Stable aerobic and anaerobic coexistence in anoxic marine zones

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zakem, E. J., Mahadevan, A., Lauderdale, J. M., & Follows, M. J. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME Journal, 14, (2019): 288–301, doi: 10.1038/s41396-019-0523-8.Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.We are grateful for the thorough and thoughtful comments of two anonymous reviewers. We also thank Andrew Babbin for helpful comments. EJZ was supported by the Simons Foundation (Postdoctoral Fellowship in Marine Microbial Ecology). AM was supported by the Office of Naval Research (ONR #N000-14-15-1-2555). JML was supported by U.S. National Science Foundation (NSF #OCE-1259388). MJF was supported by the Gordon and Betty Moore Foundation (GBMF #3778) and the Simons Foundation: the Simons Collaboration on Ocean Processes and Ecology (SCOPE #329108) and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES #549931)

A unified theory for organic matter accumulation

Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. Our framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millennial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates

Fiducial Markers Allow Accurate and Reproducible Delivery of Liver Stereotactic Body Radiation Therapy

Fiducial markers are utilized for image guided radiotherapy (IGRT) alignment during the delivery of liver stereotactic body radiosurgery (SBRT). There are limited data demonstrating the impact of matching fiducials on the accuracy of liver SBRT. This study quantifies the benefit of fiducial-based alignment and improvements in inter-observer reliability. Nineteen patients with 24 liver lesions were treated with SBRT. Target localization was performed using fiducial markers on cone-beam computed tomography (CBCT). Each CBCT procedure was retrospectively realigned to match both the liver edge and fiducial markers. The shifts were recorded by seven independent observers. Inter-observer variability was analyzed by calculating the mean error and uncertainty for the set-up. The mean absolute Cartesian error observed from fiducial and liver edge-based alignment was 1.5 mm and 5.3 mm, respectively. The mean uncertainty from fiducial and liver edge-based alignment was 1.8 mm and 4.5 mm, respectively. An error of 5 mm or greater was observed 50% of the time when aligning to the liver surface versus 5% of the time when aligning to fiducial markers. Aligning to the liver edge significantly increased the error, resulting in increased shifts when compared to alignment to fiducials. Tumors of 3 cm or farther from the liver dome had higher mean errors when aligned without fiducials (4.8 cm vs. 4.4 cm, p = 0.003). Our data support the use of fiducial markers for safer and more accurate liver SBRT

A Flux‐Based Threshold for Anaerobic Activity in the Ocean

Anaerobic microbial activity in the ocean causes losses of bioavailable nitrogen and emission of nitrous oxide to the atmosphere, but its predictability at global scales remains limited. Resource ratio theory suggests that anaerobic activity becomes sustainable when the ratio of oxygen to organic matter supply is below the ratio required by aerobic metabolisms. Here, we demonstrate the relevance of this framework at the global scale using three-dimensional ocean datasets, providing a new interpretation of existing observations. Evaluations of the location and extent of anoxic zones and a diagnostic rate of pelagic nitrogen loss are consistent with previous estimates. However, we demonstrate that a threshold based on substrate-supply fluxes is qualitatively different from a threshold based solely on the ambient oxygen concentration. This implies that use of the flux-based threshold in global biogeochemical models can result in different predictions of anaerobic activity and nitrogen loss

Redox-informed models of global biogeochemical cycles

Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments. “Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things.” –Georgia O’Keef