mcrA Gene Research Articles

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BackgroundArsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.ResultsFive ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.ConclusionsOur results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils.5-kbCdqq-d7KqfyvRVSSUfVideo

The biological mechanism of a lower carbon/nitrogen ratio increases methane emissions during vegetable waste composting

The initial carbon/nitrogen (C/N) ratio is one of the most important factors impacting composting processes, such as methane (CH4) emissions. However, the effects of the C/N ratio on CH4 emissions and the associated biological mechanisms during vegetable waste composting are largely unknown. In this study, a lab-scale experiment was conducted to investigate the effects of different C/N ratios on CH4 emissions and the mechanisms associated with methane-metabolizing microorganisms (methanogens and methanotrophs) during capsicum straw composting. The initial C/N ratios were set to 18, 30 and 50 to simulate the low (L), medium (M) and high (H) C/N ratios, respectively. The results showed that CH4 emissions were mainly concentrated in the thermophilic phase and that the cumulative CH4 emissions were significantly greater in the L treatment than in the M and H treatments by 10.8 and 15.4 times, respectively. During the methanogenic process, the relative abundance of the dominant genus Methanoculleus (47.59 % ∼ 76.92 %) was higher than in the L treatment than in the M and H treatments at the thermophilic and maturation stages, and the Chao1 index and the mcrA gene abundance followed the order of L > M > H at each composting stage. During the methanotrophic process, the dominant genus unclassified_d_bacteria (51.3 % ∼ 91.87 %), Chao1 index, pmoA gene abundance and CO2 emissions were in the order of L > M > H at each composting stage. This pattern suggests that a lower C/N ratio simultaneously enhanced CH4 production and oxidation. A structural equation model further revealed that the methanogenic community, which was driven directly by the relative contents of hemicellulose and cellulose in the substrates, as indicated by the C/N ratio, made greater contributions to CH4 emissions than did the methanotrophic community. In conclusion, a lower C/N ratio increased CH4 emissions mainly by regulating the population and composition of methanogen community.

Effects of inorganic nitrogen enrichment on soil CH4 and CO2 production in freshwater and mesohaline marshes across six estuaries in China

Eutrophication is an important environmental stressor in coastal wetlands that alters ecosystem processes including primary production and the carbon cycle. However, how different nitrogen eutrophication scenarios may affect CH4 and CO2 production along a salinity gradient in coastal wetlands is poorly known. We collected the surface soil samples from both tidal freshwater and mesohaline Phragmites australis marshes in six main estuaries in China and conducted inorganic nitrogen enrichment anaerobic incubation experiments. Background soil CH4 and CO2 production rates were strongly correlated with total nitrogen but not salinity. On average, nitrate enrichment decreased soil CH4 and CO2 production rates by ca. 20 % in freshwater marsh and 16–43 % in mesohaline marshes, whereas ammonium enrichment decreased CO2 production by ca. 26–30 % but had no effect on CH4 production. Salinity was not an important mitigating factor in either eutrophication scenario. In most cases, nitrogen addition decreased the extracellular enzyme activities of β-1,4-glucosidase and cellobiohydrolase, but increased the activity of β-N-acetyl glucosaminidase, phenol oxidase and peroxidase. Nitrate addition decreased the mcrA gene abundance on average by 34–35 % but ammonium addition had insignificant effect. Total nitrogen availability was an important driver of CH4 and CO2 production rates in these tidally influenced coastal wetlands. Our results showed that tidal marshes with salinity < 15 ppt had similar soil CH4 production rates, and increasing inorganic nitrogen eutrophication might lower soil microbial carbon gas production in both tidal freshwater and mesohaline marshes.

Biochar amendment affects the microbial genetic profile of the soil, its community structure and phospholipid fatty acid contents

Biochar (BC) amendment has been proposed as a promising strategy for mitigating greenhouse gas (GHG) emissions, specifically carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Conducting a meta-analysis to evaluate the impact of biochar on microbial genetic profile, community structure, and phospholipid fatty acid (PLFA) contents can aid in identifying key microbial groups involved in GHG production and consumption, and assessing the overall effectiveness of biochar in reducing GHG emissions. The present meta-analysis revealed that the addition of biochar resulted in a 22 % and 41 % reduction in pmoA and mcrA genes of methanogenic microorganisms, respectively. The mcrA/pmoA ratio significantly increased by 81 %. Gene abundances exhibited a positive response to biochar amendment, with increases observed in nifH, nirK, nirS, nosZ, and nosZ (nirS + nirK) genes by 13 %, 32 %, 37 %, 42 %, and 79 %, respectively. Moreover, biochar amendment influenced the microbial community structure accordingly. The concentration of PLFAs increased in response to BC treatment in the following order: A-bacteria (+49 %) < Fungi (+30 %) < Gram-pb (+21 %) < G-bacteria (+17 %) < Gram-nb (+11 %). These findings indicate that biochar amendment shapes the microbial community structure, further emphasizing its significance in enhancing soil fertility.

Effects of Fallow Season Water and Straw Management on Methane Emissions and Associated Microorganisms

The effects of fallow season water and straw management on methane (CH4) emissions during the fallow season and the subsequent rice-growing season are rarely reported, and the underlying microbial mechanisms remain unclear. A field experiment was conducted with four treatments: (1) fields flooded in both the fallow and rice seasons (FF), (2) fields drained in the fallow season and flooded in the rice season (DF), (3) FF with straw retention (FFS), and (4) DF with straw retention (DFS). The CH4 emissions in fields under different water and straw treatments were monitored using the static closed chamber method. Methanogenic and methanotrophic communities in these fields were examined using terminal restriction fragment length polymorphism (T-RFLP) analysis based on the mcrA gene and pmoA gene encoding methyl coenzyme M reductase and particulate methane monooxygenase, respectively. The results showed that CH4 emissions were significantly affected by water management, straw retention, season, and their interactions. Over 80% of CH4 emissions occurred during the rice season. Field drainage during the fallow season reduced CH4 emissions by 47.0% and 53.8% with and without straw during the rice season, respectively. Water management altered the abundance and composition of methanogens and methanotrophs, whereas the effects of straw retention were less pronounced. The quantitative polymerase chain reaction (qPCR) assay revealed that field drainage in the fallow season decreased the mcrA gene abundance by 30.0% and 23.2% with and without straw in rice season, respectively, and increased the pmoA gene abundance by 108.9% and 213.7% with and without straw in rice season, respectively. CH4 flux was significantly positively associated with mcrA gene copy number and the ratio of mcrA to pmoA gene copy number, whereas it was significantly negatively correlated with the pmoA gene copy number. Results indicated that fallow drainage greatly decreased CH4 emission not only during the fallow season but also during the subsequent rice season by altering the community composition of methanogens and methanotrophs. These findings provide scientific insight into the role of water and straw management in controlling CH4 emissions through microbial community dynamics.

Coupled reduction in arsenic methylation and methanogenesis with silicate amendment in arsenic-enriched paddy soils

Methanogens play an important role in the demethylation of arsenic. Soil amendments that inhibit methanogens can increase dimethylarsinic acid (DMA), which is responsible for straighthead disease in rice. A decrease in methanogenesis caused by silicate fertilizer may increase DMA concentration in paddy soils and rice grains; the relationship between these two factors and their impacts on DMA concentration remains unclear. We applied silicate fertilizer (2 Mg ha−1) to japonica and indica rice grown on arsenic-spiked soils and found a simultaneous reduction in methane emissions and pore-water DMA concentration, compared to no-silicate fertilization. Gene and transcript copies of mcrA and arsM, as well as dominant methanogens and arsenic-methylating microbes decreased significantly with silicate fertilization. However, the sulfate-reducing bacteria and the gene and transcript copies of dsrB did not change significantly in response to the application of silicate fertilizer to paddy soils. The abundance of arsenic methylating microbes was significantly and positively correlated with the abundance of methanogens, but not with the abundance of sulfate-reducing bacteria. Methylomonas and Methylobacter, which harbor the arsM gene, were suppressed under silicate fertilization, suggesting that they have the potential to methylate As and play a crucial role in reducing pore-water DMA in As-enriched flooded paddy soils. Increasing Fe concentration, soil pH, and Eh value decreased pore-water DMA concentration, while decreasing arsenite concentration, arsM and mcrA gene abundance decreased it. While silicate fertilization decreased arsenite and DMA concentrations in pore-water, it had no significant effect on rice DMA content, but significantly decreased arsenite content. Results reveal that methanogens and arsenic-methylating microbes have a synergistic relationship under silicate fertilization that facilitates a significant reduction in methane emissions and DMA concentration in As-enriched paddy soils.

Stand age-related effects of mangrove on archaeal methanogenesis in sediments: Community assembly and co-occurrence patterns

Mangrove sediment is a key source of methane emissions; however, archaea community structure dynamics and methanogenesis activities during long-term mangrove restoration remain unclear. In this study, microcosm incubations revealed a substantial reduction in microbial-mediated methane production potential from mangrove sediments with increasing stand age; methane production rates decreased from 0.42 ng g−1 d−1 in 6-year-old stands to 0.23 ng g−1 d−1 in 64-year-old stands. High-throughput sequencing revealed a reduction in community diversity because of specific microorganism colonization and species loss, notably a decline in the relative abundance of Bathyarchaeia in sediments of 64-year-old stands. In addition, mangrove sediments, especially those in older stands (20- and 64-year-old), had more complex and stable co-occurrence microbial networks than mudflats. Furthermore, archaea community assembly in older stands was dominated by stochastic processes wherein dispersal limitation was prominent, and that in younger stands (6- and 12-year-old) was driven by deterministic processes. The proportion of dispersal limitation of Bathyarchaeia and traditional methanogens in sediment decreased with an increase in stand age. Quantitative polymerase chain reaction analysis confirmed a decrease in Bathyarchaeia (from 3.50 to 0.54 copies g−1) and mcrA gene (from 3.83 to 0.25 copies g−1) abundance in mangrove sediments with an increase in stand age. These findings demonstrate the critical role of Bathyarchaeia in methanogenesis; the decline in microbial interactions and abundance, and the reduced proportion of dispersal limitation of Bathyarchaeia and traditional methanogens collectively contributed to the mitigation of microbial-mediated methane production potential in older mangrove stands.

The archaeal community in sediments of freshwater lakes of north-east Antarctic Peninsula: Structure and diversity

This research represents the first attempt to study the structure and diversity of the archaeal and methanogenic archaeal community in selected lakes around the Czech polar station J.G. Mendel on James Ross Island (JRI), Antarctica. Sediment samples from a total of 19 of JRI and the nearby Vega Island and Long Island, were analyzed using 16S rRNA and mcrA genes sequencing and real-time qPCR. Contrary to the sequences retrieved by 16S rRNA analysis, many more reads belonging to methanogens were found with mcrA gene sequencing. Generally, archaea represented only a small proportion (0–8.8%) of the total prokaryotic community. With the exception of lakes in the Solorina Valley and Lagoons Mesa area and Lake Esmeralda on Vega Island, methanogenic archaea made up a small proportion of the archaea present in most lakes. The genera Methanothrix and Methanosarcina were identified as the predominant methanogenic representatives in the lake samples. Sequences of representatives belonging to Methanothermobacter sp. and Methanomassiliicoccales and a high proportion of sequences belonging to Methanoperedens-like archaea, methanotrophs that associate anaerobic methane oxidation with denitrification, were recorded for the first time in Antarctica. It is also the first time that the presence of the genus Methanobacterium has been detected to such a large extent. Generally, sequences of the methanogens which might be involved in all three pathways of methane production were found in our samples, indicating the broad metabolic potential of the methanogens present. Individual lakes from one area shared much higher similarity in their methanogenic diversity with the lakes from another area rather than with the lakes within the same area, suggesting that a lake location is probably not the main factor influencing the diversity of the methanogens. Indeed, archaeal and methanogenic community structure and mcrA gene copy numbers varied even within a single lake, suggesting that more sampling within a single lake, preferably at different times of the year, will be necessary in the future for more comprehensive information. Although this is an initial study, our research unambiguously provides evidence that the lakes of the JRI and surrounding islands may be potential sources of new archaeal species or metabolic pathways.

Arsenic Reduces Methane Emissions from Paddy Soils: Insights from Continental Investigation and Laboratory Incubations.

Arsenic (As) contamination and methane (CH4) emissions co-occur in rice paddies. However, how As impacts CH4 production, oxidation, and emission dynamics is unknown. Here, we investigated the abundances and activities of CH4-cycling microbes from 132 paddy soils with different As concentrations across continental China using metagenomics and the reverse transcription polymerase chain reaction. Our results revealed that As was a crucial factor affecting the abundance and distribution patterns of the mcrA gene, which is responsible for CH4 production and anaerobic CH4 oxidation. Laboratory incubation experiments showed that adding 30 mg kg-1 arsenate increased 13CO2 production by 10-fold, ultimately decreasing CH4 emissions by 68.5%. The inhibition of CH4 emissions by As was induced through three aspects: (1) the toxicity of As decreased the abundance and activity of the methanogens; (2) the adaptability and response of methanotrophs to As is beneficial for CH4 oxidation under As stress; and (3) the more robust arsenate reduction would anaerobically consume more CH4 in paddies. Additionally, significant positive correlations were observed between arsC and pmoA gene abundance in both the observational study and incubation experiment. These findings enhance our understanding of the mechanisms underlying the interactions between As and CH4 cycling in soils.

Combined metabolomic and microbial community analyses reveal that biochar and organic manure alter soil C-N metabolism and greenhouse gas emissions

The use of biochar to reduce the gas emissions from paddy soils is a promising approach. However, the manner in which biochar and soil microbial communities interact to affect CO2, CH4, and N2O emissions is not clearly understood, particularly when compared with other amendments. In this study, high-throughput sequencing, soil metabolomics, and quantitative real-time PCR were utilized to compare the effects of biochar (BC) and organic manure (OM) on soil microbial community structure, metabolomic profiles and functional genes, and ultimately CO2, CH4, and N2O emissions. Results indicated that BC and OM had opposite effects on soil CO2 and N2O emissions, with BC resulting in lower emissions and OM resulting in higher emissions, whereas BC, OM, and their combined amendments increased cumulative CH4 emissions by 19.5 %, 31.6 %, and 49.1 %, respectively. BC amendment increased the abundance of methanogens (Methanobacterium and Methanocella) and denitrifying bacteria (Anaerolinea and Gemmatimonas), resulting in an increase in the abundance of mcrA, amoA, amoB, and nosZ genes and the secretion of a flavonoid (chrysosplenetin), which caused the generation of CH4 and the reduction of N2O to N2, thereby accelerating CH4 emissions while reducing N2O emissions. Simultaneously, OM amendment increased the abundance of the methanogen Caldicoprobacter and denitrifying Acinetobacter, resulting in increased abundance of mcrA, amoA, amoB, nirK, and nirS genes and the catabolism of carbohydrates [maltotriose, D-(+)-melezitose, D-(+)-cellobiose, and maltotetraose], thereby enhancing CH4 and N2O emissions. Moreover, puerarin produced by Bacillus metabolism may contribute to the reduction in CO2 emissions by BC amendment, but increase in CO2 emissions by OM amendment. These findings reveal how BC and OM affect greenhouse gas emissions by modulating soil microbial communities, functional genes, and metabolomic profiles.

Dual mechanism of membrane covering on GHG and NH3 mitigation during industrial-scale experiment on dairy manure composting: Inhibiting formation and blocking emissions

An industrial-scale experiment on dairy manure composting with the control group (Ctrl) and the membrane covering group (CM) was conducted to explore the effects of functional membrane covering on gas emissions, the conversion of carbon and nitrogen, and revealing the underlying mechanisms. Results indicated that CM achieved the synergistic effects on gas mitigation and improved compost product quality. CO2, CH4, N2O, and NH3 emissions were reduced by 81.8%, 87.0%, 82.6%, and 82.2%, respectively. The micro-aerobic condition formed in membrane covering compost pile together with the covering inhibiting effect dominated the mitigation effect. CM significantly downregulated the mcrA gene copies and the value of mcrA/pmoA (p < 0.01), which reduced CH4 emission. CM decreased the nirS and nirK gene copies and increased the nosZ gene copies to reduce N2O emission. Functional Annotation of Prokaryotic Taxa showed that membrane covering effectively amended part of carbon and nitrogen cycles, which stimulated the degradation of organic matter, accelerated compost maturity and reduced the gaseous emissions.

Controlling Methane Ebullition Flux in Cascade Reservoirs of the Upper Yellow River by the Ratio of mcrA to pmoA Genes

Reservoirs are an important source of methane (CH4) emissions, but the relative contribution of CH4 ebullition and diffusion fluxes to total fluxes has received little attention in the past. In this study, we systematically monitored the CH4 fluxes of nine cascade reservoirs (Dahejia, Jishixia, Huangfeng, Suzhi, Kangyang, Zhiganglaka, Lijiaxia, Nina, and Longyangxia) in the upper reaches of the Yellow River in the dry (May 2023) and wet seasons (August 2023) using the static chamber gas chromatography and headspace equilibrium methods. We also simultaneously measured environmental physicochemical properties as well as the abundance of methanogens and methanotrophs in sediments. The results showed the following: (1) All reservoirs were sources of CH4 emissions, with an average diffusion flux of 0.08 ± 0.05 mg m−2 h−1 and ebullition flux of 0.38 ± 0.41 mg m−2 h−1. Ebullition flux accounted for 78.01 ± 7.85% of total flux. (2) Spatially, both CH4 diffusion and ebullition fluxes increased from upstream to downstream. Temporally, CH4 diffusion flux in the wet season (0.09 ± 0.06 mg m−2 h−1) was slightly higher than that in the dry season (0.08 ± 0.04 mg m−2 h−1), but CH4 ebullition flux in the dry season (0.38 ± 0.48 mg m−2 h−1) was higher than that in the wet season (0.32 ± 0.2 mg m−2 h−1). (3) qPCR showed that methanogens (mcrA gene) were more abundant in the wet season (5.43 ± 3.94 × 105 copies g−1) than that in the dry season (3.74 ± 1.34 × 105 copies g−1). Methanotrophs (pmoA gene) also showed a similar trend with more abundance found in the wet season (7 ± 2.61 × 105 copies g−1) than in the dry season (1.47 ± 0.92 × 105 copies g−1. (4) Structural equation modeling revealed that the ratio of mcrA/pmoA genes, water N/P, and reservoir age were key factors affecting CH4 ebullition flux. Variation partitioning further indicated that the ratio of mcrA/pmoA genes was the main factor causing the spatial variation in CH4 ebullition flux, explaining 35.69% of its variation. This study not only reveals the characteristics and influencing factors of CH4 emissions from cascade reservoirs on the Qinghai Plateau but also provides a scientific basis for calculating fluxes and developing global CH4 reduction strategies for reservoirs.

Overlooked drivers of the greenhouse effect: The nutrient-methane nexus mediated by submerged macrophytes

Submerged macrophytes remediation is a commonly used technique for improving water quality and restoring habitat in aquatic ecosystems. However, the drivers of success in the submerged macrophytes assembly process and their specific impacts on methane emissions are poorly understood. Thus, we conducted a mesocosm experiment to test the growth plasticity and carbon fixation of widespread submerged macrophytes (Vallisneria natans) under different nutrient conditions. A refined dynamic chamber method was utilized to concurrently collect and quantify methane emission fluxes arising from ebullition and diffusion processes. Significant correlations were found between methane flux and variations in the physiological activities of V. nantas by the fluorescence imaging system. Our results show that exceeding tolerance thresholds of ammonia in the water significantly interfered with the photosynthetic systems in submerged leaves and the radial oxygen loss in adventitious roots. The recovery process of V. natans accelerated the consumption of dissolved oxygen, leading to increase in the populations of methanogen (153.3 % increase of mcrA genes) and subsequently elevating CH4 emission fluxes (23.7 %) under high nutrient concentrations. Conversely, V. natans increased the available organic carbon under low nutrient conditions by radial oxygen loss, further increasing CH4 emission fluxes (94.7 %). Quantitative genetic and modeling analyses revealed that plant restoration processes drive ecological niche differentiation of methanogenic and methane oxidation microorganisms, affecting methane release fluxes within the restored area. The speciation process of V. natans is incapable of simultaneously meeting improved water purification and reduced methane emissions goals.

Role of methanogenesis and methanotrophy in CH4 fluxes from rice paddies under elevated CO2 concentration and elevated temperature

The differential responses of methanogenesis and methanotrophy to elevated carbon dioxide concentrations ([CO2]) (e[CO2]) and elevated temperature ([T]) (e[T]) may lead to dramatic changes in the response of CH4 emissions from rice paddies to global warming. In this study, we systematically investigated the responses and mechanisms of CH4 flux from rice paddies to e[CO2] and e[T] based on the production and oxidation of CH4. The CH4 flux, soil properties, and soil methanogenesis and methanotrophy were observed under CK (ambient [CO2] + ambient [T]), EC (e[CO2] by 200 μmol mol−1 + ambient [T]), ET (ambient [CO2] + e[T] by 2 °C), and ECT (e[CO2] by 200 μmol mol−1 + e[T] by 2 °C) treatments. The results revealed that EC, ET, and ECT significantly increased the cumulative amount of CH4 (CAC) in the rice paddies by 10.63, 15.20, and 11.77 kg ha−1, respectively, compared with CK. ECT increased the CAC in the rice paddies by 1.14 kg ha−1 compared with EC. Moreover, EC, ET, and ECT significantly enhanced the methane production potential (MPP) and methane oxidation potential (MOP) and tended to increase the mcrA gene abundance of the methanogens. EC tended to prompt the pmoA gene abundance of the methanotrophs, but the effect of ET on the pmoA gene abundance was less consistent across the growth stages. ECT significantly decreased the relative abundances of Methanosarcina and Methylocystis (Type II) by 4.9 % and 14.2 %, respectively, while it increased the relative abundance of Methylosarcina (Type I) by 24.0 % compared with CK. Overall, the increased MPP/MOP, mcrA/pmoA, and microbial biomass carbon under climate change increased the CH4 flux from the rice paddies. The contribution of e[CO2] to the CH4 flux was significantly enhanced by e[T], which could further exacerbate the risk of global climate change induced by e[CO2].

Rice-crayfish integrated system enhances global warming potential via increasing methane emission mainly driven by continuous deep flooding

The conversion from rice monoculture (RM) to rice-crayfish integrated system (RCIS) could change soil physicochemical properties and microorganisms related to greenhouse gas (GHG) emissions. Nevertheless, it is still unclear the responses of GHG emissions and global warming potential (GWP) from paddy fields to RCIS. Here, we conducted a field experiment to investigate the changes in the emissions of methane (CH4) and nitrous oxide (N2O), GWP, soil physicochemical properties and the associated microbial abundances (methanogen, methanotrophs, denitrifier and nitrifier) under RCIS in Gaoyou City, Jiangsu Province, China from 2022 to 2023. There were three treatments, including RM, rice monoculture with continuous deep flooding (RMF) and RCIS. Compared with RM, RCIS and RMF all significantly increased CH4 emission and decreased N2O emission. But the effectiveness of increasing CH4 emission and decreasing N2O emission was larger under RCIS than RMF. The increased CH4 emission was due to the significantly higher mcrA gene abundance and ratio of mcrA/pmoA under RCIS. While the significantly higher nosZ gene abundance and ratio of nosZ/(amoA+nirK+nirS) under RCIS were responsible for its reduced N2O emission. Furthermore, the increases in gene abundances of mcrA and nosZ under RCIS were closely correlated with the significantly lower redox potential and pH as well as the significantly higher contents of dissolved organic carbon, ammonium and nitrate in soil. Averaged across two years, GWP under RCIS and RMF were 4.6-fold and 3.4-fold that under RM, respectively. This revealed that continuous deep flooding had a greater effectiveness in increasing GWP than crayfish culture under RCIS. Notably, the contribution rates of CH4 emission to the total GWP decreased in the order of RCIS (98.6%) > RMF (97.5%) > RM (86.2%). Besides, greenhouse gas intensity under RCIS was 5.1-fold that of RM due to its enhanced GWP and reduced rice grain yield. In summary, RCIS could enhance GWP from paddy fields through increasing CH4 emission mainly caused by the continuous deep flooding.

Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest.

Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 107copiesg-1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 105 and 104copiesg-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106cellsg-1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.

New insights for simultaneous nitrogen removal and greenhouse gas reduction by biological-electrolysis constructed wetland in the treatment of aquaculture wastewater under varied C/N

Aiming to address the challenges of poor nitrogen (N) removal and greenhouse gas (GHG) emissions in aquaculture wastewater treatment, biological-electrolysis constructed wetland (BECW) and constructed wetland (CW) were established to comparatively evaluate the N removal efficiency, the greenhouse gas (GHG) emissions, and specific microbial gene abundances under various influent C/N ratios. Increasing influent C/N ratio markedly enhanced the removal rates of COD, NH4+-N, NO3−-N, and TN, while markedly reduced N2O fluxes in CW and BECW. The integration of an electric field with CW (BECW) significantly compensated for the shortcomings of the poor NO3−-N removal efficiency and high N2O emissions when C/N < 6. However, this compensating effect gradually weakened with the continue increase of C/N. BECW simultaneously achieved the high COD (89.26 ± 6.08 %), NO3−N (97.03 ± 1.22 %), and TN (83.17 ± 3.19 %) removal rates, and low GHG emissions (486.00 ± 36.61 mg/m2/h) at C/N = 6. The BECW significantly decreased the abundance of mcrA and pmoA genes while increased the abundance of nirK, nirS, and nosZ genes, and the ratios of pmoA/mcrA and nosZ/(nirS + nirK) across all C/N condition. The emission flux of CH4 in BECW was positively correlated with C/N and the mcrA abundance but significantly negatively correlated with pmoA abundance and pmoA/mcrA. The emission flux of N2O was positively correlated with nirS and nirK abundance but significantly negatively correlated with C/N, NO3−-N removal rates, nosZ abundance, and the index of nosZ/(nirS + nirK). This research offers an innovative approach to get both low GHG emissions and high NO3−-N removal rate in aquaculture wastewater treatment.

Surprising concentrations of hydrogen and non-geological methane and carbon dioxide in the soil

Due to its potential use as a carbon-free energy resource with minimal environmental and climate impacts, natural hydrogen (H2) produced by subsurface geochemical processes is today the target of intensive research. In H2 exploration practices, bacteria are thought to swiftly consume H2 and, therefore, small near-surface concentrations of H2, even orders of 102 ppmv in soils, are considered a signal of active migration of geological gas, potentially revealing underground resources. Here, we document an extraordinary case of a widespread occurrence of H2 (up to 1 vol%), together with elevated concentrations of CH4 and CO2 (up to 51 and 27 vol%, respectively), in aerated meadow soils along Italian Alps valleys. Based on current literature, this finding would be classified as a discovery of pervasive and massive geological H2 seepage. Nevertheless, an ensemble of gas geochemical and soil microbiological analyses, including bulk and clumped CH4 isotopes, radiocarbon of CH4 and CO2, and DNA and mcrA gene quantitative polymerase chain reaction analyses, revealed that H2 was only coupled to modern microbial gas. The H2-CO2-CH4-H2S association, wet soil proximity, and the absence of other geogenic gases in soils and springs suggest that H2 derives from near-surface fermentation, rather than geological degassing. H2 concentrations up to 1 vol% in soils are not conclusive evidence of deep gas seepage. This study provides a new reference for the potential of microbial H2, CH4 and CO2 in soils, to be considered in H2 exploration guidelines and soil carbon and greenhouse-gas cycle research.

Strategies and mechanisms for improving groundwater remediation efficiency of chlorinated ethenes by controlling the particle size of polyhydroxyalkanoate

The efficacy of in-situ bioremediation of chlorinated ethenes (CEs)-contaminated groundwater is heavily contingent upon the provision of exogenous electron donors to facilitate reductive dechlorination by dechlorinating bacteria. Nonetheless, methanogenic archaea have been reported to engender competition for the limited electron donor supply, thereby diminishing dechlorination efficiency. This study proposes a novel strategy to enhance reductive dechlorination by reducing the particle size of polyhydroxyalkanoate (PHA) to the micrometer scale, thereby inhibiting methanogenic competition for electron donors. The results demonstrate that trichloroethylene (TCE) biodegradation efficiency peaked at a PHA particle size of 500 μm, significantly surpassing the efficiency observed in groups with particle sizes of 50 and 2000 μm. Furthermore, the electron utilization efficiency of dechlorinating bacteria (represented by Geobacter, Dehalobacter, Anaerolinea, etc in this study) was as high as 94.82 % over methanogenic archaea (represented by Methanobacterium) in the 500 μm group. Mechanistic analyses revealed that the 500 μm PHA particles activated dark oxygen, leading to the generation of reactive oxygen species that decreased the abundance of the methanogenic functional gene McrA and increased the abundance of dechlorinating functional gene TceA relative to the total microbial genome gene (in terms of 16S rRNA). In contrast, PHA particles of 50 μm exhibited lower TCE biodegradation efficiency due to particle aggregation, while particles of 2000 μm exhibited reduced efficiency due to lower specific surface area. This study moves a step for the in-situ microbial remediation of CEs-contaminated groundwater.

Optimization of sulfate reduction and methanogenesis via phase separation in a two-phase internal circulation reactor for the treatment of high-sulfate organic wastewater

To enhance the performance of the internal circulation (IC) reactor when treating high-sulfate organic wastewater, a laboratory-scale two-phase IC reactor with distinct phase separation capabilities was designed, and the sulfate reduction and methanogenesis processes were optimized by segregating the reactor into two specialized reaction zones. The results demonstrated that the first and second reaction areas of the two-phase IC reactor could be maintained at 4.5–6.0 and 7.5–8.5, respectively, turning them into the specialized phase for sulfate reduction and methanogenesis. Through phase separation, the two-phase IC reactor achieved a COD degradation and sulfate reduction efficiency of more than 80% when the influent sulfate concentration exceeded 5,000 mg/L, which were 32.32% and 16.04% higher than that before phase separation. Functional analyses indicated a greater activity of both the dissimilatory and assimilatory sulfate reduction pathways in the acidogenic phase, largely due to a rise in the relative abundance of the genera Desulfovibrio, Bacteroides, and Lacticaseibacillus, the primary carriers of sulfate reduction functional genes. In contrast, all the acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis pathways were inhibited in the acidogenic phase but thrived in the methanogenic phase, coinciding with shifts in the genus Methanothrix, which harbors the mcrA, mcrB, and mcrG genes essential for the final transformation step of all three methanogenesis pathways.