Comparative genomics of Sphingopyxis spp. unravelled functional attributes

Verma, Helianthous; Dhingra, Gauri; Sharma, Monika; Gupta, Vipin; Negi, Ram Krishan; Singh, Yogendra; Lal, Rup

doi:10.1016/j.ygeno.2019.11.008

Cited by 24 publications

(13 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In a study, a network analysis of degrading protein obtained from the genome of Sphingopyxis strains deciphers interaction with the core content ( Verma et al, 2020 ). Although carboxylesterase and aldehyde dehydrogenase genes from RNA-seq data were mapped for interaction with a relative set of hydrolytic proteins, the 13 genes of carboxylesterase were mapped, and interactors of catabolic and central metabolism were identified with both sets of genes.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-Guided Insights Into Plastic Degradation by the Marine Bacterium

et al. 2021

View full text Add to dashboard Cite

Polyethylene terephthalate (PET) is a common single-use plastic that accumulated in the environment because of its non-degradable characteristics. In recent years, microbes from different environments were found to degrade plastics and suggested their capability to degrade plastics under varying environmental conditions. However, complete degradation of plastics is still a void for large-scale implications using microbes because of the lack of knowledge about genes and pathways intricate in the biodegradation process. In the present study, the growth and adherence of marine Bacillus species AIIW2 on PET surface instigating structural deterioration were confirmed through weight loss and hydrophobicity reduction, as well as analyzing the change in bond indexes. The genome-wide comparative transcriptomic analysis of strain AIIW2 was completed to reveal the genes during PET utilization. The expression level of mRNA in the strain AIIW2 was indexed based on the log-fold change between the presence and absence of PET in the culture medium. The genes represent carbon metabolism, and the cell transport system was up-regulated in cells growing with PET, whereas sporulation genes expressed highly in the absence of PET. This indicates that the strain AIIW2 hydrolyzes PET and assimilated via cellular carbon metabolism. A protein–protein interaction network was built to obtain the interaction between genes during PET utilization. The genes traced to degrade PET were confirmed by detecting the hydrolytic product of PET, and genes were cloned to improve PET utilization by microbial system as an eco-friendly solution.

show abstract

Section: Discussionmentioning

confidence: 99%

Transcriptome-Guided Insights Into Plastic Degradation by the Marine Bacterium

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The complete genome of Sphingopyxis strain OPL5 comprised of one contig of 4.67 Mbp and had a GC content of 65.89% ( Table 1 ). The genome size and GC content are comparable with those of other Sphingopyxis species, the genomes of which vary considerably within the broad range of 3.0–6.0 Mbp [ 52 ]. Specifically, the genome of the closest sequenced relative of strain OPL5, Sphingopyxis QXT-31 (see Figure 2 ), was 4.3 Mbp and had a GC content of 66.5%.…”

Section: Resultsmentioning

confidence: 99%

Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves

et al. 2020

View full text Add to dashboard Cite

The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.

show abstract

“…Also, Sphingopyxis (alpha-Proteobacteria class), which was isolated from the groundwater, is a genus that comprises versatile bacteria that are present in a wide variety of environments, including seawater, wastewater treatment plants, and hydrocarbon-contaminated soils. These bacteria harbor genes that code for resistance against arsenic, metals and many efflux pumps, and some species can also use nitrate as a terminal electron acceptor in anaerobic respiration (Verma et al, 2020). Microbacterium is a genus of Actinobacteria that includes species with a high capacity for interaction with and resistance to arsenic and other metals (Kaushik et al, 2012).…”

Section: Bacterial Identificationmentioning

confidence: 99%

Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic

et al. 2021

View full text Add to dashboard Cite

Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.

show abstract

Comparative genomics of Sphingopyxis spp. unravelled functional attributes

Cited by 24 publications

References 89 publications

Transcriptome-Guided Insights Into Plastic Degradation by the Marine Bacterium

Transcriptome-Guided Insights Into Plastic Degradation by the Marine Bacterium

Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves

Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic

Contact Info

Product

Resources

About