Methanogenic octadecene degradation by syntrophic enrichment culture from brackish sediments

Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review

Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C₁₀ alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.

Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion

Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments, its degradation relies on syntrophic associations between syntrophic propionate-oxidizing bacteria (SPOB) and Archaea. However, only 10 isolated species have been identified as SPOB so far. We report syntrophic propionate oxidation in thermophilic enrichments of Candidatus Syntrophosphaera thermopropionivorans, a novel representative of the candidate phylum Cloacimonetes. In enrichment culture, methane was produced from propionate, while Ca. S. thermopropionivorans contributed 63% to total bacterial cells. The draft genome of Ca. S. thermopropionivorans encodes genes for propionate oxidation via methymalonyl-CoA. Phylogenetically, Ca. S. thermopropionivorans affiliates with the uncultured Cloacimonadaceae W5 and is more distantly related (86.4% 16S rRNA gene identity) to Ca. Cloacimonas acidaminovorans. Although Ca. S. thermopropionivorans was enriched from a thermophilic biogas reactor, Ca. Syntrophosphaera was in particular associated with mesophilic anaerobic digestion systems. 16S rRNA gene amplicon sequencng and a novel genus-specific quantitative PCR assay consistently identified Ca. Syntrophosphaera/Cloacimonadaceae W5 in 9 of 12 tested full-scale biogas reactors thereby outnumbering other SPOB such as Pelotomaculum, Smithella and Syntrophobacter. Taken together the ubiquity and abundance of Ca. Syntrophosphaera, those SPOB might be key players for syntrophic propionate metabolism that have been overlooked before.

Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation

The methanogenic alkanes-degrading enrichment culture which had been incubated for over 1,300 days amended with n-alkanes (C₁₅–C₂₀) was investigated through clone libraries of bacteria, archaea and assA, mcrA functional genes. These enrichment cultures were obtained from oily sludge after an initial incubation of the oily sludge without any carbon source and then an enrichment transfer with n-alkanes (C₁₅–C₂₀) for acclimation. Activation of alkanes, methane precursor generation and methanogenic pathways are considered as three pivotal stages for the continuous methanogenesis from degradation of alkanes. The presence of functional genes encoding the alkylsuccinate synthase α-subunit indicated that fumarate addition is most likely the one of initial activation step for degradation of n-alkanes. Degradation intermediates of n-alkanes were octadecanoate, hexadecanoate, butyrate, isobutyrate, acetate and propionate, which could provide the appropriate substrates for acetate formation. Both methyl coenzyme M reductase gene and 16S rRNA gene analysis showed that microorganisms of Methanoseata were the most dominant methanogens, capable of using acetate as the electron donor to produce methane. Bacterial clone libraries showed organisms of Anaerolineaceae (within the phylum of Chloroflexi) were predominant (45.5%), indicating syntrophically cooperation with Methanosaeta archaea was likely involved in the process of methanogenic degradation of alkanes. Alkanes may initially be activated via fumarate addition and degraded to fatty acids, then converted to acetate, which was further converted to methane and carbon dioxide by methanogens.

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.