Acute impact of agriculture on high-affinity methanotrophic bacterial populations

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils

Organic fertilizers have been shown to stimulate CH₄ uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH₄ oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO₂ and N₂O differed considerably between the treatments, CH₄ fluxes remained stable. In contrast, in vitro CH₄ oxidation showed a clear increase for all amendments over time. CO₂ fluxes were mostly dependent on the amount of organic residue that was used, while N₂O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO₂, CH₄, and/or N₂O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms

Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.

The influence of nitrogen fertiliser rate and crop rotation on soil methane flux in rain-fed potato fields in Wuchuan County, China

As one of the important greenhouse gases, the characteristics and principles of methane exchange characteristics in cultivated lands have become hot topics in current climate change research. This study examines the influences of nitrogen fertilisation, temperature and soil water content on methane exchange characteristic and methane exchange functional gene-pmoA gene abundance based on experimental observations of methane exchange fluxes using the static chamber-gas chromatographic method and measurements of methanotroph gene copy numbers in three growing periods by real-time PCR in rain-fed potato fields. The results indicate that the rain-fed potato fields were a CH4 sink with an average annual methane absorption (negative emission) of 940.8±103.2 g CH4-C/ha/year. The cumulative methane absorption first exhibited flat and subsequently increasing trend with the increase of nitrogen fertilisation from 0~135 kg N·ha(-1). Methane cumulative absorption significantly increased with the increase of temperature when temperatures were below 19.6 °C. Methane oxidation capacity (methanotroph pmoA gene copy numbers) showed an increasing and subsequently decreasing trend with the increase of soil moisture. Crop rotation was observed to increase the methane absorption in rain-fed potato fields and nearly one time higher than that under continuous cropping. A mechanism concept model of the methane exchange in rain-fed potato fields was advanced in this paper.

Environmental impacts on the diversity of methane-cycling microbes and their resultant function

Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5–15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters.

Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane

Agriculture has marked impacts on the production of carbon dioxide (CO(2)) and consumption of methane (CH(4)) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH(4). To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH(4)-oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH(4) and CO(2) at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH(4) consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH(4) consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH(4) consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO(2) emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH(4) oxidation, as compared with processes driven by widely distributed metabolic processes, like CO(2) production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

Methanotrophic communities in Brazilian ferralsols from naturally forested, afforested, and agricultural sites

Conversion of forests to farmland permanently lowers atmospheric methane consumption due to unresolved reasons. Alphaproteobacterial methanotrophs were predominant in forested soils and gammaproteobacterial species were predominant in farmland soils of subtropical ferralsols in Brazil. The capability of atmospheric methane consumption was obliterated in farmland soils, suggesting a shift from oligotrophic to copiotrophic species.

Substantial high-affinity methanotroph populations in Andisols effect high rates of atmospheric methane oxidation

Methanotrophic bacteria in soils derived from volcanic ash (Andisols) were characterized via time series (13) C-phospholipid fatty acid (PLFA) labelling. Three Andisols were incubated under 2 ppmv (13) CH4 for up to 18 weeks, thus enabling high-affinity methanotrophs to be selectively characterized and quantified. PLFA profiles from all soils were broadly similar, but the magnitude of the high-affinity methanotrophic populations determined through (13) C-PLFA-stable isotope probing displayed sizeable differences. Substantial incorporation of (13) C indicated very large high-affinity methanotrophic populations in two of the soils. Such high values are far in excess (10×) of those observed for a range of mineral soils incubated under similar conditions (Bull et al., 2000; Maxfield et al., 2006; 2008a, b). Two of the three Andisols studied also displayed high but variable CH4 oxidation rates ranging from 0.03 to 1.58 nmol CH4 g(-1) d.wt. h(-1) . These findings suggest that Andisols, a previously unstudied soil class with respect to high-affinity methanotrophic bacteria, may oxidize significant amounts of atmospheric methane despite their low areal coverage globally.

The quest for atmospheric methane oxidizers in forest soils

Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1)   DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.

Links between methanotroph community composition and CH oxidation in a pine forest soil

The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.

Aerobic methanol-oxidizing bacteria in soil

Methanol is an atmospheric compound that is primarily released from plant polymers and impacts ozone formation. The global methanol emission rate from terrestrial ecosystems is of the same order of magnitude (4.9 x 10(12) mol year(-1)) as that of methane (10 x 10(12) mol year(-1)). The major proportion of the annual plant-released methanol does not enter the atmosphere, but may be reoxidized by biological methanol oxidation, which is catalyzed by methanol-oxidizing prokaryotes. Fifty-six aerobic methanol-oxidizing species have been isolated from soils. These methylotrophs belong to the Alpha-, Beta-, and Gammaproteobacteria, Verrucomicrobia, Firmicutes, and Actinobacteria. Their ecological niches are determined by oxygen and methanol concentration, temperature, pH, the capability to utilize nitrate as an electron acceptor, and the spectrum of nitrogen sources and utilizable multicarbon substrates. Recently discovered interactions with eukaryotes indicate that their ecological niches may not solely be defined by physicochemical parameters. Nonetheless, there are still gaps in knowledge; based on global methanol budgets, methanol oxidation in soil is important, but has not been addressed adequately by biogeochemical studies. Ratios of above-ground and soil-internal methanol oxidation are not known. The contribution to methanol-oxidation by aerobic and anaerobic methylotrophs in situ also needs further research.

Physical and biological controls on the in situ kinetic isotope effect associated with oxidation of atmospheric CH4 in mineral soils

The amounts and delta(13)C values of CH4 at subambient concentrations in soil gas were determined along depth profiles in a U.K. grassland (Bronydd Mawr) and woodland (Leigh Woods). The data were used to determine in situ kinetic isotope effects (KIEs) associated with uptake of atmospheric CH4 by high-affinity methanotrophic bacteria that inha bit soil. Three independent calculation approaches yielded similar mean KIEs of 1.0211 +/- 0.0020 (n=18) for Bronydd Mawr and 1.0219 +/- 0.0010 (n=24) for Leigh Woods. Soil methanotrophy KIEs were largely invariant among oak, beech, and pine forest soils of different ages at Leigh Woods but exhibited a statistically significant relationship with methanotroph biomass in individual plots at Bronydd Mawr and Leigh Woods quantified previously by 13C stable isotope probing. This finding, albeit based upon a small data set suggests that 13C and 12C partitioning associated with the global soil sink for atmospheric CH4 may occur in part as a result of biological as well as physical processes. An accurate assessment of the relative importance of each process to the total KIE requires confirmation that significant partitioning of (13)CH4 and (12)CH4 occurs in pore spaces as a result of differences in diffusion rates.