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)

Carbon isotope budget indicates biological disequilibrium dominated ocean carbon storage at the Last Glacial Maximum.

Understanding the causes of the  ~90 ppmv atmospheric CO2 swings between glacial and interglacial climates is an important open challenge in paleoclimate research. Although the regularity of the glacial-interglacial cycles hints at a single driving mechanism, Earth System models require many independent physical and biological processes to explain the full observed CO2 signal. Here we show that biologically sequestered carbon in the ocean can explain an atmospheric CO2 change of 75 ± 40 ppmv, based on a mass balance calculation using published carbon isotopic measurements. An analysis of the carbon isotopic signatures of different water masses indicates similar regenerated carbon inventories at the Last Glacial Maximum and during the Holocene, requiring that the change in carbon storage was dominated by disequilibrium. We attribute the inferred change in carbon disequilibrium to expansion of sea-ice or change in the overturning circulation

Quantifying the drivers of ocean-atmosphere CO2 fluxes

A mechanistic framework for quantitatively mapping the regional drivers of air-sea CO2 fluxes at a global scale is developed. The framework evaluates the interplay between (1) surface heat and freshwater fluxes that influence the potential saturated carbon concentration, which depends on changes in sea surface temperature, salinity and alkalinity, (2) a residual, disequilibrium flux influenced by upwelling and entrainment of remineralized carbon- and nutrient-rich waters from the ocean interior, as well as rapid subduction of surface waters, (3) carbon uptake and export by biological activity as both soft tissue and carbonate, and (4) the effect on surface carbon concentrations due to freshwater precipitation or evaporation. In a steady state simulation of a coarse-resolution ocean circulation and biogeochemistry model, the sum of the individually determined components is close to the known total flux of the simulation. The leading order balance, identified in different dynamical regimes, is between the CO2 fluxes driven by surface heat fluxes and a combination of biologically driven carbon uptake and disequilibrium-driven carbon outgassing. The framework is still able to reconstruct simulated fluxes when evaluated using monthly averaged data and takes a form that can be applied consistently in models of different complexity and observations of the ocean. In this way, the framework may reveal differences in the balance of drivers acting across an ensemble of climate model simulations or be applied to an analysis and interpretation of the observed, real-world air-sea flux of CO2

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei

IL-24 Inhibits lung cancer cell migration and invasion by disrupting the SDF-1/CXCR4 signaling axis

© 2015 Panneerselvam et al. Background The stromal cell derived factor (SDF)-1/chemokine receptor (CXCR)-4 signaling pathway plays a key role in lung cancer metastasis and is molecular target for therapy. In the present study we investigated whether interleukin (IL)-24 can inhibit the SDF-1/CXCR4 axis and suppress lung cancer cell migration and invasion in vitro. Further, the efficacy of IL-24 in combination with CXCR4 antagonists was investigated. Methods Human H1299, A549, H460 and HCC827 lung cancer cell lines were used in the present study. The H1299 lung cancer cell line was stably transfected with doxycycline-inducible plasmid expression vector carrying the human IL-24 cDNA and used in the present study to determine the inhibitory effects of IL-24 on SDF-1/CXCR4 axis. H1299 and A549 cell lines w ere used in transient transfection studies. The inhibitory effects of IL-24 on SDF1/CXCR4 and its downstream targets were analyzed by quantitative RT-PCR, western blot, luciferase reporter assay, flow cytometry and immunocytochemistry. Functional studies included cell migration and invasion assays. Principal Findings Endogenous CXCR4 protein expression levels varied among the four human lung cancer cell lines. Doxycycline-induced IL-24 expression in the H1299-IL24 cell line resulted in reduced CXCR4 mRNA and protein expression. IL-24 post-transcriptionally regulated CXCR4 mRNA expression by decreasing the half-life of CXCR4 mRNA ( > 40%). Functional studies showed IL-24 inhibited tumor cell migration and invasion concomitant with reduction in CXCR4 and its downstream targets (pAKTS 473 , pmTORS 2448 , pPRAS40 T246 and HIF-1α). Additionally, IL-24 inhibited tumor cell migration both in the presence and absence of the CXCR4 agonist, SDF-1. Finally, IL-24 when combined with CXCR4 inhibitors (AMD3100, SJA5) or with CXCR4 siRNA demonstrated enhanced inhibitory activity on tumor cell migration. Conclusions IL-24 disrupts the SDF-1/CXCR4 signaling pathway and inhibits lung tumor cell migration and invasion. Additionally, IL-24, when combined with CXCR4 inhibitors exhibited enhanced anti-metastatic activity and is an attractive therapeutic strategy for lung metastasi

On the role of the Southern Ocean in the global carbon cycle and atmospheric CO2 change

Uncertainty about the causes of glacial-interglacial CO2 variations demonstrates our incomplete grasp of fundamental processes that govern our climate and thus one of the foremost problems in palaeoceanography and Earth System Science regards the mechanism(s) responsible for natural changes in atmospheric CO2 concentration. It is becoming clear that the Southern Ocean overturning circulation plays an important role in the global carbon cycle because altered communication between the atmosphere and abyss in the Southern Ocean is relatively well documented and often implicated in explanations of past and future climate changes, but the ambiguity of the paleoceanographic record defies interpretation of the mechanisms involved.Using a coarse resolution ocean general circulation model and coupled biogeochemistry code, an ensemble of idealised perturbations to external forcing and internal physics of the Southern Ocean is examined to explain the processes that link ocean circulation, nutrient distributions and biological productivity, and determine the extent to which the Southern Ocean governs the partitioning of CO2. Strengthened or northward-shifted winds result in oceanic outgassing and increased atmospheric carbon dioxide levels, while weakened or southward-shifted winds cause oceanic carbon uptake and reduced atmospheric carbon dioxide concentration. Driven by the work done on the ocean by the winds, changes in the rate or spatial pattern of the Southern Ocean residual overturning circulation lead to alteration of upper ocean stratification and the rate and depth from which carbon and nutrient-rich deep waters are upwelled to the surface. These surface waters, imprinted with the pattern of air-sea gas exchange, are subducted to intermediate depths in the ocean interior, not the abyss as previous suggested.These results are robust to significant alterations to surface heat and freshwater boundary conditions, mesoscale eddy activity and rates of air-sea gas exchange and represent a significant proportion of the change in glacial-interglacial CO2 that can be currently generated by altered ocean circulation in a variety of models, revealing that the upper limb of the Southern Ocean overturning circulation is important in determining atmospheric CO2 levels

On the role of the Southern Ocean in the global carbon cycle and atmospheric CO2 change

Uncertainty about the causes of glacial-interglacial CO2 variations demonstrates our incomplete grasp of fundamental processes that govern our climate and thus one of the foremost problems in palaeoceanography and Earth System Science regards the mechanism(s) responsible for natural changes in atmospheric CO2 concentration. It is becoming clear that the Southern Ocean overturning circulation plays an important role in the global carbon cycle because altered communication between the atmosphere and abyss in the Southern Ocean is relatively well documented and often implicated in explanations of past and future climate changes, but the ambiguity of the paleoceanographic record defies interpretation of the mechanisms involved. Using a coarse resolution ocean general circulation model and coupled biogeochemistry code, an ensemble of idealised perturbations to external forcing and internal physics of the Southern Ocean is examined to explain the processes that link ocean circulation, nutrient distributions and biological productivity, and determine the extent to which the Southern Ocean governs the partitioning of CO2. Strengthened or northward-shifted winds result in oceanic outgassing and increased atmospheric carbon dioxide levels, while weakened or southward-shifted winds cause oceanic carbon uptake and reduced atmospheric carbon dioxide concentration. Driven by the work done on the ocean by the winds, changes in the rate or spatial pattern of the Southern Ocean residual overturning circulation lead to alteration of upper ocean stratification and the rate and depth from which carbon and nutrient-rich deep waters are upwelled to the surface. These surface waters, imprinted with the pattern of air-sea gas exchange, are subducted to intermediate depths in the ocean interior, not the abyss as previous suggested. These results are robust to significant alterations to surface heat and freshwater boundary conditions, mesoscale eddy activity and rates of air-sea gas exchange and represent a significant proportion of the change in glacial-interglacial CO2 that can be currently generated by altered ocean circulation in a variety of models, revealing that the upper limb of the Southern Ocean overturning circulation is important in determining atmospheric CO2 levels.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Impact of Remineralization Profile Shape on the Air‐Sea Carbon Balance

The ocean's “biological pump” significantly modulates atmospheric carbon dioxide levels. However, the complexity and variability of processes involved introduces uncertainty in interpretation of transient observations and future climate projections. Much research has focused on “parametric uncertainty,” particularly determining the exponent(s) of a power‐law relationship of sinking particle flux with depth. Varying this relationship's functional form introduces additional “structural uncertainty.” We use an ocean biogeochemistry model substituting six alternative remineralization profiles fit to a reference power‐law curve, to systematically characterize structural uncertainty, which, in atmospheric pCO₂ terms, is roughly 50% of parametric uncertainty associated with varying the power‐law exponent within its plausible global range, and similar to uncertainty associated with regional variation in power‐law exponents. The substantial contribution of structural uncertainty to total uncertainty highlights the need to improve characterization of biological pump processes, and compare the performance of different profiles within Earth System Models to obtain better constrained climate projections.US National Science Foundation (Dust PIRE 1545859

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