Methane is a potent greenhouse gas, but its effects on Earth's climate remain poorly constrained, in part due to uncertainties in global methane fluxes to the atmosphere. An important source of atmospheric methane is the methane generated in organic‐rich sediments underlying surface water bodies, including lakes, wetlands, and the ocean. The fraction of the methane that reaches the atmosphere depends critically on the mode and spatiotemporal characteristics of free‐gas venting from the underlying sediments. Here we propose that methane transport in lake sediments is controlled by dynamic conduits, which dilate and release gas as the falling hydrostatic pressure reduces the effective stress below the tensile strength of the sediments. We test our model against a four‐month record of hydrostatic load and methane flux in Upper Mystic Lake, Mass., USA, and show that it captures the complex episodicity of methane ebullition. Our quantitative conceptualization opens the door to integrated modeling of methane transport to constrain global methane release from lakes and other shallow‐water, organic‐rich sediment systems, and to assess its climate feedbacks.

Methane is a potent greenhouse gas whose emission from sediments in inland waters and shallow oceans may both contribute to global warming and be exacerbated by it. The fraction of methane emitted by sediments that bypasses dissolution in the water column and reaches the atmosphere as bubbles depends on the mode and spatiotemporal characteristics of venting from the sediments. Earlier studies have concluded that hot spots—persistent, high‐flux vents—dominate the regional ebullitive flux from submerged sediments. Here the spatial structure, persistence, and variability in the intensity of methane venting are analyzed using a high‐resolution multibeam sonar record acquired at the bottom of a lake during multiple deployments over a 9 month period. We confirm that ebullition is strongly episodic, with distinct regimes of high flux and low flux largely controlled by changes in hydrostatic pressure. Our analysis shows that the spatial pattern of ebullition becomes homogeneous at the sonar's resolution over time scales of hours (for high‐flux periods) or days (for low‐flux periods), demonstrating that vents are ephemeral rather than persistent, and suggesting that long‐term, lake‐wide ebullition dynamics may be modeled without resolving the fine‐scale spatial structure of venting.

Sediments submerged beneath many inland waterways and shallow oceans emit methane, a potent greenhouse gas, but the magnitude of the methane flux to the atmosphere remains poorly constrained. In many settings, the majority of methane is released through bubbling, and the spatiotemporal heterogeneity of this ebullition both presents challenges for measurement and impacts bubble dissolution and atmospheric emissions. Here we present laboratory‐scale experiments of methane ebullition in a controlled incubation of reconstituted sediments from a eutrophic lake. Image analysis of a 0.14 m2 sediment surface area allowed identification of individual bubble outlets and resolved their location to ∼1 cm. While ebullition events were typically concentrated in bursts lasting ∼2 min, some major outlets showed persistent activity over the scale of days and even months. This persistence was surprising given the previously observed ephemerality of spatial structure at the field scale. This persistence suggests that, at the centimeter scale, conduits are reopened as a result of a drop in tensile strength due to deformation of sediments by the rising bubbles. The mechanistic insight from this work sheds light on the spatiotemporal distribution of methane venting from organic‐rich sediments and has important implications for bubble survival in the water column and associated biogeochemical pathways of methane.

BackgroundMicrobial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass decomposition, degrading the habitat of many economically important aquatic animals. Microbes then turn to alternative electron acceptors, which alter nutrient cycling and generate potent greenhouse gases. As oxygen depletion is expected to worsen with altered land use and climate change, understanding how chemical and microbial dynamics impact dead zones will aid modeling efforts to guide remediation strategies. More work is needed to understand the complex interplay between microbial genes, populations, and biogeochemistry during oxygen depletion.ResultsHere, we used 16S rRNA gene surveys, shotgun metagenomic sequencing, and a previously developed biogeochemical model to identify genes and microbial populations implicated in major biogeochemical transformations in a model lake ecosystem. Shotgun metagenomic sequencing was done for one time point in Aug., 2013, and 16S rRNA gene sequencing was done for a 5-month time series (Mar.–Aug., 2013) to capture the spatiotemporal dynamics of genes and microorganisms mediating the modeled processes. Metagenomic binning analysis resulted in many metagenome-assembled genomes (MAGs) that are implicated in the modeled processes through gene content similarity to cultured organism and the presence of key genes involved in these pathways. The MAGs suggested some populations are capable of methane and sulfide oxidation coupled to nitrate reduction. Using the model, we observe that modulating these processes has a substantial impact on overall lake biogeochemistry. Additionally, 16S rRNA gene sequences from the metagenomic and amplicon libraries were linked to processes through the MAGs. We compared the dynamics of microbial populations in the water column to the model predictions. Many microbial populations involved in primary carbon oxidation had dynamics similar to the model, while those associated with secondary oxidation processes deviated substantially.ConclusionsThis work demonstrates that the unique capabilities of resident microbial populations will substantially impact the concentration and speciation of chemicals in the water column, unless other microbial processes adjust to compensate for these differences. It further highlights the importance of the biological aspects of biogeochemical processes, such as fluctuations in microbial population dynamics. Integrating gene and population dynamics into biogeochemical models has the potential to improve predictions of the community response under altered scenarios to guide remediation efforts.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0556-7) contains supplementary material, which is available to authorized users.

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