Iron-dependent AOM

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New research using sediments from a Dutch canal has yielded important insights into the anaerobic oxidation of methane (AOM).  A group of scientists from the Institute for Water and Wetland Research at Radboud University identified archaea of the order Methanosarcinales as being responsible for AOM coupled to iron and manganese reduction.

AOM proceeds as methane is oxidised with various terminal electron acceptors including sulphate, nitrite and nitrate, and the importance of oxidised metals in the process has been investigated, but the microorganisms involved have remained unknown.  To address this, a culture of methanotrophs was established that was enriched with canal sediment.  When this culture was supplied with nitrate as the only available electron acceptor, it became dominated by AOM-associated archaea (AAA).  This culture linked methane oxidation to nitrate reduction, with N2 being the main end product, although approximately 10% of nitrate was converted to ammonium.

The enrichment culture with AAA was used for further experiments, where methane oxidation was observed following the addition of ferric citrate, nanoparticulate ferrihydrite (Fe3+) or birnessite (Mn4+).  Analysis of the AAA genome showed that it could couple methane oxidation to nitrate reduction or Fe3+ reduction, or that the reverse methanogenesis pathway could also operate.  The authors therefore suggest that AAA could act as a versatile methanotroph, switching electron acceptors depending on their availability.

The paper was jointly led by Katharina Ettwig and Baoli Zhu. One of the co-authors, Boran Kartaldescribed the possible application of their findings: “A bioreactor containing anaerobic methane and ammonium oxidizing microorganisms can be used to simultaneously convert ammonium, methane and oxidized nitrogen in wastewater into harmless nitrogen gas and carbon dioxide, which has much lower global warming potential.”  The authors conclude that their work “may also shed light on the long-standing discussion about Fe2+ -producing processes on early Earth, when AAA-related organisms may have thrived under the methane-rich atmosphere in the ferruginous Archean oceans.”

Ettwig, K.F., Zhu, B., Speth, D., Keltjens, J.T., Jetten, M.S.M., Kartal, B. 2016. Archaea catalyse iron-dependent anaerobic oxidation of methane. PNAS, doi: 10.1073/pnas.1609534113.

Image is from the paper and shows fluorescence in situ hybridization of biomass from the enrichment culture of AAA and M. oxyfera-like bacteria.

Deep microbial communities created through fracking

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A new study published in Nature Microbiology has shed light on the microbial communities inhabiting hydraulically fractured shale, at a depth of approximately 2.5 km.  The process of hydraulic fracturing relies on the high-pressure injection of water and various chemicals deep underground.

The investigation took place in two Appalachian basin shales in the USA, and involved metagenomic and metabolite analyses on input fluids to the well, as well as analyses on produced fluids over a period of 328 days.  This approach enabled changes in microbial communities and metabolites to be observed over time.

The analyses of the Marcellus shale showed that changes in microbial community corresponded to increases in salinity, and persisting halotolerant and thermotolerant members were found in various bacterial and archaeal taxa.  Additionally, the authors discovered one apparently unique bacteria and proposed the genus name Candidatus Frackibacter.  Over time, there was an increase in the concentration of glycine betaine (GB), which is used by microbes to survive osmotic stress, as well as evidence of uptake and de novo synthesis of GB by microbes.  GB could be degraded by obligate fermenters from the genera Halanaerobium or Candidatus Frackibacter which would produce trimethylamine (TMA).  In turn, it was hypothesised that TMA would be used as a methanogenic substrate by organisms in the genera Methanolous and Methanohalophilus.

The second shale (Utica) investigated was geologically and geographically distinct from the Marcellus shale.  The authors experimentally amended produced fluids from the Utica shale with GB, which resulted in enrichment of Methanohalophilus and Halanaerobium.  TMA production was detected, and the amended samples produced 6.5 times more methane per day when compared to controls that were not amended with GB.  The genomes of Methanohalophilus and Halanaerobium from the Marcellus and Utica shales were closely related, demonstrating that even though the two ecosystems were different, similarities arose in the microbial communities.

Kelly Wrighton, last author on the paper, said: “We think that the microbes in each well may form a self-sustaining ecosystem where they provide their own food sources.  Drilling the well and pumping in fracturing fluid creates the ecosystem, but the microbes adapt to their new environment in a way to sustain the system over long periods.”

Much of the previous research on hydraulic fracturing has focussed on economics and environmental impacts.  However, this new research shows that hydraulic fracturing also creates the necessary physical and chemical conditions for microbial life to persist, and that much of this is implicated in methane cycling.

Daly, R.A., Borton, M.A., Wilkins, M.J. et al. 2016. Microbial metabolisms in a 2.5km deep ecosystem created by hydraulic fracturing in shales. Nature Microbiology, 1, article number 16146.

Image is from the above paper, under a Creative Commons Attribution 4.0 International License.