Metagenomic Characterization of Candidatus Smithella cisternae Strain M82_1, a Syntrophic Alkane-Degrading Bacteria, Enriched from the Shengli Oil Field.

PubWeight™: 0.75‹?›

🔗 View Article (PMID 28781346)

Published in Microbes Environ on August 05, 2017

Authors

Qian-Shan Qin1, Ding-Shan Feng2, Peng-Fei Liu1, Qiao He1, Xia Li1, Ai-Ming Liu2, Hui Zhang1, Guo-Quan Hu1, Lei Cheng1

Author Affiliations

1: Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture.
2: Anhui Normal University.

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39

The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81

Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97

Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23

Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics (2010) 42.80

Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev (1977) 30.41

Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res (2005) 19.81

HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics (2012) 11.56

Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93

Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics (2007) 7.34

Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics (2001) 6.53

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol (2013) 6.40

Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol (2008) 4.81

Microbial biosynthesis of alkanes. Science (2010) 4.74

Understanding and exploiting C-H bond activation. Nature (2002) 4.48

ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains. FEMS Microbiol Rev (1998) 3.20

Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature (2007) 3.06

Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J (2011) 2.97

Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol (2009) 2.80

The twin-arginine translocation (Tat) protein export pathway. Nat Rev Microbiol (2012) 2.53

Methane formation from long-chain alkanes by anaerobic microorganisms. Nature (1999) 2.44

The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol (2008) 2.40

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim Biophys Acta (2012) 2.30

The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc Natl Acad Sci U S A (2007) 2.17

The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J Bacteriol (2009) 2.12

Evolution of the structure of ferredoxin based on living relics of primitive amino Acid sequences. Science (1966) 1.98

Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon. Science (2006) 1.90

Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. J Bacteriol (1996) 1.83

A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol (2011) 1.78

Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. Int J Syst Bacteriol (1999) 1.77

Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann N Y Acad Sci (2008) 1.70

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics (2012) 1.44

Pathway of propionate oxidation by a syntrophic culture of Smithella propionica and Methanospirillum hungatei. Appl Environ Microbiol (2001) 1.44

Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl Environ Microbiol (2000) 1.33

The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation. Environ Microbiol (2011) 1.33

The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol (2010) 1.32

Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol (2008) 1.31

Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl Environ Microbiol (2003) 1.31

The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol (2011) 1.29

The midgut transcriptome of Lutzomyia longipalpis: comparative analysis of cDNA libraries from sugar-fed, blood-fed, post-digested and Leishmania infantum chagasi-infected sand flies. BMC Genomics (2008) 1.28

Anaerobic degradation of n-hexane in a denitrifying bacterium: further degradation of the initial intermediate (1-methylpentyl)succinate via C-skeleton rearrangement. Arch Microbiol (2001) 1.28

The structure of iron-sulfur proteins. Prog Biophys Mol Biol (1998) 1.28

The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One (2012) 1.27

Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members. Genome (2013) 1.22

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J (2013) 1.19

Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms. Environ Microbiol Rep (2010) 1.09

Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers. Environ Sci Technol (2002) 1.08

Membrane-bound proton-translocating pyrophosphatase of Syntrophus gentianae, a syntrophically benzoate-degrading fermenting bacterium. Eur J Biochem (1998) 1.07

Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures. Environ Sci Technol (2010) 1.06

Comparison of mechanisms of alkane metabolism under sulfate-reducing conditions among two bacterial isolates and a bacterial consortium. Appl Environ Microbiol (2006) 1.03

Anaerobic n-alkane metabolism by a sulfate-reducing bacterium, Desulfatibacillum aliphaticivorans strain CV2803T. Appl Environ Microbiol (2005) 1.03

Microbial communities involved in methane production from hydrocarbons in oil sands tailings. Environ Sci Technol (2012) 0.99

Pyrosequencing analysis of eukaryotic and bacterial communities in faucet biofilms. Sci Total Environ (2012) 0.98

Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei. Microbiology (2010) 0.98

DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLoS One (2013) 0.98

A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei. PLoS One (2013) 0.98

Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings. Environ Sci Technol (2011) 0.97

Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. J Bacteriol (2006) 0.97

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions. ISME J (2014) 0.96

The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol (2014) 0.94

Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum. BMC Genomics (2012) 0.94

Anaerobic biodegradation of n-hexadecane by a nitrate-reducing consortium. Appl Environ Microbiol (2008) 0.91

Stable isotopic studies of n-alkane metabolism by a sulfate-reducing bacterial enrichment culture. Appl Environ Microbiol (2005) 0.91

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities. Biochim Biophys Acta (2014) 0.89

Trimethylsilyl transfer during electron ionization mass spectral fragmentation of some omega-hydroxycarboxylic and omega-dicarboxylic acid trimethylsilyl derivatives and the effect of chain length. Rapid Commun Mass Spectrom (2004) 0.87

Enrichment and dynamics of novel syntrophs in a methanogenic hexadecane-degrading culture from a Chinese oilfield. FEMS Microbiol Ecol (2012) 0.86

Novel bacterial groups dominate in a thermophilic methanogenic hexadecane-degrading consortium. FEMS Microbiol Ecol (2013) 0.84

Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei. Front Microbiol (2015) 0.84

Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc Natl Acad Sci U S A (2015) 0.84

Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)). Stand Genomic Sci (2012) 0.83

Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens. Environ Microbiol (2016) 0.79

Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. ISME J (2013) 0.79

Draft Genome Sequences of Three Smithella spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water. Genome Announc (2014) 0.78

Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria. Microbes Environ (2016) 0.77

Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions. Microb Ecol (2015) 0.76

The Structure and Function of OxlT, the Oxalate Transporter of Oxalobacter formigenes. J Membr Biol (2014) 0.76

[Degradation of fatty acid by syntrophic hydrocarbon-degrading consortium M82]. Wei Sheng Wu Xue Bao (2014) 0.76