How methanotrophs respond to pH: A review of ecophysiology

Black and White Fire Ash Alters Greenhouse Gas Emissions and Temporarily Reverses Carbon Source-Sink Status in Aquatic Mesocosms

Wildfire ash is transported in large quantities to receiving water bodies, where it may exert strong chemical controls on ecosystem function. To assess the role of fire ash in altering CO2 and CH4 fluxes in aquatic sediments, we designed three mesocosm experiments that compared the changing fluxes of these gases and water quality parameters under different loads and types of ash. Black ash (char) caused substantial drops in pH and increased CO2 and CH4 emissions through abiotic and biotic mechanisms, while white ash dramatically increased pH and enhanced CH4 emissions, possibly due to inhibition of methanotrophy. White ash-driven increases in pH also instigated CO2 uptake. If this abiotically driven CO2 uptake could interact with ash-driven nutrient fertilization to synergistically enhance biotic CO2 uptake in surface waters after a fire, these initial increases in pH may represent an important priming effect. Our findings suggest that strong ash flows following fires may trigger substantial pulses of heterotrophic or abiotically driven greenhouse gas emissions or uptake in recipient lentic aquatic ecosystems, which─although they may be overshadowed by autotrophic responses─may nonetheless be central to altered lake or wetland carbon balance following a fire.

Dissolved organic matter derived from long-term photodegradation of plastics alters microbial methane conversion in mangrove sediments

Highly enriched plastic debris leads to an increase in dissolved organic matter derived from the degradation of plastics (PDOM), which potentially influences the stability of methane (CH4) emissions of microorganisms in mangrove sediments. Here, microcosm incubation was conducted to reveal the impacts of two PDOM on CH4 emissions from mangrove sediments. CH4 emissions from PDOM treated sediments were reduced by 0.03-0.11 ppm within 30 days. The reduction in CH4 emissions was attributed mainly to alterations in sediment properties and bacterial communities. Phosphorus-containing lignin and proteins were the key molecular components that induce the decrease in the abundance of functional genes in the CO2 to methane pathway. The influence of PDOM on CH4 emissions may be associated with bacterial fermentation and the degradation pathways of aromatic compounds. This study enhances the understanding of the impact of PDOM on carbon cycling in mangrove ecosystems.

Iron Modulates the Growth and Activity of Nitrate-Dependent Methanotrophic Bacteria by Reprogramming Carbon Metabolism

Iron is indispensable for literally all microorganisms, yet becomes toxic at elevated levels. Protein-based iron storage compartments, such as ferritins, play a key role in maintaining iron homeostasis when the iron level surpasses microbial requirements. However, the energy-intensive nature of iron storage raises questions about how microbes balance this bioprocess between growth and metabolism. Here, using nitrate-dependent methanotrophic bacteria with the simplified metabolic system as a model, we propose a novel metabolic reprogramming pathway regulated by iron storage that controls the balance between growth and activity. Isotopic labeling and meta-omics analyses revealed a striking contrast between bacterial abundance and methane-dependent denitrification activity in "Ca. M. sinica". Using microscopy and energy dispersive spectroscopy, we identified iron-rich nanoparticles within cells exposed to 40 μM Fe2+, alongside increased expression of genes involved in iron metabolism and methane oxidation coupled with denitrification. Additionally, we observed a shift from the energy-demanding Calvin cycle to the more energy-efficient serine pathway for carbon fixation, promoting the synthesis of glycine and succinyl-CoA, which serve as key precursors for iron storage proteins. These metabolic adjustments highlight a strategy for coordinating both substance and energy metabolism in nitrate-dependent methanotrophic bacteria, thereby enhancing their capacity for simultaneous nitrogen and carbon removal. Our findings reveal that iron may act as a metabolic "switch" in microorganisms, offering new insights into the targeted manipulation of microbial metabolism to maximize their beneficial functions in both engineered and natural environments.

Effects of different proportions of organic substitution for mineral fertilizers on soil methanogenic and methanotrophic communities in paddy fields

Mineral fertilizers are widely used to improve rice yields, but their overuse has caused severe environmental problems. Replacing mineral fertilizers with organic alternatives might be an effective practice for enhancing agro-ecosystems. This study investigated treatments with varying proportions of organic substitution to determine the optimal approach for increasing soil fertility and rice yield. In addition, the relationship between soil methane emission characteristics and associated microbial communities was studied by microcosm experiments and high-throughput sequencing to assess greenhouse gas emissions. Compared with mineral fertilizers alone, treatment with organic substitution, especially at high proportions, increased soil pH, fertility, and crop yield. Treatment with a medium proportion of organic substitution increased cumulative methane (CH4) emissions by 44.8% relative to mineral fertilization alone, but that with low and high proportions showed similar emissions compared with mineral fertilization alone. Organic substitution treatment significantly increased the gene copy numbers of soil methanogens and methanotrophs, with the highest increases observed under high proportions of organic substitution. The gene copy number of methanogens increased by 4.87 times, and that of methanophiles increased by 13.11 times. Additionally, organic substitution treatment significantly changed their community compositions. High organic substitution was associated with an exceptionally high abundance of methanotrophs. Treatment with a high proportion of organic substitution enhanced the relative abundance of Type I taxa of methanotrophs and increased soil pH to trigger higher pmoA abundance, thus strengthening methane oxidation capacity without additional cumulative CH4 emissions compared with mineral fertilizers alone. Besides, treatment with a high proportion of organic substitution increased crop yield and reduced the amount of mineral fertilizers needed, resulting in less environmental pollution. This study comprehensively evaluated the effects of organic substitution for mineral fertilizers, providing an essential theoretical basis for the sustainable development of agriculture.

Biochar mitigates methane emissions from organic mulching in urban soils: Evidence from a long-term mesocosm experiment

Methane (CH₄), a potent greenhouse gas (GHG) with high global warming potential, significantly contributes to urban GHG emissions. Organic mulching, commonly practiced in urban forestry, may promote CH₄ emissions via anaerobic decomposition; yet its impact on the urban carbon budget has largely been unexamined. Biochar has shown promise in mitigating CH₄ emissions in agricultural soils, but its effectiveness in urban mulched systems remains unknown. This study employed a mesocosm experiment to investigate the effects of organic mulches (woodchips and bark) and biochar amendments (50 t/ha), applied either on the surface (top-dressed) or incorporated (mixed), on fluxes of CH₄, CO₂, and H₂O. Fluxes were measured using an off-axis integrated cavity output spectroscopy analyzer. Results indicate that mulched soils emitted CH₄ at 1.0-1.5 nmol m⁻2.s⁻1, whereas biochar amendments promoted CH₄ uptake, in the case of both woodchips (-1.65 ± 1.03 nmol m⁻2.s⁻1) and bark mulch (-0.49 ± 0.16 nmol m⁻2.s⁻1) by the second year. Mixed treatments showed greater CH₄ uptake; for instance, incorporating biochar into bark mulch led to a mean CH₄ uptake (-2.02 ± 1.02 nmol m⁻2.s⁻1), nearly fivefold greater than controls. While mulch additions reduced water loss and increased soil organic carbon-factors contributing to CH₄ emissions-biochar amendments increased CO₂ emissions by 26.7%-121.1%. Biochar-mediated CH₄ uptake correlated with substrate pH, bulk density, and C:N ratio, suggesting enhanced microbial activity and increased CO₂ release. Overall, findings indicate that biochar, combined with organic mulching, can serve as an effective GHG mitigation strategy, informing climate-smart soil management in urban landscapes.

Methane cycle in subsurface environment: A review of microbial processes

Methane is a pivotal component of the global carbon cycle. It acts both as a potent greenhouse gas and a vital energy source. While the microbial cycling of methane in subsurface environments is crucial, its impact on geological settings and related engineering projects is often underestimated. This review uniquely integrates the latest findings on methane production, oxidation, and migration processes in strata, revealing novel microbial mechanisms and their implications for environmental sustainability. We address critical issues of methane leakage and engineering safety during resource extraction, underscoring the urgent need for effective methane management strategies. This work clarifies geological factors affecting methane budgets and emissions, deepening our understanding of methane dynamics. It offers practical insights for geological engineering and sustainable natural gas hydrate exploration, paving the way for future research and applications.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BACKGROUND

The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS

Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION

The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.

Role of methanotrophic communities in atmospheric methane oxidation in paddy soils

Wetland systems are known methane (CH4) sources. However, flooded rice fields are periodically drained. The paddy soils can absorb atmospheric CH4 during the dry seasons due to high-affinity methane-oxidizing bacteria (methanotroph). Atmospheric CH4 uptake can be induced during the low-affinity oxidation of high-concentration CH4 in paddy soils. Multiple interacting factors control atmospheric CH4 uptake in soil ecosystems. Broader biogeographical data are required to refine our understanding of the biotic and abiotic factors related to atmospheric CH4 uptake in paddy soils. Thus, here, we aimed to assess the high-affinity CH4 oxidation activity and explored the community composition of active atmospheric methanotrophs in nine geographically distinct Chinese paddy soils. Our findings demonstrated that high-affinity oxidation of 1.86 parts per million by volume (ppmv) CH4 was quickly induced after 10,000 ppmv high-concentration CH4 consumption by conventional methanotrophs. The ratios of 16S rRNA to rRNA genes (rDNA) for type II methanotrophs were higher than those for type I methanotrophs in all acid-neutral soils (excluding the alkaline soil) with high-affinity CH4 oxidation activity. Both the 16S rRNA:rDNA ratios of type II methanotrophs and the abundance of 13C-labeled type II methanotrophs positively correlated with high-affinity CH4 oxidation activity. Soil abiotic factors can regulate methanotrophic community composition and atmospheric CH4 uptake in paddy soils. High-affinity methane oxidation activity, as well as the abundance of type II methanotroph, negatively correlated with soil pH, while they positively correlated with soil nutrient availability (soil organic carbon, total nitrogen, and ammonium-nitrogen). Our results indicate the importance of type II methanotrophs and abiotic factors in atmospheric CH4 uptake in paddy soils. Our findings offer a broader biogeographical perspective on atmospheric CH4 uptake in paddy soils. This provides evidence that periodically drained paddy fields can serve as the dry-season CH4 sink. This study is anticipated to help in determining and devising greenhouse gas mitigation strategies through effective farm management in paddy fields.

pH Adaptation stabilizes bacterial communities

Diverse microbes in nature play an important role in ecosystem functioning and human health. Nevertheless, it remains unclear how microbial communities are maintained. This study proposes that evolutionary changes in the pH niche of bacteria can promote bacterial coexistence. Bacteria modify the pH environment and also react to it. The optimal environmental pH level for a given species or pH niche can adaptively change in response to the changes in environmental pH caused by the bacteria themselves. Theory shows that the evolutionary changes in the pH niche can stabilize otherwise unstable large bacterial communities, particularly when the evolution occurs rapidly and diverse bacteria modifying pH in different directions coexist in balance. The stabilization is sufficiently strong to mitigate the inherent instability of system complexity with many species and interactions. This model can show a relationship between pH and diversity in natural bacterial systems.

Low-molecular-weight organic acids inhibit the methane-dependent arsenate reduction process in paddy soils

Anaerobic methane oxidation (AOM) can drive soil arsenate reduction, a process known as methane-dependent arsenate reduction (M-AsR), which is a critical driver of arsenic (As) release in soil. Low molecular weight organic acids (LMWOAs), an important component of rice root exudates, have an unclear influence and mechanism on the M-AsR process. To narrow this knowledge gap, three typical LMWOAs-citric acid, oxalic acid, and acetic acid-were selected and added to As-contaminated paddy soils, followed by the injection of 13CH4 and incubation under anaerobic conditions. The results showed that LMWOAs inhibited the M-AsR process and reduced the As(III) concentration in soil porewater by 35.1-65.7 % after 14 days of incubation. Among the LMWOAs, acetic acid exhibited the strongest inhibition, followed by oxalic and citric acid. Moreover, LMWOAs significantly altered the concentrations of ferrous iron and dissolved organic carbon in the soil porewater, consequently impacting the release of As in the soil. The results of qPCR and sequencing analysis indicated that LMWOAs inhibited the M-AsR process by simultaneously suppressing microbes associated with ANME-2d and arrA. Our findings provide a theoretical basis for modulating the M-AsR process and enhance our understanding of the biogeochemical cycling of As in paddy soils under rhizosphere conditions.

Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils

Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles in biogeochemical cycles and ecosystem functions. Despite the extensive research on soil pH as a key predictor of microbial community and composition, a limitation of these studies lies in determining whether bacterial and/or fungal communities are directly or indirectly influenced by pH. We conducted a controlled laboratory experiment to investigate the effects of soil pH amendment (+/- 1-2 units) with six levels on soil microbial communities in two contrasting Chinese agricultural soils (pH 8.43 in Dezhou, located in the North China Plain, Shandong vs pH 6.17 in Wuxi, located in the Taihu Lake region, Jiangsu, east China). Results showed that the fungal diversity and composition were related to soil pH, but the effects were much lower than the effects of soil pH on bacterial community in two soils. The diversity and composition of bacterial communities were more closely associated with soil pH in Wuxi soils compared to Dezhou soils. The alpha diversity of bacterial communities peaked near in situ pH levels in both soils, displaying a quadratic fitting pattern. Redundancy analysis and variation partition analysis indicated that soil pH affected bacterial community and composition by directly imposing a physiological constraint on soil bacteria and indirectly altering soil characteristics (e.g., nutrient availability). The study also examined complete curves of taxa relative abundances at the phylum and family levels in response to soil pH, with most relationships conforming to a quadratic fitting pattern, indicating soil pH is a reliable predictor. Furthermore, soil pH amendment affected the transformation of nitrogen and the abundances of functional genes involved in the nitrogen cycle, and methane production and consumption. Overall, results from this study would enhance our comprehension of how soil microorganisms in contrasting farmlands will respond to soil pH changes, and would contribute to more effective soil management and conservation strategies.

IMPORTANCE

This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1-2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies.

Unveiling the unique role of iron in the metabolism of methanogens: A review

Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.

Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach

Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Unraveling the impact of lanthanum on methane consuming microbial communities in rice field soils

The discovery of the lanthanide requiring enzymes in microbes was a significant scientific discovery that opened a whole new avenue of biotechnological research of this important group of metals. However, the ecological impact of lanthanides on microbial communities utilizing methane (CH4) remains largely unexplored. In this study, a laboratory microcosm model experiment was performed using rice field soils with different pH origins (5.76, 7.2, and 8.36) and different concentrations of La3+ in the form of lanthanum chloride (LaCl3). Results clearly showed that CH4 consumption was inhibited by the addition of La3+ but that the response depended on the soil origin and pH. 16S rRNA gene sequencing revealed the genus Methylobacter, Methylosarcina, and Methylocystis as key players in CH4 consumption under La3+ addition. We suggest that the soil microbiome involved in CH4 consumption can generally tolerate addition of high concentrations of La3+, and adjustments in community composition ensured ecosystem functionality over time. As La3+ concentrations increase, the way that the soil microbiome reacts may not only differ within the same environment but also vary when comparing different environments, underscoring the need for further research into this subject.

Environmental heterogeneity shapes the C and S cycling-associated microbial community in Haima's cold seeps

Environmental heterogeneity in cold seeps is usually reflected by different faunal aggregates. The sediment microbiome, especially the geochemical cycling-associated communities, sustains the ecosystem through chemosynthesis. To date, few studies have paid attention to the structuring and functioning of geochemical cycling-associated communities relating to environmental heterogeneity in different faunal aggregates of cold seeps. In this study, we profiled the microbial community of four faunal aggregates in the Haima cold seep, South China Sea. Through a combination of geochemical and meta-omics approaches, we have found that geochemical variables, such as sulfate and calcium, exhibited a significant variation between different aggregates, indicating changes in the methane flux. Anaerobic methanotrophic archaea (ANME), sulfate-reducing, and sulfide-oxidizing bacteria (SRB and SOB) dominated the microbial community but varied in composition among the four aggregates. The diversity of archaea and bacteria exhibited a strong correlation between sulfate, calcium, and silicate. Interspecies co-exclusion inferred by molecular ecological network analysis increased from non-seep to clam aggregates and peaked at the mussel aggregate. The networked geochemical cycling-associated species showed an obvious aggregate-specific distribution pattern. Notably, hydrocarbon oxidation and sulfate reduction by ANME and SRB produced carbonate and sulfide, driving the alkalization of the sediment environment, which may impact the microbial communities. Collectively, these results highlighted that geofluid and microbial metabolism together resulted in environmental heterogeneity, which shaped the C and S cycling-associated microbial community.