Baojiang Wang

A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp. P1

A pyrene-degrading bacterial consortium was obtained from deep-sea sediments of the Pacific Ocean. The consortium degraded many kinds of polycyclic aromatic hydrocarbons (PAHs), including naphthalene, phenanthrene, pyrene, acenaphthene, fluorene, anthracene, fluoranthene, 2-methylnaphthalene and 2,6-dimethylnaphthalene, but it did not grow with chrysene and benzo[alpha]pyrene. With methods of plate cultivation and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), 72 bacteria belonging to 22 genera were detected from this consortium. Among the detected bacteria, the following genera frequently occurred: Flavobacterium, Cycloclasticus, Novosphingobium, Halomonas, Achromobacter, Roseovarius and Alcanivorax. The first two genera showed the strongest bands in denaturing gradient gel electrophoresis (DGGE) profiles and appeared in all PAH treatments. By now, only one isolate designated P1 was confirmed to be a pyrene degrader. It was identified to be Cycloclasticus spirillensus (100%). Although P1 can degrade pyrene independently, other bacteria, such as Novosphingobium sp. (Band 14), Halomonas sp. (Band 16) and an unidentified bacterium (Band 35), were involved in pyrene degradation in some way; they persist in the consortium in the test of dilution to extinction if only the consortium was motivated with pyrene. However, the secondary most important member Flavobacterium sp. evaded from the community at high dilutions. As a key member of the consortium, P1 distinguished itself by both cell morphology and carbon source range among the isolates of this genus. Based on intermediate analyses of pyrene degradation, P1 was supposed to take an upper pathway different from that previously reported. Together with the results of obtained genes from P1 homology with those responsible for naphthalene degradation, its degradation to pyrene is supposed to adopt another set of genes unique to presently detected. Summarily, an efficient pyrene-degrading consortium was obtained from the Pacific Ocean sediment, in which Cycloclasticus bacterium played a key role. This is the first report to exploit the diversity of pyrene-degrading bacteria in oceanic environments.

Roseovarius pacificus sp. nov., isolated from deep-sea sediment.

An aerobic, Gram-negative, ovoid to rod-shaped bacterial isolate, strain 81-2(T), was isolated from deep-sea sediment of the Western Pacific Ocean. Strain 81-2(T) was motile, formed faint pink colonies, and was catalase-positive, weakly positive for oxidase and required NaCl for growth. It did not synthesize bacteriochlorophyll a and its DNA G+C content was 62.3 mol%. The 16S rRNA gene sequence of strain 81-2(T) indicated that it was a member of the Roseobacter clade of the class Alphaproteobacteria, with moderate bootstrap support for inclusion in the genus Roseovarius. Its closest phylogenetic neighbour was the type strain of Roseovarius nubinhibens, which shared 95.8 % 16S rRNA gene sequence similarity; strain 81-2(T) was <95.0 % similar to strains of other related species and genera. Phenotypic, chemotaxonomic and phylogenetic data support assignment of this strain to the genus Roseovarius as a representative of a novel species. The name Roseovarius pacificus sp. nov. is proposed, with strain 81-2(T) (=MCCC 1A00293(T)=CGMCC 1.7083(T)=LMG 24575(T)) as the type strain.

Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium

A taxonomic study was carried out on a Gram-negative, rod-shaped, non-motile, halophilic bacterium, designated strain W11-2B(T), which was isolated from a pyrene-degrading consortium that was enriched from sediment from the Pacific Ocean. Growth was observed at salinities of 0.5-10 % and at temperatures of 10-41 degrees C. Strain W11-2B(T) was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence comparisons showed that strain W11-2B(T) was related most closely to Oceanicola nanhaiensis SS011B1-20(T) (95.8 % similarity) and Oceanicola batsensis HTCC2597(T) (95.7 %); levels of 16S rRNA gene sequence similarity between strain W11-2B(T) and the type strains of other species tested were below 95.2 %. The dominant fatty acids of strain W11-2B(T) were C(18 : 1)omega7c (32.1 % of the total), C(19 : 0) cyclo (20.9 %), C(18 : 1)omega7c 11-methyl (19.5 %), C(18 : 0) (7.3 %), C(17 : 0) (6.6 %) and C(16 : 0) (3.8 %). The G+C content of the chromosomal DNA was 64.6 mol%. The above data were in good agreement with those of members of the genus Oceanicola. Based on morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain W11-2B(T) is considered to represent a novel species of the genus Oceanicola, for which the name Oceanicola pacificus sp. nov. is proposed. The type strain is W11-2B(T) (=CCTCC AB 208224(T)=LMG 24619(T)=MCCC 1A01034(T)).

Roseovarius nanhaiticus sp. nov., a member of the Roseobacter clade isolated from marine sediment.

An aerobic, Gram-staining-negative, rod or ovoid-shaped bacterial isolate, strain NH52J(T), was isolated from a sandy sediment sample from the South China Sea. Strain NH52J(T) exhibited tumbling motility, formed beige or faint pink colonies, gave a positive reaction in tests for catalase and oxidase and required NaCl for growth. Optimal growth was observed at pH 7.8-9.3, at 30 degrees C and in the presence of 2.0-4.0 % (w/v) NaCl. The novel strain did not synthesize bacteriochlorophyll a, and the DNA G+C content was 62 %. The major fatty acids were C(18 : 1)omega7c, C(16 : 0) and C(18 : 1)omega7c 11-methyl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52J(T) was affiliated to the genus Roseovarius of the class Alphaproteobacteria. Roseovarius pacificus and Roseovarius aestuarii were the most closely related recognized species to strain NH52J(T) with 16S rRNA gene sequence similarity values of 95.0 and 95.7 %, respectively. Sequence similarity values between strain NH52J(T) and other phylogenetically related species were all below 95.0 %. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain NH52J(T) is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius nanhaiticus sp. nov. is proposed. The type strain is NH52J(T) (=LMG 24840(T)=CCTCC AB 208317(T)=MCCC 1A03543(T)).

Leisingera nanhaiensis sp. nov., isolated from marine sediment

An aerobic, Gram-staining-negative, motile, rod-shaped bacterium, strain NH52F(T), was isolated from a sandy sediment sample taken from the South China Sea. On M2 agar medium (a complex medium), colonies were beige in colour. The isolate showed highest 16S rRNA gene sequence similarities to members of the genera Leisingera (96.7 % similarity), Phaeobacter (95.4-96.0 %) and Marinovum (94.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NH52F(T) formed a distinct cluster with Leisingera methylohalidivorans MB2(T) and Leisingera aquimarina LMG 24366(T). Optimal growth was observed at pH 7.0-8.5 and 25 degrees C and the new isolate required the presence of 1-4 % (w/v) NaCl. The major fatty acids were C(18 : 1)omega7c, C(16 : 0) 2-OH, C(10 : 0) 3-OH, C(12 : 0) 3-OH, C(16 : 0) and 11-methyl C(18 : 1)omega7c. The DNA G+C content was 60.5 mol%. The phylogenetic and chemotaxonomic characteristics of strain NH52F(T) were similar to those of the genus Leisingera. However, the differences in phenotypic properties and the 16S rRNA gene similarity values demonstrated that the new isolate differed from recognized species of the genus Leisingera. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Leisingera, for which the name Leisingera nanhaiensis sp. nov. is proposed. The type strain is NH52F(T) (=LMG 24841(T)=CCTCC AB 208316(T)=MCCC 1A04178(T)).

Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1

Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation.

Nitratireductor pacificus sp. nov., isolated from a pyrene-degrading consortium.

Strain pht-3B(T) was isolated from a pyrene-degrading consortium of an enriched sediment from the Pacific Ocean, collected during the screening of polycyclic aromatic hydrocarbon-degrading bacteria. Cells were Gram-negative, short rods that were motile by means of flagella. Growth was observed at 0-7 % NaCl and 10-41 °C. The isolate was able to reduce nitrate to nitrite, but not to nitrogen. 16S rRNA gene sequence comparisons showed that strain pht-3B(T) was most closely related to Nitratireductor aquibiodomus NL21(T) (97.3 % 16S rRNA gene sequence similarity), N. indicus C115(T) (97.1 %), N. basaltis J3(T) (96.8 %) and N. kimnyeongensis KY 101(T) (96.7 %). DNA-DNA hybridization between strain pht-3B(T) and these reference strains revealed 55, 54, 28 and 42 % DNA-DNA relatedness, respectively. The dominant fatty acids were C(19 : 0)ω8c cyclo (22.6 %) and summed feature 8 (consisting of C(18 : 1)ω7c and/or C(18 : 1)ω6c; 60.4 %). The G+C content of the chromosomal DNA was 63 mol%. These characteristics were in good agreement with those of members of the genus Nitratireductor. According to cell morphology, physiology, fatty acid composition, 16S rRNA gene sequence analysis and DNA-DNA relatedness, the isolate belonged to the genus Nitratireductor but could be readily distinguished from recognized species of the genus. Therefore a novel species is proposed to accommodate strain pht-3B(T), for which the name Nitratireductor pacificus sp. nov. is proposed. The type strain is pht-3B(T) ( = CCTCC AB 209302(T) = LMG 25541(T) = MCCC 1A01024(T)).

Arenibacter nanhaiticus sp. nov., isolated from marine sediment of the South China Sea.

An aerobic, Gram-stain-negative, rod-shaped bacterial isolate, strain NH36A(T), was isolated from a sandy sediment sample from the South China Sea. Colonies of the isolate were dark orange on M2 agar. Optimal growth was observed at pH 7.0-8.5, 30 degrees C and in the presence of 0.5-4.0 % (w/v) NaCl. The major fatty acids were C(15 : 0), iso-C(15 : 0), anteiso-C(15 : 0), iso-C(15 : 1), iso-C(15 : 0) 3-OH, iso-C(17 : 0) 3-OH and summed feature 3 (comprising iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). The DNA G+C content was 38.9 mol%. 16S rRNA gene sequence analysis revealed that strain NH36A(T) was most closely related to members of the genus Arenibacter, exhibiting 94.3-96.2 % sequence similarity to the type strains of Arenibacter species. On the basis of phenotypic, chemotaxonomic and phylogenetic data, this organism should be classified as a representative of a novel species in the genus Arenibacter. The name Arenibacter nanhaiticus sp. nov. is proposed and the type strain is NH36A(T) (=LMG 24842(T)=CCTCC AB 208315(T)=MCCC 1A04137(T)).

Bowmanella pacifica sp. nov., isolated from a pyrene-degrading consortium

A taxonomic study was carried out on a strain, designated W3-3A(T), which was isolated from a pyrene-degrading consortium, enriched from sediment of the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W3-3A(T) belonged to the genus Bowmanella, with the highest sequence similarity (99.0 %) with Bowmanella denitrificans BD1(T), whereas sequence similarities with other species were less than 93 %. The nucleotide sequence similarity of both gyrB and rpoD genes of strain W3-3A(T) and B. denitrificans BD1(T) was 81.1 %. However, the protein sequence similarities of the gyrB and rpoD genes of strain W3-3A(T) and B. denitrificans BD1(T) were 96.1 % and 91.0 %, respectively. Phylogenetic trees based on these housekeeping genes showed that strain W3-3A(T) and B. denitrificans BD1(T) formed a distinct lineage in the Gammaproteobacteria. The DNA-DNA hybridization value between strain W3-3A(T) and B. denitrificans BD1(T) was 43 %. Strain W3-3A(T) could also be differentiated from B. denitrificans BD1(T) based on the repetitive extragenic palindromic DNA-PCR fingerprint. The G+C content of the chromosomal DNA of strain W3-3A(T) was 49 mol%. The combined genotypic and phenotypic data showed that strain W3-3A(T) represents a novel species of the genus Bowmanella, for which the name Bowmanella pacifica sp. nov. is proposed, with the type strain W3-3A(T) (=CGMCC 1.7086(T)=LMG 24568(T)=MCCC 1A01018(T)).

Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China

A Gram-negative, ovoid rod-shaped bacterium that lacked bacteriochlorophyll a, designated strain Y-2(T), was isolated from seawater of the Taiwan Strait, China. The strain was oxidase- and catalase-positive, and reduced nitrate to nitrite. Optimal growth occurred at around pH 7.0 and 25 degrees C in the presence of 1-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y-2(T) belonged to the class Alphaproteobacteria and formed a coherent cluster with Donghicola eburneus SW-277(T) (96.2 % sequence similarity). The major whole-cell fatty acid was C(18 : 1)omega7c (75.42 %). Other characteristic fatty acids were C(18 : 0) (9.16 %) and C(16 : 0) (7.32 %). The DNA G+C content of strain Y-2(T) was 62.4 mol%. Therefore, based on phenotypic properties, phylogeny and genomic data, strain Y-2(T) should be placed in the genus Donghicola as representing a novel species, for which the name Donghicola xiamenensis sp. nov. is proposed. The type strain is Y-2(T) (=MCCC 1A00107(T)=LMG 24574(T)=CGMCC 1.7081(T)).