Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

Leafcutter ants enhance microbial drought resilience in tropical forest soil

We conducted a research campaign in a neotropical rainforest in Costa Rica throughout the drought phase of an El-Nino Southern Oscillation event to determine microbial community dynamics and soil C fluxes. Our study included nests of the leafcutter ant Atta cephalotes, as soil disturbances made by these ecosystem engineers may influence microbial drought response. Drought decreased the diversity of microbes and the abundance of core microbiome taxa, including Verrucomicrobial bacteria and Sordariomycete fungi. Despite initial responses of decreasing diversity and altered composition, 6 months post-drought the microbiomes were similar to pre-drought conditions, demonstrating the resilience of soil microbial communities to drought events. A. cephalotes nests altered fungal composition in the surrounding soil, and reduced both fungal mortality and growth of Acidobacteria post-drought. Drought increased CH4 consumption in soils due to lower soil moisture, and A. cephalotes nests decrease the variability of CH4 emissions in some soil types. CH4 emissions were tracked by the abundance of methanotrophic bacteria and fungal composition. These results characterize the microbiome of tropical soils across both time and space during drought and provide evidence for the importance of leafcutter ant nests in shaping soil microbiomes and enhancing microbial resilience during climatic perturbations.

Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle

Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.

The sanitary indoor environment-a potential source for intact human-associated anaerobes

A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

Methane Generation from Anthracite by Fungi and Methanogen Mixed Flora Enriched from Produced Water Associated with the Qinshui Basin in China

Biogenic coalbed methane (CBM) is generally believed to be formed by anaerobic bacteria and methanogens, while a few studies took fungi into account. Here, the microflora consisting of fungi and methanogens was enriched from the produced water associated with the Qinshui Basin using anthracite as the only carbon source. The maximum methane yield of 231 μmol/g coal was obtained after 22 days of cultivation under the optimum temperature of 35 °C, pH of 8, salinity of 0-2%, particle size of 0.075-0.150 mm, and the solid-liquid ratio of 1:30. It could remain active even after exposure to air for 24 h. Miseq results showed that the archaea were mainly composed of Methanocella, a hydrogenotrophic methanogen, followed by acetoclastic methanogen Methanosaeta and Methanosarcina, which could use various methanogenic substrates. The fungal communities mainly included Amorphotheca, Alternaria, Aspergillus, and Penicilium, which are all able to degrade complex organics such as aromatics and lignin. After cultivation, the crystal structure of anthracite became looser, as shown by XRD results, which might be due to the swelling effect caused by the destruction of the aromatic ring structure of coal under the function of fungi. The stretching vibration intensity of each functional group in coal decreased with cultivation, as revealed by FTIR. The GC-MS results showed that the concentration of alkanes and alcohols decreased significantly, which are the products of ring-opening of aromatics by fungi. These results suggested that fungi and methanogens in the coalbed also can syntrophically degrade coal effectively, especially for aromatics in coal.

Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments

Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.

Alternating Wet-Dry Cycles Rather than Sulfate Fertilization Control Pathways of Methanogenesis and Methane Turnover in Rice Straw-Amended Paddy Soil

Alternate wet-drying (AWD) and sulfate fertilization have been considered as effective methods for lowering CH₄ emissions from paddy soils. However, there is a clear knowledge gap between field studies that focus on the quantification of emissions and laboratory studies that investigate mechanisms. To elucidate mechanisms of CH₄ production and oxidation under field conditions, rice was planted in straw-amended mesocosms with or without sulfate fertilization under continuously flooded conditions (FL) or two wet-dry cycles. CO₂ and CH₄ concentrations in soil air and their natural C isotope compositions were measured at stem elongation, booting, and flowering stages. CH₄ concentration reached 51 mg C L^-1 at the flowering stage under FL, while it decreased to 0.04 mg C L^-1 under AWD. Relative ¹³C enrichment in CH₄ and depletion in CO₂ under AWD indicated CH₄ oxidation. Ample organic substrate supply may have reduced competition between sulfate-reducing bacteria and methanogenic archaea, and therefore, it explains the absence of a decrease in CH₄ concentrations in sulfate treatments. ¹³C enrichment in CO₂ over time (6 and 7‰ with and without sulfate fertilizers, respectively) under FL indicates continuous contribution of hydrogenotrophic methanogenesis to CH₄ production with ongoing rice growth. Overall, AWD could more efficiently reduce CH₄ production than sulfate fertilization in rice straw-amended paddy soils.

Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH₄ source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH₄ emissions across floodplain areas. Here, we report the in situ composition of CH₄ cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH₄ cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH₄ were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH₄ emissions in the region.

Biogeochemical transformation of greenhouse gas emissions from terrestrial to atmospheric environment and potential feedback to climate forcing

Carbon dioxide (CO₂) is mainly universal greenhouse gas associated with climate change. However, beyond CO₂, some other greenhouse gases (GHGs) like methane (CH₄) and nitrous oxide (N₂O), being two notable gases, contribute to global warming. Since 1900, the concentrations of CO₂ and non-CO₂ GHG emissions have been elevating, and due to the effects of the previous industrial revolution which is responsible for climate forcing. Globally, emissions of CO₂, CH₄, and N₂O from agricultural sectors are increasing as around 1% annually. Moreover, deforestation also contributes 12-17% of total global GHGs. Perhaps, the average temperature is likely to increase globally, at least 2 °C by 2100-by mid-century. These circumstances are responsible for climate forcing, which is the source of various human health diseases and environmental risks. From agricultural soils, rhizospheric microbial communities have a significant role in the emissions of greenhouse gases. Every year, microbial communities release approximately 1.5-3 billion tons of carbon into the atmospheric environment. Microbial nitrification, denitrification, and respiration are the essential processes that affect the nitrogen cycle in the terrestrial environment. In the twenty-first century, climate change is the major threat faced by human beings. Climate change adversely influences human health to cause numerous diseases due to their direct association with climate change. This review highlights the different anthropogenic GHG emission sources, the response of microbial communities to climate change, climate forcing potential, and mitigation strategies through different agricultural management approaches and microbial communities.

Relationship between soil solution electrochemical changes and methane and nitrous oxide emissions in different rice irrigation management systems

Rice (Oryza sativa L.) intermittent irrigation is a potential strategy to mitigate methane (CH₄) and nitrous oxide (N₂O) emissions, but the effects of dry-wetting intervals on soil electrochemical changes and plant characteristics should be considered. This study was conducted in a greenhouse evaluating CH₄ and N₂O fluxes in rice under five different irrigation management practices (continuous irrigation (CI), intermittent irrigation with flooding resumption in saturated soil condition (SSI) and soil moisture at field capacity (FCI), saturated soil and irrigation resumption with soil moisture bellow field capacity (FCS), and soil at field capacity (FCD)) and its relation to plant development and global warming potential (GWP). Soil electrochemical conditions and CH₄ and N₂O emissions were expressively affected by irrigation management. The CI system presented the greatest CH₄ flux (20.14 g m^-2) and GWP (462.7 g m^-2 eq. CO₂), whereas intermittent irrigation expressively reduced CH₄ emissions. Overall, the N₂O flux was low (bellow 20 μg m^-2 h^-1) even with N application, with greater emissions occurring at the FCD treatment at the beginning of the rice season. Soil moisture at field capacity had no CH₄ flux but presented greater GWP (271 g m^-2 eq. CO₂) than intermittent irrigation systems due to N₂O flux while compromising rice plant development. The best soil moisture condition to initiate a flooding cycle during intermittent irrigation is at saturated soil conditions.

The influence of soil temperature, methanogens and methanotrophs on methane emissions from cold waterlogged paddy fields

Paddy fields are major sources of atmospheric methane (CH₄). However, CH₄ emissions from cold-waterlogged paddy fields, a major type of paddy soil in China, remain unclear. Here we investigated the CH₄ emissions and associated influential factors in cold-waterlogged paddy fields at two sites (Yangxin County and Daye City) in Hubei Province, South China. Normal paddy fields matched with parental material and cropping system were used as the controls. The CH₄ emissions from cold-waterlogged fields were significantly higher than those from normal fields with (3.0-4.4-fold) or without (3.5-8.6-fold) rice. Rice planting increased CH₄ emissions by 59-78% in cold-waterlogged fields and by 85-247% in normal fields. CH₄ instantaneous fluxes were positively correlated with soil temperature and methanogen mcrA (methyl coenzyme M reductase alpha subunit) and methanotroph pmoA (methane monooxygenase) copy numbers at the annual scale. Under rice planting, mcrA copy number was higher in cold-waterlogged fields than in normal fields at both sites, whereas pmoA copy number had the same trend at the Daye site only. Soil temperature and water content influenced mcrA and pmoA copy numbers in the normal paddy fields, whereas soil organic matter content was more influential in the cold-waterlogged paddy fields. These findings suggest that perennial waterlogging is a prerequisite for substantial CH₄ emissions from cold-waterlogged paddy fields, and it promotes the proliferation of methanogens and methanotrophs under rice planting. Therefore, CH₄ production-oxidation processes are more active in cold-waterlogged paddy fields than in normal paddy fields.

The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China

Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.

Methylobacter accounts for strong aerobic methane oxidation in the Yellow River Delta with characteristics of a methane sink during the dry season

Recent investigations demonstrate that some coastal wetlands are atmospheric methane sinks, but the regulatory mechanisms are not clear. Here, the main pathway and operator of methane oxidation in the Yellow River Delta (YRD) wetland, a methane source in the wet season but a methane sink in the dry season, were investigated. The anaerobic oxidation of methane (AOM) and aerobic methane oxidation (AMO) abilities of wetland soil were measured, and the microbial community structure was analyzed. The experimental results showed that AMO was active throughout the year. In contrast, AOM was weak and even undetected. The microbial community analysis indicated that Methylomicrobium and Methylobacter potentially scavenged methane in oxic environments. A representative strain of Methylobacter, which was isolated from the soil, presented a strong AMO ability at high concentrations of methane and air. Overall, this study showed that active AMO performing by Methylobacter may account for methane sink in the YRD wetland during the dry season. Our research not only has determined the way in which methane sinks are formed but also identified the potential functional microbes. In particular, we confirmed the function of potential methanotroph by pure culture. Our research provides biological evidence for why some wetlands have methane sink characteristics, which may help to understand the global methane change mechanism.

Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions

Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.

Limited potential of harvest index improvement to reduce methane emissions from rice paddies

Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH₄ emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH₄ emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH₄ mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH₄ emissions under continuously flooded (CF) irrigation, it did not affect CH₄ emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH₄ emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH₄ mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management.

Hypoxia Remediation and Methane Emission Manipulation Using Surface Oxygen Nanobubbles

Algal blooms in eutrophic waters often induce anoxia/hypoxia and enhance methane (CH₄) emissions to the atmosphere, which may contribute to global warming. At present, there are very few strategies available to combat this problem. In this study, surface oxygen nanobubbles were tested as a novel approach for anoxia/hypoxia remediation and CH₄ emission control. Incubation column experiments were conducted using sediment and water samples taken from Lake Taihu, China. The results indicated that algae-induced anoxia/hypoxia could be reduced or reversed after oxygen nanobubbles were loaded onto zeolite micropores and delivered to anoxic sediment. Cumulated CH₄ emissions were also reduced by a factor of 3.2 compared to the control. This was mainly attributed to the manipulation of microbial processes using the surface oxygen nanobubbles, which potentially served as oxygen suppliers. The created oxygen-enriched environment simultaneously decreased methanogen but increased methanotroph abundances, making a greater fraction of organic carbon recycled as carbon dioxide (CO₂) instead of CH₄. The CH₄/CO₂ emission ratio decreased to 3.4 × 10^-3 in the presence of oxygen nanobubbles, compared to 11 × 10^-3 in the control, and therefore the global warming potential was reduced. This study proposes a possible strategy for anoxia/hypoxia remediation and CH₄ emission control in algal bloom waters, which may benefit global warming mitigation.

Impact of hydrochar on rice paddy CH4 and N2O emissions: A comparative study with pyrochar

Hydrothermal carbonization (HTC) thermally converts wet biomasses to carbon materials, dramatically reducing energy use for drying and improving solid product yield compared to pyrolysis process. However, researches regarding agricultural usage of hydrochar (HC) are limited. In the present study, the influence of HC amendment on CH₄ and N₂O emissions, as well as global warming potential (GWP) and greenhouse gas intensity (GHGI) were investigated. Additionally, pyrochar (PC) treatments as well as two char-free control treatments with (CKU) or without (CK) N fertilizer were also included for comparison. Chars were produced from wheat straw (WC) and saw dust (SC) and applied at different rates (0.5% and 3%, w/w). Both hydrochar and pyrochar decreased paddy CH₄ emissions when amended at a lower rate (0.5%) compared to CKU treatment, which was more obvious for pyrochar when applied at the rate of 3%. Contrarily, 3%-HC significantly stimulated CH₄ emissions, which were around 5 and 3 times higher than that of CKU for WC and SC, respectively. Furthermore, hydrochar showed the potential to decrease paddy N₂O emissions (6.06-32.32%) at both application rates. However, N₂O emissions with PC treatments varied depending on application rate (20.20-75.76%). GWP and GHGI values of 0.5%-HC and PC treatments were similar, 6.67-25.00% and 3.85-25.00% lower than those of CKU treatment, respectively. However, 3%-HC amendments led to significantly increased GWP and GHGI. This study suggested that application rate of hydrochar used in rice fields should be taken into serious consideration to fulfill its potential in GHGs mitigation and minimize environmental side effects.

Effects of turbulence on carbon emission in shallow lakes

Turbulent mixing is enhanced in shallow lakes. As a result, exchanges across the air-water and sediment-water interfaces are increased, causing these systems to be large sources of greenhouse gases. This study investigated the effects of turbulence on carbon dioxide (CO₂) and methane (CH₄) emissions in shallow lakes using simulated mesocosm experiments. Results demonstrated that turbulence increased CO₂ emissions, while simultaneously decreasing CH₄ emissions by altering microbial processes. Under turbulent conditions, a greater fraction of organic carbon was recycled as CO₂ instead of CH₄, potentially reducing the net global warming effect because of the lower global warming potential of CO₂ relative to CH₄. The CH₄/CO₂ flux ratio was approximately 0.006 under turbulent conditions, but reached 0.078 in the control. The real-time quantitative PCR analysis indicated that methanogen abundance decreased and methanotroph abundance increased under turbulent conditions, inhibiting CH₄ production and favoring the oxidation of CH₄ to CO₂. These findings suggest that turbulence may play an important role in the global carbon cycle by limiting CH₄ emissions, thereby reducing the net global warming effect of shallow lakes.

Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments

Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.

Methane emission from feather moss stands

Data from remote sensing and Eddy towers indicate that forests are not always net sinks for atmospheric CH₄ . However, studies describing specific sources within forests and functional analysis of microorganisms on sites with CH₄ turnover are scarce. Feather moss stands were considered to be net sinks for carbon dioxide, but received little attention to their role in CH₄ cycling. Therefore, we investigated methanogenic rates and pathways together with the methanogenic microbial community composition in feather moss stands from temperate and boreal forests. Potential rates of CH₄ emission from intact moss stands (n = 60) under aerobic conditions ranged between 19 and 133 pmol CH₄ h^-1 gdw^-1 . Temperature and water content positively influenced CH₄ emission. Methanogenic potentials determined under N₂ atmosphere in darkness ranged between 22 and 157 pmol CH₄ h^-1 gdw^-1 . Methane production was strongly inhibited by bromoethane sulfonate or chloroform, showing that CH₄ was of microbial origin. The moss samples tested contained fluorescent microbial cells and between 10⁴ and 10⁵ copies per gram dry weight moss of the mcrA gene coding for a subunit of the methyl CoM reductase. Archaeal 16S rRNA and mcrA gene sequences in the moss stands were characteristic for the archaeal families Methanobacteriaceae and Methanosarcinaceae. The potential methanogenic rates were similar in incubations with and without methyl fluoride, indicating that the CH₄ was produced by the hydrogenotrophic rather than aceticlastic pathway. Consistently, the CH₄ produced was depleted in ¹³ C in comparison with the moss biomass carbon and acetate accumulated to rather high concentrations (3-62 mM). The δ¹³ C of acetate was similar to that of the moss biomass, indicating acetate production by fermentation. Our study showed that the feather moss stands contained active methanogenic microbial communities producing CH₄ by hydrogenotrophic methanogenesis and causing net emission of CH₄ under ambient conditions, albeit at low rates.

Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China

Changes in land-uses and fertilization are important factors regulating methane (CH₄) emissions from paddy soils. However, the responses of soil CH₄ emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH₄ fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH₄ fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH₄ fluxes, whereas fertilization did not distinctly affect soil CH₄ fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH₄ fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH₄ fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH₄ fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH₄ emissions.

Mitigating effects of ex situ application of rice straw on CH4 and N2O emissions from paddy-upland coexisting system

The in situ application of rice straw enhances CH₄ emissions by a large margin. The ex situ application of rice straw in uplands, however, may mitigate total global warming potential (GWP) of CH₄ and N₂O emissions from paddy-upland coexisting systems. To evaluate the efficiency of this practice, two field trials were conducted in rice-rice-fallow and maize-rape cropping systems, respectively. Year-round measurements of CH₄ and N₂O emissions were conducted to evaluate the system-scaled GWP. The results showed that CH₄ accounted for more than 98% of GWP in paddy. Straw removal from paddy decreased 44.7% (302.1 kg ha⁻¹ yr⁻¹) of CH₄ emissions and 51.2% (0.31 kg ha⁻¹ yr⁻¹) of N₂O emissions, thus decreased 44.8% (7693 kg CO₂-eqv ha⁻¹ yr⁻¹) of annual GWP. N₂O accounted for almost 100% of GWP in upland. Straw application in upland had insignificant effects on CH₄ and N₂O emissions, which increased GWP only by 91 kg CO₂-eqv ha⁻¹ yr⁻¹. So, the transfer of straw from paddy to upland could decrease GWP by 7602 kg CO₂-eqv ha⁻¹ yr⁻¹. Moreover, straw retention during late rice season contributed to 88.2% of annual GWP increment. It is recommended to transfer early rice straw to upland considering GWP mitigation, nutrient recycling and labor cost.

Divergent responses of methanogenic archaeal communities in two rice cultivars to elevated ground-level O3

Inhibitive effect of elevated ground-level ozone (O3) on paddy methane (CH4) emission varies with rice cultivars. However, little information is available on its microbial mechanism. For this purpose, the responses of methane-metabolizing microorganisms, methanogenic archaea and methanotrophic bacteria to O3 pollution were investigated in the O3-tolerant (YD6) and the O3-sensitive (IIY084) cultivars at two rice growth stages in Free Air Concentration Elevation of O3 (O3-FACE) system of China. It was found that O3 pollution didn't change the abundances of Type I and Type II methanotrophic bacteria at two rice stages. For methanogenic archaea, their abundances in both cultivars were decreased by O3 pollution at the tillering stage. Furthermore, a greater negative influence on methanogenic archaeal community was observed on IIY084 than on YD6: at tillering stage, the alpha diversity indices of methanogenic archaeal community in IIY084 was decreased to a greater extent than in YD6; IIY084 shifted methanogenic archaeal community composition and decreased the abundances and the diversities of Methanosarcinaceae and Methanosaetaceae as well as the abundance of Methanomicrobiales, while the diversity of Methanocellaceae were increased in YD6. These findings indicate that the variations in the responses of paddy CH4 emission to O3 pollution between cultivars could result from the divergent responses of their methanogenic archaea.

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches

Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.

Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community

Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate

Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.

Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil

Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.

Methane dynamics in an alpine fen: a field-based study on methanogenic and methanotrophic microbial communities

Wetlands are important sources of the greenhouse gas methane (CH4). We provide an in situ study of CH4 dynamics in the permanently submerged soil of a Swiss alpine fen. Physico-chemical pore water analyses were combined with structural and microbiological analyses of soil cores at high vertical resolution down to 50 cm depth. Methanotrophs and methanogens were active throughout the depth profile, and highest abundance of active methanotrophs and methanogens [6.1 × 10(5) and 1.1 × 10(7) pmoA and mcrA transcripts (g soil)(-1), respectively] was detected in the uppermost 2 cm of the soil. Active methanotrophic communities in the near-surface zone, dominated by viable mosses, varied from the communities in the deeper zones, but further changes with depth were not pronounced. Apart from a distinct active methanogenic community in the uppermost sample, a decrease of acetoclastic Methanosaetaceae with depth was observed in concomitance with decreasing root surface area. Overall, root surface area correlated with mcrA transcript abundance and CH4 pore water concentrations, which peaked (137.1 μM) at 10 to 15 cm depth. Our results suggest that stimulation of methanogenesis by root exudates of vascular plants had a stronger influence on CH4 dynamics than stimulation of CH4 oxidation by O2 input.

Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil

The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.

Methanogenic pathway and fraction of CH(4) oxidized in paddy fields: seasonal variation and effect of water management in winter fallow season

A 2-year field and incubation experiment was conducted to investigate δ¹³C during the processes of CH₄ emission from the fields subjected to two water managements (flooding and drainage) in the winter fallow season, and further to estimate relative contribution of acetate to total methanogenesis (F_ac) and fraction of CH₄ oxidized (F_ox) based on the isotopic data. Compared with flooding, drainage generally caused CH₄, either anaerobically or aerobically produced, depleted in ¹³C. There was no obvious difference between the two in transport fractionation factor (ε_transport) and δ¹³C-value of emitted CH₄. CH₄ emission was negatively related to its δ¹³C-value in seasonal variation (P<0.01). Acetate-dependent methanogenesis in soil was dominant (60–70%) in the late season, while drainage decreased F_ac-value by 5–10%. On roots however, CH₄ was mostly produced through H₂/CO₂ reduction (60–100%) over the season. CH₄ oxidation mainly occurred in the first half of the season and roughly 10–90% of the CH₄ was oxidized in the rhizosphere. Drainage increased F_ox-value by 5–15%, which is possibly attributed to a significant decrease in production while no simultaneous decrease in oxidation. Around 30–70% of the CH₄ was oxidized at the soil-water interface when CH₄ in pore water was released into floodwater, although the amount of CH₄ oxidized therein might be negligible relative to that in the rhizosphere. CH₄ oxidation was also more important in the first half of the season in lab conditions and about 5–50% of the CH₄ was oxidized in soil while almost 100% on roots. Drainage decreased F_ox-value on roots by 15% as their CH₄ oxidation potential was highly reduced. The findings suggest that water management in the winter fallow season substantially affects F_ac in the soil and F_ox in the rhizosphere and roots rather than F_ac on roots and F_ox at the soil-water interface.

Dry/Wet cycles change the activity and population dynamics of methanotrophs in rice field soil

The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.

Eco-stoichiometric alterations in paddy soil ecosystem driven by phosphorus application

Agricultural fertilization may change processes of elemental biogeochemical cycles and alter the ecological function. Ecoenzymatic stoichiometric feature plays a critical role in global soil carbon (C) metabolism, driving element cycles, and mediating atmospheric composition in response to agricultural nutrient management. Despite the importance on crop growth, the role of phosphorous (P) in compliance with eco-stoichiometry on soil C and nitrogen (N) sequestration in the paddy field remains poorly understood in the context of climate change. Here, we collected soil samples from a field experiment after 6 years of chemical P application at a gradient of 0 (P-0), 30 (P-30), 60 (P-60), and 90 (P-90) kg ha⁻¹ in order to evaluate the role of P on stoichiometric properties in terms of soil chemical, microbial biomass, and eco-enzyme activities as well as greenhouse gas (GHG: CO₂, N₂O and CH₄) emissions. Continuous P input increased soil total organic C and N by 1.3–9.2% and 3%–13%, respectively. P input induced C and N limitations as indicated by the decreased ratio of C:P and N:P in the soil and microbial biomass. A synergistic mechanism among the ecoenzymatic stoichiometry, which regulated the ecological function of microbial C and N acquisition and were stoichiometrically related to P input, stimulated soil C and N sequestration in the paddy field. The lower emissions of N₂O and CH₄ under the higher P application (P-60 and P-90) in July and the insignificant difference in N₂O emission in August compared to P-30; however, continuous P input enhanced CO₂ fluxes for both samplings. There is a technical conflict for simultaneously regulating three types of GHGs in terms of the eco-stoichiometry mechanism under P fertilization. Thus, it is recommended that the P input in paddy fields not exceed 60 kg ha⁻¹ may maximize soil C sequestration, minimize P export, and guarantee grain yields.

Diel cycle of methanogen mcrA transcripts in rice rhizosphere

Methanogens are known to inhabit not only the anaerobic bulk soil but also the rhizosphere of rice plants. The release of root exudates, a major carbon source for CH4 production in the rhizosphere, is closely coupled to plant photosynthesis. In the present study we hypothesized that the diel cycle of plant photosynthetic activity may shape the structure and function of methanogens in the rhizosphere of rice. We performed a field experiment to determine the diel dynamics of methanogen mcrA and their transcripts in the rhizosphere and bulk soil. The chemistry of NH4 (+) , NO3 (-) , SO4 (2-) and Fe(II) in the rice rhizosphere remained constant over a diel sampling. The mcrA copy number and their transcripts were greater in the rice rhizosphere compared with the bulk soil, indicating the enhanced activity of methanogens in the rhizosphere. The hydrogenotrophic Methanomicrobiales in particular increased in the rhizosphere whereas Methanosarcinaceae were more abundant in the bulk soil. Both the phylogenetic affiliation and copy numbers of methanogen mcrA in the rice rhizosphere did not display diel dynamics. The mcrA transcripts, however, significantly increased in the night compared with the daytime. The diel pattern of physical factors like temperature appeared not to affect the methanogen dynamics. The response of mcrA transcripts is probably due to the plant attributes, which release less O2 from roots in the night and hence stimulate the methanogen gene transcription and activity compared with the daytime.

Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil

Intermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogen mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that both mcrA gene copies and mcrA transcripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance of mcrA genes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription of mcrA genes was reduced to a greater extent than the abundance of mcrA genes, resulting in very low mcrA transcript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance of mcrA transcripts than of mcrA genes in rice field soil.

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.