July 7, 2019  |  

Complete genome sequence of the petroleum-emulsifying bacterium Pseudomonas stutzeri SLG510A3-8.

Pseudomonas stutzeri SLG510A3-8, isolated from oil-contaminated soil in Shengli Oilfield, China, has the potential to be applied for microbial enhanced oil recovery. Here, we reported the complete genome sequence of this bacterium. It has a 4,650,155bp circular chromosome encoding 4450 genes, and the genome consists of genes that are involved in denitrification, chemotaxis, benzoate degradation, molecule transportation, and other functions. The genome contains a complete set of genes for type I secretion system in comparison with sequences of other P. stutzeri strains. Copyright © 2015 Elsevier B.V. All rights reserved.


July 7, 2019  |  

Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification.

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1(T) is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1(T) was sequenced as part of the DOE Joint Genome Institute Community Science Program.


July 7, 2019  |  

Genome sequence of “Candidatus Thioglobus autotrophica” Strain EF1, a chemoautotroph from the SUP05 clade of marine gammaproteobacteria.

Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we announce the complete genome sequence of “Candidatus Thioglobus autotrophica” strain EF1, the first cultured chemoautotrophic representative from the SUP05 clade. Copyright © 2015 Shah and Morris.


July 7, 2019  |  

Complete genome sequence of Bradyrhizobium japonicum J5, isolated from a soybean nodule in Hokkaido, Japan.

Soybean bradyrhizobia form root nodules on soybean plants and symbiotically fix N2 Strain J5 is phylogenetically far from well-known representatives within the Bradyrhizobium japonicum linage. The complete genome showed the largest single chromosomal (10.1 Mb) and symbiosis island (998 kb) among complete genomes of soybean bradyrhizobia. Copyright © 2017 Kanehara and Minamisawa.


July 7, 2019  |  

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.


July 7, 2019  |  

Complete genome sequence of the thermophilic bacterium Geobacillus subterraneus KCTC 3922(T) as a potential denitrifier.

Denitrification is a crucial process for the global nitrogen cycle through the reduction of nitrates by heterotrophic bacteria. Denitrifying microorganisms play an important role in eliminating fixed nitrogen pollutants from the ecosystem, concomitant with N2O emission. Although many microbial denitrifiers have been identified, little is known about the denitrifying ability of the genus Geobacillus. Here, we report the first complete genome sequences of Geobacillus subterraneus KCTC 3922(T), isolated from Liaohe oil field in China, and G. thermodenitrificans KCTC 3902(T). The strain KCTC 3922(T) contains a complete set of genes involved in denitrification, cofactor biogenesis, and transport systems, which is consistent with a denitrifying activity. On the other hand, G. thermodenitrificans KCTC 3902(T) exhibited no denitrifying activity probably due to the lack of molybdnumtransferase (moeA) and nitrite transporter (nirC) genes. Therefore, comparative genome analysis of Geobacillus strains highlights the potential impact on treatment of nitrate-contaminated environments. Copyright © 2017 Elsevier B.V. All rights reserved.


July 7, 2019  |  

Complete genome sequence of a denitrifying bacterium, Pseudomonas sp. CC6-YY-74, isolated from Arctic Ocean sediment

Pseudomonas sp. CC6-YY-74, a psychrotrophic, denitrifying bacterium isolated from Arctic Ocean sediment, uses NO3- or NH4+ as the sole nitrogen source to grow at low temperatures. Here we described the complete genome of Pseudomonas sp. CC6-YY-74. The genome has one circular chromosome of 5,040,792 bp (61.73 mol% G + C content), consisting of 4747 coding genes, 68 tRNA genes, as well as six rRNA operons as 16S-23S-5S rRNA. According to the annotation results, strain CC6-YY-74 encodes 52 proteins related to nitrogen metabolism, including a complete denitrifying pathway, and more than 20 kinds of hydrolytic enzymes.


July 7, 2019  |  

High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.

Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409(T) together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.


July 7, 2019  |  

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum (fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.


July 7, 2019  |  

High-quality draft genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, isolates from Tengchong, China.

The draft genomes of Thermus  tengchongensis YIM 77401 and T. caliditerrae YIM 77777 are 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes, respectively. Gene content and growth experiments demonstrate broad metabolic capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation, incomplete denitrification, and polysulfide reduction. Copyright © 2016 Mefferd et al.


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