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

Long-term paddy use influences response of methane production, arsenic mobility and speciation to future higher temperatures

Anaerobic microbial metabolisms make flooded paddy soils a major source of the greenhouse gas methane (CH4) and mobilize toxic arsenic (As), threatening rice production and consumption. Increasing temperatures due to climate change enhance these microbially mediated processes, increasing their related threats. Chronosequence studies show that long-term paddy use ("age") changes soil properties and redox biogeochemistry through soil organic carbon (SOC) accumulation, its association to amorphous iron (Fe) phases, and increased microbial activity. Using paddy and non-paddy soils from a chronosequence as proxies of soil development and incubating them at different temperatures, we show that paddy soil age influences the response of paddies to changes in temperature. Older paddies showed up to a 6-fold higher CH4 production with increasing temperature, compared to a 2-fold increase in young ones. Contrarily, changes in As mobility were higher in non-paddies and young paddies due to a lack of Fe-SOC-sorption sites. Temperature increased the formation of phytotoxic methylated As in all paddies, posing a risk for rice production. Mitigation strategies for future maintenance, abandonment, or management of paddy soils should include the consideration that history of use shapes the soils' biogeochemistry and microbiology and can influence the response of paddy soils to future temperature increases.

Agro-technologies for greenhouse gases mitigation in flooded rice fields for promoting climate smart agriculture

We investigated methane (CH4) and nitrous oxide (N2O), two important greenhouse gases (GHGs) emissions using the closed chamber method from a flooded rice field in Brahmaputra valley of Assam, northeast part of India. We tried to understand the factors responsible for the emission and identify appropriate agro-technologies for their mitigation. Various factors like water level, drainage management, soil organic carbon management, crop management, fertilizer amendment, cultivar type etc. affect the GHG production and emission from the flooded rice soil. In this study, six treatments were employed, namely, farmer's practice (FP), recommended fertilizer dosage (RDF), direct seeded rice (DSR), intermittent wetting drying (IWD), use of efficient methanotrophs (MTH), and use of ammonium sulfate as a nitrogen source for real-time nitrogen management using leaf color chart, (AS). GHG flux was measured through the static closed chamber technique. Soil temperature, pH, and redox potential (Eh) and other soil physico-chemical and biological properties that have a potential role in GHG emission were also assessed. The lowest CH4 flux was observed in IWD treatment. The highest CH4 but lowest N2O flux was observed in RDF thus portraying a tradeoff relationship among these two GHGs. The highest N2O flux was observed in AS. Changes in Eh strongly altered CH4 and N2O emissions. The CH4 flux for the growing season varied from 62.5 to 86.3 kg ha-1 with an average of 72.4 kg ha-1. The average N2O flux was 0.89 kg ha-1 with values fluctuating between 0.72 - and 1.08 kg ha-1. The findings of this study could assist in understanding the factors affecting the source, production, and sink of these two important GHGs. IWD, along with judicious N-based fertilizer use, could provide significant respite from GHG emissions in rice-based agriculture. These climate-smart strategies not only reduce emissions but also have the potential to improve yield.

The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity

Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.

Impact of Polyethylene-Glycol-Induced Water Potential on Methane Yield and Microbial Consortium Dynamics in the Anaerobic Degradation of Glucose

This study investigated the relationship between water potential (Ψ) and the cation-induced inhibition of methane production in anaerobic digesters. The Ψ around methanogens was manipulated using polyethylene glycol (PEG) in a batch anaerobic reactor, ranging from -0.92 to -5.10 MPa. The ultimate methane potential (Bu) decreased significantly from 0.293 to 0.002 Nm3 kg-1-VSadded as Ψ decreased. When Ψ lowered from -0.92 MPa to -1.48 MPa, the community distribution of acetoclastic Methanosarcina decreased from 59.62% to 40.44%, while those of hydrogenotrophic Methanoculleus and Methanobacterium increased from 17.70% and 1.30% to 36.30% and 18.07%, respectively. These results mirrored changes observed in methanogenic communities affected by cation inhibition with KCl. Our findings strongly indicate that the inhibitory effect of cations on methane production may stem more from the water stress induced by cations than from their direct toxic effects. This study highlights the importance of considering Ψ dynamics in understanding cation-mediated inhibition in anaerobic digesters, providing insights into optimizing microbial processes for enhanced methane production from organic substrates.

Uranium Biogeochemistry in the Rhizosphere of a Contaminated Wetland

The objective of this study was to determine if U sediment concentrations in a U-contaminated wetland located within the Savannah River Site, South Carolina, were greater in the rhizosphere than in the nonrhizosphere. U concentrations were as much as 1100% greater in the rhizosphere than in the nonrhizosphere fractions; however and importantly, not all paired samples followed this trend. Iron (but not C, N, or S) concentrations were significantly enriched in the rhizosphere. XAS analyses showed that in both sediment fractions, U existed as UO22+ coordinated with iron(III)-oxides and organic matter. A key difference between the two sediment fractions was that a larger proportion of U was adsorbed to Fe(III)-oxides, not organic matter, in the rhizosphere, where significantly greater total Fe concentrations and greater proportions of ferrihydrite and goethite existed. Based on 16S rRNA analyses, most bacterial sequences in both paired samples were heterotrophs, and population differences were consistent with the generally more oxidizing conditions in the rhizosphere. Finally, U was very strongly bound to the whole (unfractionated) sediments, with an average desorption Kd value (Usediment/Uaqueous) of 3972 ± 1370 (mg-U/kg)/(mg-U/L). Together, these results indicate that the rhizosphere can greatly enrich U especially in wetland areas, where roots promote the formation of reactive Fe(III)-oxides.

Seasonal and spatial variations of greenhouse gas (CO2, CH4 and N2O) emissions from urban ponds in Brussels

Freshwaters have been recognized as important sources of greenhouse gases (GHG) to the atmosphere. However, urban ponds have received little attention even though their number is increasing due to expanding urbanisation globally. Ponds are frequently associated to urban green spaces that provide several ecosystemic services such as cooling local climate, regulating the water cycle, and acting as small carbon sinks This study aims to identify and understand the processes producing GHGs (CO2, CH4, and N2O) in the urban ponds of the temperate European city of Brussels in Belgium. 22 relatively small ponds (0.1-4.6 ha) surrounded by contrasted landscape (strictly urban, bordered by cropland or by forest), were sampled during four seasons in 2021-2022. The mean ± standard deviation was 3,667 ± 2,904 ppm for the partial pressure of CO2 (pCO2), 2,833 ± 4,178 nmol L-1 for CH4, and 273 ± 662% for N2O saturation level (%N2O). Relationships of GHGs with oxygen and water temperature suggest that biological processes controlled pCO2, CH4 concentration and%N2O. However, pCO2 was also controlled by external inputs as indicated by the higher values of pCO2 in the smaller ponds, more subject to external inputs than larger ones. The opposite was observed for CH4 concentration that was higher in larger ponds, closer to the forest in the city periphery, and with higher macrophyte cover. N2O concentrations, as well as dissolved inorganic nitrogen, were higher closer to the city center, where atmospheric nitrogen deposition was potentially higher. The total GHG emissions from the Brussels ponds were estimated to 1kT CO2-eq per year and were equivalent to the carbon sink of urban green spaces.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Biochar impacts on carbon dioxide, methane emission, and cadmium accumulation in rice from Cd-contaminated soils; A meta-analysis

Climate change and cadmium (Cd) contamination pose severe threats to rice production and food security. Biochar (BC) has emerged as a promising soil amendment for mitigating these challenges. To investigate the BC effects on paddy soil upon GHG emissions, Cd bioavailability, and its accumulation, a meta-analysis of published data from 2000 to 2023 was performed. Data Manager 5.3 and GetData plot Digitizer software were used to obtain and process the data for selected parameters. Our results showed a significant increase of 18% in soil pH with sewage sludge BC application, while 9% increase in soil organic carbon (SOC) using bamboo chips BC. There was a significant reduction in soil bulk density (8%), but no significant effects were observed for soil porosity, except for wheat straw BC which reduced the soil porosity by 6%. Sewage sludge and bamboo chips BC significantly reduced carbon dioxide (CO2) by 7-8% while municipal biowaste reduced methane (CH4) emissions by 2%. In the case of heavy metals, sunflower seedshells-derived materials and rice husk BC significantly reduced the bioavailable Cd in paddy soils by 24% and 12%, respectively. Cd uptake by rice roots was lowered considerably by the addition of kitchen waste (22%), peanut hulls (21%), and corn cob (15%) based BC. Similarly, cotton sticks, kitchen waste, peanut hulls, and rice husk BC restricted Cd translocation from rice roots to shoots by 22%, 27%, 20%, and 19%, respectively, while sawdust and rice husk-based BC were effective for reducing Cd accumulation in rice grains by 25% and 13%. Regarding rice yield, cotton sticks-based BC significantly increased the yield by 37% in Cd-contaminated paddy soil. The meta-analysis demonstrated that BC is an effective and multi-pronged strategy for sustainable and resilient rice cultivation by lowering greenhouse gas emissions and Cd accumulation while improving yields under the increasing threat of climate change.

Changes in arsenic mobility and speciation across a 2000-year-old paddy soil chronosequence

Rice accumulates arsenic (As) when cultivated under flooded conditions in paddy soils threatening rice yield or its safety for human consumption, depending on As speciation. During long-term paddy use, repeated redox cycles systematically alter soil biogeochemistry and microbiology. In the present study, incubation experiments from a 2000-year-old paddy soil chronosequence revealed that As mobilization and speciation also change with paddy soil age. Younger paddies (≤100 years) showed the highest total As mobilization, with speciation dominated by carcinogenic inorganic oxyarsenic species and highly mobile inorganic thioarsenates. Inorganic thioarsenates formed by a high availability of reduced sulfur (S) due to low concentrations of reducible iron (Fe) and soil organic carbon (SOC). Long-term paddy use (>100 years) resulted in higher microbial activity and SOC, increasing the share of phytotoxic methylated As. Methylated oxyarsenic species are precursors for cytotoxic methylated thioarsenates. Methylated thioarsenates formed in soils of all ages being limited either by the availability of methylated As in young soils or that of reduced-S in older ones. The present study shows that via a linkage of As to the biogeochemistry of Fe, S, and C, paddy soil age can influence the kind and the extent of threat that As poses for rice cultivation.

Feeding or pen surface application of clinoptilolite with different particle sizes: impact on nitrogen utilization and manure ammonia emissions in feedlot cattle

This study investigated the effects of feeding clinoptilolite (CLN; 2.5% of diet dry matter) with a particle size of either 30- or 400-µm on ruminal fermentation characteristics, measures of nitrogen (N) utilization, and manure ammonia-N (NH3) emissions in feedlot cattle. The impact of directly applying 30- or 400-µm CLN to the pen surface (2,250 kg/ha) on manure NH3-N emissions was also evaluated. Six beef heifers were used in a replicated 3 × 3 Latin square design with 21-d periods. Dietary treatments were 1) finishing ration with no supplement (CON), 2) CON + 30-µm CLN (CLN-30), and 3) CON + 400-µm CL (CLN-400). Intake was measured daily. To evaluate fermentation characteristics, ruminal fluid was collected on day 19. Indwelling pH loggers were used to measure ruminal pH from days 15 to 21. Blood was collected 3-h post-feeding on day 21 for metabolite analysis. Fecal grab and urine spot samples were also collected from days 19 to 21 to measure nutrient digestibility, route of N excretion, and in vitro NH3 emissions. There was no diet effect (P ≥ 0.12) on nutrient intake and apparent total tract digestibility, and ruminal short-chain fatty acid profile and pH. Ruminal NH3 concentration, which was lower (P = 0.04) for CLN-30 than CON heifers, did not differ between CON and CLN-400 heifers. Although there was no diet effect (P = 0.50) on plasma urea-N (PUN) concentration, proportion of urea-N excreted in urine was lower (P = 0.01) for CLN-30 than CON and CLN-400 heifers. Urinary NH3-N excretion, which was greater (P ≤ 0.04) for CLN-400 than CON heifers, did not differ between CLN-30 and CLN-400 heifers. Feeding CLN also increased (P ≤ 0.02) fecal excretion of potassium (K) and iron (Fe) and reduced (P = 0.01) urinary excretion of calcium (Ca). There was a treatment × time interaction (P = 0.01) for NH3 emission rate, which was greatest within the first 36 h of incubation and was lower for manure from CLN-400 compared to CON and CLN-30 heifers and pen surface application treatments. Cumulative NH3 emissions were lower (P < 0.01) for manure from CLN-400 compared to CON and CLN-30 heifers and the pen surface application treatments. Although surface application was ineffective, feeding 400-µm CLN to finishing cattle could result in a beneficial decrease in manure NH3 emissions. However, changes in fecal and urine excretion of minerals like K and Ca, which suggest a decrease in bioavailability, need to be considered when feeding CLN in finishing cattle diets.

Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment

The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment

BACKGROUND

High mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment.

METHODS

Five sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks.

RESULTS

Almost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils.

CONCLUSIONS

The results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.

Greenhouse Gas Emissions and Crossbred Cow Milk Production in a Silvopastoral System in Tropical Mexico

In Mexico, pasture degradation is associated with extensive pastures; additionally, under these conditions, livestock activities contribute considerably to greenhouse gas (GHG) emissions. Among the options to improve grazing systems and reduce GHG emissions, silvopastoral systems (SPS) have been recommended. The objectives of this work were to quantify the N outflow in a soil-plant-animal interface, as well as the CH₄ emissions and milk production in an SPS with woody legumes (Leucaena leucocephala) that is associated with stargrass (Cynodon nlemfuensis). This was then compared with stargrass in a monoculture system (MS) in the seasons (dry and rainy period) over a two-year period. Dung was collected from the animals of each of the grazing systems and applied fresh to the land plots. Fresh dung and urine were collected from the cows of each grazing system and were applied to the experimental plots. In addition, the soil CH₄ and N₂O contents were measured to quantify the emissions. Average milk yield by seasons was similar: MS (7.1 kg per animal unit (AU)/day^-1) and SPS (6.31 kg per AU/day^-1). Cows in the MS had a mean N intake of 171.9 g/UA day^-1 without seasonal variation, while the SPS animals' mean N intake was 215.7 g/UA day^-1 for both seasons. For the urine applied to soil, the N₂O outflow was higher in the MS (peak value = 1623.9 μg N-N₂O m^-2 h^-1). The peak value for the SPS was 755.9 μg of N-N₂O m^-2 h^-1. The N₂O emissions were higher in the rainy season (which promotes denitrification). The values for the feces treatment were 0.05% (MS) and 0.01% (SPS). The urine treatment values were 0.52% (MS) and 0.17% (SPS). The emissions of CH₄ showed that the feces of the SPS systems resulted in a higher accumulation of gas in the rainy season (29.8 g C ha^-1), followed by the feces of the MS system in the dry season (26.0 g C ha^-1). Legumes in the SPS helped to maintain milk production, and the N₂O emissions were lower than those produced by the MS (where the pastures were fertilized with N).

Culture adaptation for enhanced biogas production from birch wood applying stable carbon isotope analysis to monitor changes in the microbial community

Birch wood is a potential feedstock for biogas production in Northern Europe; however, the lignocellulosic matrix is recalcitrant preventing efficient conversion to methane. To improve digestibility, birch wood was thermally pre-treated using steam explosion at 220 °C for 10 min. The steam-exploded birch wood (SEBW) was co-digested with cow manure for a period of 120 days in continuously fed CSTRs where the microbial community adapted to the SEBW feedstock. Changes in the microbial community were tracked by stable carbon isotopes- and 16S r RNA analyses. The results showed that the adapted microbial culture could increase methane production up to 365 mL/g VS day, which is higher than previously reported methane production from pre-treated SEBW. This study also revealed that the microbial adaptation significantly increased the tolerance of the microbial community against the inhibitors furfural and HMF which were formed during pre-treatment of birch. The results of the microbial analysis indicated that the relative amount of cellulosic hydrolytic microorganisms (e.g. Actinobacteriota and Fibrobacterota) increased and replaced syntrophic acetate bacteria (e.g. Cloacimonadota, Dethiobacteraceae, and Syntrophomonadaceae) as a function of time. Moreover, the stable carbon isotope analysis indicated that the acetoclastic pathway became the main route for methane production after long-term adaptation. The shift in methane production pathway and change in microbial community shows that for anaerobic digestion of SEBW, the hydrolysis step is important. Although acetoclastic methanogens became dominant after 120 days, a potential route for methane production could also be a direct electron transfer among Sedimentibacter and methanogen archaea.

Multiyear methane and nitrous oxide emissions in different irrigation management under long-term continuous rice rotation in Arkansas

Rice paddies are one of the major sources of anthropogenic methane (CH₄ ) emissions. The alternate wetting and drying (AWD) irrigation management has been shown to reduce CH₄ emissions and total global warming potential (GWP) (CH₄ and nitrous oxide [N₂ O]). However, there is limited information about utilizing AWD management to reduce greenhouse gas (GHG) emissions from commercial-scale continuous rice fields. This study was conducted for five consecutive growing seasons (2015-2019) on a pair of adjacent fields in a commercial farm in Arkansas under long-term continuous rice rotation irrigated with either continuously flooded (CF) or AWD conditions. The cumulative CH₄ emissions in the growing season across the two fields and 5 years ranged from 41 to 123 kg CH₄ -C ha^-1 for CF and 1 to 73 kg CH₄ -C ha^-1 for AWD. On average, AWD reduced CH₄ emissions by 73% relative to CH₄ emissions in CF fields. Compared to N₂ O emissions, CH₄ emissions dominated the GWP with an average contribution of 91% in both irrigation treatments. There was no significant variation in grain yield (7.3-11.9 Mg ha^-1 ) or growing season N₂ O emissions (-0.02 to 0.51 kg N₂ O-N ha^-1 ) between the irrigation treatments. The yield-scaled GWP was 368 and 173 kg CO₂ eq. Mg^-1 season^-1 for CF and AWD, respectively, showing the feasibility of AWD on a commercial farm to reduce the total GHG emissions while sustaining grain yield. Seasonal variations of GHG emissions observed within fields showed total GHG emissions were predominantly influenced by weather (precipitation) and crop and irrigation management. The influence of air temperature and floodwater heights on GHG emissions had high degree of variability among years and fields. These findings demonstrate that the use of multiyear GHG emission datasets could better capture variability of GHG emissions associated with rice production and could improve field verification of GHG emission models and scaling factors for commercial rice farms.

Winter drainage and film mulching cultivation mitigated CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil

Winter flooding of harvested rice fields is a typical cropping system in mountainous areas, which emits considerable amounts of CH₄. Plastic film mulching cultivation is recognized as an important rice cultivation practice in paddy field for water-saving irrigation. However, the effects of these managements on CH₄ emissions in paddy soil and the underlying microbial mechanism are unclear. A field experiment was carried out with the application of winter drainage followed by traditional rice cultivation (WD), winter drainage followed by plastic film mulching cultivation (MC), as well as winter flooding followed by traditional rice cultivation (WF) as control in hilly paddy fields. We investigated the CH₄ emissions, functional (CH₄ production rate, ¹³C isotope) and structural (abundance, structure) responses of soil methanogenic archaeal and fermenting bacterial communities during rice season. Shifting the fields from WF into WD and MC substantially mitigated CH₄ emissions by 62.3% and 59.2%, respectively, paralleled with the enhancement of soil Eh and the reductions of soil DOC content. Compared with WF, WD and MC both significantly decreased CH₄ production rates and the copy numbers of mcrA gene. Moreover, an increasing contribution of hydrogenotrophic methanogenesis (from 30.7% to 50.0%) to total CH₄ production was observed during the conversion from WF to MC under an anaerobic incubation, paralleled with the decreased acetate content and increased δ¹³C values of acetate-methyl and total acetate. The communities of methanogenic archaea and fermenting bacteria strongly responded to the shift from WF to WD, while MC only showed significant effects on the methanogenic archaeal communities. Compared with WF, WD and MC significantly increased the relative abundance of Methanothrix, Methanosarcina and Methanocella, while those of Methanoregula, Massilia and Geobacter were decreased. The co-occurrence networks showed that WD and MC induced the loss of mixed methanogenic fermentation modules, indicating the decrease in functional biodiversity and redundancy of fermenting bacterial and methanogenic archaeal communities.The findings suggest that WD and MC approach mitigate CH₄ emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil, which represent the effective management strategies considering the water availability and CH₄ mitigation in paddy-field agriculture.

Methane and carbon dioxide cycles in lakes of the King George Island, maritime Antarctica

Freshwater ecosystems are important contributors to the global greenhouse gas budget and a comprehensive assessment of their role in the context of global warming is essential. Despite many reports on freshwater ecosystems, relatively little attention has been given so far to those located in the southern hemisphere and our current knowledge is particularly poor regarding the methane cycle in non-perennially glaciated lakes of the maritime Antarctica. We conducted a high-resolution study of the methane and carbon dioxide cycle in a lake of the Fildes Peninsula, King George Island (Lat. 62°S), and a succinct characterization of 10 additional lakes and ponds of the region. The study, done during the ice-free and the ice-seasons, included methane and carbon dioxide exchanges with the atmosphere (both from water and surrounding soils) and the dissolved concentration of these two gases throughout the water column. This characterization was complemented with an ex-situ analysis of the microbial activities involved in the methane cycle, including methanotrophic and methanogenic activities as well as the methane-related marker gene abundance, in water, sediments and surrounding soils. The results showed that, over an annual cycle, the freshwater ecosystems of the region are dominantly autotrophic and that, despite low but omnipresent atmospheric methane emissions, they act as greenhouse gas sinks.

Absence of oxygen effect on microbial structure and methane production during drying and rewetting events

Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.

Ratoon rice with direct seeding improves soil carbon sequestration in rice fields and increases grain quality

Increasing both carbon (C) sequestration and food production is essential for a sustainable future. However, increasing soil C sequestration or graining yield/quality in rice (Oryza sativa L.) systems has been a tradeoff in that pursuing one goal may compromise the other goal. Field experiments were designed to evaluate methane emission and grain yield in two rice systems in southern China, including the traditional double rice with a seedling transplanting system and innovative ratoon rice with a direct seeding system. Grain yield, grain quality, methane (CH₄) emission, and total organic carbon (TOC) loss rate were investigated, and yield-scaled CH₄ gas emission was assessed. It is found that double rice has a higher grain yield than ratoon rice. However, the grain quality (processing, appearance of chalkiness degree and chalky grain percentage, and nutritional quality) of ratoon rice is superior to double rice, especially the ratoon crop. The yield-scaled CH₄ emission of ratoon rice (0.06 kg kg^-1) decreased by 49.29% than double rice (0.12 kg kg^-1) throughout the growth period. Compared with the TOC loss rate of double rice (2.95 g kg^-1), the rate of ratoon rice was lower (1.97 g kg^-1). As a result, ratoon rice with direct seeding can not only improve grain quality but also mitigate yield-scaled CH₄ gas emission and TOC loss rate of rice fields. Therefore, we suggest to use ratoon rice with a direct seeding technique to promote agricultural C sequestration.

Extended methane mitigation capacity of a mid-season drainage beyond the rice growing season: a case in Spain

Rice cultivation is a major source of methane (CH₄) emissions. Intermittent irrigation systems in rice cultivation, such as the mid-season drainage (MSD), are effective strategies to mitigate CH₄ emissions during the growing season, though the reduction rates are variable and dependent on the crop context. Aeration periods induce alteration of soil CH₄ dynamics that can be prolonged after flooding recovery. However, whether these changes persist beyond the growing season remains underexplored. A field experiment was conducted in Spain to study the effect of MSD implemented during the rice growing season on greenhouse gas (GHG) emissions in relation to the standard permanently flooded water management (PFL). Specifically, the study aimed at (1) assessing the CH₄ mitigation capacity of MSD in the studied area and (2) testing the hypothesis that the mitigating effect of MSD can be extended into the following winter flooded fallow season. Year-round GHG sampling was conducted, seasonal and annual cumulative emissions of CH₄ and N₂O as well as the global warming potential were calculated, and grain yield was measured. MSD reduced growing season CH₄ emissions by ca. 80% without yield penalties. During the flooded fallow season, MSD reduced CH₄ emissions by ca. 60%, despite both fields being permanently flooded. The novelty of our observations lies in the amplified mitigation capacity of MSD by extending the CH₄ mitigation effect to the following flooded winter fallow season. This finding becomes especially relevant in rice systems with flooded winter fallow season given the large contribution of this season to the annual CH₄ emissions.

Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes

Soil CH₄ fluxes are driven by CH₄-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH₄-cycling microbiomes to net surface CH₄ fluxes throughout a year in two grassland soils. CH₄ fluxes were highly dynamic: both soils were net CH₄ sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH₄ fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH₄ sinks. CH₄ uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH₄ emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH₄ sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH₄-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.

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.

Biochar as soil amendment: Syngas recycling system is essential to create positive carbon credit

Biochar utilization is accepted as the most cost-effective practice to mitigate global warming via increase in soil C stock. However, its utilization effect on greenhouse gas (GHG) fluxes was evaluated only within land application without considering industrial processes. To evaluate the net effect of biochar utilization on global warming within whole system boundary, swine manure-saw dust mixture was pyrolyzed under four different temperatures, and GHG fluxes were characterized under with/without syngas recycling systems. To determine GHG fluxes from biochar amended soil, 40 Mg ha^-1 of biochar was mixed with soil and incubated under flooded and dried soil conditions. Finally, the effect of biochar utilization was generalized using net global warming potential (GWP) from industrial process to land application. Under without syngas recycling system, huge amounts of GHGs were emitted during pyrolysis, and GHG fluxes highly increased with increasing pyrolysis temperature, due to direct and indirect GHG emissions from feedstock combustion and electricity, respectively. However, syngas recycling system removed most of GHGs, except for direct N₂O and indirect GHG emissions from electricity. Biochar application was very effective to mitigate GHG emissions within soil system boundary, and biochar produced at higher pyrolysis temperature showed higher effectivity in decreasing GHG fluxes. Within the whole system boundary from pyrolysis to soil application, without the installation of syngas recycling system, fresh manure application was more effective than biochar to reduce GHG emissions, regardless of soil water conditions. However, with the installation of syngas recycling system, biochar application was much more effective than fresh manure to decrease GHG fluxes. Biochar produced at higher temperature had higher effectivity to mitigate global warming impacts. In conclusion, to functionally mitigate global warming in soils, biochar should be produced in pyrolysis reactors equipped with syngas recycling system under higher temperature.

Effect of water management on microbial diversity and composition in an Italian rice field system

Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.

Ecological rice-cropping systems mitigate global warming - A meta-analysis

Ecological rice-cropping systems (ERSs) are prosperous rice ecosystems that have a profound influence on global greenhouse (GHG) effects. However, the high variation in research results requires an accurate evaluation of the ERS effects. In this study, three typical ERS modes, rice-crayfish, rice-duck, and rice-fish were selected, and a meta-analysis was conducted using the data of 34 studies to comprehensively evaluate the effects of ERSs on GHG emissions, the global warming potential (GWP), and GHG intensity (GHGI). The results showed that the ERSs reduced CH4 emissions significantly (-12.5%), but increased N2O emissions by 11.3% as compared with traditional rice-cropping systems (TRSs). Further, ERSs have slightly lower GWP, rice yield, and GHGI values (6.5%, 5.5%, and 5.6%, respectively) than TRSs. The rice-crayfish and rice-duck modes significantly alleviated the GWP by 18.0% and 11.1%, respectively, whereas the rice-fish mode enhanced the GWP by 20.8%. Moreover, the rice-duck mode significantly reduced the GHGI by 17.2%, while the ricecrayfish and rice-fish modes increased the GHGI by 9.7% and 8.8%, respectively. Further, the ERSs significantly changed the dissolved oxygen concentration in the flood water as well as the Eh, dissolved organic carbon, and ammonium nitrogen in the soil, wherein the effect sizes of the ERSs on the GHG emissions were significantly correlated with their respective increase. Considering the net ecosystem economic budget and CO2 emissions equivalent/output, ERSs were found to be effective "green technologies". Further, we found that the rice-duck ERS was a good ecological ricecropping system for global warming mitigation. Our study provided new ideas for sustainable agriculture.

Microbial Communities and Interactions of Nitrogen Oxides With Methanogenesis in Diverse Peatlands of the Amazon Basin

Tropical peatlands are hotspots of methane (CH₄) production but present high variation and emission uncertainties in the Amazon region. This is because the controlling factors of methane production in tropical peats are not yet well documented. Although inhibitory effects of nitrogen oxides (NO_x) on methanogenic activity are known from pure culture studies, the role of NO_x in the methane cycling of peatlands remains unexplored. Here, we investigated the CH₄ content, soil geochemistry and microbial communities along 1-m-soil profiles and assessed the effects of soil NO_x and nitrous oxide (N₂O) on methanogenic abundance and activity in three peatlands of the Pastaza-Marañón foreland basin. The peatlands were distinct in pH, DOC, nitrate pore water concentrations, C/N ratios of shallow soils, redox potential, and ¹³C enrichment in dissolved inorganic carbon and CH₄ pools, which are primarily contingent on H₂-dependent methanogenesis. Molecular 16S rRNA and mcrA gene data revealed diverse and novel methanogens varying across sites. Importantly, we also observed a strong stratification in relative abundances of microbial groups involved in NO_x cycling, along with a concordant stratification of methanogens. The higher relative abundance of ammonia-oxidizing archaea (Thaumarchaeota) in acidic oligotrophic peat than ammonia-oxidizing bacteria (Nitrospira) is noteworthy as putative sources of NO_x. Experiments testing the interaction of NO_x species and methanogenesis found that the latter showed differential sensitivity to nitrite (up to 85% reduction) and N₂O (complete inhibition), which would act as an unaccounted CH₄ control in these ecosystems. Overall, we present evidence of diverse peatlands likely differently affected by inhibitory effects of nitrogen species on methanogens as another contributor to variable CH₄ fluxes.

Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India

Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH₄) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH₄ utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, K_s of 1.92 ± 0.092 mg CH₄ L^-1. Besides the ability to utilize CH₄, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.

Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.

More Than a Methanotroph: A Broader Substrate Spectrum for Methylacidiphilum fumariolicum SolV

Volcanic areas emit a number of gases including methane and other short chain alkanes, that may serve as energy source for the prevailing microorganisms. The verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV was isolated from a volcanic mud pot, and is able to grow under thermoacidophilic conditions on different gaseous substrates. Its genome contains three operons encoding a particulate methane monooxygenase (pMMO), the enzyme that converts methane to methanol. The expression of two of these pmo operons is subjected to oxygen-dependent regulation, whereas the expression of the third copy (pmoCAB3) has, so far, never been reported. In this study we investigated the ability of strain SolV to utilize short-chain alkanes and monitored the expression of the pmo operons under different conditions. In batch cultures and in carbon-limited continuous cultures, strain SolV was able to oxidize and grow on C₁–C₃ compounds. Oxidation of ethane did occur simultaneously with methane, while propane consumption only started once methane and ethane became limited. Butane oxidation was not observed. Transcriptome data showed that pmoCAB1 and pmoCAB3 were induced in the absence of methane and the expression of pmoCAB3 increased upon propane addition. Together the results of our study unprecedently show that a pMMO-containing methanotroph is able to co-metabolize other gaseous hydrocarbons, beside methane. Moreover, it expands the substrate spectrum of verrucomicrobial methanotrophs, supporting their high metabolic flexibility and adaptation to the harsh and dynamic conditions in volcanic ecosystems.