Response of methanotrophic communities to afforestation and reforestation in New Zealand

Alfalfa-grass mixtures reduce greenhouse gas emissions and net global warming potential while maintaining yield advantages over monocultures

Improving forage productivity with lower greenhouse gas (GHG) emissions from limited grassland has been a hotspot of interest in global agricultural production. In this study, we analyzed the effects of grasses (tall fescue, smooth bromegrass), legume (alfalfa), and alfalfa-grass (alfalfa + smooth bromegrass and alfalfa + tall fescue) mixtures on GHG emissions, net global warming potential (Net GWP), yield-based greenhouse gas intensity (GHGI), soil chemical properties and forage productivity in cultivated grassland in northwest China during 2020-2021. Our results demonstrated that alfalfa-grass mixtures significantly improved forage productivity. The highest total dry matter yield (DMY) during 2020 and 2021 was obtained from alfalfa-tall fescue (11,311 and 13,338 kg ha^-1) and alfalfa-smooth bromegrass mixtures (10,781 and 12,467 kg ha^-1). The annual cumulative GHG emissions from mixtures were lower than alfalfa monoculture. Alfalfa-grass mixtures significantly reduced GHGI compared with the grass or alfalfa monocultures. Furthermore, results indicated that grass, alfalfa and alfalfa-grass mixtures differentially affected soil chemical properties. Lower soil pH and C/N ratio were recorded in alfalfa monoculture. Alfalfa and mixtures increased soil organic carbon (SOC) and soil total nitrogen (STN) contents. Importantly, alfalfa-grass mixtures are necessary for improving forage productivity and mitigating the GHG emissions in this region. In conclusion, the alfalfa-tall fescue mixture lowered net GWP and GHGI in cultivated grassland while maintaining high forage productivity. These advanced agricultural practices could contribute to the development of climate-sustainable grassland production in China.

Responses of soil greenhouse gas emissions to land use conversion and reversion-A global meta-analysis

Exploring the responses of greenhouse gas (GHG) emissions to land use conversion or reversion is significant for taking effective land use measures to alleviate global warming. A global meta-analysis was conducted to analyze the responses of carbon dioxide (CO₂ ), methane (CH₄ ), and nitrous oxide (N₂ O) emissions to land use conversion or reversion, and determine their temporal evolution, driving factors, and potential mechanisms. Our results showed that CH₄ and N₂ O responded positively to land use conversion while CO₂ responded negatively to the changes from natural herb and secondary forest to plantation. By comparison, CH₄ responded negatively to land use reversion and N₂ O also showed negative response to the reversion from agricultural land to forest. The conversion of land use weakened the function of natural forest and grassland as CH₄ sink and the artificial nitrogen (N) addition for plantation increased N source for N₂ O release from soil, while the reversion of land use could alleviate them to some degree. Besides, soil carbon would impact CO₂ emission for a long time after land use conversion, and secondary forest reached the CH₄ uptake level similar to that of primary forest after over 40 years. N₂ O responses had negative relationships with time interval under the conversions from forest to plantation, secondary forest, and pasture. In addition, meta-regression indicated that CH₄ had correlations with several environmental variables, and carbon-nitrogen ratio had contrary relationships with N₂ O emission responses to land use conversion and reversion. And the importance of driving factors displayed that CO₂ , CH₄ , and N₂ O response to land use conversion and reversion was easily affected by NH₄ ⁺ and soil moisture, mean annual temperature and NO₃ ^- , total nitrogen and mean annual temperature, respectively. This study would provide enlightenments for scientific land management and reduction of GHG emissions.

Soil Properties Interacting With Microbial Metagenome in Decreasing CH4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation

Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcrA and pmoA genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcrA and pmoA genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling.

Characterizing the post-monsoon CO2, CH4, N2O, and H2O vapor fluxes from a tropical wetland in the Himalayan foothill

Wetlands are emitters of greenhouse gases. However, many of the wetlands remain understudied (like temperate, boreal, and high-altitude wetlands), which constrains the global budgets. Himalayan foothill is one such data-deficient area. The present study reported (for the first time) the greenhouse gas fluxes (CO₂, CH₄, N₂O, and H₂O vapor) from the soils of the Nakraunda wetland of Uttarakhand in India during the post-monsoon season (October 2020 to January 2021). The sampling points covered six different types of soil within the wetlands. CO₂, CH₄, N₂O, and H₂O vapor emissions ranged from 82.89 to 1052.13 mg m^-2 h^-1, 0.56 to 2.25 mg m^-2 h^-1, 0.18 to 0.40 mg m^-2 h^-1, and 557.96 to 29,397.18 mg m^-2 h^-1, respectively, during the study period. Except for CO₂, the other three greenhouse gas effluxes did not show any spatial variability. Soils close to "swamp proper" emitted substantially higher CO₂ than the vegetated soils. Soil temperature exhibited exponential relationships with all the greenhouse gas fluxes, except for H₂O vapor. The Q₁₀ values for CO₂, CH₄, and N₂O varied from 3.42 to 4.90, 1.66 to 2.20, and 1.20 to 1.30, respectively. Soil moisture showed positive relationships with all the greenhouse gas fluxes, except for N₂O. The fluxes observed from Nakraunda were in parity with global observations. However, this study showed that wetlands experiencing lower temperature regime are also capable of emitting a substantial amount of greenhouse gases and thus, requires more study. Considering the seasonality of greenhouse gas fluxes should improve global wetland emission budgets.

Differential response of soil CO2 , CH4 , and N2 O emissions to edaphic properties and microbial attributes following afforestation in central China

Land use change specially affects greenhouse gas (GHG) emissions, and it can act as a sink/source of GHGs. Alterations in edaphic properties and microbial attributes induced by land use change can individually/interactively contribute to GHG emissions, but how they predictably affect soil CO₂ , CH₄ , and N₂ O emissions remain unclear. Here, we investigated the direct and indirect controls of edaphic properties (i.e., dissolved organic carbon [DOC], soil organic C, total nitrogen, C:N ratio, NH4+ -N, NO3- -N, soil temperature [ST], soil moisture [SM], pH, and bulk density [BD]) and microbial attributes (i.e., total phospholipid fatty acids [PLFAs], 18:1ω7c, nitrifying genes [ammonia-oxidizing archaea, ammonia-oxidizing bacteria], and denitrifying genes [nirS, nirK, and nosZ]) over the annual soil CO₂ , CH₄ , and N₂ O emissions from the woodland, shrubland, and abandoned land in subtropical China. Soil CO₂ and N₂ O emissions were higher in the afforested lands (woodland and shrubland) than in the abandoned land, but the annual cumulative CH₄ uptake did not significantly differ among all land use types. The CO₂ emission was positively associated with microbial activities (e.g., total PLFAs), while the CH₄ uptake was tightly correlated with soil environments (i.e., ST and SM) and chemical properties (i.e., DOC, C:N ratio, and NH4+ -N concentration), but not significantly related to the methanotrophic bacteria (i.e., 18:1ω7c). Whereas, soil N₂ O emission was positively associated with nitrifying genes, but negatively correlated with denitrifying genes especially nosZ. Overall, our results suggested that soil CO₂ and N₂ O emissions were directly dependent on microbial attributes, and soil CH₄ uptake was more directly related to edaphic properties rather than microbial attributes. Thus, different patterns of soil CO₂ , CH₄ , and N₂ O emissions and associated controls following land use change provided novel insights into predicting the effects of afforestation on climate change mitigation outcomes.

Soil aeration rather than methanotrophic community drives methane uptake under drought in a subtropical forest

Little information is available about the effects of drought on soil methane (CH₄) uptake and the underlying feedback of the soil microbial community in forest biomes. More importantly, a meta-analysis of the current literature on this topic revealed that there are virtually no data available in subtropical forests. To fill the abovementioned knowledge gap, we carried out a 3-year investigation of in situ CH₄ efflux under drought in a subtropical forest, and found that drought significantly increased soil CH₄ uptake (P < 0.001). However, drought did not change oxidation potentials and abundances of methanotrophs, and similar methanotrophic communities were observed between the drought and ambient control sites based on metagenomic sequencing analysis. Active methanotrophic communities were dominated by the genus Methylosinus based on DNA stable-isotope probing analysis. Structural equation model analysis indicated that direct drought-derived pathway, i.e., increasing soil aerations, outweighs the indirect pathway, i.e., altering methanotrophic communities and activities, and plays a predominant role in driving soil CH₄ uptake in forest ecosystems. To our knowledge, our work is the first study to investigate the effects of drought on in situ CH₄ efflux and the underlying microbial mechanisms in subtropical forests.

Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community

Soil-to-atmosphere methane (CH₄) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil–vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil/vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO₂) and CH₄ fluxes and their production/consumption at 5 cm intervals to a depth of 30 cm. All soils were sources of CO₂, ranging from 49 to 93 mg CO₂ m⁻² h⁻¹. Forest soils were strong net sinks for CH₄, at rates of up to −413 µg CH₄ m⁻² h⁻¹. Grassland soils varied, with some soils acting as sources and some as sinks, but overall averaged −97 µg CH₄ m⁻² h⁻¹. Bog soils were net sources of CH₄ (+340 µg CH₄ m⁻² h⁻¹). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis in the bog soils. Methylocystis were also detected at relatively low abundance in all soils. Our study suggests that there is a disproportionately large contribution of these ecosystems to the global soil CH₄ sink, which highlights our dependence on soil ecosystem services in remote locations driven by unique populations of soil microbes. It is paramount to explore and understand these remote, hard-to-reach ecosystems to better understand biogeochemical cycles that underpin global sustainability.

Manipulation of soil methane oxidation under drought stress

Drought events are predicted to occur more frequently, but comprehensive knowledge of their effects on methane (CH₄) oxidation by soil methanotrophs in upland ecosystems remains elusive. Here, we put forward a new conceptual model in which drought influences soil CH₄ oxidation through a direct pathway (i.e., positive effects of soil CH₄ oxidation via increasing soil aeration) and through an indirect pathway (i.e., negative effects of in planta ethylene (C₂H₄) production on soil CH₄ oxidation). Through measuring soil CH₄ efflux along a gradient of drought stress, we found that drought increases soil CH₄ oxidation, as the former outweighs the latter on soil CH₄ oxidation, based on a mesocosm experiment employing distinct levels of watering and a long-term drought field trial created by rainfall exclusion in a subtropical evergreen forest. Moreover, we used aminoethoxyvinylglycine (AVG), a C₂H₄ biosynthesis inhibitor, to reduce in planta C₂H₄ production under drought, and found that reducing in planta C₂H₄ production increased soil CH₄ oxidation under drought. To confirm these findings, we found that inoculation of plant growth-promoting rhizobacteria containing the 1-aminocyclopropane-1-carboxylate deaminase alleviated the negative effects of drought-induced in planta C₂H₄, thus increasing soil CH₄ oxidation rates. All these results provide strong evidence for the hypothesis that in planta C₂H₄ production inhibits soil CH₄ oxidation under drought. To our knowledge, this is the first study to manipulate the negative feedback between C₂H₄ production and CH₄ oxidation under drought stress. Given the current widespread extent of arid and semiarid regions in the world, combined with the projected increased frequency of drought stress in future climate scenarios, we provide a reliable means for increasing soil CH₄ oxidation in the context of global warming.

The response of methanotrophs to additions of either ammonium, nitrate or urea in alpine swamp meadow soil as revealed by stable isotope probing

Different forms of nitrogen (N) are deposited on the Qinghai-Tibetan plateau (QTP), while their differential effects on soil methanotrophs and their activity remain elusive. We constructed microcosms amended with different N fertilizers (ammonia, nitrate and urea) using the soils sampled from a swamp meadow on the QTP. The responses of active methanotrophs to different forms of nitrogen were determined by stable isotope probing with 5% 13C-methane. At the early stage of incubation, all N fertilizers, especially urea, suppressed methane oxidation compared with the control. The methane oxidation rate increased during the incubation, suggesting an adaptation and stimulation of some methanotrophs to elevated methane. At the onset of the incubation, the type II methanotrophs Methylocystis were most abundant, but decreased during the incubation and were replaced by the type Ia methanotrophs Methylomonas. Ammonia and urea had similar effects on the methanotroph communities, both characterized by an elevation in the proportion of Methylobacter and more diverse methanotroph communities. Nitrate had less effect on the methanotroph community. Our results uncovered the active methanotrophs responding to different nitrogen forms, and suggested that urea-N might have large effects on methanotroph diversity and activity in swamp meadow soils on the QTP.

Changes in soil greenhouse gas fluxes by land use change from primary forest

Primary forest conversion is a worldwide serious problem associated with human disturbance and climate change. Land use change from primary forest to plantation, grassland or agricultural land may lead to profound alteration in the emission of soil greenhouse gases (GHG). Here, we conducted a global meta-analysis concerning the effects of primary forest conversion on soil GHG emissions and explored the potential mechanisms from 101 studies. Our results showed that conversion of primary forest significantly decreased soil CO2 efflux and increased soil CH4 efflux, but had no effect on soil N2 O efflux. However, the effect of primary forest conversion on soil GHG emissions was not consistent across different types of land use change. For example, soil CO2 efflux did not respond to the conversion from primary forest to grassland. Soil N2 O efflux showed a prominent increase within the initial stage after conversion of primary forest and then decreased over time while the responses of soil CO2 and CH4 effluxes were consistently negative or positive across different elapsed time intervals. Moreover, either within or across all types of primary forest conversion, the response of soil CO2 efflux was mainly moderated by changes in soil microbial biomass carbon and root biomass while the responses of soil N2 O and CH4 effluxes were related to the changes in soil nitrate and soil aeration-related factors (soil water content and bulk density), respectively. Collectively, our findings highlight the significant effects of primary forest conversion on soil GHG emissions, enhance our knowledge on the potential mechanisms driving these effects and improve future models of soil GHG emissions after land use change from primary forest.

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.

Eutrophication influences methanotrophic activity, abundance and community structure in freshwater lakes

Lake is an important natural source of methane, a potential greenhouse gas, in the atmosphere. Aerobic methanotrophs can consume a notable proportion of the methane produced in lacustrine ecosystems. However, previous studies mainly focused on aerobic methanotrophs in deep and oligotrophic lakes, while little is known about these organisms in shallow and eutrophic lakes. Lake eutrophication leads to more abundant substrates for methanogenesis, and a subsequent higher methane flux. Therefore, the methanotrophs in eutrophic lakes might play a more important role in mediating lacustrine methane emission. In the current study, aerobic methanotrophs in the sediments of two adjacent shallow freshwater lakes at different trophic status (mesotrophic and eutrophic, respectively) were investigated. Abundant methanotrophs and active aerobic methane oxidation were observed in both lakes. While the eutrophic lake harbored a higher abundance of methanotrophs. The result of pmoA-based high-throughput sequencing suggested that methanotrophic communities in the two studied lakes were dominated by unique groups (Type Ib and Type II), dependent on lake and season. But generally, eutrophication might lead to a higher proportion of Type II methanotrophs. The abundance and uniqueness of methanotrophic community could be attributed to lake eutrophication, and were regulated by environmental variables of both sediment and overlying water. This work provides a new insight towards methanotrophs in shallow freshwater lake impacted by eutrophication.

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities

The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of forest soil advances our understanding of forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.

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.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Changes in soil moisture drive soil methane uptake along a fire regeneration chronosequence in a eucalypt forest landscape

Disturbance associated with severe wildfires (WF) and WF simulating harvest operations can potentially alter soil methane (CH4 ) oxidation in well-aerated forest soils due to the effect on soil properties linked to diffusivity, methanotrophic activity or changes in methanotrophic bacterial community structure. However, changes in soil CH4 flux related to such disturbances are still rarely studied even though WF frequency is predicted to increase as a consequence of global climate change. We measured in-situ soil-atmosphere CH4 exchange along a wet sclerophyll eucalypt forest regeneration chronosequence in Tasmania, Australia, where the time since the last severe fire or harvesting disturbance ranged from 9 to >200 years. On all sampling occasions, mean CH4 uptake increased from most recently disturbed sites (9 year) to sites at stand 'maturity' (44 and 76 years). In stands >76 years since disturbance, we observed a decrease in soil CH4 uptake. A similar age dependency of potential CH4 oxidation for three soil layers (0.0-0.05, 0.05-0.10, 0.10-0.15 m) could be observed on incubated soils under controlled laboratory conditions. The differences in soil CH4 uptake between forest stands of different age were predominantly driven by differences in soil moisture status, which affected the diffusion of atmospheric CH4 into the soil. The observed soil moisture pattern was likely driven by changes in interception or evapotranspiration with forest age, which have been well described for similar eucalypt forest systems in south-eastern Australia. Our results imply that there is a large amount of variability in CH4 uptake at a landscape scale that can be attributed to stand age and soil moisture differences. An increase in severe WF frequency in response to climate change could potentially increase overall forest soil CH4 sinks.

Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties

Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAIC(c) = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAIC(c) = 12.02], and the abundance of one denitrifier genotype [ΔAIC(c) = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). This approach provides a valuable tool for explicitly linking microbial communities to ecosystem functioning. By making this link, we have demonstrated that including aspects of microbial community structure and diversity in biogeochemical models can improve predictions of nutrient cycling in ecosystems and enhance our understanding of ecosystem functionality.

Landscape position influences microbial composition and function via redistribution of soil water across a watershed

Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R = 0.72, P < 0.001) and negatively with soil oxygen (R = -0.53, P = 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.

Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application

Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing, and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over 2 months. Unexpectedly, after amendments with specific residues, we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

To what extent can zero tillage lead to a reduction in greenhouse gas emissions from temperate soils?

Soil tillage practices have a profound influence on the physical properties of soil and the greenhouse gas (GHG) balance. However there have been very few integrated studies on the emission of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) and soil biophysical and chemical characteristics under different soil management systems. We recorded a significantly higher net global warming potential under conventional tillage systems (26-31% higher than zero tillage systems). Crucially the 3-D soil pore network, imaged using X-ray Computed Tomography, modified by tillage played a significant role in the flux of CO2 and CH4. In contrast, N2O flux was determined mainly by microbial biomass carbon and soil moisture content. Our work indicates that zero tillage could play a significant role in minimising emissions of GHGs from soils and contribute to efforts to mitigate against climate change.

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.

Evidence of microbial regulation of biogeochemical cycles from a study on methane flux and land use change

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.

Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients

The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.