Coastal environments have long been recognized as significant sources of methane, a potent greenhouse gas that substantially contributes to global warming. Recent research has uncovered new insights into the biological processes driving methane emissions from these regions, revealing the pivotal role of a group of microorganisms called aerotolerant methanogens. These methanogens utilize metabolites derived from seaweed and seagrass, fundamentally reshaping our understanding of methane dynamics in coastal sediments.
Methane production in marine sediments is traditionally associated with strictly anaerobic archaea, which generate methane under oxygen-depleted conditions. However, this dogma is challenged in the latest studies, demonstrating that certain methanogens not only tolerate oxygen but may actively thrive in the oxygen-variable environments characteristic of coastal sands laden with decomposing macrophytes. This discovery diverges from conventional models, proposing that these aerotolerant methanogens exploit a unique niche enriched with organic compounds sourced from decaying seaweed and seagrass.
To investigate this phenomenon, fieldwork was meticulously carried out across diverse sites in Australia and Denmark, each selected for differing levels of macrophyte accumulation. Researchers collected sediment and seawater samples from locations including Werribee, St Kilda, Shoreham, and Avernakø, employing careful methodologies designed to preserve dissolved gases and prevent contamination. These in situ measurements aimed to capture dissolved methane concentrations through precise gas chromatography approaches, complemented by comprehensive sediment analyses that detailed grain size distributions and oxygen profiles at varying depths.
Particularly innovative was the use of flow-through reactors (FTRs), which simulated natural sediment environments under controlled laboratory conditions. These reactors were charged with homogenized sandy sediments and seawater, alongside macrophyte extracts prepared from locally sourced mixed seaweeds and seagrasses. By adjusting oxygen levels and macrophyte metabolite concentrations within the FTRs, the team was able to delineate the relationship between methane production and organic substrate availability, as well as the influence of oxygen exposure on methanogenic activity.
Analytical techniques extended beyond gas measurements; metabolomic profiling via liquid chromatography–mass spectrometry (LC–MS) identified and quantified methylated compounds, including trimethylamine and dimethylsulfoniopropionate, shed from decomposing macrophytes. Understanding these metabolites was crucial because they serve as substrates fueling the pathways of methane generation in methanogenic archaea. The metabolomic insights thus provided a molecular basis linking macrophyte breakdown to methanogen metabolism.
Genomic and metagenomic analyses played a central role in characterizing the methanogenic communities inhabiting the sediments. Using state-of-the-art sequencing technologies, the researchers extracted and sequenced DNA from sediment samples and cultures enriched for methanogens. Genome assembly and annotation revealed genes encoding key enzymes in methane cycling, such as methyl coenzyme M reductase (mcrA), signifying active methanogenesis. Notably, the presence of genes indicative of aerobic tolerance suggested unique adaptations that permit survival and metabolism in oxygen-penetrated sediment layers.
Crucially, the isolation of two methanogen strains from sediments highly impacted by macrophyte inputs highlighted the taxa responsible for methane production in these environments. These strains, designated DA (from Denmark) and SH (from Australia), were cultivated in media supplemented with trimethylamine and subjected to oxygen pulse experiments. Results demonstrated that despite exposure to oxygen, these strains maintained methane production capabilities, confirming their aerotolerant nature and challenging prior assumptions that oxygen presence inhibits methanogenesis.
Methane flux rates calculated from environmental data and laboratory experiments suggested that coastal sands with substantial macrophyte accumulation can emit methane at rates significantly higher than previously estimated. The formulae utilized incorporated wind speed, gas solubility, and concentration gradients, reflecting realistic dispersal conditions. Moreover, flux normalization based on reactor production rates projected maximum methane emission potentials that position these coastal systems as underestimated contributors to atmospheric methane loads.
The implications of these findings are profound for understanding global methane budgets and climate change feedbacks. Coastal sediments, particularly those influenced by seaweed and seagrass decay, may act as hot spots for methane emissions mediated by resilient methanogens capable of anaerobic metabolism in otherwise oxic conditions. This biogeochemical process underscores the complexity of coastal methane sources and emphasizes the necessity to include macrophyte-derived substrates and oxygen-tolerant methanogens in predictive climate models.
Furthermore, the research establishes connections between methane production pathways and specific biochemical substrates, such as methylphosphonate degradation. Experiments adding methylphosphonate and other compounds to sediment slurries provided evidence that this pathway contributes to overall methane output, expanding the recognized metabolic versatility of coastal methanogen assemblages. The biodegradation of such organophosphorus compounds may thus represent a previously underappreciated mechanism driving coastal methane emissions.
Technological advancements in oxygen sensing and chemical analyses facilitated the accurate depiction of oxygen gradients and methane dynamics within sediment microenvironments. Miniature oxygen loggers buried at stratified depths discerned the fluctuating oxygen availability, while flow-through sensors monitored real-time oxygen and pH changes within reactors. These high-resolution measurements support the concept of dynamic, microoxic zones fostering methanogenic activity within sandy sediments exposed to wave and wind-driven mixing.
Sediment characterization itself revealed varied grain size distributions influencing permeability and substrate transport, essential parameters for modeling methane production and emission. By integrating these physical and chemical sediment properties with microbial and biochemical data, the study presents a holistic framework describing the interplay of environmental and biological factors controlling methane fluxes in coastal settings.
In sum, this groundbreaking investigation redefines the ecological niches of methanogens in coastal sands, demonstrating their capability to metabolize methylated compounds from macrophyte decay under oxygenated conditions. The findings challenge the traditional binary view of methane production restricted to strictly anaerobic zones, highlighting an adaptive microbial strategy that sustains methane emissions in fluctuating redox environments. This nuanced understanding promises to refine global methane emission estimates and inform mitigation strategies targeting coastal greenhouse gas sources.
As coastal ecosystems face increasing anthropogenic pressures and climate change impacts, comprehending the microbial underpinnings of methane emissions becomes imperative. The interplay among macrophyte litter, sediment chemistry, microbial community structure, and environmental dynamics manifests in elevated methane release, potentially accelerating climate feedback loops. Future research aimed at quantifying these interactions at broader spatial and temporal scales will be critical for developing comprehensive greenhouse gas inventories and fostering sustainable coastal management.
Subject of Research: Methane emissions in coastal sediments driven by aerotolerant methanogens metabolizing seaweed and seagrass-derived compounds.
Article Title: Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites.
Article References:
Hall, N., Wong, W.W., Lappan, R. et al. Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites. Nat. Geosci. (2025). https://doi.org/10.1038/s41561-025-01768-3
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