Microbial ecology of anaerobic biodegradation of benzoate : microbial communities and processes

Abstract

Microbial conversion of hydrocarbons and other aromatic compounds has been studied extensively under various electron accepting conditions, by investigating cultured microorganisms and by using samples collected directly from diverse environments. However, the functions of the principal microbial organisms taking part in the biodegradation process are not fully understood, especially when the organisms comprise complex microbial communities. The focus of the research reported here is the identification of a microbial community enriched during methanogenic benzoate degradation using inocula from two contrasting environments, river sediment and oil sands. Benzoate is a monoaromatic compound used extensively as a model compound in studies of hydrocarbons and other aromatics. The microorganisms which were most abundant and which had been shown by earlier work to take part in syntrophic benzoate degradation were investigated. Their functional potential was also investigated using metagenomic approaches. It was found that enrichments from different environments contained different microbial communities, different members of which were thought to take part in the syntrophic degradation of benzoate. In benzoate enrichments with Tyne sediment, two types of methanogen were enriched: hydrogenotrophic Methanofollis and acetoclastic Methanosaeta. In contrast, in oil sands enrichments with benzoate, the most abundant methanogens were metabolically versatile Methanosarcina spp. The primary benzoate degrader in enrichments with Tyne sediment was Syntrophus, most likely Syntrophus aciditrophicus as was suggested by 99% sequence identity. In oil sands enrichments the supposed primary benzoate degrader was an unknown species of Desulfotomaculum. Syntrophic acetate oxidisers (e.g. Syntrophomonas) were not found in abundance in Tyne sediment cocultures with benzoate. Instead, the conversion of acetate into hydrogen and carbon dioxide appeared to be mediated by acetoclastic methanogenesis, which utilised acetate directly as has been evidenced by the enrichment of acetoclastic methanogens Methanosaeta and Methanosarcina. In the oil sands, syntrophic acetate oxidation was likely to have been carried out by the known acetoclastic methanogen Methanosarcina. However, it was conjectured that unclassified Sphingobacteriales clone WCHB1.69 could have taken part in the acetate utilisation. Regardless of the observed differences between the microbial communities, investigation of the metabolic potential showed the presence of the same pathways, key genes and enzymes that are known to take part in the degradation of benzoate iv and the production of methane. The same four pathways were found in both sets of methanogenic enrichments, namely the benzoate degradation pathway and hydrogenotrophic, acetoclastic and methylotrophic methanogenesis pathways. The same key genes that take part in benzoate degradation, namely dienoyl-CoA hydratase (dch), β-hydroxyacyl-CoA dehydrogenase (had) and β-oxoacyl-CoA hydrolase (oah) were found in high abundance in both enrichment cultures. The same key genes coding for essential proteins involved in methanogenesis were also found in high abundance in all the methanogenic archaea tested in both Tyne sediment and oil sands methanogenic enrichment cultures with benzoate, namely tetrahydromethanopterin S-methyltransferase (mtrA), methyl-coenzyme M reductase A (mcrA) and heterodisulfide reductase subunit A (hdrA). Other genes found in high abundance were methanogenic pathway specific genes, namely formylmethanofuran dehydrogenase, subunit A (fmdA) involved in hydrogenotrophic methanogenesis, phosphate acetyltransferase (pta), acetate kinase (ackA) and acetyl-CoA synthetase (ACSS) involved in acetoclastic methanogenesis and coenzyme M methyltransferase (mtaA) involved in methylotrophic methanogenesis. These results suggest that the functional capabilities of the microorganisms in different environments remain constant but the communities might vary from one environment to another. In addition, a comparison was made between two sequencing platforms, Illumina MiSeq and Ion Torrent PGM. The result suggested that, overall, the two sequencers concurred. The sequencers found the same most abundant taxa, but there were instances where both sequencers detected some microorganisms which were not detected by the other sequencer. Syntrophic degradation of many different types of compound such as alcohols, saturated and unsaturated fatty acids, hydrocarbons and aromatic compounds has been identified in methanogenic environments, suggesting the global importance of this process and of the microorganisms involved. Further work on the syntrophic processes, including methanogenesis, would clarify which microorganisms take part in syntrophy, in which environments syntrophy occurs, what substrates can be utilised, which members of the microbial community participate and how. Such knowledge would be useful in understanding the processes that attenuate the contamination of industrial land and the development of strategies for bioremediation. A quantitative model of syntrophic biodegradation could also assist in understanding the processes that release greenhouse gases. There is also a likelihood that microbial degradation could find a use in the development of sustainable and environmentally innocuous sources of energy.