Abstract:
:Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism. The genomic characteristics could provide information for further study of oil-degrading microbes for recovery of crude oil polluted environment.
journal_name
Stand Genomic Scijournal_title
Standards in genomic sciencesauthors
Chang S,Zhang G,Chen X,Long H,Wang Y,Chen T,Liu Gdoi
10.1186/s40793-017-0249-zsubject
Has Abstractpub_date
2017-07-27 00:00:00pages
45issn
1944-3277pii
249journal_volume
12pub_type
abstract::The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyroba...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0243-5
更新日期:2017-05-10 00:00:00
abstract::Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease in desert tortoises, Gopherus agassizii. We sequenced the genome of M. testudineum BH29T (ATCC 700618T = MCCM 03231T), isolated from the upper respiratory tract of a Mojave desert tortoise with upper respiratory tract disease...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-018-0309-z
更新日期:2018-04-11 00:00:00
abstract::The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a publ...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2205004
更新日期:2011-12-31 00:00:00
abstract::Strain M27-SA2 was isolated from the deep-sea salt-saturated anoxic lake Medee, which represents one of the most hostile extreme environments on our planet. On the basis of physiological studies and phylogenetic positioning this extremely halophilic euryarchaeon belongs to a novel genus 'Halanaeroarchaeum' within the ...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0155-9
更新日期:2016-05-13 00:00:00
abstract::Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T)) is a marine bacterium belonging to the Roseobacter group of the family Rhodobacteraceae within the class Alphaproteobacteria. The strain was isolated from sea water surrounding cultivated oysters 2-3 miles off the Mediterrane...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0141-2
更新日期:2016-02-29 00:00:00
abstract::Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draf...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.4998989
更新日期:2014-03-15 00:00:00
abstract::Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogen...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.831993
更新日期:2010-06-15 00:00:00
abstract::A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2705996
更新日期:2012-05-25 00:00:00
abstract::Thioalkalivibrio thiocyanoxidans strain ARh 2(T) is a sulfur-oxidizing bacterium isolated from haloalkaline soda lakes. It is a motile, Gram-negative member of the Gammaproteobacteria. Remarkable properties include the ability to grow on thiocyanate as the sole energy, sulfur and nitrogen source, and the capability of...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-015-0078-x
更新日期:2015-10-26 00:00:00
abstract::Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0263-1
更新日期:2017-08-31 00:00:00
abstract::Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain,...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1463589
更新日期:2011-04-29 00:00:00
abstract::Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained fro...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0217-z
更新日期:2017-01-05 00:00:00
abstract::Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is exce...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0298-3
更新日期:2017-12-13 00:00:00
abstract::Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very few M. loti strains able to form effective nodules on the agriculturally important legume Lotus pedunculatus...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-9-7
更新日期:2014-12-08 00:00:00
abstract::Dyadobacter tibetensis Y620-1 is the type strain of the species Dyadobacter tibetensis, isolated from ice at a depth of 59 m from a high altitude glacier in China (5670 m above sea level). It is psychrotolerant with growth temperature ranges of 4 to 35°C. Here we describe the features of this organism, together with t...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.5649756
更新日期:2014-03-15 00:00:00
abstract::We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 p...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0098-6
更新日期:2015-11-20 00:00:00
abstract::The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain 10.1601/nm.1463 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The gen...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0283-x
更新日期:2017-12-05 00:00:00
abstract::Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0194-2
更新日期:2016-09-10 00:00:00
abstract::Sphingomonas paucimobilis strain LCT-SP1 is a glucose-nonfermenting Gram-negative, chemoheterotrophic, strictly aerobic bacterium. The major feature of strain LCT-SP1, isolated from the Chinese spacecraft Shenzhou X, together with the genome draft and annotation are described in this paper. The total size of strain LC...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0136-z
更新日期:2016-02-24 00:00:00
abstract::Methanoculleus bourgensis strain MAB1 has been identified as the hydrogenotrophic partner of mesophilic acetate-oxidising bacteria, a syntrophic relationship operating close to the thermodynamic equilibrium and of considerable importance in ammonia-rich engineered biogas processes. Methanoculleus bourgensis strain MAB...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0199-x
更新日期:2016-10-12 00:00:00
abstract::Mucilaginibacter pedocola TBZ30T (= CCTCC AB 2015301T = KCTC 42833T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn2+ and Cd2+ during cultivation. In addition, strain...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-018-0337-8
更新日期:2018-11-28 00:00:00
abstract::The Roseophages, a group of marine viruses that uniquely infect the Roseobacter clade of bacteria, play a significant role in marine ecosystems. Here we present a complete genomic sequence of an N4 phage 'vB_DshP-R1', which infects Dinoroseobacter shibae DFL12, together with its structural and genomic features. vB_Dsh...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-6
更新日期:2015-01-21 00:00:00
abstract::Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by th...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1042812
更新日期:2010-07-29 00:00:00
abstract::Natrinema altunense strain AJ2T, a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembl...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0237-3
更新日期:2017-03-01 00:00:00
abstract::A strain of a hyperthermophilic filamentous archaeon was isolated from a sample of Kamchatka hot spring sediment. Isolate 1807-2 grew optimally at 85 °C, pH 6.0-6.5, the parameters being close to those at the sampling site. 16S rRNA gene sequence analysis placed the novel isolate in the crenarchaeal genus Thermofilum;...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-015-0105-y
更新日期:2015-12-09 00:00:00
abstract::Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and ann...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0052-7
更新日期:2015-08-13 00:00:00
abstract::Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolat...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.5429581
更新日期:2014-03-15 00:00:00
abstract::Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the genus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary producer in the temperature range of 45-75 °C (o...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2465574
更新日期:2011-12-31 00:00:00
abstract::This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, hig...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2876184
更新日期:2012-05-25 00:00:00
abstract::The tenacious association between strains of the heterotrophic alphaproteobacterial genus Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron oxidizing mixed culture derived from a pilot plant fo...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0040-y
更新日期:2015-08-19 00:00:00