Methanogenic Soil Research Articles

Reindeer shape soil methanogenic and methanotrophic communities in subarctic fen peatlands, with a minor impact on methane emissions — A field study

Laboratory and field studies with other grazer species suggest that reindeer (Rangifer tarandus L.) grazing on northern peatlands could shape the peat soil microbial communities and lead to higher ecosystem methane (CH4) emissions. We investigated this at two sedge fens in northern Finland, Lompolojänkkä and Halssiaapa, in experiments where reindeer grazing presence or absence was achieved with exclosure fences, and the effects of reindeer droppings were evaluated comparing dropping additions either on peat surface or trampled into the peat to controls with no droppings. Active soil methanogen and methanotroph communities were analyzed by metatranscriptomics. Soil CH4 fluxes were quantified with manual chambers and portable gas analyzer. Reindeer presence and dropping additions were both connected to differences in the soil communities as compared to controls (no presence or no droppings). The responses differed between the two fens. Activity of rumen microbes in peat could not be detected. Structural equation models indicated that the ecosystem CH4 flux in both fens depended on measurement year and sedge leaf area. At Halssiaapa trampled droppings, and at Lompolojänkkä both surface and trampled droppings reduced the sedge leaf area. While at Halssiaapa the dropping effect was not altogether statistically significant, in Lompolojänkkä surface droppings reduced the CH4 flux both directly and through the reduced leaf area. In conclusion, while both reindeer presence and dropping addition were diversely reflected in the active soil communities, reindeer effects on the CH4 flux were indirect and mediated via vegetation. The results contrast our earlier laboratory findings, and i) caution against liberal generalizations from lab studies to field conditions in peatlands, as well as ii) point to a need for rigorous multivariate analyses for deciphering the complex interactions governing the functions of these ecosystems.

Effects of ant nests on soil CH4 emissions from Syzygium oblatum communities of a secondary tropical forest.

Exploring the effects of ant nests on soil CH4 emissions in the secondary tropical forests is of great scientific significance to understand the contribution of soil faunal activities to greenhouse gas emissions. With static chamber-gas chromatography method, we measured the dry-wet seasonal dynamics of CH4 emissions from ant nests and control soils in the secondary forest of Syzygium oblatum communities in Xishuangbanna. We also examined the linkages of ant-mediated changes in functional microbial diversity and soil physicochemical properties with CH4 emissions. The results showed that: 1) Ant nests significantly accelerated soil CH4 emissions, with average CH4 emissions in the ant nests being 2.6-fold of that in the control soils. 2) The CH4 emissions had significant dry-wet seasonal variations, which was a carbon sink in the dry seasons (from -0.29±0.03 to -0.53±0.02 μg·m-2·h-1) and a carbon source in the wet seasons (from 0.098±0.02 to 0.041±0.009 μg·m-2·h-1). The CH4 emissions were significantly higher in ant nests than in control soils. The CH4 emissions from the ant nests had smaller dry-wet seasonal variation (from -0.38±0.01 to 0.12±0.02 μg·m-2·h-1) than those in the control soils (from -0.65±0.04 to 0.058±0.006 μg·m-2·h-1). 3) Ant nests significantly increased the values (6.2%-37.8%) of soil methanogen diversity (i.e., Ace and Shannon indices), temperature and humidity, carbon pools (i.e., total, easily oxidizable, and microbial carbon), and nitrogen pools (i.e., total, hydrolyzed, ammonium, and microbial biomass nitrogen), but decreased the diversity (i.e., Ace and Chao1 indices) of methane-oxidizing bacteria by 21.9%-23.8%. 4) Results of the structural equation modeling showed that CH4 emissions were promoted by soil methanogen diversity, temperature and humidity, and C and N pools, but inhibited by soil methane-oxidizing bacterial diversity. The explained extents of soil temperature, humidity, carbon pool, nitrogen pool, methanogen diversity, and methane-oxidizing bacterial diversity for the CH4 emission changes were 6.9%, 21.6%, 18.4%, 15.2%, 14.0%, and 10.8%, respectively. Therefore, ant nests regulated soil CH4 emission dynamics through altering soil functional bacterial diversities, micro-habitat, and carbon and nitrogen pools in the secondary tropical forests.

Differences in Methanogenic Pathways and Communities in Paddy Soils Under Three Typical Cropping Modes

AbstractThe methane (CH4) production process in paddy fields varies depending on different cropping modes. However, there is limited knowledge on the changes in anaerobically produced CH4 isotopic ratios (δ13CH4), the methanogenic pathways, and the dominant communities of methanogens in paddy soils under different modes. To address this, we conducted experiments using anaerobic incubation methods, stable carbon isotope fractionation through inhibition studies with fluoromethane, and high‐throughput sequencing. These methods allowed us to measure the CH4 production potential (MPP), the relative contribution of acetoclastic methanogenesis to CH4 production (fac), and the composition of the methanogen community in paddy soils under three typical cropping modes: Rice‐Wheat (RW), Rice‐Fallow (RF), and Double‐Rice (DR) in China. The results showed that MPP was 30.7 μg CH4 g−1 d−1 in DR soil, around 57% and 66% higher than that in RW and RF soils, respectively, possibly due to the lower pH, clay content, and higher abundance of the mcrA gene. Moreover, RF soil had the highest value of produced δ13CH4 (−43.9‰) but the lowest value of produced δ13CO2 (−26.3‰). Based on the carbon isotope fractionation associated with methanogenesis via H2/CO2 reduction (1.049–1.062), the values of fac estimated in the RF soil (80%–98%) were much higher than that in the RW (39%–60%) and DR soils (52%–75%). This could be supported by the finding showing that Methanosarcina, the acetoclastic methanogens, were dominant in RF soil, while Methanosarcina and Methanobacterium (the hydrogenotrophic methanogens) dominated in RW and DR soils. Redundancy analysis revealed that the community structure of methanogens was significantly affected by soil pH. The findings suggest that differences in the abundance and composition of methanogens, possibly driven by soil pH, play a key role in regulating methanogenesis in the paddy soils, and further provide valuable insights into the process of CH4 production in different cropping modes.

Integrating low levels of organic fertilizer improves soil fertility and rice yields in paddy fields by influencing microbial communities without increasing CH4 emissions

Although organic fertilizer is usually recommended for improving soil quality and crop yields, it inevitably enhances methane (CH4) emissions. Effective measures to mitigate CH4 emissions while ensuring crop yields are urgently needed. A two-year experiment was performed to examine the effects of organic-inorganic fertilizer combinations on CH4 emissions, the CH4-related microbial community, soil biochemical characteristics, and rice yields during dual rice growing seasons in 2020–2021 at two locations (i.e., Nanning and Yulin City, Southern, China). The treatments were as follows: no N fertilizer (Neg-CF), 100 % chemical fertilizer (CF) (Pos-CF), 60 % cattle manure (CM) + 40 % CF (High-CM), 30 % CM + 70 % CF (Low-CM), 60 % poultry manure (PM) + 40 % CF (High-PM), and 30 % PM + 70 % CF (Low-PM). CH4 fluxes and related functional microorganism abundances were investigated using the closed chamber method and molecular procedures, respectively. The addition of organic manure significantly improved rice grain yields and soil properties, including total nitrogen (TN), soil organic carbon (SOC), and pH compared to the Pos-CF. Similarly, integrating organic and inorganic fertilizers led to significant increases in seasonal CH4 emissions, global warming potential (GWP), and the abundance of CH4-related soil microbes. Average increases in SOC, TN, CH4 emissions, and GWP in the High-PM treatment relative to the Pos-CF were 44.7, 36.4, 20.6, and 24.4 %, respectively, in Nanning; and 28.9, 33.3, 23.4, and 20.8 % in Yulin City, averaged across the years. Moreover, co-fertilization resulted in the highest increase in methanogenic diversity and abundance relative to Pos-CF only. Applying high proportions of manure improved the abundance of methanogenic soil archaea related to CH4 production compared with the plots with low proportions of manure. Interestingly, lower manure amendments produced the highest rice grain yields and lowest CH4 emissions while maintaining high soil qualities. In addition, regression analysis exhibited that SOC was highly positively associated with CH4 emissions. Above all, controlling the proportions of organic manure and CF may be a feasible approach for enhancing rice yields and soil quality while mitigating CH4 emissions. Of the treatments tested, the combination of 30 % organic manure (i.e., CM or PM) with 70 % CF (urea) performed the best. This study showed that combining manure and CF at a 30:70 ratio was the most effective approach for improving soil health and rice yields while ensuring environmental sustainability.

Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with in situ CH4 fluxes and soil edaphic factors measurements and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harboring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity, and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Effects of Pig Manure and Its Organic Fertilizer Application on Archaea and Methane Emission in Paddy Fields

Paddy fields account for 10% of global CH4 emissions, and the application of manure may increase CH4 emissions. In this study, high-throughput sequencing technology was used to investigate the effects of manure application on CH4 emissions and methanogens in paddy soil. Three treatments were studied: a controlled treatment (CK), pig manure (PM), and organic fertilizer (OF). The results showed that the contents of Zn, Cr and Ni in paddy soil increased with the application of manure, but the contents of heavy metals gradually decreased with the growth of rice. The Shannon index and Ace index showed that the application of pig manure and organic fertilizer less affected the diversity and richness of soil Archaea. The results of community composition analysis showed that Methanobacterium, Methanobrevibacter, Methanosphaera, Methanosarcina and Rice_Cluster_I were the main methanogens in paddy soil after manure and organic fertilizer application. Soil environmental factors were changed after applied manure, among which total potassium (TK) and total nitrogen (TN) were the main environmental factors affecting methanogens in paddy soil. The changes of soil environmental factors affected the community composition of methanogens, and the increase of the relative abundance of methanogens maybe the main reason for the increase of CH4 emission flux. The relative abundance of methanogens and CH4 emission flux in paddy soil were increased by both pig manure and organic fertilizer application, and pig manure had a bigger impact than organic manure.

Microbe-mediated reduction of methane emission in rice-frog crop ecosystem

Rice–frog crop ecosystem (RFCE) can significantly reduce CH4 emission from paddy soils to mitigate global warming. However, information on the correlation of soil microbial communities with paddy soil CH4 emission in RFCEs remains limited. This study evaluated the influence of frogs on CH4 flux, paddy soil/water properties, and abundance/community composition of methanogens and methanotrophs in an RFCE between 2018 and 2019. The study parameters were compared between “with frogs” (RFCE; 15,000 frogs ha−1) and “without frogs” (control check [CK]) conditions. Frogs in paddies significantly decreased the CH4 flux during the rice-growing seasons (p < 0.05) but increased the paddy water/soil dissolved oxygen (DO) concentration, redox potential (Eh), and soil organic carbon (SOC) content. Compared with the CK, the RFCE significantly decreased the relative abundance of the soil methanogen species Candidatus Methanoperedens nitroreducens and Methanocella arvoryzae, genera Candidatus Methanoperedens and Methanocella, and families Methanoperedenaceae and Methanocellaceae (p < 0.05); however, it significantly increased the abundance of the soil methanotroph species Methylosinus sp. LW2, Methylocystis sp. KS3, and Methylocystis sp. KS30; genera Methylosinus and Methylocystis; and family Methylocystaceae (p < 0.05). Furthermore, variation partitioning analysis revealed that oxygen (DO and Eh) explained 41.2% of the variation in the abundance of soil methanogens, which was greater than the effects of C/N (38.2%) and SOC content (38.1%). For soil methanotrophs, oxygen (DO and Eh) explained 45.6% of the variation, which was more than the effects of C/N or pH. Oxygen concentration in the paddy soil/water was the driving factor for the change in the composition of soil methanogenic and methanotrophic microbial communities. Bioturbation due to the frogs increased oxygen availability in the paddy soil, decreased CH4 production by soil methanogens, and increased CH4 oxidation by type II methanotrophs, all of which reduced CH4 emission. Thus, this study provides strong evidence for the microbial mechanisms underlying the reduction of CH4 emission from RFCE.

Mitigation of Paddy Field Soil Methane Emissions by Betaproteobacterium &lt;i&gt;Azoarcus&lt;/i&gt; Inoculation of Rice Seeds

Paddy fields are a major source of atmospheric methane, a greenhouse gas produced by methanogens and consumed by methanotrophs in flooded soil. The inoculation of rice seeds with the bacterium Azoarcus sp. KH32C alters the rice root-associated soil bacterial community composition. The present study investigated the effects of KH32C-inoculated rice cultivation on soil methanogens and methanotrophs involved in methane emissions from a rice paddy field. KH32C-inoculated and non-inoculated rice (cv. Nipponbare) were cultivated in a Japanese rice paddy with and without nitrogen fertilizer. Measurements of methane emissions and soil solution chemical properties revealed increases in methane flux over the waterlogged period with elevations in the concentrations of dissolved methane, dissolved organic carbon, and ferrous iron, which is an indicator of soil reduction levels. Reverse transcription quantitative PCR and amplicon sequencing were used to assess the transcription of the methyl-coenzyme M reductase gene (mcrA) from methanogens and the particulate methane monooxygenase gene (pmoA) from methanotrophs in paddy soil. The results obtained showed not only the transcript copy numbers, but also the compositions of mcrA and pmoA transcripts were related to methane flux. KH32C-inoculated rice cultivation recruited soil methanogens and methanotrophs that suppressed high methane synthesis, increased methane consumption, and decreased methane emissions by 23.5 and 17.2% under non-fertilized and nitrogen-fertilized conditions, respectively, while maintaining rice grain yield. The present study demonstrated the mitigation of paddy field methane emissions arising from the use of KH32C in rice cultivation due to its influence on the compositions of soil methanogen and methanotroph populations.

Microbial Community Structure of Soil Methanogens and Methanotrophs During Degradation and Restoration of Reed Wetlands in the Songnen Plain

Wetlands are an important global source and sink of methane. However, human activities and climatic conditions are causing serious degradation of wetlands in China. In response to this, the relevant departments have progressively carried out wetland restoration projects over the past few years. To investigate the response of microbial communities of bacteria, methanogens, and methanotrophs during degradation and restoration of wetlands, soil samples were collected from undegraded reed wetlands, degraded reed wetlands, and restored reed wetlands in the Songnen Plain. Microbial diversity and community composition were studied by high-throughput sequencing based on the 16S rRNA gene of bacteria, the mcrA gene of methanogens, and the pmoA gene of methanotrophs. The results indicate that the degradation of reed wetlands results in a decrease in bacterial and methanogenic α-diversity and an increase in methanotrophic α-diversity. Bacterial α-diversity and methanogenic α-diversity were both significantly positively correlated with soil water content. At different taxonomic levels, higher relative abundances of Rhizobiales and Methanobacteriaceae were detected in the undegraded wetland soils. Wetland degradation decreased the relative abundance of Rhizobiales but increased that of the pathogenic bacteria Burkholderiaceae and microorganisms resistant to harsh and extreme environments including Sphingomonas, Rubrobacter, Methylobacter, Methylomonas, and Methylococcus. In the restored wetland soils, the relative abundances of Bacillus, Methanosarcinaceae, Methanomicrobiaceae, and the type Ⅱ methanotroph Methylocystis were higher. Therefore, different wetland conditions can indirectly change soil properties and, consequently, change the community structure of methanogens and methanotrophs.

Generation of High Current Densities in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor.

ABSTRACTGeobacter sulfurreducens is commonly employed as a model for the study of extracellular electron transport mechanisms in the Geobacter species. Deletion of pilB, which is known to encode the pilus assembly motor protein for type IV pili in other bacteria, has been proposed as an effective strategy for evaluating the role of electrically conductive pili (e-pili) in G. sulfurreducens extracellular electron transfer. In those studies, the inhibition of e-pili expression associated with pilB deletion was not demonstrated directly but was inferred from the observation that pilB deletion mutants produced lower current densities than wild-type cells. Here, we report that deleting pilB did not diminish current production. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are expressed heterologously from the G. sulfurreducens pilin gene in Escherichia coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing a pilin monomer with a His tag continued to express His tag-labeled filaments when pilB was deleted. These results suggest that a reinterpretation of the results of previous studies on G. sulfurreducens pilB deletion strains may be necessary.IMPORTANCE Geobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes, such as the reduction of Fe(III) oxides in soils and sediments, bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity, direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments, and metal corrosion. Elucidating the phenotypes associated with gene deletions is an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that we cannot replicate the key phenotype reported for a gene deletion that has been central to the development of models for long-range electron transport in G. sulfurreducens.

A new approach to suppress methane emissions from rice cropping systems using ethephon

Rice is the main staple food for more than half of the world's population. Yet, rice cultivation is subjected to criticism because of its important role in methane (CH4) emissions. Although several agronomic practices such as controlled irrigation and conservation tillage have been widely adopted to mitigate CH4 emissions from rice cultivation, the benefits gained by these practices are highly dependent on site-specific soil and climate conditions, and often offset by yield reduction. The use of plant growth regulating compounds having the potential to increase the crop yield and mitigate CH4 emissions may be an innovative approach to sustainable agriculture. Ethylene (C2H4), a plant growth regulator is known to have a strong inhibitory effect on methanogenesis. However, due to gaseous form and low water solubility, C2H4 has not been used to suppress methanogenesis in paddy fields. To develop C2H4 as a prospective soil amendment for reducing methane (CH4) emissions, ethephon (2-Chloroethylphosphonic acid), a precursor of C2H4 was tested. We found that ethephon reduced CH4 formation by 43%, similar to other well known methanogenic inhibitors (2-Bromoethanesulfonate, 2-Chlomoethanesulfonate, 2-Mercaptoethanesulfonate). However, ethephon rapidly hydrolyzed to C2H4 and methanogenic activity recuperated completely after C2H4 removal. To slow down the release of C2H4, ethephon was mixed with bio-degradable polymers such as cellulose acetate and applied to paddy soils. We found that compared with the control, the C2H4 release of ethephon slowed down to 90 days, and the CH4 emissions were reduced by 90%. The application of ethephon at lower concentrations did not significantly alter bacterial communities, their relative abundance, and the abundance of methanotrophs, but it significantly reduced archaeal communities and the relative abundance and expression level of methanogens in paddy soils. Results suggest that cellulose acetate-mixed ethephon has great promise to suppress CH4 emissions in rice paddies while ensuring sustainable yields.

Community Characteristics of Methanogens and Methanogenic Pathways in Salt-tolerant Rice Soil

It is known that methanogens play a critical role in the carbon cycle in soil, while methanogen community characteristics and their environmental influencing factors in the soil planted with salt-tolerant rice remain unclear. In this study, methanogen abundance, community composition, and relationships with environmental factors in soils planted with the salt-tolerant rice (YC1703) and ordinary rice (Lindao 10) were evaluated in the rice improvement demonstration base of Qingdao Wisdom Agricultural Industry using real-time fluorescence quantitative PCR and Illumina high-throughput sequencing. The results indicated that the abundance and community richness of methanogens in Lindao 10 soil were significantly higher than those in YC1703 soil, and methanogens in YC1703 soil exhibited higher diversity. The combined effects of rice varieties, rice growth period, and environmental factors had impacts on the methanogen community. The hydrogenotrophic methanogens were dominant in the YC1703 and Lindao 10 soils; thus, we speculated that the dominant pathway of methane production in these soils was hydrogenotrophic methanogenesis.

Effects of Soil Moisture and Temperature on Microbial Regulation of Methane Fluxes in a Poplar Plantation

Improved mechanistic understanding of soil methane (CH4) exchange responses to shifts in soil moisture and temperature in forest ecosystems is pivotal to reducing uncertainty in estimates of the soil-atmospheric CH4 budget under climate change. We investigated the mechanism behind the effects of soil moisture and temperature shifts on soil CH4 fluxes under laboratory conditions. Soils from the Huai River Basin in China, an area that experiences frequent hydrological shifts, were sampled from two consecutive depths (0–20 and 20–50 cm) and incubated for 2 weeks under different combinations of soil moisture and temperature. Soils from both depths showed an increase in soil moisture and temperature-dependent cumulative CH4 fluxes. CH4 production rates incubated in different moisture and temperature in surface soil ranged from 1.27 to 2.18 ng g−1 d−1, and that of subsurface soil ranged from 1.18 to 2.34 ng g−1 d−1. The Q10 range for soil CH4 efflux rates was 1.04–1.37. For surface soils, the relative abundance and diversity of methanotrophs decreased with moisture increase when incubated at 5 °C, while it increased with moisture increase when incubated at 15 and 30 °C. For subsurface soils, the relative abundance and diversity of methanotrophs in all samples decreased with moisture increase. However, there was no significant difference in the diversity of methanogens between the two soil depths, while the relative abundance of methanogens in both depths soils increased with temperature increase when incubated at 150% water-filled pore space (WFPS). Microbial community composition exhibited large variations in post incubation samples except for one treatment based on the surface soils incubated at 15 °C, which showed a decrease in the total and unique species number of methanotrophs with moisture increase. In contrast, the unique species number of methanogens in surface soils increased with moisture increase. The analysis of distance-based redundancy analysis (db-RDA) showed that soil pH, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), microbial biomass carbon (MBC), NO3−-N, and NH4+-N mainly performed a significant effect on methanotrophs community composition when incubated at 60% WFPS, while they performed a significant effect on methanogens community composition when incubated at 150% WFPS. Overall, our findings emphasized the vital function of soil hydrology in triggering CH4 efflux from subtropical plantation forest soils under future climate change.

The process of methanogenesis in paddy fields under different elevated CO2 concentrations

Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH4 production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO2 concentrations (e[CO2]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH4 flux in paddy fields under various (e[CO2]). CH4 flux and CH4 production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO2 concentration), C1 (C + 160 ppm CO2), and C2 (C + 200 ppm CO2) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C2 treatment significantly increased CH4 flux and MPP at the tillering stage. E[CO2] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO2] did not significantly change the overall community structure and diversity of methanogens, C2 treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH4 flux under e[CO2]. Overall, our results demonstrated that CH4 flux in paddy fields under e[CO2] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

BackgroundSoil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks.ResultsThe network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa.ConclusionsThese results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions.C3W-7jXtk5xnWLKMZMf8GXVideo abstract

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

Response of methane emissions to litter input manipulation in a temperate freshwater marsh, Northeast China

The photograph of the field experiment of different litter input manipulations in situ and the treatment effects on CH 4 fluxes during observations in 2015 and 2016. Abbreviations: NL, no aboveground litter; DL, double litter; CK, control; AR, standing litter removal. • We conducted a two seasons litter input manipulation experiment in a freshwater marsh. • Litter input manipulations obviously affected CH 4 emission and surface DOC contents. • Litter removal induced higher soil temperature, DOC content and CH 4 emission. • The abundance of methanogens in surface soil relied on the ways of litter manipulation. Plant litter plays an important role in regulating CH 4 emission in wetland ecosystems. Our knowledge of the impacts of plant litter on CH 4 budget is important for understanding the response and feedbacks of wetland ecosystems to climate warming. Nevertheless, the effects of plant litter on CH 4 emission and temperature sensitivity (Q 10 ) are not clear under the background of global change. In this study, a field litter inputs manipulation experiment with four treatments including no aboveground litter (NL), standing litter removal (AR), doubled litter input (DL) and controls (CK) was conducted to study the effects of litter manipulations on CH 4 emission in a seasonal inundated freshwater marsh over two growing seasons of 2015 and 2016 in the Sanjiang Plain, Northeast China. Results showed that CH 4 emission was significantly associated with altered litter input over the observation period. Compared with CK, the cumulative CH 4 emission increased by 105.83%, 42.20% and 42.50% for NL, AR and DL treatments, respectively, in 2015, and the values were 199.04%, 115.55% and 17.55%, in 2016. Variances of CH 4 emission were more sensitive to litter removal effects. Altered litter input also significantly affected the dissolved organic carbon (DOC) concentration ([DOC]) in surface pore water. DL and CK treatments with lower soil temperature had lower [DOC] than litter removal treatments of NL and AR. The abundance of methanogens among the four treatments exhibited synchronous change with DOC over the observation period. The Q 10 values of CH 4 emission didn’t show consistent changing patterns with those of DOC among different litter input treatments, which was probably due to the different temperature sensitivity of dominant methanogen types. Due to its great effects on soil microclimate, substrate availability and the concomitant variation in temperature sensitivity, our results highlighted that plant litter effects should be incorporated into the current process-based CH 4 biogeochemical models to predict future CH 4 fluxes from natural wetlands under the background of global change.

Effect of phosphorus amendments on rice rhizospheric methanogens and methanotrophs in a phosphorus deficient soil

Methane emission can be affected by soil fertility, but little is known about the influence of soil phosphorus (P) nutrition on methane production and oxidation processes. In this study, a pot experiment was conducted to explore the effects of P amendments on activity, abundance and community composition of soil methanogens and methanotrophs using P deficient paddy soil. The abundance and community composition of methanogens and methanotrophs, methane production and oxidation potentials were investigated by real-time quantitative PCR, Miseq high-throughput sequencing and biochemical assays, respectively. The results showed that although P amendments induced increases of both methanogenic and methanotrophic abundances and potential activities within bulk soils, the increases were relatively small. In contrast, P applications resulted in large and significant increases in the copy numbers and potential activity of methanogens within rhizosphere soils, whereas, this phenomenon was not detected for methanotrophs. Moreover, the methanogenic community structure remained similar amongst the P amendment treatments for both rhizosphere and bulk soils. For methanotrophs, P application induced clear shifts in the community composition within rhizosphere soils but not in bulk soils, where the relative abundance of type I methanotrophs increased whilst type II decreased. Our data indicate that the application of phosphate to P deficient paddy soils could preferentially stimulate the abundance and activity of methanogens over methanotrophs within the rice rhizosphere. Ultimately, improving plant growth by P input may accelerate methane emissions through stimulating rhizosphere methanogenic populations without a concomitant increase in the methanotrophic compartment.

Evaluating the effect of different biochar application sizes on methane emission reduction from rice cultivation

Application of biochar to the soil has been reported as one of the mitigation technologies of CH4 emission from rice cultivation due to its unique characteristics of high porosity and surface area. The application of small particle size of biochar is rich in surface area that may enhance the mitigation potential. Rice cultivation and soil incubation experiments were conducted to evaluate the effect of two groups of biochar particle size on CH4 emission and production in order to show the mitigation potential. This experiment consists of three treatments including no biochar (CT), small particle size (0.5-2 mm) biochar (SB), and large particle size (2-4 mm) biochar (LB). Both biochar sizes were amended at 10 t ha−1 equivalent rate and all treatments were applied chemical fertilizer at 100 kg N ha−1 equivalent rate. The results demonstrated that SB and LB reduced cumulative CH4 emission by 24.0% and 17.1% and cumulative CH4 production by 24.6% and 15.0% as compared to CT, respectively. Our results showed that SB achieved higher mitigation potential than LB by an average of 8.47%, although it was not significant. The mitigation of both biochar sizes was supported by the significant change of soil methanogens and methanotrophs abundances. The suppression of methanogens abundance and the stimulation of methanotrophs abundance indicated in the ratio of mcrA to pmoA was significantly reduced in SB (68.0%) which higher than in LB (56.3%) as compared to CT. Both application sizes also increased soil oxidation capacity through soil Eh increase which no difference between SB and LB. In term of grain yield, SB and LB were not different and both did not show the significant change as relative to CT. The application of small size biochar in this study affected more mitigation potential of CH4 emission as compared to larger size, therefore there is a need of further study on typical size of biochar in order to recommend the most mitigation potential of biochar application.

Effects of domestic sewage from different sources on greenhouse gas emission and related microorganisms in straw-returning paddy fields

Reusing domestic sewage for crop irrigation is a promising practice, particularly in developing countries, since it is a substitute for chemical fertilizer and reduces water contamination. More attention was paid to the effect of sewage irrigation on crop yield and soil nutrients, but little attention was paid to greenhouse gas (GHG) emission from straw-returning paddy fields. In this study, a soil column monitoring experiment was conducted to assess the effects of untreated domestic sewage (dominated with ammonia) and treated domestic sewage (dominated with nitrate) irrigation on methane (CH4), nitrous oxide (N2O) emission, and related soil microorganisms in straw-returning paddy fields. Results showed that straw-returning dramatically promoted CH4 emission but had little effect on N2O emission. Both untreated and treated domestic sewage irrigation decreased CH4 emission of straw-returning paddy whether nitrogen fertilizer applied or not. The mitigating effect of treated sewage irrigation on CH4 emission was greater than untreated sewage irrigation. CH4 emission had a significant correlation with the abundance of soil methanogens and methanogens/methanotrophs. N2O emission increased with untreated or treated domestic sewage irrigation, although the total N input, including the N carried by sewage water, was the same for all treatments. No significant correlation between N2O and denitrification functional genes was found in this study. Treated domestic sewage irrigation reduced the global warming potential (GWP) by 66.7%, but untreated domestic sewage had no evident influence on the GWP. Results indicated that treated domestic sewage irrigation could significantly inhibit CH4 emission and the GWP by decreasing the ratio of methanogens to methanotrophs, and is promising in mitigating GWP from straw-returned paddy fields.