Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn

The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.

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.

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Lake surface cooling drives littoral-pelagic exchange of dissolved gases

The extent of littoral influence on lake gas dynamics remains debated in the aquatic science community due to the lack of direct quantification of lateral gas transport. The prevalent assumption of diffusive horizontal transport in gas budgets fails to explain anomalies observed in pelagic gas concentrations. Here, we demonstrate through high-frequency measurements in a eutrophic lake that daily convective horizontal circulation generates littoral-pelagic advective gas fluxes one order of magnitude larger than typical horizontal fluxes used in gas budgets. These lateral fluxes are sufficient to redistribute gases at the basin-scale and generate concentration anomalies reported in other lakes. Our observations also contrast the hypothesis of pure, nocturnal littoral-to-pelagic exchange by showing that convective circulation transports gases such as oxygen and methane toward both the pelagic and littoral zones during the daytime. This study challenges the traditional pelagic-centered models of aquatic systems by showing that convective circulation represents a fundamental lateral transport mechanism to be integrated into gas budgets.

Greenhouse gas emissions from Daihai Lake, China: Should eutrophication and salinity promote carbon emission dynamics?

Greenhouse gases (GHGs) emitted or absorbed by lakes are an important component of the global carbon cycle. However, few studies have focused on the GHG dynamics of eutrophic saline lakes, thus preventing a comprehensive understanding of the carbon cycle. Here, we conducted four sampling analyses using a floating chamber in Daihai Lake, a eutrophication saline lake in Inner Mongolia Autonomous Region, China, to explore its carbon dioxide (CO2) and methane (CH4) emissions. The mean CO2 emission flux (FCO2) and CH4 emission flux (FCH4) were 17.54 ± 14.54 mmol/m2/day and 0.50 ± 0.50 mmol/m2/day, respectively. The results indicated that Daihai Lake was a source of CO2 and CH4, and GHG emissions exhibited temporal variability. The mean CO2 partial pressure (pCO2) and CH4 partial pressure (pCH4) were 561.35 ± 109.59 µatm and 17.02 ± 13.45 µatm, which were supersaturated relative to the atmosphere. The regression and correlation analysis showed that the main influencing factors of pCO2 were wind speed, dissolved oxygen (DO), total nitrogen (TN) and Chlorophyll a (Chl.a), whereas the main influencing factors of pCH4 were water temperature (WT), Chl.a, nitrate nitrogen (NO3--N), TN, dissolved organic carbon (DOC) and water depth. Salinity regulated carbon mineralization and organic matter decomposition, and it was an important influencing factor of pCO2 and pCH4. Additionally, the trophic level index (TLI) significantly increased pCH4. Our study elucidated that salinity and eutrophication play an important role in the dynamic changes of GHG emissions. However, research on eutrophic saline lakes needs to be strengthened.

Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin

The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.

Fluxes in CO2 and CH4 and influencing factors at the sediment-water interface in a eutrophic saline lake

Although saline aquatic ecosystems are significant emitters of greenhouse gases (GHGs), dynamic changes in GHGs at the sediment-water interface remain unclear. The present investigation carried out a total of four sampling campaigns in Daihai Lake, which is a eutrophic saline lake situated in a semi-arid area of northern China. The aim of this study was to investigate the spatio-temporal dynamics of carbon dioxide (CO2) and methane (CH4) fluxes at the sediment-water interface and the influencing factors. The mean concentrations of porewater CO2 and CH4 were 44.98 ± 117.99 μmol L-1 and 124.36 ± 97.00 μmol L-1, far exceeding those in water column of 11.14 ± 2.16 μmol L-1 and 0.33 ± 0.23 μmol L-1, respectively. The CO2 and CH4 fluxes at the sediment-water interface (FS-WCO2 and FS-WCH4) exhibited significant spatial and temporal variations, with mean values of 9.24 ± 13.84 μmol m-2 d-1 and 3.53 ± 4.36 μmol m-2 d-1, respectively, indicating that sediment is the source of CO2 and CH4 in the water column. However, CO2 and CH4 fluxes were much lower than those measured at the water-air interface in a companion study (17.54 ± 14.54 mmol m-2d-1 and 0.50 ± 0.50 mmol m-2d-1, respectively), indicating that the diffusive flux of gases at the sediment-water interface was not the primary source of CO2 and CH4 emissions to the atmosphere. Regression and correlation analyses revealed that salinity (Sal) and nutrients were the most influential factors on porewater gas concentrations, and that gas fluxes increased with increasing gas concentrations and porosity. The microbial activity of sediment is greatly affected by nutrients and Sal. Additionally, Sal has the ability to regulate biogeochemical processes, thereby regulating GHG emissions. The present investigation addresses the research gap concerning GHG emissions from sediments of eutrophic saline lakes. The study suggests that controlling the eutrophication and salinization of lakes could be a viable strategy for reducing carbon emissions from lakes. However, further investigations are required to establish more conclusive results.

Global change effects on biogeochemical mercury cycling

Past and present anthropogenic mercury (Hg) release to ecosystems causes neurotoxicity and cardiovascular disease in humans with an estimated economic cost of $117 billion USD annually. Humans are primarily exposed to Hg via the consumption of contaminated freshwater and marine fish. The UNEP Minamata Convention on Hg aims to curb Hg release to the environment and is accompanied by global Hg monitoring efforts to track its success. The biogeochemical Hg cycle is a complex cascade of release, dispersal, transformation and bio-uptake processes that link Hg sources to Hg exposure. Global change interacts with the Hg cycle by impacting the physical, biogeochemical and ecological factors that control these processes. In this review we examine how global change such as biome shifts, deforestation, permafrost thaw or ocean stratification will alter Hg cycling and exposure. Based on past declines in Hg release and environmental levels, we expect that future policy impacts should be distinguishable from global change effects at the regional and global scales.

Water column dynamics control nitrite-dependent anaerobic methane oxidation by Candidatus "Methylomirabilis" in stratified lake basins

We investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins of Lake Lugano, Switzerland. Both basins accumulate large amounts of methane in the water column below their chemoclines, but methane oxidation efficiently prevents methane from reaching surface waters. Here we show that in the meromictic North Basin water column, a substantial fraction of methane was eliminated through anaerobic methane oxidation (AOM) coupled to nitrite reduction by Candidatus Methylomirabilis. Incubations with ¹⁴CH₄ and concentrated biomass from this basin showed enhanced AOM rates with nitrate (+62%) and nitrite (+43%). In the more dynamic South Basin, however, aerobic methanotrophs prevailed, Ca. Methylomirabilis was absent in the anoxic water column, and no evidence was found for nitrite-dependent AOM. Here, the duration of seasonal stratification and anoxia seems to be too short, relative to the slow growth rate of Ca. Methylomirabilis, to allow for the establishment of anaerobic methanotrophs, in spite of favorable hydrochemical conditions. Using 16 S rRNA gene sequence data covering nearly ten years of community dynamics, we show that Ca. Methylomirabilis was a permanent element of the pelagic methane filter in the North Basin, which proliferated during periods of stable water column conditions and became the dominant methanotroph in the system. Conversely, more dynamic water column conditions led to a decline of Ca. Methylomirabilis and induced blooms of the faster-growing aerobic methanotrophs Methylobacter and Crenothrix. Our data highlight that physical (mixing) processes and ecosystem stability are key drivers controlling the community composition of aerobic and anaerobic methanotrophs.

Eutrophic levels and algae growth increase emissions of methane and volatile sulfur compounds from lakes

Eutrophic lakes are hot spots of CH₄ and volatile sulfur compound (VSC) emissions, especially during algal blooms and decay. However, the response of CH₄ and VSC emissions to lake eutrophication and algae growth as well as the underlying mechanisms remain unclear. In this study, the emissions of CH₄ and VSCs from four regions of Lake Taihu with different eutrophic levels were investigated in four months (i.e., March, May, August and December). The CH₄ emissions ranged from 20.4 to 126.9 mg m^-2 d^-1 in the investigated sites and increased with eutrophic levels and temperature. H₂S and CS₂ were the dominant volatile sulfur compounds (VSCs) emitted from the lake. The CH₄ oxidation potential of water ranged from 2.1 to 14.9 μg h^-1 L^-1, which had positive correlations with trophic level index and the environmental variables except for the NH₄⁺-N concentration. Eutrophic levels could increase the abundances of bacteria and methanotrophs in lake water. α-Proteobacteria methanotroph Methylocystis was more abundant than γ-Proteobacteria methanotrophs in March and May, while the latter was more abundant in August and November. The relative abundance of Cyanobacteria, including Microcystis, A. granulata var. angustissima and Cyanobium had significantly positive correlations with temperature, turbidity, SO₄^2--S, and total sulfur. Partial least squares path modelling revealed that the algal growth could promote VSC emissions, which had a positive correlation with CH₄ oxidation potential, likely due to the positive correlation between the CH₄ and VSC emissions from lakes. These findings indicate that water eutrophication and algae growth could increase the emissions of CH₄ and VSCs from lakes. Controlling algae growth might be an effective way to mitigate the emissions of CH₄ and VSCs from freshwater lakes.

Methane Emission From Global Lakes: New Spatiotemporal Data and Observation-Driven Modeling of Methane Dynamics Indicates Lower Emissions

Lakes have been highlighted as one of the largest natural sources of the greenhouse gas methane (CH₄) to the atmosphere. However, global estimates of lake CH₄ fluxes over the last 20 years exhibit widely different results ranging from 6 to 185 Tg CH₄ yr^-1, which is to a large extent driven by differences in lake areas and thaw season lengths used. This has generated uncertainty regarding both lake fluxes and the global CH₄ budget. This study constrains global lake water CH₄ emissions by using new information on lake area and distribution and CH₄ fluxes distinguished by major emission pathways; ecoclimatic lake type; satellite-derived ice-free emission period length; and diel- and temperature-related seasonal flux corrections. We produced gridded data sets at 0.25° latitude × 0.25° longitude spatial resolution, representing daily emission estimates over a full annual climatological cycle, appropriate for use in global CH₄ budget estimates, climate and Earth System Models, bottom-up biogeochemical models, and top-down inverse model simulations. Global lake CH₄ fluxes are 41.6 ± 18.3 Tg CH₄ yr^-1 with approximately 50% of the flux contributed by tropical/subtropical lakes. Strong temperature-dependent flux seasonality and satellite-derived freeze/thaw dynamics limit emissions at high latitudes. The primary emission pathway for global annual lake fluxes is ebullition (23.4 Tg) followed by diffusion (14.1 Tg), ice-out and spring water-column turnover (3.1 Tg), and fall water-column turnover (1.0 Tg). These results represent a major contribution to reconciling differences between bottom-up and top-town estimates of inland aquatic system emissions in the global CH₄ budget.

Methanethiol Consumption and Hydrogen Sulfide Production by the Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum SolV

Methanotrophs aerobically oxidize methane to carbon dioxide to make a living and are known to degrade various other short chain carbon compounds as well. Volatile organic sulfur compounds such as methanethiol (CH₃SH) are important intermediates in the sulfur cycle. Although volatile organic sulfur compounds co-occur with methane in various environments, little is known about how these compounds affect methanotrophy. The enzyme methanethiol oxidase catalyzing the oxidation of methanethiol has been known for decades, but only recently the mtoX gene encoding this enzyme was identified in a methylotrophic bacterium. The presence of a homologous gene in verrucomicrobial methanotrophs prompted us to examine how methanotrophs cope with methanethiol. Here, we show that the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV consumes methanethiol and produces H₂S, which is concurrently oxidized. Consumption of methanethiol is required since methanethiol inhibits methane oxidation. Cells incubated with ∼15 μM methanethiol from the start clearly showed inhibition of growth. After depletion of methanethiol, growth resumed within 1 day. Genes encoding a putative methanethiol oxidase were found in a variety of methanotrophs. Therefore, we hypothesize that methanethiol degradation is a widespread detoxification mechanism in methanotrophs in a range of environments.

Methane-Derived Carbon as a Driver for Cyanobacterial Growth

Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH₄ oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO₂) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ¹³C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO₂ released by MOB. On the other hand, ¹³C-CH₄ labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH₄) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH₄ oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH₄ gdw^–1 day^–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH₄ oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH₄ emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH₄ oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

The role of methanotrophy in the microbial carbon metabolism of temperate lakes

Previous stable isotope and biomarker evidence has indicated that methanotrophy is an important pathway in the microbial loop of freshwater ecosystems, despite the low cell abundance of methane-oxidizing bacteria (MOB) and the low methane concentrations relative to the more abundant dissolved organic carbon (DOC). However, quantitative estimations of the relative contribution of methanotrophy to the microbial carbon metabolism of lakes are scarce, and the mechanism allowing methanotrophy to be of comparable importance to DOC-consuming heterotrophy remained elusive. Using incubation experiments, microscopy, and multiple water column profiles in six temperate lakes, we show that MOB play a much larger role than their abundances alone suggest because of their larger cell size and higher specific activity. MOB activity is tightly constrained by the local methane:oxygen ratio, with DOC-rich lakes with large hypolimnetic volume fraction showing a higher carbon consumption through methanotrophy than heterotrophy at the whole water column level. Our findings suggest that methanotrophy could be a critical microbial carbon consumption pathway in many temperate lakes, challenging the prevailing view of a DOC-centric microbial metabolism in these ecosystems.

Seasonal dynamics of methanotrophic bacteria in a boreal oil sands end-pit lake

Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for five years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 10⁴ cells mL^-1 of water (median 0.5 × 10³) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover, and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH₄/O₂ microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH₄ and O₂. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. Importance statement: The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multi-season and multi-year dataset is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end-pit lakes, but we propose that the dynamics are typical of boreal stratified lakes, and widely applicable in microbial ecology and limnology. Methane oxidising bacteria are important model organisms in microbial ecology, and have implications for global climate change.

Synthetically engineered microbial scavengers for enhanced bioremediation

Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.

The Influence of Above-Ground Herbivory on the Response of Arctic Soil Methanotrophs to Increasing CH4 Concentrations and Temperatures

Rising temperatures in the Arctic affect soil microorganisms, herbivores, and peatland vegetation, thus directly and indirectly influencing microbial CH₄ production. It is not currently known how methanotrophs in Arctic peat respond to combined changes in temperature, CH₄ concentration, and vegetation. We studied methanotroph responses to temperature and CH₄ concentration in peat exposed to herbivory and protected by exclosures. The methanotroph activity was assessed by CH₄ oxidation rate measurements using peat soil microcosms and a pure culture of Methylobacter tundripaludum SV96, qPCR, and sequencing of pmoA transcripts. Elevated CH₄ concentrations led to higher CH₄ oxidation rates both in grazed and exclosed peat soils, but the strongest response was observed in grazed peat soils. Furthermore, the relative transcriptional activities of different methanotroph community members were affected by the CH₄ concentrations. While transcriptional responses to low CH₄ concentrations were more prevalent in grazed peat soils, responses to high CH₄ concentrations were more prevalent in exclosed peat soils. We observed no significant methanotroph responses to increasing temperatures. We conclude that methanotroph communities in these peat soils respond to changes in the CH₄ concentration depending on their previous exposure to grazing. This “conditioning” influences which strains will thrive and, therefore, determines the function of the methanotroph community.

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes

Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.

Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates

Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.

High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water

The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH₄ oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L⁻¹). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH₄. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates.

Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.

Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived, especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in clusters of orthologous groups (COG) categories L (replication, recombination and repair) and S (function unknown) were relatively high in metagenome-assembled genomes representing Methylococcales clearly thriving below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. By contrast, genes in COG category N (cell motility) were relatively high in metagenome-assembled genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.

From nature to nurture: Essence and methods to isolate robust methanotrophic bacteria

Methanotrophic bacteria are entities with innate biocatalytic potential to biofilter and oxidize methane into simpler compounds concomitantly conserving energy, which can contribute to copious industrial applications. The future and efficacy of such industrial applications relies upon acquiring and/or securing robust methanotrophs with taxonomic and phenotypic diversity. Despite several dramatic advances, isolation of robust methanotrophs is still a long-way challenging task with several lacunae to be filled in sequentially. Methanotrophs with high tolerance to methane can be isolated and cultivated by mimicking natural environs, and adopting strategies like adaptive metabolic evolution. This review summarizes existent and innovative methods for methanotrophic isolation and purification, and their respective applications. A comprehensive description of new insights shedding light upon how to isolate and concomitantly augment robust methanotrophic metabolism in an orchestrated fashion follows.