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

Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality

Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

BACKGROUND

The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).

RESULTS

The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.

CONCLUSIONS

The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.

Water level of inland saline wetlands with implications for CO2 and CH4 fluxes during the autumn freeze-thaw period in Northeast China

Zhalong wetland is the largest inland saline wetland in Asia and susceptible to imbalance and frequent flooding during the freeze-thaw period. Changes in water level and temperature can alter the rate of greenhouse gas release from wetlands and have the potential to alter Earth's carbon budget. However, there are few reports on how water level, temperature, and their interactions affect greenhouse gas flux in inland saline wetland during the freeze-thaw period. This study revealed the characteristics of CO₂ and CH₄ fluxes in Zhalong saline wetlands at different water levels during the autumn freeze-thaw period and clarifies the response of CO₂ and CH₄ fluxes to water levels. The significance analysis of cumulative CO₂ fluxes at different water levels showed that water levels did not have a significant effect on cumulative CO₂ release fluxes from wetlands. Water levels, temperature, soil moisture content, soil nitrate, and ammonium nitrogen content and organic carbon content could explain 24.5-98.9% of CO₂ and CH₄ flux variation. There were significant differences in the average and cumulative CH₄ fluxes at different water levels. The higher the water levels, the higher the CH₄ fluxes. In short, water level had a significant effect on wetland methane fluxes, but not on carbon dioxide fluxes.

Fertilization and Global Warming Impact on Paddy CH4 Emissions

INTRODUCTION

This study aimed to assess the influence of experimental warming and fertilization on rice yield and paddy methane emissions.

METHODS

A free-air temperature increase system was used for the experimental warming treatment (ET), while the control treatment used ambient temperature (AC). Each treatment contained two fertilization strategies, (i) normal fertilization with N, P and K fertilizers (CN) and (ii) without N fertilizer input (CK).

RESULTS

The yield was remarkably dictated by fertilization (p < 0.01), but not warming. Its value with CN treatment increased by 76.24% compared to CK. Also, the interactive effect of warming and fertilization on CH₄ emissions was insignificant. The seasonal emissions from warming increased by 36.93% compared to AC, while the values under CN treatment increased by 79.92% compared to CK. Accordingly, the ET-CN treatment obtained the highest CH₄ emissions (178.08 kg ha^-1), notably higher than the other treatments. Also, the results showed that soil fertility is the main driver affecting CH₄ emissions rather than soil microorganisms.

CONCLUSIONS

Fertilization aggravates the increasing effect of warming on paddy methane emissions. It is a daunting task to optimize fertilization to ensure yield and reduce methane emissions amid global warming.

Effects of periodic drying-wetting on microbial dynamics and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in intertidal wetland sediments

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH₄) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH₄, which may help accurately project CH₄ emission from intertidal wetlands under different tidal scenarios.

Effects of Water and Fertilizer Management Practices on Methane Emissions from Paddy Soils: Synthesis and Perspective

Water and fertilizer management practices are considered to have great influence on soil methane (CH₄) emissions from paddy fields. However, few studies have conducted a quantitative analysis of the effects of these management practices. Here, we selected 156 observations of water management from 34 articles and 288 observations of fertilizer management from 37 articles and conducted a global meta-analysis of the effects of water and fertilizer management practices on soil CH₄ emissions in paddy fields. In general, compared with traditional irrigation (long-term flooding irrigation), water-saving irrigation significantly decreased soil CH₄ emissions but increased rice yield. Among the different practices, intermittent irrigation had the fewest reductions in CH₄ emissions but the greatest increase in rice yield. In addition, fertilization management practices such as manure, mixed fertilizer (mixture), and straw significantly enhanced CH₄ emissions. Rice yields were increased under fertilization with a mixture, traditional fertilizer, and controlled release fertilizer. Our results highlight that suitable agricultural water and fertilizer management practices are needed to effectively reduce CH₄ emissions while maintaining rice yields. We also put forward some prospects for mitigating soil CH₄ emissions from paddy fields in the context of global warming in the future.

Nitrogen input promotes denitrifying methanotrophs' abundance and contribution to methane emission reduction in coastal wetland and paddy soil

Denitrifying anaerobic methane oxidation (DAMO) microorganisms, using nitrate/nitrite to oxidize methane, have been proved to be an important microbial methane sink in natural habitats. Increasing nitrogen deposit around the globe brings increased availability of substrates for these microorganisms. However, how elevated nitrogen level affects denitrifying methanotrophs has not been elucidated. In this study, sediment/soil samples from coastal wetland with continuous nitrogen input and paddy field with periodic nitrogen input were collected to investigate the influence of nitrogen input on the abundance and activity of denitrifying methanotrophs. The results indicated that nitrogen input significantly promoted DAMO microorganisms' abundance and contribution to methane emission reduction. In the coastal wetland, the contribution rate of DAMO process to methane removal increased from 12.1% to 33.5% along with continuously elevated nitrogen level in the 3-year tracking study. In the paddy field, the DAMO process accounted for 71.9% of total methane removal when nitrogen fertilizer was applied during the growing season, exceeding the aerobic methane oxidation process. This work would help us better understand the microbial methane cycle and reduce uncertainties in the estimations of the global methane emission.

Sink or Source: Alternative Roles of Glacier Foreland Meadow Soils in Methane Emission Is Regulated by Glacier Melting on the Tibetan Plateau

Glacier foreland soils have long been considered as methane (CH₄) sinks. However, they are flooded by glacial meltwater annually during the glacier melting season, altering their redox potential. The impacts of this annual flooding on CH₄ emission dynamics and methane-cycling microorganisms are not well understood. Herein, we measured in situ methane flux in glacier foreland soils during the pre-melting and melting seasons on the Tibetan Plateau. In addition, high-throughput sequencing and qPCR were used to investigate the diversity, taxonomic composition, and the abundance of methanogenic archaea and methanotrophic bacteria. Our results showed that the methane flux ranged from -10.11 to 4.81 μg·m^-2·h^-1 in the pre-melting season, and increased to 7.48-22.57 μg·m^-2·h^-1 in the melting season. This indicates that glacier foreland soils change from a methane sink to a methane source under the impact of glacial meltwater. The extent of methane flux depends on methane production and oxidation conducted by methanogens and methanotrophs. Among all the environmental factors, pH (but not moisture) is dominant for methanogens, while both pH and moisture are not that strong for methanotrophs. The dominant methanotrophs were Methylobacter and Methylocystis, whereas the methanogens were dominated by methylotrophic Methanomassiliicoccales and hydrogenotrophic Methanomicrobiales. Their distributions were also affected by microtopography and environmental factor differences. This study reveals an alternative role of glacier foreland meadow soils as both methane sink and source, which is regulated by the annual glacial melt. This suggests enhanced glacial retreat may positively feedback global warming by increasing methane emission in glacier foreland soils in the context of climate change.

Elevated CO2 does not necessarily enhance greenhouse gas emissions from rice paddies

Elevated atmospheric carbon dioxide (eCO₂) greatly impacts greenhouse gas (GHG) emissions of CH₄ and N₂O from rice fields. Although eCO₂ generally stimulates GHG emissions in the short term (<5 years) experiments, the responses to long-term (≥10 years) eCO₂ remain poorly known. Here we show, through a series of experiments and meta-analysis, that the eCO₂ does not necessarily increase CH₄ and N₂O emissions from rice paddies. In an experiment of free-air CO₂ enrichment for 13-15 years, CH₄ and N₂O emissions were decreased by 11-54% and 33-54%, respectively. The decline of CH₄ emissions was related to the reduction of CH₄ production and enhancement of CH₄ oxidation via raising soil Eh and soil-water interface [O₂] under eCO₂. Moreover, the eCO₂ significantly decreased NH₄⁺-N content, suggesting a reduction of soil nitrification and thereby N₂O emissions. A meta-analysis showed that CH₄ and N₂O emissions were stimulated under short-term eCO₂ while reduced under long-term eCO₂. The eCO₂-induced increase in yield and biomass and the ratio of mcrA genes/pmoA genes declined with eCO₂ duration, indicating an eCO₂-stimulation of methanogenesis lower than that of methanotrophy over time by fewer increased substrates. Upscaling the results of meta-analysis, the eCO₂-induced global paddy CH₄ and N₂O emissions shifted from an increase (+0.17 Pg CO₂-eq year^-1) in the short term into a decrease (-0.11 Pg CO₂-eq year^-1) in the long term. Our findings suggest that the effect of eCO₂ on GHG emissions changes over time, and this should be considered in future climate change research.

Hyperthermophilic composting significantly decreases methane emissions: Insights into the microbial mechanism

Methane (CH₄) emissions from thermophilic composting (TC) are a substantial contributor to climate change. Hyperthermophilic composting (HTC) can influence CH₄-related microbial communities at temperatures up to 80 °C, and thus impact the CH₄ emissions during composting. This work investigated CH₄ emissions in sludge-derived HTC, and explored microbial community succession with quantitative PCR and high-throughput sequencing. Results demonstrated that HTC decreased CH₄ emissions by 52.5% compared with TC. In HTC, the CH₄ production potential and CH₄ oxidation potential were nearly 40% and 64.1% lower than that of TC, respectively. There was a reduction in the quantity of mcrA (3.7 × 10⁸ to 0 g^-1 TS) in HTC, which was more significant than the reduction in pmoA (2.0 × 10⁵ to 2.1 × 10⁴ g^-1 TS), and thus lead to reduce CH₄ emissions. It was found that the abundance of most methanogens and methanotrophs was inhibited in the hyperthermal environment, with a decline in Methanosarcina, Methanosaeta and Methanobrevibacter potentially being responsible for reducing the CH₄ emissions in HTC. This work provides important insight into mitigating CH₄ emissions in composting.

The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance

The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.

Resilience of methane cycle and microbial functional genes to drought and flood in an alkaline wetland: A metagenomic analysis

Alkaline wetlands distributed in arid or semi-arid areas are hotspots of methane (CH₄) emissions. Periods of drought and flood, although regular, are stressful events encountered by methanogenic anaerobes in alkaline wetlands. To investigate the response of the CH₄ cycle of alkaline wetlands to such stresses, we take Zhalong wetland as an example, then determined the CH₄ flux and soil microbiomes in the wetland during wet, dry, and flooded periods. The in-situ CH₄ flux in the wet period was 9.55-17.29 mg‧m^-2‧h^-1, but sharply degraded to 3.37-6.61 mg‧m^-2‧h^-1 in the dry period. It resumed to 4.51-20.80 mg‧m^-2‧h^-1 when the wetland was flooded again, which indicated that methanogenesis is quite resilient to drought. Syntrophic acetogenesis, and subsequently aceticlastic methanogenesis, were the dominant methanogenic pathways and resisted drought. Members belonging to Syntrophobacterales were the dominant syntrophic acetogens. They enter a viable but non-culturable (VBNC) state to resist drought. The dominant Methanosarcinales have the ability to repair reactive oxygen species damage during dry periods. The community of CH₄ sink was governed by anaerobic methanotrophs, which entered a VBNC state or used repair systems to survive dry periods. This study revealed the responses of the CH₄ cycle and microbial functional genes to drought and flood in alkaline wetlands.

Limited aerenchyma reduces oxygen diffusion and methane emission in paddy

Greenhouse gasses (GHG) emission from the agricultural lands is a serious threat to the environment. Plants such as rice (Oryza sativa L.) that are cultivated in submerged conditions (paddy field) contribute up to 19% of CH₄ emission from agricultural lands. Such plants have evolved lysigenous aerenchyma in their root system which facilitates the exchange of O₂ and GHG between aerial parts of plant and rhizosphere. Currently, the regulation of GHG and O₂ via aerenchyma formation is poorly understood in plants, especially in rice. Here, a reverse genetic approach was employed to reduce the aerenchyma formation by analyzing two mutants i.e., oslsd1.1-m12 and oslsd1.1-m51 generated by Tos17 and T-DNA insertion. The wild-type (WT) and the mutants were grown in paddy (flooded), non-paddy and hydroponic system to assess phenotypic traits including O₂ diffusion, GHG emission and aerenchyma formation. The mutants exhibited significant reductions in several morphophysiological traits including 20-60% aerenchyma formation at various distances from the root apex, 25% root development, 50% diffusion of O₂ and 27-36% emission of methane (CH₄) as compared to WT. The differential effects of the oslsd1.1 mutants in aerenchyma-mediated CH₄ mitigation were also evident in the diversity of (pmoA, mcrA) methanotrophs in the rhizosphere. Our results indicate the novel pathway in which reduced aerenchyma in rice is responsible for the mitigation of CH₄, diffusion of O₂ and the root growth in rice. Limited aerenchyma mediated approach to mitigate GHG specially CH₄ mitigation in agriculture is helpful technique for sustainable development.

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China-the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

The Impact of Antimicrobial Substances on the Methanogenic Community during Methane Fermentation of Sewage Sludge and Cattle Slurry

This study showed the effect of amoxicillin (AMO), and oxytetracycline (OXY) at a concentration of 512 µg mL−1, and sulfamethoxazole (SMX), and metronidazole (MET) at a concentration of 1024 µg mL−1 on the efficiency of anaerobic digestion (AD) of sewage sludge (SS) and cattle slurry (CS). The production of biogas and methane (CH4) content, and the concentration of volatile fatty acids (VFAs) was analyzed in this study. Other determinations included the concentration of the mcrA gene, which catalyzes the methanogenesis, and analysis of MSC and MST gene concentration, characteristic of the families Methanosarcinaceae and Methanosaetaceae (Archaea). Both substrates differed in the composition of microbial communities, and in the sensitivity of these microorganisms to particular antimicrobial substances. Metronidazole inhibited SS fermentation to the greatest extent (sixfold decrease in biogas production and over 50% decrease in the content of CH4). The lowest concentrations of the mcrA gene (106 gD−1) were observed in CS and SS digestates with MET. A decline in the number of copies of the MSC and MST genes was noted in most of the digestate samples with antimicrobials supplementation. Due to selective pressure, antimicrobials led to a considerably lowered efficiency of the AD process and induced changes in the structure of methanogenic biodiversity.

Shifts in short-chain fatty acid profile, Fe(III) reduction and bacterial community with biochar amendment in rice paddy soil

Biochar, a valuable product from the pyrolysis of agricultural and forestry residues, has been widely applied as soil amendment. However, the effect of different types of biochar on soil microorganisms and associated biochemical processes in paddy soil remains ambiguous. In this study, we investigated the impact of biochars derived from different feedstocks (rice straw, orange peel and bamboo powder) on the dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in paddy soil within 90 days of anaerobic incubation. Results showed that biochar amendment overall inhibited the accumulation of SCFAs while accelerating the Fe(III) reduction process in paddy soil. In addition, 16S rRNA gene sequencing results demonstrated that the α-diversity of the bacterial community significantly decreased in response to biochar amendments at day 1 but was relatively unaffected at the end of incubation, and incubation time was the major driver for the succession of the bacterial community. Furthermore, significant correlations between parameters (e.g. SCFAs and iron concentration) and bacterial taxa (e.g. Clostridia, Syntrophus, Syntrophobacter and Desulfatiglans) were observed. Overall, our findings demonstrated amendment with different types of biochar altered SCFA profile, Fe(III) reduction and bacterial biodiversity in rice paddy soil.

Methane Production in Soil Environments-Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation

Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O₂, anaerobic processes such as CH₄ production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O₂. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH₄. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O₂ to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH₄ production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH₄, probably due to the peculiarities of the resident methanotrophic bacteria.

Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄ )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

Effects of livestock manure properties and temperature on the methanogen community composition and methane production during storage

Livestock slurry stored in ponds is an important source of methane emission, which is influenced by environmental factors. In this study, the effect of slurry properties and temperature on methane flux and methanogen community composition was investigated. The methanogen community composition in swine slurry was more sensitive to temperature and significantly different from that of cattle slurry (ANOSIM, P < 0.05), especially for the phylotypes affiliated with Methanobrevibacter, Methanocorpusculaceae and Methanocorpusculum. These different methanogen communities partially accounted for the differences in methane flux between swine and cattle slurries. Methanogen abundance seemed to not be affected by slurry properties or temperature, but the mcrA (encoding the alpha subunit of methyl coenzyme M reductase) transcript/gene ratio was significantly increased at 30°C and was higher in swine slurry than in cattle slurry (t-test, P < 0.05). This study reveals that higher temperatures increased methane production by promoting the transcription of mcrA rather than by increasing methanogen cell numbers.

Long-term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil

Nitrogen (N) deposition is a component of global change that has considerable impact on belowground carbon (C) dynamics. Plant growth stimulation and alterations of fungal community composition and functions are the main mechanisms driving soil C gains following N deposition in N-limited temperate forests. In N-rich tropical forests, however, N deposition generally has minor effects on plant growth; consequently, C storage in soil may strongly depend on the microbial processes that drive litter and soil organic matter decomposition. Here, we investigated how microbial functions in old-growth tropical forest soil responded to 13 years of N addition at four rates: 0 (Control), 50 (Low-N), 100 (Medium-N), and 150 (High-N) kg N ha^-1  year^-1 . Soil organic carbon (SOC) content increased under High-N, corresponding to a 33% decrease in CO₂ efflux, and reductions in relative abundances of bacteria as well as genes responsible for cellulose and chitin degradation. A 113% increase in N₂ O emission was positively correlated with soil acidification and an increase in the relative abundances of denitrification genes (narG and norB). Soil acidification induced by N addition decreased available P concentrations, and was associated with reductions in the relative abundance of phytase. The decreased relative abundance of bacteria and key functional gene groups for C degradation were related to slower SOC decomposition, indicating the key mechanisms driving SOC accumulation in the tropical forest soil subjected to High-N addition. However, changes in microbial functional groups associated with N and P cycling led to coincidentally large increases in N₂ O emissions, and exacerbated soil P deficiency. These two factors partially offset the perceived beneficial effects of N addition on SOC storage in tropical forest soils. These findings suggest a potential to incorporate microbial community and functions into Earth system models considering their effects on greenhouse gas emission, biogeochemical processes, and biodiversity of tropical ecosystems.

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Geobacillus strains that have potential value in microbial enhanced oil recovery

Bacteria from the genus Geobacillus are generally obligately thermophilic, with a unique bioenergy production capacity and unique enzymes. Geobacillus species were isolated primarily from hot springs, oilfields, and associated soils. They often exhibit unique survival patterns in these extreme oligotrophic environments. With the development of the microbial resources found in oilfields, Geobacillus spp. have been proven as valuable bacteria in many reports related to oilfields. After the isolation of Geobacillus by culture methods, more evidence was found that they possess the abilities of hydrocarbon utilization and bioemulsifier production. This paper mainly summarizes some characteristics of the Geobacillus species found in the oilfield environment, focusing on the inference and analysis of hydrocarbon degradation and bioemulsifier synthesis based on existing research, which may reveal their potential value in microbial enhanced oil recovery. It also provides references for understanding microbes in extreme environments.

Intermittent agitation of liquid manure: effects on methane, microbial activity, and temperature in a farm-scale study

Liquid manure storages are a significant source of methane (CH₄) emissions. Farmers commonly agitate (stir) liquid manure prior to field application to homogenize nutrients and solids. During agitation, manure undergoes mechanical stress and is exposed to the air, disrupting anaerobic conditions. This on-farm study aimed to better understand the effects of agitation on CH₄ emissions, and explore the potential for intentional agitation (three times) to disrupt the exponential increase of CH₄ emissions in spring and summer. Results showed that agitation substantially increased manure temperature in the study year compared to the previous year, particularly at upper- and mid-depths of the stored manure. The temporal pattern of CH₄ emissions was altered by reduced emissions over the subsequent week, followed by an increase during the second week. Microbial analysis indicated that the activity of archaea and methanogens increased after each agitation event, but there was little change in the populations of methanogens, archaea, and bacteria. Overall, CH₄ emissions were higher than any of the previous three years, likely due to warmer manure temperatures that were higher than the previous years (despite similar air temperatures). Therefore, intermittent manure agitation with the frequency, duration, and intensity used in this study is not recommended as a CH₄ emission mitigation practice. Implications: The potential to mitigate methane emissions from liquid manure storages by strategically timed agitation was evaluated in a detailed farm-scale study. Agitation was conducted with readily-available farm equipment, and targeted at the early summer to disrupt methanogenic communities when CH₄ emissions increase exponentially. Methane emissions were reduced for about one week after agitation. However, agitation led to increased manure temperature, and was associated with increased activity of methanogens. Overall, agitation was associated with similar or higher methane emissions. Therefore, agitation is not recommended as a mitigation strategy.

Three-Source Partitioning of Methane Emissions from Paddy Soil: Linkage to Methanogenic Community Structure

Identification of the carbon (C) sources of methane (CH₄) and methanogenic community structures after organic fertilization may provide a better understanding of the mechanism that regulate CH₄ emissions from paddy soils. Based on our previous field study, a pot experiment with isotopic ¹³C labelling was designed in this study. The objective was to investigate the main C sources for CH₄ emissions and the key environmental factor with the application of organic fertilizer in paddies. Results indicated that 28.6%, 64.5%, 0.4%, and 6.5% of ¹³C was respectively distributed in CO₂, the plants, soil, and CH₄ at the rice tillering stage. In total, organically fertilized paddy soil emitted 3.51 kg·CH₄ ha⁻¹ vs. 2.00 kg·CH₄ ha⁻¹ for the no fertilizer treatment. Maximum CH₄ fluxes from organically fertilized (0.46 mg·m⁻²·h⁻¹) and non-fertilized (0.16 mg·m⁻²·h⁻¹) soils occurred on day 30 (tillering stage). The total percentage of CH₄ emissions derived from rice photosynthesis C was 49%, organic fertilizer C < 0.34%, and native soil C > 51%. Therefore, the increased CH₄ emissions from paddy soil after organic fertilization were mainly derived from native soil and photosynthesis. The 16S rRNA sequencing showed Methanosarcina (64%) was the dominant methanogen in paddy soil. Organic fertilization increased the relative abundance of Methanosarcina, especially in rhizosphere. Additionally, Methanosarcina sp. 795 and Methanosarcina sp. 1H1 co-occurred with Methanobrevibacter sp. AbM23, Methanoculleus sp. 25XMc2, Methanosaeta sp. HA, and Methanobacterium sp. MB1. The increased CH₄ fluxes and labile methanogenic community structure in organically fertilized rice soil were primarily due to the increased soil C, nitrogen, potassium, phosphate, and acetate. These results highlight the contributions of native soil- and photosynthesis-derived C in paddy soil CH₄ emissions, and provide basis for more complex investigations of the pathways involved in ecosystem CH₄ processes.

Microbial communities controlling methane and nutrient cycling in leach field soils

Septic systems inherently rely on microbial communities in the septic tank and leach field to attenuate pollution from household sewage. Operating conditions of septic leach field systems, especially the degree of water saturation, are likely to impact microbial biogeochemical cycling, including carbon (C), nitrogen (N), and phosphorus (P), as well as greenhouse gas (GHG) emissions to the atmosphere. To study the impact of flooding on microbial methane (CH₄) and nutrient cycling, two leach field soil columns were constructed. One system was operated as designed and the other was operated in both flooded and well-maintained conditions. CH₄ emissions were significantly higher in flooded soils (with means between 0.047 and 0.33 g CH₄ m^-2 d^-1) as compared to well-drained soils (means between -0.0025 and 0.004 g CH₄ m^-2 d^-1). Subsurface CH₄ profiles were also elevated under flooded conditions and peaked near the wastewater inlet. Gene abundances of mcrA, a biomarker for methanogens, were also greatest near the wastewater inlet. In contrast, gene abundances of pmoA, a biomarker for methanotrophs, were greatest in surface soils at the interface of CH₄ produced subsurface and atmospheric oxygen. 16S rRNA, mcrA, and pmoA amplicon library sequencing revealed microbial community structure in the soil columns differed from that of the original soils and was driven largely by CH₄ fluxes and soil VWC. Additionally, active microbial populations differed from those present at the gene level. Flooding did not appear to affect N or P removals in the soil columns (between 75 and 99% removal). COD removal was variable throughout the experiment, and was negatively impacted by flooding. Our study shows septic system leach field soils are dynamic environments where CH₄ and nutrients are actively cycled by microbial populations. Our results suggest proper siting, installation, and routine maintenance of leach field systems is key to reducing the overall impact of these systems on water and air quality.

NanoFe3O4 as Solid Electron Shuttles to Accelerate Acetotrophic Methanogenesis by Methanosarcina barkeri

Magnetite nanoparticles (nanoFe₃O₄) have been reported to facilitate direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens thereby improving syntrophic methanogenesis. However, whether or how nanoFe₃O₄ affects acetotrophic methanogenesis remain unknown. Herein, we demonstrate the unique role of nanoFe₃O₄ in accelerating methane production from direct acetotrophic methanogenesis in Methanosarcina-enriched cultures, which was further confirmed by pure cultures of Methanosarcina barkeri. Compared with other nanomaterials of higher electrical conductivity such as carbon nanotubes and graphite, nanoFe₃O₄ with mixed valence Fe(II) and Fe(III) had the most significant stimulatory effect on methane production, suggesting its redox activity rather than electrical conductivity led to enhanced methanogenesis by M. barkeri. Cell morphology and spectroscopy analysis revealed that nanoFe₃O₄ penetrated into the cell membrane and cytoplasm of M. barkeri. These results provide the unprecedented possibility that nanoFe₃O₄ in the cell membrane of methanogens serve as electron shuttles to facilitate intracellular electron transfer and thus enhance methane production. This work has important implications not only for understanding the mechanisms of mineral-methanogen interaction but also for optimizing engineered methanogenic processes.

Nanoparticles in mitigating gaseous emissions from liquid dairy manure stored under anaerobic condition

A number of mitigation techniques exist to reduce the emissions of pollutant gases and greenhouse gases (GHGs) from anaerobic storage of livestock manure. Nanoparticle (NP) application is a promising mitigating treatment option for pollutant gases, but limited research is available on the mode of NP application and their effectiveness in gaseous emission reduction. In this study, zinc silica nanogel (ZnSNL), copper silica nanogel (CuSNL), and N-acetyl cysteine (NACL) coated zinc oxide quantum dot (Qdot) NPs were compared to a control lacking NPs. All three NPs tested significantly reduced gas production and concentrations compared to non-treated manure. Overall, cumulative gas volumes were reduced by 92.73%-95.83%, and concentrations reduced by 48.98%-99.75% for H₂S, and 20.24%-99.82% for GHGs. Thus, application of NPs is a potential treatment option for mitigating pollutant and GHG emissions from anaerobically stored manure.

Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing

Metatranscriptomics is a powerful tool for capturing gene expression patterns in microbial communities and investigating their responses to environmental conditions. Stable isotope probing (SIP) is a method to target specific functional groups of microorganisms in environmental samples. The combination of RNA-SIP with metatranscriptomic analysis enhances the detection and identification of mRNA from target microorganisms. In this chapter we provide a protocol for RNA-SIP, mRNA enrichment, and mRNA preparation for high-throughput sequencing using an example of targeting methanotrophs in rice field soil.

Reduction in Methane Emissions From Acidified Dairy Slurry Is Related to Inhibition of Methanosarcina Species

Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH₄ emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A (mcrA) genes/transcripts, respectively. When compared with untreated slurries, acidification resulted in 69–84% reductions of cumulative CH₄ emissions. The abundance, activity, and proportion of bacterial communities did not vary with manure acidification. However, the abundance and activity of methanogens (as estimated from mcrA gene and transcript copies, respectively) in acidified slurries were reduced by 6 and 20%, respectively. Up to 21% reduction in mcrA transcript/gene ratios were also detected in acidified slurries. Regardless of treatment, Methanocorpusculum predominated archaeal 16S rRNA and mcrA gene and transcript libraries. The proportion of Methanosarcina, which is the most metabolically-diverse methanogen, was the significant discriminant feature between acidified and untreated slurries. In acidified slurries, the relative proportions of Methanosarcina were ≤ 10%, whereas in untreated slurries, it represented up to 24 and 53% of the mcrA gene and transcript libraries, respectively. The low proportions of Methanosarcina in acidified slurries coincided with the reductions in CH₄ emissions. The results suggest that reduction of CH₄ missions achieved by acidification was due to an inhibition of the growth and activity of Methanosarcina species.

Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions

Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH₄) and nitrous oxide (N₂O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH₄ and N₂O cycling. Functional genes were used to target populations producing and consuming GHGs, specifically methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) for CH₄ and nitric oxide reductase (cnorB) and nitrous oxide reductase (nosZ) for N₂O. All biomarker genes were found in all soil samples regardless of treatment (leach field, sand filter, or control) or depth (surface or subsurface). In general, biomarker genes were more abundant in surface soils than subsurface soils suggesting the majority of GHG cycling is occurring in near-surface soils. Ratios of production to consumption gene abundances showed a positive relationship with CH₄ emissions (mcrA:pmoA, p < 0.001) but not with N₂O emission (cnorB:nosZ, p > 0.05). Of the three measured soil parameters (volumetric water content (VWC), temperature, and conductivity), only VWC was significantly correlated to a biomarker gene, mcrA (p = 0.0398) but not pmoA or either of the N₂O cycling genes (p > 0.05 for cnorB and nosZ). 16S rRNA amplicon library sequencing results revealed soil VWC, CH₄ flux and N₂O flux together explained 64% of the microbial community diversity between samples. Sequencing of mcrA and pmoA amplicon libraries revealed treatment had little effect on diversity of CH₄ cycling organisms. Overall, these results suggest GHG cycling occurs in all soils regardless of whether or not they are associated with a leach field system.

Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium

The aim of this work was to study the effects of key trace elements (i.e., iron, copper and molybdenum) on the development of co-cultured n-damo and methanogenic bacteria consortium, which could realize in situ CH₄ production and utilization. The results showed that rational dosage, which was 50 mg/L of Fe, 1 mg/L of Cu and 5 mg/L of Mo, significantly stimulated the removal of NO₂^-. However, the activity of microbes was noticeably inhibited at 5 mg/L of Cu and 1 mg/L of Mo. Microbial community analysis indicated that the abundances of n-damo bacteria and methanogens showed a positive response to the rational dosage. Furthermore, the expression of key functional genes was enhanced under the rational dosage condition.

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

BACKGROUND

The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web.

RESULTS

Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype.

CONCLUSIONS

Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.

Cryptic CH4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea

Methane in the seabed is mostly oxidized to CO₂ with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO₂ by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.

Stimulatory Effect of Magnetite Nanoparticles on a Highly Enriched Butyrate-Oxidizing Consortium

Syntrophic oxidation of butyrate is catabolized by a few bacteria specialists in the presence of methanogens. In the present study, a highly enriched butyrate-oxidizing consortium was obtained from a wetland sediment in Tibetan Plateau. During continuous transfers of the enrichment, the addition of magnetite nanoparticles (nanoFe3O4) consistently enhanced butyrate oxidation and CH4 production. Molecular analysis revealed that all bacterial sequences from the consortium belonged to Syntrophomonas with the closest relative of Syntrophomonas wolfei and 96% of the archaeal sequences were related to Methanobacteria with the remaining sequences to Methanocella. Addition of graphite and carbon nanotubes for a replacement of nanoFe3O4 caused the similar stimulatory effect. Silica coating of nanoFe3O4 surface, however, completely eliminated the stimulatory effect. The control experiment with axenic cultivation of a Syntrophomonas strain and two methanogen strains showed no effect by nanoFe3O4. Together, the results in the present study support that syntrophic oxidation of butyrate is likely facilitated by direct interspecies electron transfer in the presence of conductive nanomaterials.

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

Paddy soil accounts for 10% of global atmospheric methane (CH₄) emissions. Many types of fertilizers may enhance CH₄ emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH₄ and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha^-1. Paddy CH₄, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH₄ emissions were significantly higher in OT (145.31 kg ha^-1) than MT (84.62 kg ha^-1), CT (77.88 kg ha^-1) or ctrl (32.19 kg ha^-1). Soil organic acids were also increased by organic fertilization. CH₄ effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH₄ production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH₄ emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha^-1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.

Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil

Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime

Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6 years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change.

Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem

Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO₂). Rice fields represent the major source of methane (CH₄) emission as the recent estimates range from 34 to 112 Tg CH₄ per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH₄ emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.

Stimulation of long-term ammonium nitrogen deposition on methanogenesis by Methanocellaceae in a coastal wetland

Atmospheric nitrogen deposition caused by human activities has been receiving much attention. Here, after long-term simulated ammonium and nitrate nitrogen deposition (NH₄Cl, KNO₃, and NH₄NO₃) in the Yellow River Delta (YRD), a sensitive coastal wetland ecosystem typified by a distinct wet and dry season, methane fluxes were measured, by adopting a closed static chamber technique. The results showed that deposition of ammonium nitrogen accelerated methane emissions all year round. Ammonium nitrogen deposition transformed the YRD from a methane sink into a source during the dry season. Methanocellaceae is the only methanogen with increased abundance after the application of NH₄Cl and NH₄NO₃, which promoted methane emissions, during the wet season. The findings suggested that Methanocellaceae may facilitate methane emissions in response to increased ammonium nitrogen deposition. Other methanogens might have profited from ammonium supplementation, such as Methanosarcinaceae. Deposition of nitrate nitrogen did not affect methane flux significantly. To the best of our knowledge, this study is the first to show that Methanocellaceae may be responsible for methane production in coastal wetland system. This study highlights the significant effect of ammonium nitrogen and slight effect of nitrate nitrogen on methane emission in the YRD and it will be helpful to understand the microbial mechanism responding to increased nitrogen deposition in the sensitive coastal wetland ecosystem.

Reduction of greenhouse gases emissions during anoxic wastewater treatment by strengthening nitrite-dependent anaerobic methane oxidation process

Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered process performed by NC10 phylum, which plays an important role in greenhouse gases (GHG) reduction. In this study, co-existence of n-damo bacteria and methanogens was successfully achieved by using upflow anaerobic sludge blanket (UASB) reactor. Reactor with inorganic carbon source (CO₂/H₂) showed the highest abundance of n-damo bacteria and the highest n-damo potential activity, resulted in its highest nitrogen removal rate. Significant reduction in GHG was obtained after introduction of n-damo process, especially for N₂O. Furthermore, GHG emissions decreased with the increase of n-damo bacteria abundance. Community structure analysis found carbon source could influence the diversity of n-damo bacteria indirectly. And phylogenetic analysis showed that all the obtained sequences were assigned to group B, mainly due to in situ production and consumption of CH₄.

Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand

Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ¹³C of organic carbon and of CH₄ and CO₂ produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH₄ production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.

Characterization of zinc oxide nanoparticle (nZnO) alginate beads in reducing gaseous emission from swine manure

Hydrogen sulfide (H₂S) and greenhouse gases' emission from livestock production facilities are of concern to human welfare and the environment. Application of nanoparticles (NPs) has emerged as a potential option for minimizing these gaseous emissions. Application of bare NPs, however, could have an adverse effect on plants, soil, human health, and the environment. To minimize NPs' exposure to the environment by recovering them, NPs were entrapped in polymeric beads for treating livestock manure. The objectives of the research were to understand the mechanism of gaseous reduction in swine manure treated for 33 days with zinc oxide nanoparticles (nZnO) or nZnO-entrapped alginate (alginate-nZnO) beads by different characterization techniques. Headspace gases from treated manure flasks were collected in 2-6-day intervals during the experimental period and were analyzed for methane (CH₄), carbon dioxide (CO₂), and H₂S concentrations. The microbial analysis of manure was carried out using bacterial plate counts and Real-Time Polymerase Chain Reaction methods. Morphology and chemical composition of alginate-nZnO beads were analyzed by Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and X-ray Photoelectron Spectroscopy (XPS). Alginate-nZnO beads or bare nZnO proved to be an effective NP in reducing H₂S (up to 99%), CH₄ (49-72%), and CO₂ (46-62%) from manure stored under anaerobic conditions and these reductions are likely due to the microbial inhibitory effect from nZnO, as well as chemical conversion. Both SEM-EDS and XPS analysis confirmed the presence of zinc sulfide (ZnS) in the beads, which is likely formed by reacting nZnO with H₂S.

Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils

The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated with Geobacter species, but sequences most closely related to putative e-pilin genes from genera such as Desulfobacterium, Deferribacter, Geoalkalibacter, and Desulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered with Geobacter species, and the finding that Geobacter spp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribed Geobacter genes. In addition, homologs of genes encoding OmcS, a c-type cytochrome associated with the e-pili of G. sulfurreducens and required for DIET, were also highly expressed in the soils. Methanothrix species in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO₂ reduction in Methanothrix Thus, these results are consistent with a model in which Geobacter species were providing electrons to Methanothrix species for methane production through electrical connections of e-pili.IMPORTANCEMethanothrix species are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons for Methanothrix in methanogenic rice paddy soils is important because it demonstrates that the contribution that Methanothrix makes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that when Methanothrix species receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus, Methanothrix growth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason that Geobacter species are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation with Methanothrix spp., and possibly other methanogens, via DIET.

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice

Azolla caroliniana Willd. is widely used as a green manure accompanying rice, but its ecological importance remains unclear, except for its ability to fix nitrogen in association with cyanobacteria. To investigate the impacts of Azolla cultivation on methane emissions and environmental variables in paddy fields, we performed this study on the plain of Dongting Lake, China, in 2014. The results showed that the dual cropping of Azolla significantly suppressed the methane emissions from paddies, likely due to the increase in redox potential in the root region and dissolved oxygen concentration at the soil-water interface. Furthermore, the floodwater pH decreased in association with Azolla cultivation, which is also a factor significantly correlated with the decrease in methane emissions. An increase in methanotrophic bacteria population (pmoA gene copies) and a reduction in methanogenic archaea (16S rRNA gene copies) were observed in association with Azolla growth. During rice cultivation period, dual cropping of Azolla also intensified increasing trend of 1/Simpson of methanogens and significantly decreased species richness (Chao 1) and species diversity (1/Simpson, 1/D) of methanotrophs. These results clearly demonstrate the suppression of CH₄ emissions by culturing Azolla and show the environmental and microbial responses in paddy soil under Azolla cultivation.

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil

Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.