CH4 oxidation in a boreal lake during the development of hypolimnetic hypoxia

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.

The concentration of CH4, N2O and CO2 in the Pearl River estuary increased significantly due to the sediment particle resuspension and the interaction of hypoxia

Hypoxia and sediment particle resuspension (SPR) alter the biogeochemical cycle of estuarine and coastal seas, which in turn affects the production and emission of methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) greenhouse gases (GHGs) in estuaries. Despite the importance of CH4, N2O and CO2 in estuarine ecosystems, little is known about their magnitude and spatiotemporal variation under the combined influence of hypoxia and SPR. This study utilized continuous mooring observations to investigate the temporal and spatial variations of GHGs before and after hypoxia in the Pearl River Estuary (PRE). The results showed that the concentration of GHGs in the water column increased significantly following hypoxia as compared to its absence. The synergistic effect of SPR and hypoxia significantly enhances GHGs production and accumulation in bottom water. Anaerobic mineralization of organic matter (OM) in an environment with severely low dissolved oxygen (DO) is the primary determinant for increased CH4 concentration, while OM and CH4 oxidation are the main drivers for maintaining high CO2 concentration in subsurface water. Hypoxic development enhanced denitrification N2O production in the water column. The presence of SPR enhanced oxygen-consuming coupled hypoxia significantly stimulated the increase of CH4, N2O and CO2 concentrations in the water column. Hypoxic development results in an increased water-air GHGs flux, but this effect may be masked by runoff plumes with high GHGs concentrations in the regions near the river outlets. This study highlights that hypoxia leads to significant increases in anaerobic GHGs production and subsequent emissions from estuarine water columns.

Research on aerobic oxidation of methane bacteria and its influencing factors in Chongqing central city section of the Yangtze River, China

Bacterial communities play an important role in the carbon cycle of freshwater ecosystems. In order to understand the influencing factors of bacterial community in the process of carbon cycle and search for measures to reduce carbon emissions, Chongqing central city section of the Yangtze River and its tributaries were selected to be the study area in this research. High-throughput sequencing was applied to study aerobic oxidation of methane bacteria (MOB) in sampling area. The results showed that there were spatial differences in the community diversity of aerobic MOB in the Yangtze River in central Chongqing. The Shannon index in the sediment (2.389-2.728) was higher than that in the water (1.820-2.458), and the community diversity in the middle reaches of the main river was higher than that in the upstream and the downstream. The aerobic MOB community was mainly dominated by Type II (Methylocystis). Most of operational taxonomic units (OTUs) in the top ten had high homology with MOB from river and lake sediments, and a few OTUs had high homology with MOB from paddy fields, forests and wetland soils. The main environmental factors affecting the community structure of aerobic MOB were NH4+-N, dissolved oxygen (DO), temperature (T, p ≤ 0.001), pH (p ≤ 0.05), methane (CH4) and carbon dioxide (CO2).

Oxygen micro-nanobubbles for mitigating eutrophication induced sediment pollution in freshwater bodies

Sediment hypoxia is a growing problem and has negative ecological impacts on the aquatic ecosystem. Hypoxia can disturb the biodiversity and biogeochemical cycles of both phosphorus (P) and nitrogen (N) in water columns and sediments. Anthropogenic eutrophication and internal nutrient release from lakebed sediment accelerate hypoxia to form a dead zone. Thus, sediment hypoxia mitigation is necessary for ecological restoration and sustainable development. Conventional aeration practices to control sediment hypoxia, are not effective due to high cost, sediment disturbance and less sustainability. Owing to high solubility and stability, micro-nanobubbles (MNBs) offer several advantages over conventional water and wastewater treatment practices. Clay loaded oxygen micro-nanobubbles (OMNBs) can be delivered into deep water sediment by gravity and settling. Nanobubble technology provides a promising route for cost-effective oxygen delivery in large natural water systems. OMNBs also have the immense potential to manipulate biochemical pathways and microbial processes for remediating sediment pollution in natural waters. This review article aims to analyze recent trends employing OMNBs loaded materials to mitigate sediment hypoxia and subsequent pollution. The first part of the review highlights various minerals/materials used for the delivery of OMNBs into benthic sediments of freshwater bodies. Release of OMNBs at hypoxic sediment water interphase (SWI) can provide significant dissolved oxygen (DO) to remediate hypoxia induced sediment pollution Second part of the manuscript unveils the impacts of OMNBs on sediment pollutants (e.g., methylmercury, arsenic, and greenhouse gases) remediation and microbial processes for improved biogeochemical cycles. The review article will facilitate environmental engineers and ecologists to control sediment pollution along with ecological restoration.

Batch Experiments Demonstrating a Two-Stage Bacterial Process Coupling Methanotrophic and Heterotrophic Bacteria for 1-Alkene Production From Methane

Methane (CH₄) is a sustainable carbon feedstock for value-added chemical production in aerobic CH₄-oxidizing bacteria (methanotrophs). Under substrate-limited (e.g., oxygen and nitrogen) conditions, CH₄ oxidation results in the production of various short-chain organic acids and platform chemicals. These CH₄-derived products could be broadened by utilizing them as feedstocks for heterotrophic bacteria. As a proof of concept, a two-stage system for CH₄ abatement and 1-alkene production was developed in this study. Type I and Type II methanotrophs, Methylobacter tundripaludum SV96 and Methylocystis rosea SV97, respectively, were investigated in batch tests under different CH₄ and air supplementation schemes. CH₄ oxidation under either microaerobic or aerobic conditions induced the production of formate, acetate, succinate, and malate in M. tundripaludum SV96, accounting for 4.8–7.0% of consumed carbon from CH₄ (C-CH₄), while M. rosea SV97 produced the same compounds except for malate, and with lower efficiency than M. tundripaludum SV96, accounting for 0.7–1.8% of consumed C-CH₄. For the first time, this study demonstrated the use of organic acid-rich spent media of methanotrophs cultivating engineered Acinetobacter baylyi ADP1 ‘tesA-undA cells for 1-alkene production. The highest yield of 1-undecene was obtained from the spent medium of M. tundripaludum SV96 at 68.9 ± 11.6 μmol mol C_substrate^–1. However, further large-scale studies on fermenters and their optimization are required to increase the production yields of organic acids in methanotrophs.

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.

Greenhouse gas emissions from Baltic coastal lakes

Coastal lakes (CL) act as limnetic-β-oligohaline systems located on non-tidal coastlines in fresh and salt water mixing zone. Owing to considerable terrestrial nutrient input and a high autochthonous productivity CLs release greenhouse gases (GHG) to the ambient atmosphere, however, neither emission from the system was assessed nor controls on the emission were recognized so far. In this study we attempted to quantify diffusive emissions of CH₄, CO₂ and N₂O from CLs based on data collected from seven lakes located on a south coast of the Baltic Sea in Poland. Lake water samples were collected with quarterly resolution along salinity, water depth and wind fetch gradients. From our data it emerged that the concentrations of GHGs were determined by temperature. CH₄ showed dependence on salinity, lake water depth and wind fetch. N₂O was controlled by dissolved O₂ and NO₃^- and CO₂ was largely related to wind fetch. It also appeared that concentrations of N₂O and CO₂ were influenced by terrestrial nutrient input. The mean fluxes of CH₄, CO₂ and N₂O for the whole system were 21.7 mg·m^-2·d^-1, 12.7 g·m^-2·d^-1 and 0.74 mg·m^-2·d^-1, respectively which was equivalent to 7.9 g CH₄·m^-2·y^-1, 4.6 kg CO₂·m^-2·y^-1 and 269 mg N₂O·m^-2·y^-1. CH₄ and N₂O were released throughout the year and CO₂ was predominantly emitted during winter. We showed that diffusive emissions of the GHGs showed relationships to the surface area of the lakes as well as the ratio of catchment area to lake area (CA/LA). The study would benefit from further extension with higher resolution analyses of the lakes over longer timescales and quantification of ebullitive GHG emission (CH₄ in particular).

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.