The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Abstract

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic ‘Candidatus Methanothrix paradoxum’, which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, ‘Candidatus Methanoperedens nitroreducens’ ANME-2d archaea and ‘Candidatus Methylomirabilis oxyfera’ bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although ‘Candidatus Methanoperedens nitroreducens’ and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.

Increases in temperature and nutrient availability positively affect methane‐cycling microorganisms in Arctic thermokarst lake sediments

“…For the H 2 /CO 2 incubation the maximum Q 10 coefficient of 2.0 was obtained after 52 days. Cell‐specific methanogenesis rates had only minor differences between 4°C and 10°C on acetate (8.1 and 7.7 fmol cell −1 d −1 for 4°C and 10°C respectively) and TMA (51 and 40 fmol cell −1 d −1 for 4°C and 10°C respectively) and are all in the range of previously observed methane production rates (Supporting Information Table S6) (in ‘t Zandt et al ., ).…”

“…B), which indicated on average a 10% increase in CH 4 consumption rate at 10°C. Cell‐specific rates were 83 and 112 fmol cell −1 h −1 for 4°C and 10°C, which is within the range previously reported for aerobic methanotrophs (Supporting Information Table S6) (in ‘t Zandt et al ., ).…”

2038 – When microbes rule the Earth

“…As mentioned above, we are still learning about microbial processes like methanogenesis, but there are many other biogeochemical processes that are predicted to be driven by microbes, about which we need to learn a lot more. This search was articulated as ‘the hunt for the most‐wanted chemolithoautotrophic spookmicrobes ’ (In ′t Zandt et al ., ). The hunt for spookmicrobes generally starts with biogeochemical evidence, such as co‐localized depletion, which could not be explained by physical processes, of two compounds that could react to generate energy, and may include stable‐ and radio‐isotopic evidence of microbial involvement.…”

“…The hunt for spookmicrobes generally starts with biogeochemical evidence, such as co‐localized depletion, which could not be explained by physical processes, of two compounds that could react to generate energy, and may include stable‐ and radio‐isotopic evidence of microbial involvement. A classic example is the discovery of anaerobic methane oxidation (see In ′t Zandt et al ., ), for which we now know the microbes that couple the oxidation of methane to terminal electron acceptors such as sulfate, nitrate and nitrite, while the Archaea that use Fe(III) as terminal electron acceptor evaded identification until very recently (Cai et al ., ). Genomic reconstruction of ‘ Candidatus Methylomirabilis oxyfera’, the dominant member of a culture carrying out nitrite‐dependent anaerobic oxidation of methane, has revealed a fascinating mechanism whereby it converts nitrite to nitric oxide, which is dismutated to nitrogen and oxygen, and the latter is then used to oxidize methane by the well‐known aerobic pathway (Ettwig et al .…”

A novel mesocosm set-up reveals strong methane emission reduction in submerged peat moss Sphagnum cuspidatum by tightly associated methanotrophs

“…However, not all of the CH 4 produced reaches the atmosphere, due to methanotrophs that oxidize CH 4 to CO 2 [14, 15]. The oxidation of CH 4 is performed both aerobically (e-acceptor: O 2 ) by CH 4 -oxidizing bacteria (MOB), and anaerobically (AOM) by Archaea and bacteria (e-acceptors: nitrite, nitrate, metal-oxides, humic acids, and sulfate [16]). Both aerobic and anaerobic CH 4 oxidation contribute to the reduction of CH 4 emissions from peatlands [12, 17–19].…”