Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
PLoS One
2019 Apr 18;144:e0215396. doi: 10.1371/journal.pone.0215396.
Show Gene links
Show Anatomy links
Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting.
Silva NM
,
de Oliveira AMSA
,
Pegorin S
,
Giusti CE
,
Ferrari VB
,
Barbosa D
,
Martins LF
,
Morais C
,
Setubal JC
,
Vasconcellos SP
,
da Silva AM
,
de Oliveira JCF
,
Pascon RC
,
Viana-Niero C
.
???displayArticle.abstract???
Hydrocarbons are important environmental pollutants, and the isolation and characterization of new microorganisms with the ability to degrade these compounds are important for effective biodegradation. In this work we isolated and characterized several bacterial isolates from compost, a substrate rich in microbial diversity. The isolates were obtained from selective culture medium containing n-hexadecane, aiming to recover alkane-degraders. Six isolates identified as Gordonia by MALDI-TOF and 16S rRNA sequencing had the ability to degrade n-hexadecane in three days. Two isolates were selected for genomic and functional characterization, Gordonia paraffinivorans (MTZ052) and Gordonia sihwensis (MTZ096). The CG-MS results showed distinct n-hexadecane degradation rates for MTZ052 and MTZ096 (86% and 100% respectively). The genome sequence showed that MTZ052 encodes only one alkane degrading gene cluster, the CYP153 system, while MTZ096 harbors both the Alkane Hydroxylase (AH) and the CYP153 systems. qPCR showed that both gene clusters are induced by the presence of n-hexadecane in the growth medium, suggesting that G. paraffinivorans and G. sihwensis use these systems for degradation. Altogether, our results indicate that these Gordonia isolates have a good potential for biotransformation of hydrocarbons.
???displayArticle.pubmedLink???
30998736
???displayArticle.pmcLink???PMC6472744 ???displayArticle.link???PLoS One
Fig 1. Phylogenetic analysis of MTZ052 and MTZ096.Maximum likelihood-based inference phylogenetic trees were reconstructed based on 57 gene families shared by the indicated bacterial species. Millisia brevis NBRC 105863 and Skermania piniformis NBRC 15059 were used as an outgroup. Branch bootstrap values are at least 80%, unless otherwise indicated.
Fig 2. Schematic comparison of the two main gene clusters for alkane degradation in MTZ052 and MTZ096.(A) Alkane hydroxylase cluster genes: alkane monooxygenase (red), rubredoxin (blue) and reductase (yellow). (B) CYP153 cluster genes: 2Fe-2S ferredoxin (red), cytochrome P450 (blue) and ferredoxin reductase (yellow). Transcriptional regulators colored in gray and pink are indicated. Comparison between the strains studied in this work (underlined) and available strains in IMG/M are shown.
Fig 3. Transcriptional pattern by real-time PCR.AH, (B) CYP153 gene clusters in G. sihwensis MTZ096 and (C) transcriptional pattern of CYP153 gene cluster in G. paraffinivorans MTZ052.
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997, Pubmed
Altschul,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
1997,
Pubmed
Amgarten,
Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages.
2017,
Pubmed
Antunes,
Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics.
2016,
Pubmed
Arenskötter,
Biology of the metabolically diverse genus Gordonia.
2004,
Pubmed
Assefa,
ABACAS: algorithm-based automatic contiguation of assembled sequences.
2009,
Pubmed
Auch,
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison.
2010,
Pubmed
Brown,
Draft Genome Sequence of Gordonia sihwensis Strain 9, a Branched Alkane-Degrading Bacterium.
2016,
Pubmed
Chen,
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.
2019,
Pubmed
Chevreux,
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
2004,
Pubmed
Contreras-Moreira,
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.
2013,
Pubmed
Drzyzga,
The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential.
2012,
Pubmed
Drzyzga,
Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge.
2009,
Pubmed
Ferrera-Rodríguez,
Hydrocarbon-degrading potential of microbial communities from Arctic plants.
2013,
Pubmed
Fujii,
Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from Gordonia sp. TF6.
2004,
Pubmed
Guo,
Isolation of PAH-degrading bacteria from mangrove sediments and their biodegradation potential.
2005,
Pubmed
Hilpert,
Infiltration and evaporation of small hydrocarbon spills at gas stations.
2014,
Pubmed
Indest,
A TaqMan polymerase chain reaction method for monitoring RDX-degrading bacteria based on the xplA functional gene.
2007,
Pubmed
Jurado,
Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting.
2014,
Pubmed
Kausar,
Isolation and screening of potential actinobacteria for rapid composting of rice straw.
2011,
Pubmed
Kolinko,
A bacterial pioneer produces cellulase complexes that persist through community succession.
2018,
Pubmed
Kubota,
Phylogenetic analysis of long-chain hydrocarbon-degrading bacteria and evaluation of their hydrocarbon-degradation by the 2,6-DCPIP assay.
2008,
Pubmed
Kurtz,
Versatile and open software for comparing large genomes.
2004,
Pubmed
Lemos,
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting.
2017,
Pubmed
Liang,
Regulation of the Alkane Hydroxylase CYP153 Gene in a Gram-Positive Alkane-Degrading Bacterium, Dietzia sp. Strain DQ12-45-1b.
2016,
Pubmed
Lima-Junior,
Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U.
2016,
Pubmed
,
Echinobase
Linh,
Characterization and functional expression of a rubber degradation gene of a Nocardia degrader from a rubber-processing factory.
2017,
Pubmed
Livak,
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
2001,
Pubmed
Lo Piccolo,
Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes.
2011,
Pubmed
López-González,
Dynamics of bacterial microbiota during lignocellulosic waste composting: Studies upon its structure, functionality and biodiversity.
2015,
Pubmed
Mapelli,
Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms.
2017,
Pubmed
Martins,
Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms.
2013,
Pubmed
Martínková,
Biodegradation potential of the genus Rhodococcus.
2009,
Pubmed
Meier-Kolthoff,
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
2013,
Pubmed
Nguyen,
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
2015,
Pubmed
Oliveira,
Halotolerant bacteria in the São Paulo Zoo composting process and their hydrolases and bioproducts.
2015,
Pubmed
,
Echinobase
Parashar,
Optimization of procedures for isolation of mycobacteria from soil and water samples obtained in northern India.
2004,
Pubmed
Parks,
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
2015,
Pubmed
Partanen,
Bacterial diversity at different stages of the composting process.
2010,
Pubmed
Pascon,
Amylolytic microorganism from são paulo zoo composting: isolation, identification, and amylase production.
2011,
Pubmed
,
Echinobase
Procópio,
Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain.
2013,
Pubmed
Ramos,
A Tropical Composting Operation Unit at São Paulo Zoo as a Source of Bacterial Proteolytic Enzymes.
2019,
Pubmed
,
Echinobase
Richter,
Shifting the genomic gold standard for the prokaryotic species definition.
2009,
Pubmed
Rojo,
Degradation of alkanes by bacteria.
2009,
Pubmed
Ron,
Enhanced bioremediation of oil spills in the sea.
2014,
Pubmed
Sowani,
An insight into the ecology, diversity and adaptations of Gordonia species.
2018,
Pubmed
Vargas-García,
Compost as a source of microbial isolates for the bioremediation of heavy metals: in vitro selection.
2012,
Pubmed
Varjani,
Microbial degradation of petroleum hydrocarbons.
2017,
Pubmed
Vasconcellos,
The potential for hydrocarbon biodegradation and production of extracellular polymeric substances by aerobic bacteria isolated from a Brazilian petroleum reservoir.
2011,
Pubmed
,
Echinobase
Xue,
Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well.
2003,
Pubmed
