Impact of land-use changes on the methanotrophic community structure

Methane (CH4) is one of the most potent greenhouse gases and its increasing concentration in the Earth’s atmosphere is linked to today’s global warming. The types of land and land-use have an impact on net CH4 fluxes, e.g. wetlands are generally net CH4 emitters while upland forest soils are a sink for CH4. This project aimed to elucidate the effect of afforestation and reforestation on net CH4 fluxes and to determine the control of the CH4-oxidising bacteria (methanotrophs) on net CH4 flux rate. This was investigated using a combination of molecular (T-RFLP, cloning/sequencing, microarray) and activity-specific (PLFA-SIP) approaches. Several sites were selected to analyse soil methanotrophs under shrubs regenerating after a fire compared to a native mature forest (in New Zealand), and under bog, grass, heath, pine and birch vegetation (in Scotland). Furthermore, a simple bottom-up approach was applied to seasonal measurements of local net CH4 fluxes in Scotland. These were upscaled to annual values in order to estimate the contribution to the national CH4 budget for each habitat investigated. The effect on CH4 mitigation of the conversion of different types of non-forested habitat to forests was then estimated. Afforestation/reforestation was always found to induce net CH4 oxidation at rates much faster than previously estimated. This preliminary analysis suggests that heathland conversion to birch forest was beneficial in term of CH4 sinks but it also induced large and permanent losses of soil C. However, bog afforestation with pine trees can potentially neutralise the national CH4 emissions from non-forested areas, while preserving soil C stocks. This project also revealed that changes in net CH4 flux due to land-use changes were closely related to shifts in the structure of the methanotrophic community. The relative abundance of members of the USCα cluster (high-affinity methanotrophs) was a strong predictor of net CH4 fluxes. Finally, the sole presence of trees suggested a niche-specific adaptation of the methanotrophs, which may have been correlated to some of the soil characteristics

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate

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The fate of carbon in a mature forest under carbon dioxide enrichment

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1 5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3 5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7 10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7 11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests. © 2020, The Author(s), under exclusive licence to Springer Nature Limited

One fold, two functions: cytochrome P460 and cytochrome c′-β from the methanotroph Methylococcus capsulatus (Bath)

Nature is adept at utilising highly similar protein folds to carry out very different functions, yet the mechanisms by which this functional divergence occurs remain poorly characterised. In certain methanotrophic bacteria, two homologous pentacoordinate c-type heme proteins have been identified: a cytochrome P460 (cyt P460) and a cytochrome c′-β (cyt cp-β). Cytochromes P460 are able to convert hydroxylamine to nitrous oxide (N2O), a potent greenhouse gas. This reactivity is similar to that of hydroxylamine oxidoreductase (HAO), which is a key enzyme in nitrifying and methanotrophic bacteria. Cyt P460 and HAO both have unusual protein-heme cross-links, formed by a Tyr residue in HAO and a Lys in cyt P460. In contrast, cyts cp-β (the only known cytochromes c′ with a β-sheet fold) lack this crosslink and appears to be optimized for binding non-polar molecules (including NO and CO) without enzymatic conversion. Our bioinformatics analysis supports the proposal that cyt cp-β may have evolved from cyt P460 via a gene duplication event. Using high-resolution X-ray crystallography, UV-visible absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy, we have characterized the overall protein folding and active site structures of cyt cp-β and cyt P460 from the obligate methanotroph, Methylococcus capsulatus (Bath). These proteins display a similar β-sheet protein fold, together with a pattern of changes to the heme pocket regions and localised tertiary structure that have converted a hydroxylamine oxidizing enzyme into a gas-binding protein. Structural comparisons provide insights relevant to enzyme redesign for synthetic enzymology and engineering of gas sensor proteins. We also show the widespread occurrence of cyts cp-β and characterise their phylogeny

Microbial mechanisms of carbon priming effects revealed during the interaction of crop residue and nutrient inputs in contrasting soils

Agronomic practices such as crop residue return and additional nutrient supply are recommended to increase soil organic carbon (SOC) in arable farmlands. However, changes in the priming effect (PE) on native SOC mineralization in response to integrated inputs of residue and nutrients are not fully known. This knowledge gap along with a lack of understanding of microbial mechanisms hinders the ability to constrain models and reduce the uncertainty to predict carbon (C) sequestration potential. Using a 13C‐labelled wheat residue, this 126‐day incubation study examined the dominant microbial mechanisms that underpin the PE response to inputs of wheat residue and nutrients (nitrogen, phosphorus and sulfur) in two contrasting soils. The residue input caused positive PE through “co‐metabolism”, supported by increased microbial biomass, C and nitrogen (N) extracellular enzyme activities (EEAs), and gene abundance of certain microbial taxa (Eubacteria, β‐Proteobacteria, Acidobacteria, and Fungi). The residue input could have induced nutrient limitation, causing an increase in the PE via “microbial nutrient mining” of native soil organic matter, as suggested by the low C‐to‐nutrient stoichiometry of EEAs. At the high residue, exogenous nutrient supply (cf. no‐nutrient) initially decreased positive PE by alleviating nutrient mining, which was supported by the low gene abundance of Eubacteria and Fungi. However, after an initial decrease in PE at the high residue with nutrients, the PE increased to the same magnitude as without nutrients over time. This suggests the dominance of “microbial stoichiometry decomposition”, supported by higher microbial biomass and EEAs, while Eubacteria and Fungi increased over time, at the high residue with nutrients cf. no‐nutrient in both soils. Our study provides novel evidence that different microbial mechanisms operate simultaneously depending on organic C and nutrient availability in a residue‐amended soil. Our results have consequences for SOC modelling and integrated nutrient management employed to increase SOC in arable farmlands

Methane, microbes and models : fundamental understanding of the soil methane cycle for future predictions

Methane is an important greenhouse gas and microbes in the environment play major roles in both global methane emissions and terrestrial sinks. However, a full mechanistic understanding of the response of the methane cycle to global change is lacking. Recent studies suggest that a number of biological and environmental processes can influence the net flux of methane from soils to the atmosphere but the magnitude and direction of their impact are still debated. Here, we synthesize recent knowledge on soil microbial and biogeochemical process and the impacts of climate change factors on the soil methane cycle. We focus on (i) identification of the source and magnitude of methane flux and the global factors that may change the flux rate and magnitude in the future, (ii) the microbial communities responsible for methane production and terrestrial sinks, and (iii) how they will respond to future climatic scenarios and the consequences for feedback responses at a global scale. We also identify the research gaps in each of the topics identified above, provide evidence which can be used to demonstrate microbial regulation of methane cycle and suggest that incorporation of microbial data from emerging -omic technologies could be harnessed to increase the predictive power of simulation models