Microbacterium yannicii strain.

Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost

A Gram-positive, aerobic, non-motile, short rod, designated SMC46T, was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46T was a member of the family Microbacteriaceae ; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46T and other members of the family Microbacteriaceae was ≤97 %, the highest sequence similarity being with Frigoribacterium faeni 801T and Frondihabitans australicus E1HC-02T (both 97.0 %). Some chemotaxonomic properties of strain SMC46T were consistent with those of the family Microbacteriaceae : MK-11 and MK-12 as the predominant menaquinones, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46T contained a B-type peptidoglycan not previously found in the family Microbacteriaceae . The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46T was considered to represent a novel genus and species in the family Microbacteriaceae , for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46T ( = KACC 13354T  = NBRC 106304T).

Gryllotalpicola gen. nov., with descriptions of Gryllotalpicola koreensis sp. nov., Gryllotalpicola daejeonensis sp. nov. and Gryllotalpicola kribbensis sp. nov. from the gut of the African mole cricket, Gryllotalpa africana, and reclassification of Curtobacterium ginsengisoli as Gryllotalpicola ginsengisoli comb. nov

Strains RU-16T, RU-28, RU-04T and PU-02T were isolated from the gut of the African mole cricket, Gryllotalpa africana. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belonged to the family Microbacteriaceae . All four strains were most closely related to Curtobacterium ginsengisoli DCY26T (below 97 % 16S rRNA gene sequence similarity). These isolates were Gram-stain-positive, motile (by gliding), rod-shaped and exhibited ivory-coloured colonies. Their chemotaxonomic properties included MK-11 as the major respiratory quinone, ornithine as the cell-wall diamino acid, acetyl as the acyl type of the peptidoglycan, cyclohexyl-C17 : 0 as the major fatty acid and phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, we propose a new genus in the family Microbacteriaceae , Gryllotalpicola gen. nov., with three novel species, Gryllotalpicola daejeonensis sp. nov. (type strain RU-04T  = KCTC 13809T  = JCM 17590T), Gryllotalpicola koreensis sp. nov. (type strain RU-16T  = KCTC 13810T  = JCM 17591T) and Gryllotalpicola kribbensis sp. nov. (type strain PU-02T  = KCTC 13808T  = JCM 17593T). Gryllotalpicola koreensis is the type species of the genus. Additionally, we propose that Curtobacterium ginsengisoli should be reclassified in the genus as Gryllotalpicola ginsengisoli comb. nov. (type strain DCY26T  = KCTC 13163T  = JCM 14773T).

Colonization of tomato seedlings by bioluminescent Clavibacter michiganensis subsp. michiganensis under different humidity regimes

Tomato bacterial canker, caused by Clavibacter michiganensis subsp. michiganensis, is transmitted by infected or infested seed and mechanically from plant to plant. Wounds occurring during seedling production and crop maintenance facilitate the dissemination of the pathogen. However, the effects of environmental factors on C. michiganensis subsp. michiganensis translocation and growth as an endophyte have not been fully elucidated. A virulent, stable, constitutively bioluminescent C. michiganensis subsp. michiganensis strain BL-Cmm 17 coupled with an in vivo imaging system allowed visualization of the C. michiganensis subsp. michiganensis colonization process in tomato seedlings in real time. The dynamics of bacterial infection in seedlings through wounds were compared under low (45%) and high (83%) relative humidity. Bacteria multiplied rapidly in cotyledon petioles remaining after clip inoculation and moved in the stem toward both root and shoot. Luminescent signals were also observed in tomato seedling roots over time, and root development was reduced in inoculated plants maintained under both humidity regimes. Wilting was more severe in seedlings under high-humidity regimes. A strong positive correlation between light intensity and bacterial population in planta suggests that bioluminescent C. michiganensis subsp. michiganensis strains will be useful in evaluating the efficacy of bactericides and host resistance.

Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite

A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25(T), was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25(T) belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3(T) (97.0%). However, strain Cr8-25(T) could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness value of only 37.2%. Strain Cr8-25(T) contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25(T) were C(15:0) anteiso (64.6%) and iso-C(16:0) (22.5%) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25(T) (=DSM 23737(T)=LMG 26215(T)).

Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae

A Gram-positive, non-motile bacterium, designated KSL51201-037T, was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037T belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17T, 96.0 % to Leifsonia ginsengi wged11T and 95.9 % to Microterricola viridarii KV-677T. The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037T had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C15 : 0 (47.8 %) and iso-C16 : 0 (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037T represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037T (=KEMC 51201-037T=JCM 16463T).

Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic

Strain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).