Methane formation driven by reactive oxygen species across all living organisms

Synchronous influence of soil amendments on alkylmercury and methane emissions in mercury-contaminated paddy soil

Mercury (Hg) alkylation and methane (CH4) emissions pose significant global concerns. Paddy soil, due to its long-term anaerobic conditions and abundant organic matter, is hotspots for soil Hg alkylation and CH4 emissions. However, the relevance between Hg alkylation and CH4 emissions, especially their simultaneous reduction strategies, remains poorly understood. Here, we investigated the effects of biochar (BC), selenium (Se) and rice straw (RS) amendments on Hg alkylation and CH4 emissions in paddy soil, and the accumulation of Hg speciation. Results found that both BC and RS amendments significantly increased the levels of soil organic carbon (SOC) and humification index (HIX). Furthermore, BC decreased the concentrations of Hg(II), methylmercury (MeHg) and ethylmercury (EtHg) by 63.1%, 53.6% and 100% in rice grains. However, RS increased Hg(II) concentration but decreased the total Hg (THg), MeHg and EtHg concentrations in rice grains. Compared to the CK, RS significantly increased CH4 emissions, while BC decreased CH4 emissions, and Se showed no significant difference. Se amendment increased the Hg(II) and EtHg concentrations by 20.3% and 17.0% respectively, and decreased the MeHg concentration in grains by 58.3%. Both BC and RS impacted the abundance of methanogens by enhancing SOC and HIX, subsequently modulating the relevance between Hg alkylation and CH4 emissions. These findings provide insights into the relevance between Hg alkylation and CH4 emissions and propose potential mitigation mechanisms in Hg-contaminated paddy soil.

Iron driven organic carbon capture, pretreatment, recovery and upgrade in wastewater: Process technologies, mechanisms, and implications

Wastewater treatment plants face significant challenges in transitioning from energy-intensive systems to carbon-neutral, energy-saving systems, and a large amount of chemical energy in wastewater remains untapped. Iron is widely used in modern wastewater treatment. Research shows that leveraging the coupled redox relationship of iron and carbon can redirect this energy (in the form of carbon) towards resource utilization. Therefore, re-examining the application of iron in existing wastewater carbon processes is particularly important. In this review, we investigate the latest research progress on iron for wastewater carbon flow restructuring. During the iron-based chemically enhanced primary treatment (CEPT) process, organic carbon is captured into sludge and its bioavailability is enhanced through iron-based advanced oxidation processes (AOP) pretreatment, further being recovered or upgraded to value-added products in anaerobic biological processes. We discuss the roles and mechanisms of iron in CEPT, AOP, anaerobic biological processes, and biorefining in driving organic carbon conversion. The dosage of iron, as a critical parameter, significantly affects the recovery and utilization of sludge carbon resources, particularly by promoting effective electron transfer. We propose a pathway for beneficial conversion of wastewater organic carbon driven by iron and analyze the benefits of the main products in detail. Through this review, we hope to provide new insights into the application of iron chemicals and current wastewater treatment models.

S-containing molecular markers of dissolved organic carbon attributing to riverine dissolved methane production across different land uses

The emission of methane (CH4) from streams and rivers contributes significantly to its global inventory. The production of CH4 is traditionally considered as a strictly anaerobic process. Recent investigations observed a "CH4 paradox" in oxic waters, suggesting the occurrence of oxic methane production (OMP). Human activities promoted dissolved organic carbon (DOC) in streams and rivers, providing significant substrates for CH4 production. However, the underlying DOC molecular markers of CH4 production in river systems are not well known. The identification of these markers will help to reveal the mechanism of methanogenesis. Here, Fourier transform ion cyclotron mass spectrometry and other high-quality DOC characterization, ecosystem metabolism, and in-situ net CH4 production rate were employed to investigate molecular markers attributing to riverine dissolved CH4 production across different land uses. We show that endogenous CH4 production supports CH4 oversaturation and positively correlates with DOC concentrations and gross primary production. Furthermore, sulfur (S)-containing molecules, particularly S-aliphatics and S-peptides, and fatty acid-like compounds (e.g., acetate homologs) are characterized as markers of water-column aerobic and anaerobic CH4 production. Watershed characterization, including riverine discharge, allochthonous DOC input, turnover, as well as autochthonous DOC, affects the CH4 production. Our study helps to understand riverine aerobic or anaerobic CH4 production relating to DOC molecular characteristics across different land uses.

Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome

Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.

Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle

Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.

Global atmospheric methane uptake by upland tree woody surfaces

Methane is an important greenhouse gas1, but the role of trees in the methane budget remains uncertain2. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base3,4, it has also been suggested that upland trees can serve as a net sink for atmospheric methane5,6. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.

Methane sink of subterranean space in an integrated atmosphere-soil-cave system

CH4 serves as an important greenhouse gas, yet limited knowledge is available in global and regional CH4 cycling, particularly in widely distributed karst terrain. In this study, we investigated an upland in Puding Karst Ecosystem Research Station, and explored CH4 concentration and/or flux in atmosphere, soil and cave using a closed static chamber method and an eddy covariance system. Meanwhile, we monitored atmospheric temperature, precipitation, temperature and wind velocity in the cave entrance. The results demonstrated that atmospheric CH4 and actual soil CH4 fluxes in the source area of eddy covariance system were -0.19 ± 8.64 nmols-1m-2 and -0.16 nmols-1m-2 respectively. The CH4 concentrations in Shawan Cave exhibited 10 ∼ 100-fold lower than that of the external atmosphere. CH4 oxidation rate dominated by methane-oxidizing bacteria was 1.98 nmols-1m-2 in Shawan Cave when it combined with temperature difference between cave and external atmosphere. Therefore, CH4 sink in global karst subterranean spaces was estimated at 106.2 Tg CH4 yr-1. We supplemented an understanding of CH4 cycling paths and fluxes in karst terrain, as well as CH4 sinks in karst subterranean space. Further works require to establish a karst ecosystem observation network to conduct long-term integrated studies on CH4 fluxes regarding atmosphere, soils, plants and caves.

Photo-methanification of aquatic dissolved organic matters with different origins under aerobic conditions: Non-negligible role of hydroxyl radicals

Lingering inconsistencies in the global methane (CH4) budget and ambiguity in CH4 sources and sinks triggered efforts to identify new CH4 formation pathways in natural ecosystems. Herein, we reported a novel mechanism of light-induced generation of hydroxyl radicals (•OH) that drove the production of CH4 from aquatic dissolved organic matters (DOMs) under ambient conditions. A total of five DOM samples with different origins were applied to examine their potential in photo-methanification production under aerobic conditions, presenting a wide range of CH4 production rates from 3.57 × 10-3 to 5.90 × 10-2 nmol CH4 mg-C-1 h-1. Experiments of •OH generator and scavenger indicated that the contribution of •OH to photo-methanificaiton among different DOM samples reached about 4∼42 %. In addition, Fourier transform infrared spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry showed that the carbohydrate- and lipid-like substances containing nitrogen-bonded methyl groups, methyl ester, acetyl groups, and ketones, were the potential precursors for light-induced CH4 production. Based on the experimental results and simulated calculations, the contribution of photo-methanification of aquatic DOMs to the diffusive CH4 flux across the water-air interface in a typical eutrophic shallow lake (e.g., Lake Chaohu) ranged from 0.1 % to 18.3 %. This study provides a new perspective on the pathways of CH4 formation in aquatic ecosystems and a deeper understanding on the sources and sinks of global CH4.

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.

Abiotic Methane Production Driven by Ubiquitous Non-Fenton-Type Reactive Oxygen Species

Abiotic CH4 production driven by Fenton-type reactive oxygen species (ROS) has been confirmed to be an indispensable component of the atmospheric CH4 budget. While the chemical reactions independent of Fenton chemistry to ROS are ubiquitous in nature, it remains unknown whether the produced ROS can drive abiotic CH4 production. Here, we first demonstrated the abiotic CH4 production at the soil-water interface under illumination. Leveraging this finding, polymeric carbon nitrides (CNx) as a typical analogue of natural geobattery material and dimethyl sulfoxide (DMSO) as a natural methyl donor were used to unravel the underlying mechanisms. We revealed that the ROS, photocatalytically produced by CNx, can oxidize DMSO into CH4 with a high selectivity of 91.5 %. Such an abiotic CH4 production process was further expanded to various non-Fenton-type reaction systems, such as electrocatalysis, pyrocatalysis and sonocatalysis. This work provides insights into the geochemical cycle of abiotic CH4, and offers a new route to CH4 production via integrated energy development.

Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake

Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.

Oxygen is an essential gasotransmitter directly sensed via protein gasoreceptors

The current restrictive criteria for gasotransmitters exclude oxygen (O2) as a gasotransmitter in vertebrates. In this manuscript, I propose a revision of gasotransmitter criteria to include O2 per se as a signaling molecule and 'essential gasotransmitter' for vertebrates. This revision would enable us to search for protein-based O2-binding sensors (gasoreceptors) in all cells in the brain or other tissues rather than specialized tissues such as the carotid body or gills. If microorganisms have protein-based O2-binding sensors or gasoreceptors such as DosP or FixL or FNR with diverse signaling domains, then eukaryotic cells must also have O2-binding sensors or gasoreceptors. Just as there are protein-based receptor(s) for nitric oxide (GUCY1A, GUCY1B, CLOCK, NR1D2) in cells of diverse tissues, it is reasonable to consider that there are protein-based receptors for O2 in cells of diverse tissues as well. In mammals, O2 must be acting as a gasotransmitter or gaseous signaling molecule via protein-based gasoreceptors such as androglobin that very likely mediate acute sensing of O2. Accepting O2 as an essential gasotransmitter will enable us to search for gasoreceptors not only for O2 but also for other nonessential gasotransmitters such as hydrogen sulfide, ammonia, methane, and ethylene. It will also allow us to investigate the role of environment-derived metal ions in acute gas (or solute) sensing within and between organisms. Finally, accepting O2 per se as a signaling molecule acting via gasoreceptors will open up the field of gasocrinology.

Microbial methanogenesis in aerobic water: A key driver of surface methane enrichment in a deep reservoir

Significant amounts of the greenhouse gas methane (CH4) are released into the atmosphere worldwide via freshwater sources. The surface methane maximum (SMM), where methane is supersaturated in surface water, has been observed in aquatic systems and contributes significantly to emissions. However, little is known about the temporal and spatial variability of SMM or the mechanisms underlying its development in artificial reservoirs. Here, the community composition of methanogens as major methane producers in the water column and the mcrA gene was investigated, and the cause of surface methane supersaturation was analyzed. In accordance with the findings, elevated methane concentration of SMM in the transition zone, with an annually methane emission flux 2.47 times higher than the reservoir average on a large and deep reservoir. In the transition zone, methanogens with mcrA gene abundances ranging from 0.5 × 103-1.45 × 104 copies/L were found. Methanobacterium, Methanoseata and Methanosarcina were the three dominate methanogens, using both acetic acid and H2/CO2 pathways. In summary, this study contributes to our comprehension of CH4 fluxes and their role in the atmospheric methane budget. Moreover, it offers biological proof of methane generation, which could aid in understanding the role of microbial methanogenesis in aerobic water.

Optimization strategy of Co3O4 nanoparticles in biomethane production from seaweeds and its potential role in direct electron transfer and reactive oxygen species formation

In the present study, three process parameters optimization were assessed as controlling factors for the biogas and biomethane generation from brown algae Cystoceira myrica as the substrate using RSM for the first time. The biomass amount, Co3O4NPs dosage, and digestion time were assessed and optimized by RSM using Box-Behnken design (BBD) to determine their optimum level. BET, FTIR, TGA, XRD, SEM, XPS, and TEM were applied to illustrate the Co3O4NPs. FTIR and XRD analysis established the formation of Co3O4NPs. The kinetic investigation confirmed that the modified model of Gompertz fit the research results satisfactorily, with R2 ranging between 0.989-0.998 and 0.879-0.979 for biogas and biomethane production, respectively. The results recommended that adding Co3O4NPs at doses of 5 mg/L to C. myrica (1.5 g) significantly increases biogas yield (462 mL/g VS) compared to all other treatments. The maximum biomethane generation (96.85 mL/g VS) was obtained with C. myrica at (0 mg/L) of Co3O4NPs. The impacts of Co3O4NPs dosages on biomethane production, direct electron transfer (DIET) and reactive oxygen species (ROS) were also investigated in detail. The techno-economic study results demonstrate the financial benefits of this strategy for the biogas with the greatest net energy content, which was 2.82 kWh with a net profit of 0.60 USD/m3 of the substrate and was produced using Co3O4NPs (5 mg/L).

Plant-mediated CH4 exchange in wetlands: A review of mechanisms and measurement methods with implications for modelling

Plant-mediated CH4 transport (PMT) is the dominant pathway through which soil-produced CH4 can escape into the atmosphere and thus plays an important role in controlling ecosystem CH4 emission. PMT is affected by abiotic and biotic factors simultaneously, and the effects of biotic factors, such as the dominant plant species and their traits, can override the effects of abiotic factors. Increasing evidence shows that plant-mediated CH4 fluxes include not only PMT, but also within-plant CH4 production and oxidation due to the detection of methanogens and methanotrophs attached to the shoots. Despite the inter-species and seasonal differences, and the probable contribution of within-plant microbes to total plant-mediated CH4 exchange (PME), current process-based ecosystem models only estimate PMT based on the bulk biomass or leaf area index of aerenchymatous plants. We highlight five knowledge gaps to which more research efforts should be devoted. First, large between-species variation, even within the same family, complicates general estimation of PMT, and calls for further work on the key dominant species in different types of wetlands. Second, the interface (rhizosphere-root, root-shoot, or leaf-atmosphere) and plant traits controlling PMT remain poorly documented, but would be required for generalizations from species to relevant functional groups. Third, the main environmental controls of PMT across species remain uncertain. Fourth, the role of within-plant CH4 production and oxidation is poorly quantified. Fifth, the simplistic description of PMT in current process models results in uncertainty and potentially high errors in predictions of the ecosystem CH4 flux. Our review suggest that flux measurements should be conducted over multiple growing seasons and be paired with trait assessment and microbial analysis, and that trait-based models should be developed. Only then we are capable to accurately estimate plant-mediated CH4 emissions, and eventually ecosystem total CH4 emissions at both regional and global scales.

Engineering Clinically Relevant Probiotics with Switchable "Nano-Promoter" and "Nano-Effector" for Precision Tumor Therapy

Probiotics have the potential as biotherapeutic agents for cancer management in preclinical models and human trials by secreting antineoplastic or immunoregulatory agents in the tumor microenvironment (TME). However, current probiotics lack the ability to dynamically respond to unique TME characteristics, leading to limited therapeutic accuracy and efficacy. Although progress has been made in customizing controllable probiotics through synthetic biology, the engineering process is complex and the predictability of production is relatively low. To address this, here, for the first time, this work adopts pH-dependent peroxidase-like (POD-like) artificial enzymes as both an inducible "nano-promoter" and "nano-effector" to engineer clinically relevant probiotics to achieve switchable control of probiotic therapy. The nanozyme initially serves as an inducible "nano-promoter," generating trace amounts of nonlethal reactive oxygen species (ROS) stress to upregulate acidic metabolites in probiotics. Once metabolites acidify the TME to a threshold, the nanozyme switches to a "nano-effector," producing a great deal of lethal ROS to fight cancer. This approach shows promise in subcutaneous, orthotopic, and colitis-associated colorectal cancer tumors, offering a new methodology for modulating probiotic metabolism in a pathological environment.

Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget

Biological methane, a major source of global methane budget, is traditionally thought to be produced in anaerobic environments. However, the recent reports about methane supersaturation occurring in oxygenated water layer, termed as "methane paradox", have challenged this prevailing paradigm. Significantly, growing evidence has indicated that phytoplankton including prokaryotic cyanobacteria and eukaryotic algae are capable of generating methane under aerobic conditions. In this regard, a systematic review of aerobic methane production by phytoplankton is expected to arouse the public attention, contributing to the understanding of methane paradox. Here, we comprehensively summarize the widespread phenomena of methane supersaturation in oxic layers. The remarkable correlation relationships between methane concentration and several key indicators (depth, chlorophyll a level and organic sulfide concentration) indicate the significance of phytoplankton in in-situ methane accumulation. Subsequently, four mechanisms of aerobic methane production by phytoplankton are illustrated in detail, including photosynthesis-driven metabolism, reactive oxygen species (ROS)-driven demethylation of methyl donors, methanogenesis catalyzed by nitrogenase and demethylation of phosphonates catalyzed by CP lyase. The first two pathways occur in various phytoplankton, while the latter two have been specially discovered in cyanobacteria. Additionally, the effects of four crucial factors on aerobic methane production by phytoplankton are also discussed, including phytoplankton species, light, temperature and crucial nutrients. Finally, the measures to control global methane emissions from phytoplankton, the precise intracellular mechanisms of methane production and a more complete global methane budget model are definitely required in the future research on methane production by phytoplankton. This review would provide guidance for future studies of aerobic methane production by phytoplankton and emphasize the potential contribution of aquatic ecosystems to global methane budget.

Gas-sensing riboceptors

Understanding how cells sense gases or gaseous solutes is a fundamental question in biology and is pivotal for the evolution of molecular and organismal life. In numerous organisms, gases can diffuse into cells, be transported, generated, and sensed. Controlling gases in the cellular environment is essential to prevent cellular and molecular damage due to interactions with gas-dependent free radicals. Consequently, the mechanisms governing acute gas sensing are evolutionarily conserved and have been experimentally elucidated in various organisms. However, the scientific literature on direct gas sensing is largely based on hemoprotein-based gasoreceptors (or sensors). As RNA-based G-quadruplex (G4) structures can also bind to heme, I propose that some ribozymes can act as gas-sensing riboceptors (ribonucleic acid receptors). Additionally, I present a few other ideas for non-heme metal ion- or metal cluster-based gas-sensing riboceptors. Studying riboceptors can help understand the evolutionary origins of cellular and gasocrine signaling.

Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production

Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.

Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes

Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, eutrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in 13C-CH4 and 2H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with 13C- and 2H-labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emission to the atmosphere.

Physiological responses and altered halocarbon production in Phaeodactylum tricornutum after exposure to polystyrene microplastics

Oceanic emissions are a major source of atmospheric, very short-lived, ozone-depleting, brominated substances. These substances can be produced by marine microalgae, estimates of their current and future emissions are imperfect, because the processes by which marine microalgae respond to environmental changes are rarely account for environmental pollutants. Here, concurrent measurements of the potential effects of polystyrene (PS) microplastics with concentrations of 25-100 mg/L on the growth of Phaeodactylum tricornutum and their volatile halocarbons (VHCs) production were made over a 20-day culture period. The maximum inhibition rates (IR) due to 0.1 µm and 0.5 µm PS microplastics on cell density were 40.11 % and 32.87 %, on Chl a content were 25.89 % and 20.73 %, and on Fv/Fm were 9.74 % and 9.00 %, respectively. All IR showed dose-dependent effects with maxima occurring in the logarithmic phase. However, in the stationary phase, P. tricornutum exposed to PS microplastics exhibited improved attributes. Enhanced biogenesis of VHCs was induced by the excess reactive oxygen species in algal cells due to microplastics exposure, and their production rates were higher in the logarithmic phase than stationary phase. This represents that oxidative stress to cells plays a dominant role in determining the release of CHBrCl2, CHBr2Cl, and CHBr3. Hence, we suggest that the widespread microplastics in the ocean may be partly responsible for the increase in the emission of VHCs by marine phytoplankton, thereby affecting the ozone layer recovery in the future.

Phosphonate consumers potentially contributing to methane production in Brazilian soda lakes

Oxic methane production (OMP) has been reported to significantly contribute to methane emissions from oxic surface waters. Demethylation of organic compounds, photosynthesis-associated methane production, and (bacterio)chlorophyll reduction activity are some of the investigated mechanisms as potential OMP sources related to photosynthetic organisms. Recently, cyanobacteria have often been correlated with methane accumulation and emission in freshwater, marine, and saline systems. The Brazilian Pantanal is the world's largest wetland system, with approximately 10,000 shallow lakes, most of which are highly alkaline and saline extreme environments. We initiated this study with an overall investigation using genetic markers, from which we explored metagenomic and limnological data from the Pantanal soda for five potential OMP pathways. Our results showed a strong positive correlation between dissolved methane concentrations and bloom events. Metagenomic data and nutrients, mainly orthophosphate, nitrogen, iron, and methane concentrations, suggest that the organic phosphorous demethylation pathway has the most potential to drive OMP in lakes with blooms. A specialized bacterial community was identified, including the Cyanobacteria Raphidiopsis, although the bloom does not contain the genes to carry out this process. These data showed enough evidence to infer the occurrence of an OMP pathway at Pantanal soda lakes, including the microbial sources and their relation to the cyanobacterial blooms.

Stable Isotope Approach to Assess the Production and Consumption of Methylphosphonate and Its Contribution to Oxic Methane Formation in Surface Waters

Recent studies in aquatic environments have indicated that microbial methane production is not limited to strictly anoxic conditions and is widespread in the oxic water column. Based on recent investigations proposing linkage between the microbial turnover of methylphosphonate (MPn) and the widespread methane oversaturation in surface waters, we conducted an MPn/13C-MPn tracer approach that combines liquid chromatography-mass spectrometry and gas chromatography-stable isotope ratio mass spectrometry to assess concentrations of the MPn tracer and its contribution to oxic methane formation. In our study, conducted during summer 2020 in the Baltic Sea, we show that MPn is a potent methanogenic substrate in the surface water. However, we found that MPn was produced within the surface and subthermocline water bodies and that its turnover was not limited to the phosphorus-stressed and cyanobacteria-rich surface water. However, our study revealed that most of the MPn was probably degraded via alternative pathways, not releasing methane. Our assessment indicates that the contribution of the MPn degradation pathway only contributed marginally to oxic methane production at the study site in the Baltic Sea and that a variety of methanogenic pathways are probably responsible for the surface-water methane enrichments.

Supersulfide biology and translational medicine for disease control

For decades, the major focus of redox biology has been oxygen, the most abundant element on Earth. Molecular oxygen functions as the final electron acceptor in the mitochondrial respiratory chain, contributing to energy production in aerobic organisms. In addition, oxygen-derived reactive oxygen species including hydrogen peroxide and nitrogen free radicals, such as superoxide, hydroxyl radical and nitric oxide radical, undergo a complicated sequence of electron transfer reactions with other biomolecules, which lead to their modified physiological functions and diverse biological and pathophysiological consequences (e.g. oxidative stress). What is now evident is that oxygen accounts for only a small number of redox reactions in organisms and knowledge of biological redox reactions is still quite limited. This article reviews a new aspects of redox biology which is governed by redox-active sulfur-containing molecules-supersulfides. We define the term 'supersulfides' as sulfur species with catenated sulfur atoms. Supersulfides were determined to be abundant in all organisms, but their redox biological properties have remained largely unexplored. In fact, the unique chemical properties of supersulfides permit them to be readily ionized or radicalized, thereby allowing supersulfides to actively participate in redox reactions and antioxidant responses in cells. Accumulating evidence has demonstrated that supersulfides are indispensable for fundamental biological processes such as energy production, nucleic acid metabolism, protein translation and others. Moreover, manipulation of supersulfide levels was beneficial for pathogenesis of various diseases. Thus, supersulfide biology has opened a new era of disease control that includes potential applications to clinical diagnosis, prevention and therapeutics of diseases.

Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic

Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.

Conjugation with Tris Decreases the Risk of Ketoprofen-Induced Mucosal Damage and Reduces Inflammation-Associated Methane Production in a Rat Model of Colitis

We have designed a new compound from the non-steroidal anti-inflammatory drug (NSAID) ketoprofen (Ket) and 2-amino-2-(hydroxymethyl)-1,3-propanediol (Tris) precursors, with the aim to reduce the gastrointestinal (GI) side effects of NSAID therapies. We investigated mucosal reactions in a standard rat model of colitis together with methane generation as a possible indicator of pro-inflammatory activation under this condition (approval number: V./148/2013). Whole-body methane production (photoacoustic spectroscopy) and serosal microcirculation (intravital videomicroscopy) were measured, and mucosal damage was assessed (conventional histology; in vivo laser-scanning endomicroscopy). Inflammatory markers were measured from tissue and blood samples. Colitis induced an inflammatory response, morphological colonic damage and increased methane output. Ket treatment lowered inflammatory activation and colonic mucosal injury, but macroscopic gastric bleeding and increased methane output were present. Ket-Tris reduced inflammatory activation, methane emission and colonic mucosal damage, without inducing gastric injury. Conjugation with Tris reduces the GI side effects of Ket and still decreases the inflammatory response in experimental colitis. Methane output correlates with the mucosal inflammatory response and non-invasively demonstrates the effects of anti-inflammatory treatments.

High antipersister activity of a promising new quinolone drug candidate in eradicating uropathogenic Escherichia coli persisters and persistent infection in mice

AIMS

To develop more potent drugs that eradicate persister bacteria and cure persistent urinary tract infections (rUTIs).

METHODS AND RESULTS

We synthesized eight novel clinifloxacin analogs and measured minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), the time-kill curves in uropathogenic Escherichia coli (UPEC) UTI89, and applied the candidate drugs and combinations against biofilm bacteria in vitro and in mice. Transcriptomic analysis was performed for UPEC after candidate drug treatment to shed light on potential mechanism of action. We identified Compound 2, named Qingdafloxacin (QDF), which was more potent than clinafloxacin and clinically used levofloxacin and moxifloxacin, with an MIC of < 0.04 μg ml-1 and an MBC of 0.08∼0.16 μg ml-1. In drug combination studies, QDF + gentamicin + nitrofuran combination but not single drugs completely eradicated all stationary phase bacteria containing persisters and biofilm bacteria, and all bacteria in a persistent UTI mouse model. Transcriptome analysis revealed that the unique antipersister activity of QDF was associated with downregulation of genes involved in bacterial stress response, DNA repair, protein misfolding repair, pyrimidine metabolism, glutamate, and glutathione metabolism, and efflux.

CONCLUSIONS

QDF has high antipersister activity and its drug combinations proved highly effective against biofilm bacteria in vitro and persistent UTIs in mice, which may have implications for treating rUTIs.

Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay

Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.

Methane formation driven by light and heat prior to the origin of life and beyond

Methane is a potent greenhouse gas, which likely enabled the evolution of life by keeping the early Earth warm. Here, we demonstrate routes towards abiotic methane and ethane formation under early-earth conditions from methylated sulfur and nitrogen compounds with prebiotic origin. These compounds are demethylated in Fenton reactions governed by ferrous iron and reactive oxygen species (ROS) produced by light and heat in aqueous environments. After the emergence of life, this phenomenon would have greatly intensified in the anoxic Archean by providing methylated sulfur and nitrogen substrates. This ROS-driven Fenton chemistry can occur delocalized from serpentinization across Earth's humid realm and thereby substantially differs from previously suggested methane formation routes that are spatially restricted. Here, we report that Fenton reactions driven by light and heat release methane and ethane and might have shaped the chemical evolution of the atmosphere prior to the origin of life and beyond.

Radical-Driven Methane Formation in Humans Evidenced by Exogenous Isotope-Labeled DMSO and Methionine

Methane (CH₄), which is produced endogenously in animals and plants, was recently suggested to play a role in cellular physiology, potentially influencing the signaling pathways and regulatory mechanisms involved in nitrosative and oxidative stress responses. In addition, it was proposed that the supplementation of CH₄ to organisms may be beneficial for the treatment of several diseases, including ischemia, reperfusion injury, and inflammation. However, it is still unclear whether and how CH₄ is produced in mammalian cells without the help of microorganisms, and how CH₄ might be involved in physiological processes in humans. In this study, we produced the first evidence of the principle that CH₄ is formed non-microbially in the human body by applying isotopically labeled methylated sulfur compounds, such as dimethyl sulfoxide (DMSO) and methionine, as carbon precursors to confirm cellular CH₄ formation. A volunteer applied isotopically labeled (²H and ¹³C) DMSO on the skin, orally, and to blood samples. The monitoring of stable isotope values of CH₄ convincingly showed the conversion of the methyl groups, as isotopically labeled CH₄ was formed during all experiments. Based on these results, we considered several hypotheses about endogenously formed CH₄ in humans, including physiological aspects and stress responses involving reactive oxygen species (ROS). While further and broader validation studies are needed, the results may unambiguously serve as a proof of concept for the endogenous formation of CH₄ in humans via a radical-driven process. Furthermore, these results might encourage follow-up studies to decipher the potential physiological role of CH₄ and its bioactivity in humans in more detail. Of particular importance is the potential to monitor CH₄ as an oxidative stress biomarker if the observed large variability of CH₄ in breath air is an indicator of physiological stress responses and immune reactions. Finally, the potential role of DMSO as a radical scavenger to counteract oxidative stress caused by ROS might be considered in the health sciences. DMSO has already been investigated for many years, but its potential positive role in medical use remains highly uncertain.

The greenhouse effect of antibiotics: The influence pathways of antibiotics on methane release from freshwater sediment

The impact of antibiotics on methane (CH₄) release from sediment involves both CH₄ production and consumption processes. However, most relevant studies lack a discussion of the pathways by which antibiotics affect CH₄ release and do not highlight the role played by the sediment chemical environment in this influence mechanism. Here, we collected field surface sediments and grouped them with various antibiotic combination concentration gradients (50, 100, 500, 1000 ng g^-1) under a 35-day indoor anaerobic constant temperature incubation. We found that the positive effect of antibiotics on sediment CH₄ release potential appeared later than the positive effect on sediment CH₄ release flux. Still, the positive effect of high-concentration antibiotics (500, 1000 ng g^-1) occurred with a lag in both processes. Also, the positive effect of high-concentration antibiotics was significantly higher than low-concentration antibiotics (50, 100 ng g^-1) in the later incubation period (p < 0.05). We performed a multi-collinearity assessment of sediment biochemical indicators, followed by a generalized linear model with negative binomial regression (GLM-NB) to obtain essential variables. In particular, we conducted the interaction analysis on CH₄ release potential and flux regression for the influence pathways construction. The partial least-squares path modeling (PLS-PM) demonstrated that the positive effect of antibiotics on CH₄ release (Total effect = 0.2579) was primarily attributed to their effect on the sediment chemical environment (Direct effect = 0.5107). These findings greatly expand our understanding of the antibiotic greenhouse effect in freshwater sediment. Further studies should more carefully consider the effects of antibiotics on the sediment chemical environment, and continuously improve the mechanistic studies of antibiotics on sediment CH₄ release.

A methane-cGMP module positively influences adventitious rooting

KEY MESSAGE

Endogenous cGMP operates downstream of CH₄ control of adventitious rooting, following by the regulation in the expression of cell cycle regulatory and auxin signaling-related genes. Methane (CH₄) is a natural product from plants and microorganisms. Although exogenously applied CH₄ and cyclic guanosine monophosphate (cGMP) are separately confirmed to be involved in the control of adventitious root (AR) formation, the possible interaction still remains elusive. Here, we observed that exogenous CH₄ not only rapidly promoted cGMP synthesis through increasing the activity of guanosine cyclase (GC), but also induced cucumber AR development. These responses were obviously impaired by the removal of endogenous cGMP with two GC inhibitors. Anatomical evidence showed that the emerged stage (V) among AR primordia development might be the main target of CH₄-cGMP module. Genetic evidence revealed that the transgenic Arabidopsis that overexpressed the methyl-coenzyme M reductase gene (MtMCR) from Methanobacterium thermoautotrophicum not only increased-cGMP production, but also resulted in a pronounced AR development compared to wild-type (WT), especially with the addition of CH₄ or the cell-permeable cGMP derivative 8-Br-cGMP. qPCR analysis confirmed that some marker genes associated with cell cycle regulatory and auxin signaling were closely related to the brand-new CH₄-cGMP module in AR development. Overall, our results clearly revealed an important function of cGMP in CH₄ governing AR formation by modulating auxin-dependent pathway and cell cycle regulation.

Evaluation of the methane paradox in four adjacent pre-alpine lakes across a trophic gradient

Contrasting the paradigm that methane is only produced in anoxic conditions, recent discoveries show that oxic methane production (OMP, aka the methane paradox) occurs in oxygenated surface waters worldwide. OMP drivers and their contribution to global methane emissions, however, are not well constrained. In four adjacent pre-alpine lakes, we determine the net methane production rates in oxic surface waters using two mass balance approaches, accounting for methane sources and sinks. We find that OMP occurs in three out of four studied lakes, often as the dominant source of diffusive methane emissions. Correlations of net methane production versus chlorophyll-a, Secchi and surface mixed layer depths suggest a link with photosynthesis and provides an empirical upscaling approach. As OMP is a methane source in direct contact with the atmosphere, a better understanding of its extent and drivers is necessary to constrain the atmospheric methane contribution by inland waters.

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

Analysis of the Scale of Global Human Needs and Opportunities for Sustainable Catalytic Technologies

We analyzed the enormous scale of global human needs, their carbon footprint, and how they are connected to energy availability. We established that most challenges related to resource security and sustainability can be solved by providing distributed, affordable, and clean energy. Catalyzed chemical transformations powered by renewable electricity are emerging successor technologies that have the potential to replace fossil fuels without sacrificing the wellbeing of humans. We highlighted the technical, economic, and societal advantages and drawbacks of short- to medium-term decarbonization solutions to gauge their practicability, economic feasibility, and likelihood for widespread acceptance on a global scale. We detailed catalysis solutions that enhance sustainability, along with strategies for catalyst and process development, frontiers, challenges, and limitations, and emphasized the need for planetary stewardship. Electrocatalytic processes enable the production of solar fuels and commodity chemicals that address universal issues of the water, energy and food security nexus, clothing, the building sector, heating and cooling, transportation, information and communication technology, chemicals, consumer goods and services, and healthcare, toward providing global resource security and sustainability and enhancing environmental and social justice.

The ro-vibrational ν2 mode spectrum of methane investigated by ultrabroadband coherent Raman spectroscopy

We present the first experimental application of coherent Raman spectroscopy (CRS) on the ro-vibrational ν₂ mode spectrum of methane (CH₄). Ultrabroadband femtosecond/picosecond (fs/ps) CRS is performed in the molecular fingerprint region from 1100 to 2000 cm^-1, employing fs laser-induced filamentation as the supercontinuum generation mechanism to provide the ultrabroadband excitation pulses. We introduce a time-domain model of the CH₄ ν₂ CRS spectrum, including all five ro-vibrational branches allowed by the selection rules Δv = 1, ΔJ = 0, ±1, ±2; the model includes collisional linewidths, computed according to a modified exponential gap scaling law and validated experimentally. The use of ultrabroadband CRS for in situ monitoring of the CH₄ chemistry is demonstrated in a laboratory CH₄/air diffusion flame: CRS measurements in the fingerprint region, performed across the laminar flame front, allow the simultaneous detection of molecular oxygen (O₂), carbon dioxide (CO₂), and molecular hydrogen (H₂), along with CH₄. Fundamental physicochemical processes, such as H₂ production via CH₄ pyrolysis, are observed through the Raman spectra of these chemical species. In addition, we demonstrate ro-vibrational CH₄ v₂ CRS thermometry, and we validate it against CO₂ CRS measurements. The present technique offers an interesting diagnostics approach to in situ measurement of CH₄-rich environments, e.g., in plasma reactors for CH₄ pyrolysis and H₂ production.

Quantifying biochar-induced greenhouse gases emission reduction effects in constructed wetlands and its heterogeneity: A multi-level meta-analysis

Zero-waste biochar is an emerging tool for carbon neutralization, but the role of biochar in reducing greenhouse gases (GHGs) emissions from CWs were controversy and uncertainty. Yet, no previous study has integrated multiple research systems to quantitatively examine biochar-mediated GHGs emission reduction potential in CWs. Here we synthesized 114 studies to quantify biochar-induced declines ability of GHGs in the CWs by using the multi-level meta-analysis, reveal the variation of GHGs emission effect in different biochar-CWs and its response relationship with biochar, and identify the moderating variables that had a strong explanatory effect on the emission reduction effect of biochar. We showed that biochar remarkably affect CO₂ mitigation (p < 0.05), but has insignificant and heterogeneous effects on CH₄ and N₂O. Pyrolysis time, influent dissolved oxygen (DO), influent NO₃^--N concentration, hydraulic retention time (HRT) and wetland type can significantly affect the effect of biochar on CH₄ emission reduction. Particularly, the importance of HRT and wetland type was 0.89 and 0.85, respectively. Specially, the surface batch CWs modified by biochar could significantly promote the emission of CH₄ (p < 0.001), and the effect size was up to 89.59. For N₂O, biochar diameter, biochar addition ratio, influent COD/TN ratio, plant name, and removal efficiency of NO₃^--N/TN/COD were significant moderators. Among them, influent COD/TN ratio and plant name showed a stronger explanation. Planting Cyperus alternifolius L. significantly enhanced the N₂O emission reduction capacity by biochar (p < 0.001), and effect size was as low as -24.32. 700-900 °C biochar can promote CH₄ flux but inhibit N₂O flux. This study provides an important theoretical basis and valuable strategic guidance for more accurate estimation and improvement of synergistic emission reduction benefits between CH₄ and N₂O of biochar in CWs.

Methane Production by Facultative Anaerobic Wood-Rot Fungi via a New Halomethane-Dependent Pathway

The greenhouse gas methane (CH4) is of pivotal importance for Earth's climate system and as a human energy source. A significant fraction of this CH4 is produced by anaerobic Archaea. Here, we describe the first CH4 production by facultative anaerobic wood-rot fungi during growth on hydroxylated/carboxylated aromatic compounds, including lignin and lignite. The amount of CH4 produced by fungi is positively correlated with the amount of CH3Cl produced during the rapid growth period of the fungus. Biochemical, genetic, and stable isotopic tracer analyses reveal the existence of a novel halomethane-dependent fungal CH4 production pathway during the degradation of phenol and benzoic acid monomers and polymers and utilization of cyclic sugars. Even though this halomethane-dependent pathway may only play a side role in anaerobic fungal activity, it could represent a globally significant, previously overlooked source of biogenic CH4 in natural ecosystems. IMPORTANCE Here, we demonstrate that wood-rot fungi produce methane anaerobically without the involvement of methanogenic archaea via a new, halomethane-dependent pathway. These findings of an anaerobic fungal methane formation pathway open another avenue in methane research and will further assist with current efforts in the identification of the processes involved and their ecological implications.

Phytomelatonin and gasotransmitters: a crucial combination for plant physiological functions

Melatonin, a molecule that was first identified in animal tissues, has been confirmed to be involved as a potential phytohormone in a variety of plant physiological responses. It is considered primarily as an antioxidant with important actions in controlling reactive oxygen and reactive nitrogen species. In addition to its role in regulating plant growth and development, phytomelatonin is involved in protection against abiotic and biotic stresses. The 'gasotransmitter'-that is, a gaseous signaling molecule-is a new concept that has been advanced in the past two decades, with functions in animal and plant physiological regulation. Gasotransmitters including nitric oxide, carbon monoxide, hydrogen sulfide, methane, and, more recently identified, hydrogen gas are critical and indispensable in a wide range of biological processes. This review investigates the interrelationship between phytomelatonin and the above-mentioned gasotransmitters from the perspective of biosynthetic origin and functions. Moreover, the potential future research directions for phytomelatonin and gasotransmitters interactions are discussed.

Suppressing Methane Production to Boost High-Purity Hydrogen Production in Microbial Electrolysis Cells

Hydrogen gas (H₂) is an attractive fuel carrier due to its high specific enthalpy; moreover, it is a clean source of energy because in the combustion reaction with oxygen (O₂) it produces water as the only byproduct. The microbial electrolysis cell (MEC) is a promising technology for producing H₂ from simple or complex organics present in wastewater and solid wastes. Methanogens and non-archaeal methane (CH₄)-producing microorganisms (NAMPMs) often grow in the MECs and lead to rapid conversion of produced H₂ to CH₄. Moreover, non-archaeal methane production (NAMP) catalyzed by nitrogenase of photosynthetic bacteria was always overlooked. Thus, suppression of CH₄ production is required to enhance H₂ yield and production rate. This review comprehensively addresses the principles and current state-of-the-art technologies for suppressing methanogenesis and NAMP in MECs. Noteworthy, specific strategies aimed at the inhibition of methanogenic enzymes and nitrogenase could be a more direct approach than physical and chemical strategies for repressing the growth of methanogenic archaea. In-depth studies on the multiomics of CH₄ metabolism can possibly provide insights into sustainable and efficient approaches for suppressing metabolic pathways of methanogenesis and NAMP. The main objective of this review is to highlight key concepts, directions, and challenges related to boosting H₂ generation by suppressing CH₄ production in MECs. Finally, perspectives are briefly outlined to guide and advance the future direction of MECs for production of high-purity H₂ based on genetic and metabolic engineering and on the interspecific interactions.

Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO₂, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX₅₈) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO₂ were significantly related to microbial community composition, with CO₂ inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO₂ production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.

Magnitude and Drivers of Oxic Methane Production in Small Temperate Lakes

Methanogenesis is traditionally considered as a strictly anaerobic process. Recent evidence suggests instead that the ubiquitous methane (CH₄) oversaturation found in freshwater lakes is sustained, at least partially, by methanogenesis in oxic conditions. Although this paradigm shift is rapidly gaining acceptance, the magnitude and regulation of oxic CH₄ production (OMP) have remained ambiguous. Based on the summer CH₄ mass balance in the surface mixed layer (SML) of five small temperate lakes (surface area, SA, of 0.008-0.44 km²), we show that OMP (range of 0.01 ± 0.01 to 0.52 ± 0.04 μmol L^-1 day^-1) is linked to the concentrations of chlorophyll-a, total phosphorus, and dissolved organic carbon. The stable carbon isotopic mass balance of CH₄ (δ¹³C-CH₄) indicates direct photoautotrophic release as the most likely source of oxic CH₄. Furthermore, we show that the oxic CH₄ contribution to the SML CH₄ saturation and emission is an inverse function of the ratio of the sediment area to the SML volume in lakes as small as 0.06 km². Given that global lake CH₄ emissions are dominated by small lakes (SA of <1 km²), the large contribution of oxic CH₄ production (up to 76%) observed in this study suggests that OMP can contribute significantly to global CH₄ emissions.

W Single-Atom Catalyst for CH4 Photooxidation in Water Vapor

Solar-driven high-efficiency and direct conversion of methane into high-value-added liquid oxygenates against overoxidation remains a great challenge. Herein, facile and mass fabrication of low-cost tungsten single-atom photocatalysts is achieved by directly calcining urea and sodium tungstate under atmosphere (W-SA-PCN-m, urea amount m = 7.5, 15, 30, and 150 g). The single-atom photocatalysts can manage H₂ O₂ in situ generation and decomposition into ·OH, thus achieving highly efficient CH₄ photooxidation in water vapor under mild conditions. Systematic investigations demonstrate that integration of multifunctions of methane activation, H₂ O₂ generation, and decomposition into one photocatalyst can dramatically promote methane conversion to C1 oxygenates with a yield as high as 4956 µmol g_cat ^-1 , superior to that of the most reported non-precious photocatalysts. Liquid-solid phase transition can induce the products to facilely switch in from HCOOH to CH₃ OH by pulling the catalyst above water with CH₃ OH/HCOOH ratio from 10% (in H₂ O) to 80% (above H₂ O).

Tumor microbiome metabolism: A game changer in cancer development and therapy

Accumulating recent evidence indicates that the human microbiome plays essential roles in pathophysiological states, including cancer. The tumor microbiome, an emerging concept that has not yet been clearly defined, has been proven to influence both cancer development and therapy through complex mechanisms. Small molecule metabolites produced by the tumor microbiome through unique biosynthetic pathways can easily diffuse into tissues and penetrate cell membranes through transporters or free diffusion, thus remodeling the signaling pathways of cancer and immune cells by interacting with biomacromolecules. Targeting tumor microbiome metabolism could offer a novel perspective for not only understanding cancer progression but also developing new strategies for the treatment of multiple cancer types. Here, we summarize recent advances regarding the role the tumor microbiome plays as a game changer in cancer biology. Specifically, the metabolites produced by the tumor microbiome and their potential effects on the cancer development therapy are discussed to understand the importance of the microbial metabolism in the tumor microenvironment. Finally, new anticancer therapeutic strategies that target tumor microbiome metabolism are reviewed and proposed to provide new insights in clinical applications.

ROS-driven cellular methane formation: Potential implications for health sciences

Recently it has been proposed that methane might be produced by all living organisms via a mechanism driven by reactive oxygen species that arise through the metabolic activity of cells. Here, we summarise details of this novel reaction pathway and discuss its potential significance for clinical and health sciences. In particular, we highlight the role of oxidative stress in cellular methane formation. As several recent studies also demonstrated the anti-inflammatory potential for exogenous methane-based approaches in mammalians, this article addresses the intriguing question if ROS-driven methane formation has a general physiological role and associated diagnostic potential.

Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina

Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides.

IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.

Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens

In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.