Abstract
Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.
Highlights
Many hydrocarbon compounds are both toxic to living organisms and difficult to remove from the environment
In order to determine the syntrophic potential of hydrocarbon resource environments based on examining syntroph associated gene families in metagenomes, metagenomes were obtained which were sequenced and publically available on both the Hydrocarbon Metagenomics Project (HMP) website and the IMG database [10,16]
Hydrocarbon resource environments containing microbial communities typically associated with syntrophic processes (Deltaproteobacteria, Firmicutes, and Epsilonproteobacteria together with Euryarchaeota, primarily consisting of methanogens) and sampled from locations where anaerobic, methanogenic conditions dominate were classified as
Summary
Many hydrocarbon compounds are both toxic to living organisms and difficult to remove from the environment. Anaerobic electron acceptors such as nitrate (NO3 ́ ), iron (Fe3+ ), and sulfate (SO4 2 ́ ) are rapidly utilized, leaving an environment with recalcitrant hydrocarbons which is depleted in electron acceptors [1] Under these energy-limited methanogenic conditions, mechanisms of hydrocarbon biodegradation are poorly understood, though this is thought to be the main biodegradation process in contaminated environments [2,3]. Certain anaerobic bacteria (typically Deltaproteobacteria and Firmicutes, though other groups such as Epsilonbacteria may play a role) are capable of breaking down hydrocarbon compounds under anoxic conditions, generating simple molecules such as hydrogen and acetate [4,5,6] Though possible, these conversions are energetically unfavorable under standard conditions [3,5]. Known as Microorganisms 2016, 4, 5; doi:10.3390/microorganisms4010005 www.mdpi.com/journal/microorganisms
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