Abstract
Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’
INTRODUCTION
Alkanes are saturated hydrocarbons that are derived from both natural and anthropogenic sources. Due to their apolar C-H σbonds, alkanes are considered to be among the least chemically reactive organic compounds. The activation or functionalization of alkanes is initiated via cleavage of a C-H bond. Aerobic microorganisms achieve this step via monooxygenase or dioxygenase enzymes, in which oxygen serves as both the physiological terminal electron acceptor and as a reactant (for review of mechanisms and enzymes see ). The role of oxygen in the functionalization of alkanes led to the belief for many years that anaerobic microorganisms would be unable to activate and utilize these compounds as growth substrates. However, research during the last 25 years has demonstrated that anaerobic microorganisms have their own novel mechanisms of activating alkanes.
ANAEROBIC OXIDATION OF METHANE
The shortest alkane, methane, is the most environmentally relevant hydrocarbon due to its biological production by methanogenic archaea in freshwater systems, swamps, landfills, marine sediments and seeps, rice fields, and other anaerobic environments, as well as its role as a greenhouse gas (). Anaerobic methane oxidation (AOM) is thought to account for the removal of over 300 Tg of methane per year in oceanic systems (; Reeburgh, 2007). Therefore, from the perspective of climate change, AOM serves as a significant greenhouse “sink.” AOM can be coupled to the reduction of sulfate, nitrate and nitrite (for reviews see ; Shen et al., 2012), manganese (), and iron (; ; Sivan et al., 2011; ; Zhu et al., 2012). Although the mechanisms of aerobic methane oxidation are well-described (), the mechanisms of AOM have been hotly debated.
REVERSE METHANOGENESIS
To date, several studies have revealed that AOM coupled to sulfate reduction is mediated by consortia of archaeal anaerobic methane oxidizers (ANME-1, ANME-2, and ANME-3) and sulfate-reducing bacteria (SRB) (). AOM with sulfate as the terminal electron acceptor appears to proceed via “reverse methanogenesis” (Zehnder and Brock, 1979; ; ) and is catalyzed by a homolog of methyl-coenzyme M reductase (MCR), the Ni-containing enzyme responsible for the last step of methanogenesis (Krüger et al., 2003; Scheller et al., 2010a; Figure 1A). MCR homologues have been found in high concentrations in methanotrophic archaea associated with SRB (; Krüger et al., 2003; ; Mayr et al., 2008; Nunoura et al., 2008). In a recent study, an ANME-1 MCR complex was isolated from a Black Sea microbial mat, and the X-ray structure was reported (Shima et al., 2012). Compared to the methanogenic MCR, the ANME-1 MCR complex is similar in overall structure and contains coenzyme M and coenzyme B. However, it differs from the methanogenic MCR in that it contains an F430 variant, as well as a cysteine-rich region and an altered post-translational amino acid modification pattern (Shima et al., 2012). Although not clearly elucidated, the role of the cysteine-rich region between the F430 and the protein surface may be to operate as a redox-relay system for electron or H+/e- transport for the reduction of ANME-1 MCR from the inactive Ni2+ to the active Ni1+ oxidation state (Mayr et al., 2008; Shima et al., 2012), whereas, the altered post-translational amino acid modifications may reflect phylogenetic adaptation to environmental conditions (Shima et al., 2012) based on the distribution of different ANME groups within microbial mats (Krüger et al., 2008).
FIGURE 1
The “reversibility” of MCR is supported by thermodynamic and kinetic considerations (Thauer, 2011), as well as activity assays with purified MCR from Methanothermobacter marburgensis (Scheller et al., 2010a). However, there are still several hypotheses regarding the reaction intermediates of both methane formation and methane oxidation by MCR. The two main competing theories argue either for an organometallic methyl-NiIIIF430 intermediate (
ALTERNATIVE AOM MECHANISMS UNDER SULFATE-REDUCING CONDITIONS
There has been tremendous debate regarding the interspecies intermediates of sulfate-dependent AOM, and several mechanisms have been proposed for consortia of ANME and SRB. One hypothesis proposes the formation of acetic acid and H2 from methane and water by methane-oxidizing archaea, with subsequent utilization of the acetic acid and H2 by SRB (Valentine and Reeburgh, 2000). Another variation of this process was previously proposed as “reverse acetoclastic methanogenesis” in which methane-oxidizing archaea produce acetate from CO2 and CH4, and the acetate is utilized by SRB (Zehnder and Brock, 1980;
NEW MODEL FOR AOM MECHANISM UNDER SULFATE-REDUCING CONDITIONS: ZERO-VALENT SULFUR AS A KEY INTERMEDIATE
The studies focusing on the identification of AOM intermediates under sulfate-reducing conditions (see above) have mainly been predicated on the hypothesis that the ANME/SRB consortia catalyze AOM via an obligate syntrophic mechanism (for review see
NITRITE-DEPENDENT ANAEROBIC METHANE OXIDATION (“INTRA-AEROBIC DENITRIFICATION”)
Anaerobic methane oxidation coupled to denitrification through “reverse methanogenesis” was first proposed for a consortium (“Twente”) enriched from Twentekanaal sediment (Netherlands) (Raghoebarsing et al., 2006). The culture consisted of a bacterium belonging to the candidate division, “NC10,” and archaea distantly related to Methanosaeta and ANME–II (Raghoebarsing et al., 2006;
METHANE ADDITION TO FUMARATE
The addition of non-methane alkanes to fumarate (i.e., fumarate addition) is a prevalent anaerobic alkane activation mechanism observed under nitrate- and sulfate-reducing conditions (see below). Although the majority of studies have focused on longer-chain alkanes, a few investigations have revealed that short alkanes, such as propane, are also added to fumarate terminally or subterminally under sulfate-reducing conditions (
Whether AOM via fumarate addition proceeds with sulfate versus nitrate or nitrite as the terminal electron acceptor has also been debated. It is hypothesized that the majority or all of the free energy generated from this process with sulfate as the terminal electron acceptor (δG°′ = -21 kJ/mol) would be dissipated as heat in the initial activation step, which would not allow enough energy for subsequent reactions, whereas the free energy change using nitrate or nitrite as a terminal electron acceptor is more energetically favorable (Thauer and Shima, 2008).
ANAEROBIC OXIDATION OF NON-METHANE ALKANES
ALKANE ADDITION TO FUMARATE
One of the most well characterized mechanisms of anaerobic alkane activation and degradation is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates. This was first demonstrated in a sulfate-reducing, dodecane-utilizing enrichment culture (Kropp et al., 2000) and was subsequently found to be applicable to a range of n-alkane and cycloalkane substrates (C3–C16) in several sulfate-reducing and nitrate-reducing isolates and cultures (Rabus et al., 2001; Wilkes et al., 2002, 2003; Rios-Hernandez et al., 2003;
FIGURE 2

(A) Proposed pathway and stereochemistry for the anaerobic activation and degradation of hexane via subterminal addition to fumarate (adapted from
Analogous to the glycyl radical mechanism of benzylsuccinate synthase (BSS) and its homologs, which catalyze the addition of aromatic hydrocarbons to fumarate (for reviews see
The discoveries of ASS and MAS have enabled the interrogation of hydrocarbon-impacted environments as well as isolates and enrichment cultures (
INTRA-HYDROXYLATION
An “intra-aerobic” pathway of alkane oxidation similar to that of ‘Methylomirabilis oxyfera’ has also been proposed to be involved in the functionalization of n-hexadecane by the Gammaproteobacterium HdN1 (Figure 2B; Zedelius et al., 2011). Unlike ‘Methylomirabilis oxyfera,’ HdN1 contains genes for the complete denitrification pathway. The genome of strain HdN1 does not contain genes that encode an alkane-activating glycyl radical enzyme, but does contain genes that may encode a di-iron monooxygenase, a P450-type monooxygenase and a putative third type of monooxygenase (Zedelius et al., 2011). Consistent with the absence of an alkane-activating glycyl radical enzyme, alkyl-substituted succinates were not detected via metabolite profiling, but 1-hexadecanol was detected when the anaerobic culture was exposed to air. Based on these findings and growth experiments, the authors proposed a mechanism in which NO2-, NO or an unknown product of NO2- reduction may be required for alkane activation. Specifically, the dismutation of NO2- [ΔG°′= -55.2 kJ (mole O2)-1] or NO [ΔG°′= -173.1 kJ (mole O2)-1)] would provide O2, which could then be used to hydroxylate the alkane via one of the putative monooxygenases. Alternatively, N-O species could behave as strongly oxidizing electron acceptors to generate a reactive state of a factor or enzyme site that is involved in the activation of the alkane, or an N-O species may be directly involved in the activation of the alkane (Zedelius et al., 2011).
ANAEROBIC HYDROXYLATION FOLLOWED BY CARBOXYLATION
Finally, there appears to be at least one additional pathway of anaerobic alkane oxidation. Early studies of the sulfate-reducing bacterium Desulfococcus oleovorans Hxd3 demonstrated that incubation with an alkane with an odd number of C atoms yielded predominantly fatty acids with an even number of C atoms, and vice versa (
With the continual evolution of sequencing technologies, however, genome-enabled analyses are yielding new hypotheses. Consistent with the above experimental observations, the genome of Hxd3 does not contain genes encoding an alkane-activating glycyl radical enzyme. Interestingly, the genome contains genes that encode an ethylbenzene dehydrogenase-like complex (
CONCLUSION
The anaerobic oxidation of alkanes plays an important role in the biogeochemical cycling of methane and the bioremediation of hydrocarbon-impacted environments. As we look to the future, advances in next-generation sequencing and annotation will facilitate genome-enabled transcriptomic and proteomic investigations of anaerobic alkane oxidation. The complete genome sequences of several model alkane utilizers are now publicly available and include: Desulfatibacillum alkenivorans AK-01, Desulfococcus oleovorans Hxd3, ‘Candidatus Methylomirabilis. oxyfera,’ and the Gammaproteobacterium, strain HdN1. Future work will rely on these model organisms for the purification and characterization of relevant enzymes.
Statements
Acknowledgments
The author would like to thank Rachel N. Austin, Johann Heider, Jana Milucka, and Mark A. Nanny for editorial comments and suggestions. The preparation of this review was funded by a National Science Foundation grant (MCB-0921265).
Conflict of interest
The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
anaerobic, oxidation, alkanes, methane, paraffins
Citation
Callaghan AV (2013) Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front. Microbiol. 4:89. doi: 10.3389/fmicb.2013.00089
Received
14 December 2012
Accepted
31 March 2013
Published
14 May 2013
Volume
4 - 2013
Edited by
Rachel N. Austin, Bates College, USA
Reviewed by
Julia Foght, University of Alberta, Canada; Amy M. Grunden, North Carolina State University, USA; Ian M. Head, Newcastle University, UK
Copyright
© Callaghan.
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
*Correspondence: Amy V. Callaghan, Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA. e-mail: acallaghan@ou.edu
This article was submitted to Frontiers in Microbiological Chemistry, a specialty of Frontiers in Microbiology.
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