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Comment
. 2014 Dec;8(12):2353-6.
doi: 10.1038/ismej.2014.87. Epub 2014 May 27.

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions

Boonfei Tan  1 , Camilla Nesbø  2 , Julia Foght  1
Affiliations
Comment

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions

Boonfei Tan et al. ISME J. 2014 Dec.
No abstract available

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Figures

Figure 1
Figure 1
Sequence alignment of translated putative assA in Smithella spp. with reference AssA sequences. Sequences were aligned using Muscle 3.3 in Geneious R7, with conserved sequence motifs highlighted in black. Pairwise percentage identity of the nucleotide alignment is shown in Supplementary Table S1.
Figure 2
Figure 2
Maximum likelihood tree of six translated glycyl radical enzyme genes in the draft Smithella ME-1 genome (Embree et al., 2013) recovered through tblastn searches (shown in boldface, with the SCADC assA sequence); sequence length is shown in parentheses. Closely related sequences were recovered from the NCBI nr-database through BLASTX searches and all sequences were aligned using MAFFT, followed by phylogenetic tree construction using PhyML (Guindon et al., 2010) with LG model and 100 bootstrap replicates in Geneious R7 (www.geneious.com). Bootstrap support ⩾70% is indicated. The tree was rooted by midpoint rooting. The assA sequences from clones (indicated on tree) were not full length and ranged from 414–662 bp. All other sequences used in the tree were full length (>2400 bp). A tree with the same overall topology was obtained when including only full-length sequences and removing gaps (not shown).
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References

    1. Aitken CM, Jones DM, Maguire MJ, Gray ND, Sherry A, Bowler BFJ, et al. Evidence that crude oil alkane activation proceeds by different mechanisms under sulfate-reducing and methanogenic conditions. Geochim Cosmochim Acta. 2013;109:162–174.
    1. Callaghan AV, Morris BEL, Pereira IAC, McInerney MJ, Austin RN, Groves JT, et al. The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation. Environ Microbiol. 2012;14:101–113. - PubMed
    1. Callaghan AV. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol. 2013;4:89. - PMC - PubMed
    1. Cheng L, Ding C, Li Q, He Q, Dai LR, Zhang H. DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLoS One. 2013;8:e66784. - PMC - PubMed
    1. Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J. 2013;8:757–767. - PMC - PubMed

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