Characterization of plasmids from plant pathogenic pseudomonads

Physical characterization of the resident plasmids from Pseudomonas tabaci, P. angulata, and P. coronafaciens strains indicated that they harbored five different plasmid DNA species. Two ATCC strains of P. tabaci contained indistinguishable plasmids that we have named pJP1 and pJP2. An isolate of one of these strains contained a spontaneous variant of pJP1, pJP1¹, which contains an insertion of 3.9 Mdal. This 3.9-Mdal region did not hybridize to pJP1 indicating that the region was foreign DNA and not a duplication of a segment of DNA already present in pJP1. Another P. tabaci strain, PT27881, contained a third plasmid species, pJP27, which had few similarities to pJP1 or pJP2, but was indistinguishable from the plasmids from all three P. angulata strains. pJP27 and pJP1 had a small region, 8.8 Mdal, of sequence homology. The one strain of P. coronafaciens examined contained a plasmid, pJP50, which was different from the P. tabaci plasmids, but had the 8.8-Mdal region and additional regions of sequence homology with pJP1 and pJP27 as well as homology with a portion of the pJP1¹ insertion. A fourth strain of P. tabaci, PTBR-2, a pathogen on beans, contained plasmid pBW, the only plasmid that lacked detectable regions of homology with the other plasmids.     

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 Idiomarina xiamenensis Type Strain 10-D-4

Idiomarina xiamenensis strain 10-D-4^T was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4^T, which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 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.     

Thalassococcus lentus sp. nov., an alphaproteobacterium isolated from seawater of a seaweed farm

A Gram-negative, non-motile and rod- or ovoid-shaped bacterial strain, designated YCS-24^T, was isolated from seawater of a seaweed farm in the South Sea, South Korea. Strain YCS-24^T grew optimally at 25–28 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Strain YCS-24^T exhibited the highest 16S rRNA gene sequence similarity values of 97.5 and 97.1 % to the type strains of Thalassobius maritimus and Thalassococcus halodurans, respectively. The neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain YCS-24^T clustered with the type strain of T. halodurans. The DNA G+C content of strain YCS-24^T was 58.0 mol% and its DNA–DNA relatedness values with T. halodurans JCM 13833^T and T. maritimus GSW-M6^T were 17 ± 6.2 and 23 ± 9.2 %, respectively. The predominant ubiquinone found in strain YCS-24^T was Q-10 and the predominant fatty acid of strain YCS-24^T was C_18:1 ω7c. The major polar lipids of strain YCS-24^T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain YCS-24^T is distinguished from T. halodurans. On the basis of the data presented, strain YCS-24^T (= KCTC 32084^T = CCUG 62791^T) represents a novel species of the genus Thalassococcus, for which the name Thalassococcus lentus sp. nov. is proposed.     

Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity

Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04^T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04^T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794^T, Streptomyces laculatispora NRRL B-24909^T, and Streptomyces brevispora NRRL B-24910^T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04^T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04^T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04^T (=DSM 111306^T = CCM 9048^T) as the type strain.     

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.     

一株溶藻细菌对海洋原甲藻的溶藻效应

从深圳大鹏湾南澳赤潮爆发海域的表层海水中分离得到1株对海洋原甲藻(Prorocentrum micans)具有溶藻活性的海洋细菌,菌株编号为N10。利用液相感染法研究了该溶藻细菌的溶藻效果和溶藻作用方式。结果表明,菌株N10能使藻细胞失去运动活性,并膨胀变形,细胞膜内物质聚集于一端,藻细胞最终破裂死亡。菌悬液接种到藻液中的量越大,初始细菌密度越高,其溶藻效果越强。菌悬液以1∶10的体积比接种到藻液中时,藻细胞在24 h的死亡率为83%,至72 h全部溶解死亡;体积比为1∶20的藻细胞在24 h的死亡率为71%,之后藻细胞密度略有波动,120 h时死亡率达77%;而体积比为1∶100的藻细胞密度在前24 h有所下降,死亡率达39%,之后藻细胞密度又开始明显上升;对照组的藻细胞密度均呈明显上升趋势。菌悬液过滤液和高温加热处理后的菌悬液过滤液对海洋原甲藻均无溶藻活性,表明菌株N10的溶藻方式为直接溶藻。通过16S rRNA序列分析并与GenBank数据进行同源性检索,并结合细菌形态及生理生化特征,菌株N10隶属于黄杆菌科(Flavobacteriaceae)中的Muricauda sp.。     

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.     

Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey

A study of 91 isolates from fish farms in Turkey showed that isolates P7^T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7^T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16–88.29% and 38.10–38.20%, respectively. These data confirm that isolates P7^T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7^T as a type strain (=CCUG 74260^T= and CECT30107^T).     

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.     

Mechanism of cyanide and thiocyanate decomposition by an association of Pseudomonas putida and Pseudomonas stutzeri strains

The intermediate and terminal products of cyanide and thiocyanate decomposition by individual strains of the genus Pseudomonas, P. putida strain 21 and P. stutzeri strain 18, and by their association were analyzed. The activity of the enzymes of nitrogen and sulfur metabolism in these strains was compared with that of the collection strains P. putida VKM B-2187^T and P. stutzeri VKM B-975^T. Upon the introduction of CN⁻ and SCN⁻ into cell suspensions of strains 18 and 21 in phosphate buffer (pH 8.8), the production of NH ₄ ⁺ was observed. Due to the high rate of their utilization, NH₃, NH ₄ ⁺ , and CNO⁻ were absent from the culture liquids of P. putida strain 21 and P. stutzeri strain 18 grown with CN⁻ or SCN⁻. Both Pseudomonas strains decomposed SCN⁻ via cyanate production. The cyanase activity was 0.75 μmol/(min mg protein) for P. putida strain 21 and 1.26 μmol/(min mg protein) for P. stutzeri strain 18. The cyanase activity was present in the cells grown with SCN⁻ but absent in cells grown with NH ₄ ⁺ . Strain 21 of P. putida was a more active CN⁻ decomposer than strain 18 of P. stutzeri. Ammonium and CO₂ were the terminal nitrogen and carbon products of CN⁻ and SCN⁻ decomposition. The terminal sulfur products of SCN⁻ decomposition by P. stutzeri strain 18 and P. putida strain 21 were thiosulfate and tetrathionate, respectively. The strains utilized the toxic compounds in the anabolism only, as sources of nitrogen (CN⁻ and SCN⁻) and sulfur (SCN⁻). The pathway of thiocyanate decomposition by the association of bacteria of the genus Pseudomonas is proposed based on the results obtained. Original Russian Text ? N.V. Grigor’eva, T.F. Kondrat’eva, E.N. Krasil’nikova, G.I. Karavaiko, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 3, pp. 320–328.     

Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.

Peptoniphilus obesi strain ph1^T sp. nov., is the type strain of P. obesi sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. P. obesi strain ph1^T is a Gram-positive, obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,774,150 bp long genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA genes, including 5 rRNA genes.     

Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence,and proposal of Streptomyces pratensis sp. nov.

The Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) contains isolates obtained from grassy fields, as well as Streptomyces flavogriseus ATCC 33331 and strain CGMCC 4.1868. This latter strain was received as Streptomyces griseoplanus but was subsequently found to be mislabeled, and S. flavogriseus ATCC 33331 (=IAF-45-CD) was shown to be clearly distinct from the type strain S. flavogriseus ATCC 25452^T (=CGMCC 4.1884^T). In order to evaluate the taxonomic position of phylogroup pratensis further, sequences of the 16S rRNA gene and five protein-coding housekeeping genes (atpD, gyrB, recA, rpoB and trpB) were determined for six strains of the phylogroup and type strains of 19 related species, which were selected by a BLAST search based on the sequences of the phylogroup. The 16S rRNA gene sequences for the phylogroup were identical to those of eight species belonging to cluster I of the S. griseus clade. However, in all the individual protein-coding gene and MLSA phylogenies, the phylogroup strains without exception formed an obviously distinct cluster that could be equated with a new species status. The phylogenetic evidence for the new species assignment was also supported by corresponding DNA–DNA hybridization values and by phenotypic characteristics. It is therefore proposed that the phylogroup should be classified as Streptomyces pratensis sp. nov., and the type strain is ch24^T (=CGMCC 4.6829^T = NRRL B-24916^T).     

Arthrobacter pokkalii sp nov,a Novel Plant Associated Actinobacterium with Plant Beneficial Properties,Isolated from Saline Tolerant Pokkali Rice,Kerala, India

A novel yellow colony-forming bacterium, strain P3B162^T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162^T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162^T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137^T, Arthrobacter pascens DSM 20545^T and Arthrobacter liuii DSXY973^T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864^T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813^T and 88.7% to Arthrobacter pascens LMG 16255^T. However, the DNA-DNA hybridization values between strain P3B162^T, Arthrobacter globiformis LMG 3813^T, Arthrobacter pascens LMG 16255^T and Arthrobacter liuii JCM 19864^T was below 50%. In addition, the novel strain P3B162^T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the classification of strain P3B162^T as a novel Arthrobacter species and we propose Arthrobacter pokkalii sp.nov.as its name. The type strain is P3B162^T (= KCTC 29498^T = MTCC 12358^T).     

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.     

A multiple plasmid-containing Escherichia coli strain: convenient source of size reference plasmid molecules.

A strain of Escherichia coli is described that contains eight plasmid species ranging in size from 1.36 × 10⁶ to 35.8 × 10⁶ daltons. This strain can be employed as a single source of covalently closed circular deoxyribonucleic acid molecules of different sizes for use as references in agarose gel electrophoretic analysis.     

Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.

Clostridium jeddahense strain JCD^T (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m²). Clostridium jeddahense strain JCD^T is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462 protein-coding and 53 RNA genes, including 4 rRNA genes.     

Paenibacillus hordei sp. nov., isolated from naked barley in Korea

A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24^T, was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24^T was observed at 4–40 °C (optimum: 35–37 °C) and at pH 5.0–9.0 (optimum: pH 6.0–7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G + C content: 53.5 mol %; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB_15:0 and CB_16:0B) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24^T belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24^T was most closely related to Paenibacillus hunanensis FeL05^T and Paenibacillus illinoisensis NRRL NRS-1356^T with similarities of 94.64 and 94.54 %, respectively. On the basis of phenotypic and molecular properties, strain RH-N24^T represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24^T (=KACC 15511^T = JCM 17570^T).