Exploring the biodiversity, interactions and controls of prokaryotic communities driving methane flux in marine sediments.

Lead Research Organisation: Cardiff University
Department Name: School of Earth and Ocean Sciences

Abstract

Methane is a potent greenhouse gas, second in importance only to carbon dioxide. Most methane is produced by microorganisms and methane concentrations in the atmosphere had been increasing rapidly, but now is quite variable. This is important to understand as atmospheric methane increases in the geological past have been linked to global warming. Global methane production in marine sediments is very significant and these sediments contain the largest, global reservoir of methane. This includes huge stores of methane in an ice matrix called hydrates, which might be a future energy store, as well as being a sensitive trigger for rapid climate change. Surprisingly, we know relatively little about the methanogens in ocean sediments that produce this methane, as only a few have been isolated and studied (11 species, representing less than 10% of cultured methanogen species). Also uncultured and little understood, are the microbes related to methanogens, which currently remove approximately 80% of all methane produced in sediments before it can enter the ocean and atmosphere above. These two groups of microbes are intimately connected and together have major influence on the flux of methane from sediments. There are even suggestions that anaerobic methane production and consumption may be due to the same microbes, but nobody knows for sure. Hence, our lack of understanding of the microbes controlling methane flux in marine sediments severely limits our ability to predict controls and future changes in the extremely important global methane cycle. We intend to significantly increase knowledge of the controls on ocean methane flux, and the microorganisms driving this process, by investigating methane production in high-pressure systems. These systems mimic sediment conditions, and within which both methane-producing and methane-consuming microbial communities are active. We will conduct similar experiments with microbial communities from marine gas hydrate sediments to determine their response to temperature and pressure changes, the supply of compounds for methane oxidation or production, and other factors controlling methane concentrations. From these experiments and a range of marine sediments we will isolate a number of methanogens, many of which may be new marine types, as their presence has been indicated by DNA surveys. Study sites include coastal sediments which are strongly influenced by human activity, globally significant gas hydrate sediments and mud volcanoes, which have recently been suggested as being an important potential source of methane. We will identify the physiology and metabolism of these methanogens to significantly increase our knowledge of the biodiversity and function of this important group of microorganisms. This will include, for the first time, investigating their response to high pressure.

Publications

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Timmis, Kenneth N.; Lorenzo, Victor De; McGenity, Terry J.; Van Der Meer, Jan Roelof; Timmis, Kenneth N. (2009) Handbook of Hydrocarbon and Lipid Microbiology

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Watkins AJ (2014) Glycine betaine as a direct substrate for methanogens (Methanococcoides spp.). in Applied and environmental microbiology

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Watkins AJ (2012) Choline and N,N-dimethylethanolamine as direct substrates for methanogens. in Applied and environmental microbiology

 
Description 1) Biodiversity of methanogens in marine sediments. Sediments studied included tidal-flats, a shallow bay, deep-water mud volcanoes and Guaymas Basin hydrothermal sediments. Nine of the sixteen recognised methanogen genera were cultured, ranging from only one methanogen genus at mud volcano sites to eight in tidal-flats. At a number of these sites, methanogens were either not detected or showed low diversity using culture-independent techniques (16S rRNA and mcrA gene sequences). Acetate and hydrogen utilizing methanogens (including two strains of the genus Methanococcus) were cultured from marine sediments with high sulphate content. But, surprisingly, by far the most abundant genus was methylotrophic Methanococcoides being isolated from seven of the sites investigated, including the deepest (in terms of water depth) non-thermophilic methanogens so far isolated. Study of newly isolated Methanococcoides strains has extended the substrate range of methanogens by identifying four new directly utilized methylated substrates (choline, dimethylethanolamine, betaine and methyliodide). The substrate range of Methanococcoides has also been extended by demonstrating dimethylsulphide utilization, only previously known as a substrate in closely related genera. Representative strains from each of the sites were physiologically characterized and this showed that members of Methanococcoides are mesophilic/psychrotolerant, neutrophilic, halotolerant, and for the first time piezotolerant (up to 70 MPa).
2) Investigation of the organisms involved in net methane production in marine sediments, their interactions and environmental controls. Studies of salt marsh creek sediments demonstrated a close relationship between the depth distribution of methanogenic substrate utilization and specific methanogens that can utilize these compounds, including for non-competitive substrates. Surprisingly, there was no evidence for anaerobic methane oxidation (AOM), and acetate methanogenesis dominated areal rates of methanogenesis (99%) yet CH4 stable carbon isotopic values were atypical for acetate methanogenesis (mean d13C=71‰). The methanogenic community diversity (16S rRNA and mcrA gene) was also in accordance with the depth distribution of the H2/CO2 and acetate methanogenesis in the Mediterranean Amsterdam mud volcano, acetoclastic methanogenesis again dominated, but in this case due to very high pore water acetate concentrations. Methylotrophic methanogenesis was consistently present, whilst Methanococcoides was cultured from shallow sediment layers. In contrast, in the brine-impacted Napoli mud volcano, hydrogenotrophic methanogenesis was the dominant pathway below 50 cm with only low rates of acetoclastic methanogenesis, whilst methylotrophic methanogenesis was the only significant methanogenic pathway in shallow sediments (0-40 cm), and Methanococcoides was again detected. Surprisingly, however, no active methanogenesis (acetoclastic or hydrogenotrophic) could be detected in the sulphate-methane transition zone (SMTZ) sediments of Aarhus Bay (Denmark), but characteristic SMTZ prokaryotes could be maintained in long-term mixed heterotrophic cultivation, providing new information about their physiology, including for those with few or no cultivated representatives. Stable isotope probing of prokaryotic DNA in tidal flat sediment slurries under methanogenic conditions showed that although Bacteria were labelled, Archaea were not, despite suggestions that they are adapted to low-energy conditions.
3) To test the hypotheses that methane hydrate sediments contain distinct prokaryotic communities and to explore the biogeochemical processes they catalyse. Although, the high concentrations of both H2 and acetate, characteristic of many deep hydrate deposits could be produced in elevated pressure sediment slurry incubations, it proved difficult to link this to AOM, although many AOM associated prokaryotes were present. Comparison of incubations in all glass systems, new pressure vessels and previously used vessels suggested that microbial enhanced corrosion might be responsible for H2 formation and subsequent acetate production via autotrophic acetogenesis. Addition of a range of metals to anaerobic incubations demonstrated the significant effect they can have on anaerobic processes, as steel and iron stimulated H2, CH4 and acetate formation, and sulphate reduction, but to varying extents. Even the anti-seize compound, which has to be used to stop pressure vessel metal-metal joints from "welding" has a marked affect on anaerobic prokaryotic processes. This complicates anaerobic experiments in pressure vessels, but may also point to novel processes occurring in some anaerobic environments.
Exploitation Route In microbial ecology of anaerobes and methanogenesis.
Sectors Environment