Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil

Shinella sedimenti sp. nov., isolated from sediment of Zhairuo Island located in the East China Sea

A Gram-negative, rod-shaped and aerobic bacterial strain B3.7T, was isolated from the sediment of Zhairuo Island, Zhoushan city, Zhejiang Province, PR China. Maximum growth of strain B3.7T was observed at 30 °C when cultured in a medium containing 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain B3.7T belonged to the genus Shinella; it showed the highest sequence similarity of 98.47 % to Shinella kummerowiae CCBAU 25048T. The average nucleotide identity and digital DNA-DNA hybridization values between strain B3.7T and its reference strains were 82.9-84.2 % and 26.1-27.3 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was Q-10 and the predominant cellular fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C18 : 1  ω7c 11-methyl and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two unidentified aminolipids. Collectively, strain B3.7T can be considered to represent a novel species, for which the name Shinella sedimenti sp. nov. is proposed. The type strain is B3.7T (=MCCC 1K07163T=LMG 32559T).

Shinella lacus sp. nov., a novel microcystin-degrading alphaproteobacterium containing the bla carbapenemase gene

A Gram-stain-negative, rod-shaped, microcystin-degrading bacterium, designated as CPCC 100929T, was isolated from a fresh water reservoir in Sichuan Province, PR China. This isolate grew well at 4–37 °C and pH 6.0–8.0, with optimal growth at 28–32 °C and pH 7.0, respectively. The major cellular fatty acids were C18:1 ω7c/C18:1 ω6c, C16:0, C18:1 ω7c 11-methyl and C19:0 cyclo ω8c. The predominant respiratory quinone was Q-10. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine were detected in the polar lipids extraction. The 16S rRNA gene sequence of strain CPCC 100929T was closely related to those of members of the genus Shinella , with the highest similarity of 98.6 % to Shinella zoogloeoides DSM 287T and 97.4–98.4 % with other identified Shinella members. In the phylogenetic trees based on 16S rRNA gene sequences and the core-genes analysis, strain CPCC 100929T was included within the clade of the genus Shinella . The values of average nucleotide identity (81.4–86.7 %) and digital DNA–DNA hybridization (25.4–44.6 %) between strain CPCC 100929T and other Shinella species were all below the thresholds for bacterial species delineation, respectively. The genomic DNA G+C content of strain CPCC 100929T was 63.6 %. The genomic sequence analysis indicated that this species contained genes encoding peroxidase, bla carbapenemase and the key enzyme for microcystin bio degradation, as well as rich carbohydrate-active enzyme coding genes, which might endow the micro-organism with properties to adapt to diverse environments. Based on its phenotypic and genetic properties, we propose that strain CPCC 100929T (=T1A350T=KCTC 72957T) is the type strain of a novel species with the name Shinella lacus sp. nov.

Draft genome sequence data and analysis of Shinella sp. strain JR1-6 isolated from nitrate- and radionuclide-contaminated groundwater in Russia

Shinella sp. strain JR1-6 is a Gram-negative, facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium isolated from radionuclide- and nitrate-contaminated groundwater. This bacterium reduces nitrate to N2. Strain JR1-6 has potential for removal of nitrate contamination, which is the main reason for the interest in sequencing its genome. Here, we present a set of features of Shinella sp. strain JR1-6, together with the description of its genomic sequencing and annotation. The draft genome of strain JR1-6 has a size of ∼7.09 Mb and contains 6,945 genes, including 62 RNA genes. In the genome of strain JR1-6, the genes were revealed encoding nitrate reduction to N2, as well as the genes associated with metal resistance, showing its adaptation to the conditions of the environment and possible role in nitrate removal from contaminated groundwater. The draft genome sequence of Shinella sp. strain JR1-6 is available at DDBJ/EMBL/GenBank under the accession no. SHMI00000000.