Genome Sequence of Nitratireductor indicus Type Strain C115

Nitratireductor indicus strain C115^T was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. Here, we present the draft genome of strain C115^T, which contains 4,992,479 bp with a G+C content of 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.     

Genome Sequence of Galbibacter marinum Type Strain ck-I2-15

Galbibacter marinum strain ck-I2-15^T was isolated from an arsenite-resistant consortium enriched from the deep sea sediment of a hydrothermal vent field on the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain ck-I2-15^T, which contains 3,572,447 bp with a G+C content of 37.04% and contains 3,099 protein-coding genes and 38 tRNA genes.     

Genome Sequence of Nitratireductor pacificus Type Strain pht-3B

Nitratireductor pacificus strain pht-3B^T was isolated from a pyrene-degrading consortium enriched from the deep sea sediment of the Pacific Ocean. Here, we present the draft genome of strain pht-3B^T, which contains 4,466,205 bp with a G+C content of 65.51% and contains 4,197 protein-coding genes and 46 tRNA genes.     

Genome Sequence of Gallaecimonas xiamenensis Type Strain 3-C-1

Gallaecimonas xiamenensis 3-C-1^T was isolated from a crude-oil-degrading consortium enriched from the surface seawater around Xiamen Island. Here, we present the draft genome of strain 3-C-1^T, which contains 4,062,282 bp with a G+C content of 60.58% and contains 3,798 protein-coding genes and 65 tRNAs.     

Genome Sequence of Thalassospira profundimaris Type Strain WP0211

Thalassospira profundimaris WP0211^T was isolated from a pyrene-degrading consortium, enriched from deep-sea sediment collected from the West Pacific Ocean. Here, we present the draft genome of strain WP0211^T, which contains 4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes and 45 tRNAs.     

Genome Sequence of Thalassospira xiamenensis Type Strain M-5

Thalassospira xiamenensis M-5^T was isolated from the surface water of a waste oil pool at the oil storage dock in the city of Xiamen, Fujian Province, China. Here, we present the draft genome of strain M-5^T, which contains 4,705,237 bp with a G+C content of 54.65% and contains 4,343 protein-coding genes and 46 tRNA genes.     

Genome Sequence of Legionella tunisiensis Strain LegMT,a New Legionella Species Isolated from Hypersaline Lake Water

Legionella tunisiensis is a gammaproteobacterium from the class Legionellaceae, growing in amoebae. We sequenced the genome from strain LegM^T. It is composed of 3,508,121 bp and contains 4,747 protein-coding genes and 38 RNA genes, including 3 rRNA genes.     

Genome Sequence of Oceanibaculum indicum Type Strain P24

Oceanibaculum indicum type strain P24 was isolated from a polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a deep-seawater sample collected from the Indian Ocean. Here we present the draft genome of strain P24^T, which contains 3,952,792 bp with a G+C content of 65.5% and contains 3,755 protein-coding genes and 45 tRNAs.     

Genome Sequence of Afipia birgiae,a Rare Bacterium Associated with Amoebae

Afipia birgiae is an alphaproteobacterium from the family Bradyrhizobiaceae, growing in amoebae, and a potential human pathogen. We sequenced the genome of type strain 34632^T. It is composed of 5,325,467 bp and contains 5,160 protein-coding genes and 53 RNA genes, including 3 rRNA genes.     

The Genome of the Moderate Halophile Amycolicicoccus subflavus DQS3-9A1T Reveals Four Alkane Hydroxylation Systems and Provides Some Clues on the Genetic Basis for Its Adaptation to a Petroleum Environment

The moderate halophile Amycolicicoccus subflavus DQS3-9A1^T is the type strain of a novel species in the recently described novel genus Amycolicicoccus, which was isolated from oil mud precipitated from oil produced water. The complete genome of A. subflavus DQS3-9A1^T has been sequenced and is characteristic of harboring the genes for adaption to the harsh petroleum environment with salinity, high osmotic pressure, and poor nutrient levels. Firstly, it characteristically contains four types of alkane hydroxylases, including the integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153, a long-chain alkane monooxygenase (LadA) and propane monooxygenase. It also accommodates complete pathways for the response to osmotic pressure. Physiological tests proved that the strain could grow on n-alkanes ranging from C10 to C36 and propane as the sole carbon sources, with the differential induction of four kinds of alkane hydroxylase coding genes. In addition, the strain could grow in 1–12% NaCl with the putative genes responsible for osmotic stresses induced as expected. These results reveal the effective adaptation of the strain DQS3-9A1^T to harsh oil environment and provide a genome platform to investigate the global regulation of different alkane metabolisms in bacteria that are crucially important for petroleum degradation. To our knowledge, this is the first report to describe the co-existence of such four types of alkane hydroxylases in a bacterial strain.     

New metabolites of Azotobacter vinelandii exhibiting antifungal activity

New metabolites exhibiting antifungal activity were isolated from the culture liquid of Azotobacter vinelandii strain IB 4. The metabolites were characterized by IR and ¹³C-NMR spectroscopy and defined as sucrose polythiophosphates of tetraamine (α-D-2,3-diaminoglucopyranosyl-β-D-3,4-diaminofructofuranose).     

Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae,isolated from coral reef seawater off Ishigaki Island,Japan

Two phylogenetically distinct Vibrionaceae strains C4II189^T and C4V358^T isolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189^T (=DSM 101554^T = JCM 31629^T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358^T (=DSM 101555^T = JCM 31630^T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.     

Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42

The complete genome sequence of Bacillus amyloliquefaciens type strain DSM7^T is presented. A comparative analysis between the genome sequences of the plant associated strain FZB42 (Chen et al., 2007) with the genome of B. amyloliquefaciens DSM7^T revealed obvious differences in the variable part of the genomes, whilst the core genomes were found to be very similar. The strains FZB42 and DSM7^T have in common 3345 genes (CDS) in their core genomes; whilst 547 and 344 CDS were found to be unique in DSM7^T and FZB42, respectively. The core genome shared by both strains exhibited 97.89% identity on amino acid level. The number of genes representing the core genome of the strains FZB42, DSM7^T, and Bacillus subtilis DSM10^T was calculated as being 3098 and their identity was 92.25%. The 3,980,199 bp genome of DSM7^T contains numerous genomic islands (GI) detected by different methods. Many of them were located in vicinity of tRNA, glnA, and glmS gene copies. In contrast to FZB42, but similar to B. subtilis DSM10^T, the GI were enriched in prophage sequences and often harbored transposases, integrases and recombinases. Compared to FZB42, B. amyloliquefaciens DSM7^T possessed a reduced potential to non-ribosomally synthesize secondary metabolites with antibacterial and/or antifungal action. B. amyloliquefaciens DSM7^T did not produce the polyketides difficidin and macrolactin and was impaired in its ability to produce lipopeptides other than surfactin. Differences established within the variable part of the genomes, justify our proposal to discriminate the plant-associated ecotype represented by FZB42 from the group of type strain related B. amyloliquefaciens soil bacteria.     

Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae

Timonella senegalensis strain JC301^T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301^T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301^T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301^T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels.     

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601^T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601^T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601^T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601^T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601^T. Genes involved in cyclohexanol degradation were only found in strain K601^T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.     

Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov

Anaerococcus senegalensis strain JC48^T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate anaerobic coccus. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid) contains 1,721 protein-coding and 53 RNA genes including 5 rRNA genes     

Definition of a novel symbiovar (sv. retamae) within Bradyrhizobium retamae sp. nov., nodulating Retama sphaerocarpa and Retama monosperma

In this paper we analyze through a polyphasic approach several Bradyrhizobium strains isolated in Spain and Morocco from root nodules of Retama sphaerocarpa and Retama monosperma. All the strains have identical 16S rRNA genes and their closest relative species is Bradyrhizobium lablabi CCBAU 23086^T, with 99.41% identity with respect to the strain Ro19^T. Despite the closeness of the 16S rRNA genes, the housekeeping genes recA, atpD and glnII were divergent in Ro19^T and B. lablabi CCBAU 23086^T, with identity values of 95.71%, 93.75% and 93.11%, respectively. These differences were congruent with DNA–DNA hybridization analysis that revealed an average of 35% relatedness between the novel species and B. lablabi CCBAU 23086^T. Also, differential phenotypic characteristics of the new species were found with respect to the already described species of Bradyrhizobium. Based on the genotypic and phenotypic data obtained in this study, we propose to classify the group of strains isolated from R. sphaerocarpa and R. monosperma as a novel species named Bradyrhizobium retamae sp. nov. (type strain Ro19^T = LMG 27393^T = CECT 8261^T). The analysis of symbiotic genes revealed that some of these strains constitute a new symbiovar within genus Bradyrhizobium for which we propose the name “retamae”, that mainly contains nodulating strains isolated from Retama species in different continents.     

Roseibacterium beibuensis sp. nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

A novel aerobic, bacteriochlorophyll-containing bacteria strain JLT1202r^T was isolated from Beibu Gulf in the South China Sea. Cells were gram-negative, non-motile, and short-ovoid to rod-shaped with two narrower poles. Strain JLT1202r^T formed circular, opaque, wine-red colonies, and grew optimally at 3–4?% NaCl, pH 7.5–8.0 and 28–30?°C. The strain was catalase, oxidase, ONPG, gelatin, and Voges–Proskauer test positive. In vivo absorption spectrum of bacteriochlorophyll a presented two peaks at 800 and 877?nm. The predominant cellular fatty acid was C_18:1 ω7c and significant amounts of C_16:0, C_18:0, C_10:0 3-OH, C_16:0 2-OH, and 11-methyl C_18:1 ω7c were present. Strain JLT1202r^T contained Q-10 as the major respiratory quinone and the genomic DNA G+C content was 76.3?mol%. Phylogenetic analysis based on 16S rRNA gene sequences of various species with validly published names showed that strain JLT1202r^T fell within the genus Roseibacterium, family Rhodobacteraceae, sharing the highest similarity with Roseibacterium elongatum OCh 323^T (97.9?% similarity), followed by Dinoroseobacter shibae DFL 12^T (95.4?% similarity). The phylogenetic distance of pufM genes between strain JLT1202r^T and R. elongatum OCh 323^T was 9.4?%, suggesting that strain JLT1202r^T was distinct from the only strain of the genus Roseibacterium. Based on the variabilities of phylogenetic and phenotypic characteristics, strain JLT1202r^T stands for a novel species of the genus Roseibacterium and the name R. beibuensis sp. nov. is proposed with JLT1202r^T as the type strain (=JCM 18015^T?=?CGMCC 1.10994^T).     

Micromonospora violae sp. nov., isolated from a root of Viola philippica Car

A novel actinomycete, designated strain NEAU-zh8^T, was isolated from a root of Viola philippica Car collected in China and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-zh8^T belongs to the genus Micromonospora, being most closely related to Micromonospora chokoriensis 2-9(6)^T (99.9 %), Micromonospora saelicesensis Lupac 09^T (99.3 %) and Micromonospora lupini Lupac 14N^T (99.0 %). gyrB gene analysis also indicated that strain NEAU-zh8^T should be assigned to the genus Micromonospora. The cell-wall peptidoglycan consisted of meso-diaminopimelic acid and glycine. The major menaquinones were MK-10(H₄), MK-10(H₂) and MK-10(H₆). The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were iso-C_15:0, C_16:0 and C_17:0 10-methyl. A combination of DNA–DNA hybridization results and some physiological and biochemical properties indicated that strain NEAU-zh8^T could be readily distinguished from the closest phylogenetic relatives. Therefore, it is proposed that strain NEAU-zh8^T represents a novel Micromonospora species, for which the name Micromonospora violae sp. nov. is proposed. The type strain is NEAU-zh8^T (=CGMCC 4.7102^T=DSM 45888^T).