The genome sequence of Desulfatibacillum alkenivorans AK‐01: a blueprint for anaerobic alkane oxidation

Abstract

Desulfatibacillum alkenivorans AK-01 serves as a model organism for anaerobic alkane biodegradation because of its distinctive biochemistry and metabolic versatility. The D. alkenivorans genome provides a blueprint for understanding the genetic systems involved in alkane metabolism including substrate activation, CoA ligation, carbon-skeleton rearrangement and decarboxylation. Genomic analysis suggested a route to regenerate the fumarate needed for alkane activation via methylmalonyl-CoA and predicted the capability for syntrophic alkane metabolism, which was experimentally verified. Pathways involved in the oxidation of alkanes, alcohols, organic acids and n-saturated fatty acids coupled to sulfate reduction and the ability to grow chemolithoautotrophically were predicted. A complement of genes for motility and oxygen detoxification suggests that D. alkenivorans may be physiologically adapted to a wide range of environmental conditions. The D. alkenivorans genome serves as a platform for further study of anaerobic, hydrocarbon-oxidizing microorganisms and their roles in bioremediation, energy recovery and global carbon cycling.

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

“…In D. alkenivorans AK-01, these reactions are presumably catalyzed by AssK, a putative methylmalonyl-CoA mutase, and a putative methylmalonyl-CoA carboxyl transferase before β-oxidation (Callaghan et al, 2012). We found BLAST or Pfam matches to these genes in all three metagenomes (Figure 2, Supplementary Table S3).…”

“…Genes encoding anaerobic hydrocarbon-degrading enzymes (for example, bssA, assA) have been detected in hydrocarbon-degrading methanogenic cultures (for example Aitken et al, 2013;Cheng et al, 2013;Fowler et al, 2012;Washer and Edwards, 2007) as well as genes involved in syntrophic processes such as H 2 and formate transfer, and flagella, amino-acid and coenzyme biosynthesis (Kato et al, 2009;Walker et al, 2009). Despite recent reports of hydrocarbon-degrading co-cultures of sulfate reducers and methanogens (Callaghan et al, 2012;Lyles et al, 2014), the diversity of key enzymes and genes involved in methanogenic hydrocarbon metabolism are not yet well described.…”

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

“…Currently, little is known about the enzymes that catalyze anaerobic alkane oxidation and, to date, only two genomes, Desulfococcus oleovorans Hxd3 and Desulfatibacillum alkenivorans AK-01 (both Deltaproteobacteria), are available among anaerobic alkane oxidizers. Of these two organisms, only the mechanism of alkane activation for D. alkenivorans AK-01 is known (Callaghan et al, 2012). The activation of alkanes by D. alkenivorans AK-01 is catalyzed by an alkylsuccinate synthase that was also identified in the TT107 metagenome (Figure 1; Callaghan et al, 2008).…”

“…Such organisms include acetogens, methanogens, sulfate reducing bacteria (SRB), ammoniaoxidizing planctomycetes, an autotrophic archaeal SRB, Archaeoglobales (Berg, 2011), anaerobic facultative autotrophs (Schauder et al, 1988) and, reversibly, with heterotrophs using carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase to oxidize acetyl-CoA (Rabus et al, 2006). Callaghan et al (2012) have also postulated that a reversed Wood-Ljungdahl pathway is carried out during the complete oxidation of alkanes under anaerobic conditions. The ΔG of many of the dominant anaerobic Based upon cell counts using DAPI (Simkus et al, 2015).…”

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

“…This cluster was one of the longest and most obvious stretches of ORFs identified (encoding at least 20 ORFs) in our data set, whereby no homologues in known DEH could be identified by BLASTP analyses, yet was downstream of known DEH genes. We hypothesise that the heterodisulfide reductase-like enzymes have important roles in cytoplasmic electron transfer and energy conserving mechanisms, like in other anaerobes such as sulphate reducers, acetogens and methanogens (Stojanowic et al, 2003;Strittmatter et al, 2009;Kaster et al, 2011b;Callaghan et al, 2012). These complexes might be especially important for transferring reducing equivalents released during beta-oxidation and/or conversions of succinate to acetyl-CoA (via the methylmalonyl-CoA pathway), to and from ferredoxins or NADH, possibly by electron bifurcating/confurcating mechanisms that may be linked to other metabolic steps (Buckel and Thauer, 2012;Grein et al, 2012).…”