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

Tan, BoonFei; Nesbø, Camilla; Foght, Julia M.

doi:10.1038/ismej.2014.87

Cited by 72 publications

(50 citation statements)

References 11 publications

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“…However, Tan et al proposed that Smithella sp. activate the initial degradation of hexadecane by fumarate addition based on reanalysis of the draft genome of Smithella ME-1 [53].…”

Section: Discussionmentioning

confidence: 99%

Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions

Ding

et al. 2015

Microb Ecol

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Anaerobic alkane degradation via methanogenesis has been intensively studied under mesophilic and thermophilic conditions. While there is a paucity of information on the ability and composition of anaerobic alkane-degrading microbial communities under low temperature conditions. In this study, we investigated the ability of consortium Y15, enriched from Shengli oilfield, to degrade hydrocarbons under different temperature conditions (5-35 °C). The consortium could use hexadecane over a low temperature range (15-30 °C). No growth was detected below 10 °C and above 35 °C, indicating the presence of cold-tolerant species capable of alkane degradation. The preferential degradation of short chain n-alkanes from crude oil was observed by this consortium. The structure and dynamics of the microbial communities were examined using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and Sanger sequencing of 16S rRNA genes. The core archaeal communities were mainly composed of aceticlastic Methanosaeta spp. Syntrophaceae-related microorganisms were always detected during consecutive transfers and dominated the bacterial communities, sharing 94-96 % sequence similarity with Smithella propionica strain LYP(T). Phylogenetic analysis of Syntrophaceae-related clones in diverse methanogenic alkane-degrading cultures revealed that most of them were clustered into three sublineages. Syntrophaceae clones retrieved from this study were mainly clustered into sublineage I, which may represent psychrotolerant, syntrophic alkane degraders. These results indicate the wide geographic distribution and ecological function of syntrophic alkane degraders.

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“…However, Tan et al proposed that Smithella sp. activate the initial degradation of hexadecane by fumarate addition based on reanalysis of the draft genome of Smithella ME-1 [53].…”

Section: Discussionmentioning

confidence: 99%

Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions

Ding

et al. 2015

Microb Ecol

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“…Based on single-cell genome and metatransciptome analyses, Embree et al [2014] came to the conclusion that Smithella as a dominant bacterial member of an n -hexadecane-degrading methanogenic community is not activating the hydrocarbon via addition to fumarate. This was subsequently disputed by Tan et al [2014], who came to the opposite conclusion based on reanalysis of the Smithella draft genome and metatranscriptomes. In a couple of metagenomic studies, these authors provided evidence that methanogenic communities originating from oil sands tailings ponds and gas condensate-contaminated aquifer sediments harbor fermentative syntrophs and sulfate reducers capable of degrading n -, iso-and cycloalkanes via their addition to fumarate [Tan et al, 2013[Tan et al, , 2015a.…”

Section: Insights From Genomic and Proteomic Studiesmentioning

confidence: 99%

Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria

Wilkes

Buckel

Golding³

et al. 2016

Microb Physiol

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The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1′R) and (2R,1′R). Experiments with stereospecifically deuterated n-(2,5-²H₂)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a S_N2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.

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“…some Clostridia and Proteobacteria) first transform hydrocarbons into smaller molecules such as short-chain fatty acids, alcohols or H 2. The involvement of Smithella and other related genera has gained general acceptance [Gray et al, 2011;Tan et al, 2014;Zengler et al, 1999]. Hydrocarbons first need to be activated (e.g.…”

Section: Methanogenic Hydrocarbon Degradationmentioning

confidence: 99%

“…Hydrocarbons first need to be activated (e.g. by addition of fumarate) to be further degraded [Heider, 2007;Tan et al, 2014]. Many of the involved reactions are endergonic and only become energetically feasible if the end products (formate, acetate or hydrogen) are kept at relatively low concentrations .…”

Section: Methanogenic Hydrocarbon Degradationmentioning

confidence: 99%

Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies

et al. 2016

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Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO₂, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.

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

Cited by 72 publications

References 11 publications

Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions

Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions

Metabolism of Hydrocarbons in <b><i>n</i></b>-Alkane-Utilizing Anaerobic Bacteria

Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies

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