Numerical modeling of methane venting from lake sediments

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2010.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (p. 91-96).The dynamics of methane transport in lake sediments control the release of methane into the water column above, and the portion that reaches the atmosphere may contribute significantly to the greenhouse effect. The observed dynamics are poorly understood. In particular, variations in the hydrostatic load on the sediments, from both water level and barometric pressure, appear to trigger free gas bubbling (ebullition). We develop a model of methane bubble ow through the sediments, forced by changes in hydrostatic load. The mechanistic, numerical model is tuned to and compared against ebullition data from Upper Mystic Lake, MA, and the predictions match the daily temporal character of the observed gas releases. We conclude that the combination of plastic gas cavity deformation and ow through "breathing" gas conduits explains methane venting from lake sediments. This research lays the groundwork for integrated modeling of methane transport in the sediment and water column to constrain the atmospheric flux from methane-generating lakes.by Benjamin P. Scandella.S.M

Ephemerality of discrete methane vents in lake sediments

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.National Science Foundation (U.S.) (1045193)United States. Department of Energy (DE-FE001399

A conduit dilation model of methane venting from lake sediments

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 38 (2011): L06408, doi:10.1029/2011GL046768.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.This work was supported by the U.S. Department of Energy (grants DE‐FC26‐06NT43067 and DE‐AI26‐05NT42496), an NSF Doctoral Dissertation Research grant (0726806), a GSA Graduate Student Research grant, and MIT Martin, Linden and Ippen fellowships

The Neurotrophic Receptor Ntrk2 Directs Lymphoid Tissue Neovascularization during Leishmania donovani Infection

The neurotrophic tyrosine kinase receptor type 2 (Ntrk2, also known as TrkB) and its ligands brain derived neurotrophic factor (Bdnf), neurotrophin-4 (NT-4/5), and neurotrophin-3 (NT-3) are known primarily for their multiple effects on neuronal differentiation and survival. Here, we provide evidence that Ntrk2 plays a role in the pathologic remodeling of the spleen that accompanies chronic infection. We show that in Leishmania donovani-infected mice, Ntrk2 is aberrantly expressed on splenic endothelial cells and that new maturing blood vessels within the white pulp are intimately associated with F4/80hiCD11bloCD11c+ macrophages that express Bdnf and NT-4/5 and have pro-angiogenic potential in vitro. Furthermore, administration of the small molecule Ntrk2 antagonist ANA-12 to infected mice significantly inhibited white pulp neovascularization but had no effect on red pulp vascular remodeling. We believe this to be the first evidence of the Ntrk2/neurotrophin pathway driving pathogen-induced vascular remodeling in lymphoid tissue. These studies highlight the therapeutic potential of modulating this pathway to inhibit pathological angiogenesis

Spatiotemporal variability of methane ebullition from lake sediments

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 130-140).Methane is a potent greenhouse gas, and natural sources to the atmosphere include inland waterways and shallow oceans. However, the magnitude of these emissions and their potential for feedbacks with climate change remain poorly constrained. In many settings the majority of atmospheric methane emissions is delivered by bubbles, and the spatiotemporal heterogeneity of ebullition makes measurement challenging and impacts bubble dissolution and atmospheric emissions. In this thesis, we present an analysis of both the episodicity and spatial structure of methane venting from soft sediments in a eutrophic lake over a range of spatial scales, from 1 cm to 20 m, and using a combination of field observations and laboratory experiments. Field-scale measurements of ebullition were acquired at the bottom of Upper Mystic Lake, MA, USA, using a high-resolution multibeam sonar during multiple deployments over a 9-month period. The sonar was calibrated to estimate the gas flow rates throughout a 330 m2 lateral observation area with resolution of 0.5 m. The results confirm that ebullition is strongly episodic, with distinct regimes of high- and low-flux largely controlled by changes in hydrostatic pressure. Statistical analysis shows that the spatial pattern of ebullition becomes homogeneous at the sonar's resolution over timescales of hours (for high-flux periods) or days (for low-flux periods), demonstrating that meter-scale methane vents are ephemeral rather than persistent. Laboratory-scale measurements were made in a controlled incubation of reconstituted sediments from the same field site. Image analysis of the 0.14 m2 observation 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 ephemerality of spatial structure at the field-scale. It suggests that, at the centimeter scale, conduits are re-used as a result of a drop in tensile strength due to deformation of sediments by the rising bubbles. By combining novel measurement techniques at different scales, we elucidate the mechanisms governing bubble growth and mobility, thereby supporting estimates of global methane fluxes from lakes and how their magnitude may vary with climate change.by Benjamin Paul Scandella.Ph. D

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake

Background Microbial 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. Results Here, 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. Conclusions This 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

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake

Abstract Background Microbial 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. Results Here, 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. Conclusions This 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