Project description:Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its' potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.
Project description:BACKGROUND:Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. METHODS:We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions. RESULTS:The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses. CONCLUSIONS:This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).
Project description:Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.
Project description:Sphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA.The TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100%) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided.Sphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level.
Project description:We report here the draft genome sequence of Sphingomonas ginsengisoli KCTC 12630T. The draft genome has a size of 3,045,889?bp and a G+C content of 67.1%. The availability of the genome sequence will provide a better understanding of strain KCTC 12630T and the genus Sphingomonas.
Project description:Here, we report the whole-genome sequence of Sphingomonas sp. strain FARSPH, isolated from an insect cell line as a contaminant. FARSPH shared high identity with Sphingomonas melonis and Sphingomonas aquatilis strains. Due to this finding, we recommend taking this genus into consideration for cell culture quality control.
Project description:Members of the Sphingomonas genus are often isolated from petroleum-contaminated soils due to their unique abilities to degrade polycyclic aromatic hydrocarbons (PAHs), which are important for in situ bioremediation. In this study, a combined phenotypic and genotypic approach using streptomycin-containing medium and Sphingomonas-specific PCR was developed to isolate and identify culturable Sphingomonas strains present in petroleum-contaminated soils in the Shenfu wastewater irrigation zone. Of the 15 soil samples examined, 12 soils yielded yellow streptomycin-resistant colonies. The largest number of yellow colony-forming units (CFUs) could reach 10(5)CFUsg(-1)soil. The number of yellow CFUs had a significant positive correlation (p<0.05) with the ratio of PAHs to total petroleum hydrocarbons (TPH), indicating that Sphingomonas may play a key role in degrading the PAH fraction of the petroleum contaminants at this site. Sixty yellow colonies were selected randomly and analyzed by colony PCR using Sphingomonas-specific primers, out of which 48 isolates had PCR-positive signals. The 48 positive amplicons generated 8 distinct restriction fragment length polymorphism (RFLP) patterns, and 7 out of 8 phylotypes were identified as Sphingomonas by 16S rRNA gene sequencing of the representative strains. Within these 7 Sphingomonas strains, 6 strains were capable of using fluorene as the sole carbon source, while 2 strains were phenanthrene-degrading Sphingomonas. To the best of our knowledge, this is the first report to evaluate the relationship between PAHs contamination levels and culturable Sphingomonas in environmental samples.
Project description:As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the α-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future.
Project description:Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164T), Pseudomonas mosselii (DSM 17497T), Pseudomonas plecoglossicida (DSM 15088T), Pseudomonas taiwanensis (DSM 21245T) and Pseudomonas vranovensis (DSM 16006T). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species.