Correlation of methane production and functional gene transcriptional activity in a peat soil

The interplay of soil physicochemical properties, methanogenic diversity, and abundance governs methane production potential in paddy soil subjected to multi-decadal straw incorporation

Straw incorporation holds significant promise for enhancing soil fertility and mitigating air pollution stemming from straw burning. However, this practice concurrently elevates the production and emission of methane (CH4) from paddy ecosystems. Despite its environmental impact, the precise mechanisms behind the heightened CH4 production resulting from long-term straw incorporation remain elusive. In a 32-year field experiment featuring three fertilization treatments (CFS-chemical fertilizer with wheat straw, CF-chemical fertilizer, and CK-unamended), we investigated the impact of abiotic (soil physicochemical properties) and biotic (methanogenic abundance, diversity, and community composition) factors on CH4 production in paddy fields. Results revealed a significantly higher CH4 production potential under CFS treatment compared to CF and CK treatments. The partial least squares path model revealed that soil physicochemical properties (path coefficient = 0.61), methanogenic diversity (path coefficient = -0.43), and methanogenic abundance (path coefficient = 0.29) collectively determined CH4 production potential, explaining 77% of the variance. Enhanced soil organic carbon content and water content, resulting from straw incorporation, emerged as pivotal factors positively correlated with CH4 production potential. Under CFS treatment, lower Shannon index of methanogens, compared to CF and CK treatments, was attributed to increased Methanosarcina. Notably, the Shannon index and relative abundance of Methanosarcina exhibited negative and positive correlations with CH4 production potential, respectively. Methanogenic abundance, bolstered by straw incorporation, significantly amplified overall potential. This comprehensive analysis underscores the joint influence of abiotic and biotic factors in regulating CH4 production potential during multi-decadal straw incorporation.

Rapid shift in greenhouse forcing of emerging arctic peatlands

In this study, we hypothesised that the actual development stage (i.e., current age of the ecosystem) is a determining factor for the magnitude of methane production and emissions in young, northern high-latitude peatlands. We demonstrate that the earliest development of peat soil imposes a sink-to-source shift in the greenhouse warming potential of emerging peatlands in response to climate change that holds feedback mechanisms of importance for short-term (< 100 years) climate warming.

pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization

Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self-alkaline conditions of pH up to 10.80. Manually lowering the pH to a range of 9.00-10.00 dramatically decreased the nitrate-to-nitrite transformation ratio to <20%, showing a significant role of high pH in denitratation. Metagenomics combined with metatranscriptomics indicated that six microorganisms, including a Thauera member, dominated the community and encoded the various genes responsible for hydrogen oxidation and the complete denitrification process. During denitratation at high pH, transcription of periplasmic genes napA, nirS, and nirK, whose products perform nitrate and nitrite reduction, decreased sharply compared to that under neutral conditions, while narG, encoding a membrane-associated nitrate reductase, remained transcriptionally active, as were genes involved in intracellular proton homeostasis. Together with no reduction in only nitrite-amended samples, these results disproved the electron competition between reductions of nitrate and nitrite but highlighted a lack of protons outside cells constraining biological nitrite reduction. Overall, our study presents a stably efficient strategy for nitrite production and provides a major advance in the understanding of denitratation.

Responses of Fermentation Characteristics and Microbial Communities to Vitamin B12 Supplementation in In Vitro Ruminal Cultures

Vitamin B12, an important cofactor involved in propionate formation, is synthesized exclusively by bacteria and archaebacteria. Humans need to intake vitamin B12 through food, and dairy products are generally the best source of vitamin B12. In the present study, the effects of vitamin B12 supplementation in diets on in vitro ruminal fermentation characteristics and microbial communities were investigated to provide a reference for increasing the vitamin B12 content in milk by dietary supplementation. A completely randomized design was carried out using the in vitro rumen culture technique, and 5 vitamin B12 dose levels (0, 0.5, 1.0, 2.0, and 4 mg/g of dry matter) were used. The results showed that vitamin B12 supplementation in diets decreased acetate: propionate ratio and butyrate concentration. The change in the acetate: propionate ratio can be attributed to the increased relative abundances of the Proteobacteria phylum and the Negativicutes class, both of which are involved in propionate metabolism. The decrease in butyrate concentration can likely be attributed to a reduction in relative abundance of species belonging to the Clostridia class, which are known as the predominant butyrate producers in the mammalian intestine. In addition, vitamin B12 supplementation in diets reduced the CH4 production by altering the species composition of the archaeal community. In conclusion, dietary supplementation of vitamin B12 resulted in rumen perturbation. In vivo studies should be conducted cautiously when evaluating the effects of vitamin B12 supplementation on the synthesis and absorption of it, as well as its content in milk.

A novel partial denitrification, anammox-biological phosphorus removal, fermentation and partial nitrification (PDA-PFPN) process for real domestic wastewater and waste activated sludge treatment

A novel process was developed for real domestic wastewater and waste activated sludge (WAS) treatment based on partial denitrification, anammox-biological phosphorus removal, fermentation and partial nitrification (PDA-PFPN). After 246 days of operation, the effluent concentrations of NH₄⁺-N, NO₂^--N and NO₃^--N were below detection limits (0.1 mg/L), and the effluent concentration of PO₄^3--P was 0.1 mg/L without the addition of external carbon source in PDA-PFPN system. Moreover, the sludge reduction efficiency reached 48.1% due to fermentation. The nitrite accumulation ratios by ammonia oxidation and nitrate reduction pathway were 60.6% and 87%, respectively. Intracellular metabolites measured by liquid chromatography mass spectrometer (LC-MS/MS) suggested that different intracellular amino acids were stored and consumed at different duration, and intracellular Valine, Glycine and Lysine were not utilized in oxic stage. Results of flow cytometry showed that the proportion of intact cells decreased from 94.7% to 82.9%, and necrotic cells increased from 5.3% to 17.1% with the increase of DNA content in sludge supernatant and cell decay rate, indicating the occurrence of cell death and lysis and leading to WAS reduction. Analysis of transcriptional community composition revealed that partial denitrification bacteria (Thauera), anammox bacteria (Candidatus Brocadia and Candidatus Kuenenia), simultaneous phosphorus removal and fermentation bacteria (Tetrasphaera) and partial nitrification bacteria (Nitrosomonas) coexisted and actually worked in PDA-PFPN system. The novel PDA-PFPN process simultaneously achieved highly efficient nitrogen and phosphorus removal and WAS reduction without the addition of external carbon source, which greatly reduced the operation cost of carbon source dosing and WAS treatment in wastewater treatment.

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

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

Methanogen and nitrifying genes dynamics in immersed membrane bioreactors during anaerobic co-digestion of different organic loading rates food waste

This work was aimed to evaluate the distinctive food waste (FW) organic loading rates (OLR) on methanogen and nitrifying genes dynamics and its correlation with identified relative abundance of bacterial dynamics during the anaerobic digestion. This experiment were carried out in the digesters at high OLR of food wastes at (4 to 8 g volatile solids/liter/day reactor R1) and (6 to 10 g volatile solids/liter/day reactor R2). The results shown that the relative abundance of mcrA, mcrB and mcrG genes were richest in the first day of both R1 and R2. In addition, the most of nitrifying genes were greater in after 34 days digestion in R2, while these genes did not show the specific regularity in R1. Finally, the correlation figure shows that Clostridium and Lactobacillus genera were significantly correlated with the different organic acids and methanogen and nitrifying genes dynamics.

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

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

Source or sink? A study on the methane flux from mangroves stems in Zhangjiang estuary, southeast coast of China

Mangrove ecosystems are an important component of "blue carbon". However, it is not clear whether the stems play roles in the CH₄ budget of mangrove ecosystems. This study investigated the CH₄ emission from mangrove stems and its potential driving factors. We set up six sample plots in the Zhangjiang Estuary National Mangrove Nature Reserve, where Kandelia obovata, Avicennia marina and Aegiceras corniculata are the main mangrove tree species. Soil properties such as total carbon content, redox potential and salinity were determined in each plot. The dynamic chamber method was used to measure mangrove stems and soil CH₄ fluxes. Combined field survey results with Principal Component Analysis (PCA) of soil properties, we divided the six plots into two sites (S1 and S2) to perform statistical analyses of stem CH₄ fluxes. Then the CH₄ fluxes from mangrove tree stems and soil were further scaled up to the ecosystem level through the mapping model. Under different backgrounds of soil properties, salinity and microbial biomass carbon were the main factors modified soil CH₄ fluxes in the two sites, and further affected the stem CH₄ fluxes of mangroves. The soil of both sites are sources of CH₄, and the soil CH₄ emission of S2 was about twice higher than that of S1. Results of upscaling model showed that mangrove stems in S1 were CH₄ sinks with -105.65 g d^-1. But stems in S2 were CH₄ sources around 1448.24 g d^-1. Taken together, our results suggested that CH₄ emission from mangrove soils closely depends on soils properties. And mangrove stems were found to act as both CH₄ sources and CH₄ sinks depend on soil CH₄ production. Therefore, when calculating the CH₄ budget of the mangrove ecosystem, the contribution of mangrove plant stems cannot be ignored.

Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems

Freshwater ecosystems are responsible for an important part of the methane (CH₄) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH₄ flux measurements, CH₄ production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H₂/CO₂, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H₂/CO₂-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H₂/CO₂ (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H₂/CO₂-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H₂-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.

Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.

Nitrogen addition decreases methane uptake caused by methanotroph and methanogen imbalances in a Moso bamboo forest

Forest soils play an important role in controlling global warming by reducing atmospheric methane (CH₄) concentrations. However, little attention has been paid to how nitrogen (N) deposition may alter microorganism communities that are related to the CH₄ cycle or CH₄ oxidation in subtropical forest soils. We investigated the effects of N addition (0, 30, 60, or 90 kg N ha⁻¹ yr⁻¹) on soil CH₄ flux and methanotroph and methanogen abundance, diversity, and community structure in a Moso bamboo (Phyllostachys edulis) forest in subtropical China. N addition significantly increased methanogen abundance but reduced both methanotroph and methanogen diversity. Methanotroph and methanogen community structures under the N deposition treatments were significantly different from those of the control. In N deposition treatments, the relative abundance of Methanoculleus was significantly lower than that in the control. Soil pH was the key factor regulating the changes in methanotroph and methanogen diversity and community structure. The CH₄ emission rate increased with N addition and was negatively correlated with both methanotroph and methanogen diversity but positively correlated with methanogen abundance. Overall, our results suggested that N deposition can suppress CH₄ uptake by altering methanotroph and methanogen abundance, diversity, and community structure in subtropical Moso bamboo forest soils.

Methane emissions respond to soil temperature in convergent patterns but divergent sensitivities across wetlands along altitude

Among the global coordinated patterns in soil temperature and methane emission from wetlands, a declining trend of optimal soil temperature for methane emissions from low to high latitudes has been witnessed, while the corresponding trend along the altitudinal gradient has not yet been investigated. We therefore selected two natural wetlands located at contrasting climatic zones from foothill and mountainside of Nepal Himalayas, to test: (1) whether the optimal temperature for methane emissions decreases from low to high altitude, and (2) whether there is a difference in temperature sensitivity of methane emissions from those wetlands. We found significant spatial and temporal variation of methane emissions between the two wetlands and seasons. Soil temperature was the dominant driver for seasonal variation in methane emissions from both wetlands, though its effect was perplexed by the level of standing water, aquatic plants, and dissolved organic carbon, particularly in the deep water area. When integrative comparison was conducted by adding the existing data from wetlands of diverse altitudes, and the latitude-for-altitude effect was taken into account, we found the baseline soil temperatures decrease whilst the altitude rises with respect to a rapid increase in methane emission from all wetlands, however, remarkably higher sensitivity of methane emissions to soil temperature (apparent Q₁₀ ) was found in mid-altitude wetland. We provide the first evidence of an apparent decline in optimal temperature for methane emissions with increasing elevation. These findings suggest a convergent pattern of methane emissions with respect to seasonal temperature shifts from wetlands along altitudinal gradient, while a divergent pattern in temperature sensitivities exhibits a single peak in mid-altitude.

Temporal, Spatial, and Temperature Controls on Organic Carbon Mineralization and Methanogenesis in Arctic High-Centered Polygon Soils

Warming temperatures in continuous permafrost zones of the Arctic will alter both hydrological and geochemical soil conditions, which are strongly linked with heterotrophic microbial carbon (C) cycling. Heterogeneous permafrost landscapes are often dominated by polygonal features formed by expanding ice wedges: water accumulates in low centered polygons (LCPs), and water drains outward to surrounding troughs in high centered polygons (HCPs). These geospatial differences in hydrology cause gradients in biogeochemistry, soil C storage potential, and thermal properties. Presently, data quantifying carbon dioxide (CO₂) and methane (CH₄) release from HCP soils are needed to support modeling and evaluation of warming-induced CO₂ and CH₄ fluxes from tundra soils. This study quantifies the distribution of microbial CO₂ and CH₄ release in HCPs over a range of temperatures and draws comparisons to previous LCP studies. Arctic tundra soils were initially characterized for geochemical and hydraulic properties. Laboratory incubations at −2, +4, and +8°C were used to quantify temporal trends in CO₂ and CH₄ production from homogenized active layer organic and mineral soils in HCP centers and troughs, and methanogen abundance was estimated from mcrA gene measurements. Results showed that soil water availability, organic C, and redox conditions influence temporal dynamics and magnitude of gas production from HCP active layer soils during warming. At early incubation times (2–9 days), higher CO₂ emissions were observed from HCP trough soils than from HCP center soils, but increased CO₂ production occurred in center soils at later times (>20 days). HCP center soils did not support methanogenesis, but CH₄-producing trough soils did indicate methanogen presence. Consistent with previous LCP studies, HCP organic soils showed increased CO₂ and CH₄ production with elevated water content, but HCP trough mineral soils produced more CH₄ than LCP mineral soils. HCP mineral soils also released substantial CO₂ but did not show a strong trend in CO₂ and CH₄ release with water content. Knowledge of temporal and spatial variability in microbial C mineralization rates of Arctic soils in response to warming are key to constraining uncertainties in predictive climate models.

Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman

Serpentinization can generate highly reduced fluids replete with hydrogen (H₂) and methane (CH₄), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH₄ in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH₄ in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH₄ cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H₂- and CH₄-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH₄ production and in microbial CH₄ oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH₄ cycling in aquifers that undergo low-temperature serpentinization.IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH₄) cycling, including the abiotic production of hydrogen (H₂) and possibly CH₄ Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth's history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H₂ and CH₄ These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH₄ in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.

Simultaneous detection of transcribed functional assA gene and the corresponding metabolites of linear alkanes (C4, C5, and C7) in production water of a low-temperature oil reservoir

Methanogenic hydrocarbon degradation is an important biogeochemical process in oil reservoirs; however, genomic DNA-based analysis of microorganisms and metabolite detection are not conclusive for identification of the ongoing nature of this bioprocess. In this study, a suite of analyses, involving the study of microbial community and selective gene quantification of both genomic DNA and RNA together with signature metabolites, were performed to comprehensively advance the understanding of the methanogenic biodegradation of hydrocarbons in a low-temperature oilfield. The fumarate addition products for alkanes-C₄, C₅, and C₇-alkylsuccinates-and transcribed assA and mcrA genes were simultaneously detected in the production water sample, providing robust and convincing evidence for both the initial activation of n-alkanes and methane metabolism in this oilfield. The clone library of assA gene transcripts showed that Smithella was active and most likely responsible for the addition of fumarate to n-alkanes, whereas Methanoculleus and Methanothrix were the dominant and active methane-producers via CO₂ reduction and acetoclastic pathways, respectively. Additionally, qPCR results of assA and mcrA genes and their transcribed gene copy numbers revealed a roughly similar transcriptional activity in both n-alkanes-degraders and methane producers, implying that they were the major participants in the methanogenic degradation of n-alkanes in this oilfield. To the best of our knowledge, this is the first report presenting sufficient speculation, through detection of signature intermediates, corresponding gene quantification at transcriptional levels, and microbial community analysis, of methanogenic degradation of n-alkanes in production water of an oil reservoir.

Assessment of microbial diversity associated with CH4 emission from sugarcane vinasse storage and transportation systems

Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH₄) emission during storage and transportation stages. Considering that CH₄ emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH₄ patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH₄ emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH₄ production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 10⁷ and 4.3 × 10¹⁰) and subsequent positive correlation with CH₄ emissions (R² = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH₄ emissions, thereby making bioethanol a greener biofuel.

Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs)

Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.

Transcriptional responses of Candidatus Accumulibacter clades to environmental dynamics in enhanced biological phosphorus removal

The dynamic response mechanism of Candidatus Accumulibacter clades to environmental factors in enhanced biological phosphorus removal (EBPR) was unclear. This study investigated the relationship between the transcriptional responses of Candidatus Accumulibacter clades and environmental dynamics. Results suggested that Candidatus Accumulibacter clade IIA only responded in initial 20 and 30 min of P-release and P-uptake stage, respectively, and was also the first clade to stop responding among the six Candidatus Accumulibacter clades. Clade IIC and IID responded at rising stage of P-release and P-uptake rate. Clade IA and IIB responded at decreasing stage of P-release and P-uptake rate. The transcriptional response duration of clade IIF was the longest, which constantly responded throughout anaerobic, anoxic and oxic phase. The transcriptional responses of Candidatus Accumulibacter clades to environmental dynamics revealed the microorganisms actually working in P-release and P-uptake, and gave a new insight into the transcriptional responses related to the EBPR performance.

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.

Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms

Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities 'map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping in organisms. We identify two insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of searching 'agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Microbial community at transcription level in the synergy of GAOs and Candidatus Accumulibacter for saving carbon source in wastewater treatment

The microbial community in endogenous denitrification and denitrifying phosphorus removal treatment at transcription level was unknown. This study first confirmed the expression of actually active bacteria in endogenous denitrification and denitrifying phosphorus removal system to treat low C/N municipal wastewater. No external carbon source was added to influent wastewater. The cDNA high throughput sequencing showed that Candidatus Accumulibacter was the most effective polyphosphate accumulating organisms (PAOs) that actually worked rather than Dechloromonas, which was different from the result at gene level. Reverse transcriptional PCR (RT-PCR) and analysis of Variance (ANOVA) suggested that the ratios of dead or dormant bacteria could monitor wastewater treatment process. Identification of active microbial community at transcription level demonstrated that the synergy of endogenous denitrification by glycogen accumulating organisms (GAOs) and denitrifying phosphorus removal by Candidatus Accumulibacter fully utilized the internal carbon source, and effectively solved the problem of carbon source deficiency in municipal wastewater treatment.

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.

Analysis of microbial community in a continuous flow process at gene and transcription level to enhance biological nutrients removal from municipal wastewater

In biological municipal wastewater treatment, gene level analysis of community structure could not determine functional genes that actually played a role and expression of viable microorganism. In this study, reverse transcriptional PCR (RT-PCR), cDNA high throughput sequencing and transcriptional activity analysis were conducted to investigate active microbial community with nitrogen and phosphorus removal from municipal wastewater. RT-PCR and correlation heatmap analysis suggested that transcriptional activities of bacteria had strong correlation with performance of nitrogen and phosphorus removal, they might be therefore regarded as an indicator for wastewater treatment monitoring. When DO concentration were raised from 0.6 mg/L to 2 mg/L and C/N ratio from 3-4 to 5, the increase of population abundance and transcriptional activities of denitrifying genes improved the removal efficiencies of COD and TN. The species with relatively high abundance at gene level were not really active species at transcription level, and vice versa.

Impact of Warming on Greenhouse Gas Production and Microbial Diversity in Anoxic Peat From a Sphagnum-Dominated Bog (Grand Rapids, Minnesota, United States)

Climate warming is predicted to increase heterotrophic metabolism in northern peatland soils leading to enhanced greenhouse gas emissions. However, the specific relationships between temperature and the greenhouse gas producing microbial communities are poorly understood. Thus, in this study, the temperature dependence of carbon dioxide (CO2) and methane (CH4) production rates along with abundance and composition of microbial communities were investigated in peat from a Sphagnum-dominated peatland, S1 bog (Minnesota, United States). Whereas CH4 production rates increased with temperature up to 30°C, CO2 production did not, resulting in a lower CO2:CH4 ratio with increasing temperature. CO2 production showed both psychrophilic and mesophilic maxima at 4 and 20°C, respectively, and appears to be mediated by two anaerobic microbial communities, one that operates under psychrophilic conditions that predominate for much of the year, and another that is more active under warmer conditions during the growing season. In incubations at 10°C above the ambient range, members of the Clostridiaceae and hydrogenotrophic methanogens of the Methanobacteriaceae dominated. Moreover, a significant negative correlation between temperature and microbial diversity was observed. Results indicate that the potential consequences of warming surface peat in northern peatlands include a large stimulation in CH4 production and a significant loss of microbial diversity.

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.

Quantitative analysis of methane monooxygenase (MMO) explains process robustness in continuous and feast-famine bioreactors treating methane

The ability of methanotrophs to rapidly respond to intentional or accidental stress conditions caused by operational failures or process fluctuations is of utmost importance to guarantee the robustness of CH₄ abatement biotechnologies. In this study, the performance of a continuous and two feast-famine (5:5 days feast-famine cycles) stirred tank reactors treating diluted CH₄ emissions (4-5% v/v) was comparatively assessed for 149 days. The robustness of the three bioreactors towards a 5 days CH₄ deprivation episode was thoroughly evaluated at a molecular level (pmoA gene expression level) and correlated to macroscopic process performance. The bioreactors recovered their steady-state abatement performance (in terms of CH₄ elimination capacity and CO₂ production rate) within 1.5-2 h following CH₄ supply resumption concomitantly with a maximum in pmoA gene expression, regardless of the previous operational mode. However, while methanotrophs from the continuous unit maintained higher basal levels of pmoA expression as a strategy for a rapid CH₄ metabolism initiation, the strategy of the feast-famine adapted-methanotrophs consisted on a more accurate regulation of their pmoA transcripts levels along with a higher and/or more rapid induction of the pmoA gene by CH₄ availability.

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.

Shifts of Hydrogen Metabolism From Methanogenesis to Propionate Production in Response to Replacement of Forage Fiber With Non-forage Fiber Sources in Diets in vitro

The rumen microbial complex adaptive mechanism invalidates various methane (CH₄) mitigation strategies. Shifting the hydrogen flow toward alternative electron acceptors, such as propionate, was considered to be a meaningful mitigation strategy. A completely randomized design was applied in in vitro incubation to investigate the effects of replacing forage fiber with non-forage fiber sources (NFFS) in diets on methanogenesis, hydrogen metabolism, propionate production and the methanogenic and bacterial community. There are two treatments in the current study, CON (a basic total mixed ration) and TRT (a modified total mixed ration). The dietary treatments were achieved by partly replacing forage fiber with NFFS (wheat bran and soybean hull) to decrease forage neutral detergent fiber (fNDF) content from 24.0 to 15.8%, with the composition and inclusion rate of other dietary ingredients remaining the same in total mixed rations. The concentrations of CH₄, hydrogen (H₂) and volatile fatty acids were determined using a gas chromatograph. The archaeal and bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the relative abundance of methanogenic and bacterial communities. The results revealed that the concentration of propionate was significantly increased, while the concentration of acetate and the acetate to propionate ratio were not affected by treatments. Compared with CON, the production of H₂ increased by 8.45% and the production of CH₄ decreased by 14.06%. The relative abundance of Methanomassiliicoccus was significantly increased, but the relative abundance of Methanobrevibacter tended to decrease in TRT group. At the bacterial phylum level, the TRT group significantly decreased the relative abundance of Firmicutes and tended to increase the relative abundance of Bacteroidetes. The replacement of forage fiber with NFFS in diets can affect methanogenesis by shifting the hydrogen flow toward propionate, and part is directed to H₂ in vitro. The shift was achieved by a substitution of Firmicutes by Bacteroidetes, another substitution of Methanobrevibacter by Methanomassiliicoccus. Theoretical predictions of displacements of H₂ metabolism from methanogenesis to propionate production was supported by the dietary intervention in vitro.

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.

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.

Active and total microbial community dynamics and the role of functional genes bamA and mcrA during anaerobic digestion of phenol and p-cresol

The aim of the present work was to investigate the dynamics of microbial community at DNA and RNA level and the role of bamA and mcrA gene during anaerobic digestion of phenol and p-cresol. Anaerobic digestion was conducted in batch reactors and microbial community dynamics was analysed. Results showed that active microbial community was quite dissimilar in comparison to the total microbial community. Syntrophorhabdus and Bacillus were the dominant active bacterial genera whereas Methanosaeta together with Methanobacterium showed the highest potential activity in the Archaea domain indicating a relevant role of these microorganisms in the anaerobic process. Ecological Networks revealed dissimilar interactions at DNA and RNA level, being the latter a better descriptor of the known roles of dominant OTUs. QRT-PCR results showed that expression of bamA gene correlated positively with instantaneous degradation rate proving for first time its functionality and its relationship with the kinetics of the process.

Climate-driven shifts in sediment chemistry enhance methane production in northern lakes

Freshwater ecosystems are a major source of methane (CH₄), contributing 0.65 Pg (in CO₂ equivalents) yr⁻¹ towards global carbon emissions and offsetting ~25% of the terrestrial carbon sink. Most freshwater CH₄ emissions come from littoral sediments, where large quantities of plant material are decomposed. Climate change is predicted to shift plant community composition, and thus change the quality of inputs into detrital food webs, with the potential to affect CH₄ production. Here we find that variation in phenol availability from decomposing organic matter underlies large differences in CH₄ production in lake sediments. Production is at least 400-times higher from sediments composed of macrophyte litter compared to terrestrial sources because of inhibition of methanogenesis by phenol leachates. Our results now suggest that earth system models and carbon budgets should consider the effects of plant communities on sediment chemistry and ultimately CH₄ emissions at a global scale.

Methane emissions from lakes vary by orders of magnitude, leaving large uncertainty in regional and global carbon budgets. Here the authors show that phenols from forest litter act as a latch to suppress microbial activity and produce over 400-times less methane than the decomposition of aquatic plant litter.

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes

Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10⁵ to 10⁹ copies g^-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

About half of the global methane (CH₄ ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH₄ emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

Plane of nutrition affects the phylogenetic diversity and relative abundance of transcriptionally active methanogens in the bovine rumen

Methane generated during enteric fermentation in ruminant livestock species is a major contributor to global anthropogenic greenhouse gas emissions. A period of moderate feed restriction followed by ad libitum access to feed is widely applied in cattle management to exploit the animal’s compensatory growth potential and reduce feed costs. In the present study, we utilised microbial RNA from rumen digesta samples to assess the phylogenetic diversity of transcriptionally active methanogens from feed-restricted and non-restricted animals. To determine the contribution of different rumen methanogens to methanogenesis during dietary restriction of cattle, we conducted high-throughput mcrA cDNA amplicon sequencing on an Illumina MiSeq and analysed both the abundance and phylogenetic origin of different mcrA cDNA sequences. When compared to their unrestricted contemporaries, in feed-restricted animals, the methanogenic activity, based on mcrA transcript abundance, of Methanobrevibacter gottschalkii clade increased while the methanogenic activity of the Methanobrevibacter ruminantium clade and members of the Methanomassiliicoccaceae family decreased. This study shows that the quantity of feed consumed can evoke large effects on the composition of methanogenically active species in the rumen of cattle. These data potentially have major implications for targeted CH₄ mitigation approaches such as anti-methanogen vaccines and/or tailored dietary management.

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils

While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production.

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil

The enrichment of H₂-oxidizing bacteria (HOB) by H₂ generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H₂, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H₂ mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H₂ exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H₂ while enhancing community level carbon substrate utilization potential and lowering CH₄ uptake activity in soil. We found that H₂ triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H₂ exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H₂ on soil microbial communities will lead to a better understanding of the H₂ fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H₂ diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH₄ oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H₂ rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.

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.

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

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

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

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

Incubation of innovative methanogenic communities to seed anaerobic digesters

The methanogenic communities in alternative inocula and their potential to increase CH₄ production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH₄ produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH₄ production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH₄ than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.

Relating Anaerobic Digestion Microbial Community and Process Function

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

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.

RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis

Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that are key to using these tools to further define the science of ruminal methanogenesis.