Integrating functional diversity, food web processes, and biogeochemical carbon fluxes into a conceptual approach for modeling the upper ocean in a high-CO2 world

Marine food webs influence climate by channeling carbon below the permanent pycnocline, where it can be sequestered. Because most of the organic matter exported from the euphotic zone is remineralized within the "upper ocean" (i.e., the water column above the depth of sequestration), the resulting CO2 would potentially return to the atmosphere on decadal timescales. Thus ocean-climate models must consider the cycling of carbon within and from the upper ocean down to the depth of sequestration, instead of only to the base of the euphotic zone. Climate-related changes in the upper ocean will influence the diversity and functioning of plankton functional types. In order to predict the interactions between the changing climate and the ocean's biology, relevant models must take into account the roles of functional biodiversity and pelagic ecosystem functioning in determining the biogeochemical fluxes of carbon. We propose the development of a class of models that consider the interactions, in the upper ocean, of functional types of plankton organisms (e.g., phytoplankton, heterotrophic bacteria, microzooplankton, large zooplankton, and microphagous macrozooplankton), food web processes that affect organic matter (e.g., synthesis, transformation, and remineralization), and biogeochemical carbon fluxes (e.g., photosynthesis, calcification, respiration, and deep transfer). Herein we develop a framework for this class of models, and we use it to make preliminary predictions for the upper ocean in a high-CO2 world, without and with iron fertilization. Finally, we suggest a general approach for implementing our proposed class of models

Growth responses of Ulva prolifera to inorganic and organic nutrients: Implications for macroalgal blooms in the southern Yellow Sea, China

International audienceThe marine macrophyte Ulva prolifera is the dominant green-tide-forming seaweed in the southern Yellow Sea, China. Here we assessed, in the laboratory, the growth rate and nutrient uptake responses of U. prolifera to different nutrient treatments. The growth rates were enhanced in incubations with added organic and inorganic nitrogen [i.e. nitrate (NO3−), ammonium (NH4+), urea and glycine] and phosphorus [i.e. phosphate (PO43−), adenosine triphosphate (ATP) and glucose 6-phosphate (G-6-P)], relative to the control. The relative growth rates of U. prolifera were higher when enriched with dissolved organic nitrogen (urea and glycine) and phosphorus (ATP and G-6-P) than inorganic nitrogen (NO3− and NH4+) and phosphorus (PO43−). In contrast, the affinity was higher for inorganic than organic nutrients. Field data in the southern Yellow Sea showed significant inverse correlations between macroalgal biomass and dissolved organic nutrients. Our laboratory and field results indicated that organic nutrients such as urea, glycine and ATP, may contribute to the development of macroalgal blooms in the southern Yellow Sea

Nutrient and phytoplankton responses to external forcing in a Mediterranean coastal area unbiased by terrestrial inputs and local activities (Calvi, Corsica)

Despite its relative oligotrophy, the northwestern Mediterranean exhibits rich biodiversity and traditional fishing that are fueled by phytoplankton at the basis of the food web. However, long-term observations of phytoplankton biomass reveal high interannual variability controlled by mechanisms that are still poorly understood, but have implications for the way we study and manage coastal zones in a changing world. Here we present a synthesis of a long-term high-resolution study of nutrient and phytoplankton bloom dynamics performed between 1979 and 2011 at a permanent station in the Bay of Calvi (Corsica, northwestern Mediterranean). The ecosystem of the Bay is known to be very sensitive to climate forcing but preserved from local anthropogenic stressors. As a distinctive feature of the area, the winter-spring phytoplankton bloom of the Bay of Calvi is characterized by a very large interannual variability reaching one order of magnitude from one year to another. In order to understand mechanisms controlling this variability, we defined a winter intensity index (WII) that integrates wind stress intensity and water temperature. WII does not evidence any trend over the 1979-2011 period but is closely correlated to nutrient delivery from deep waters and to phytoplankton production. We synthesize our current understanding of phytoplankton response to the combination of external forcings and discuss the impact of expected environmental changes on the pelagic food web in a region that is predicted to be particularly sensitive to long-term changes driven by human activities

Evolving paradigms in biological carbon cycling in the ocean

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g., CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced “omics”, and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean’s response to climate change makes an integrative understanding of the MCP, BCP and ML a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future

The Dual of the Least-Squares Method

The least-squares method was firmly established as a scientific approach by Gauss, Legendre and Laplace within the space of a decade, at the beginning of the nineteenth century.  Legendre was the first author to name the approach, in 1805, as "méthode des moindres carrés," a "least-squares method."  Gauss, however, is credited to have used it as early as 1795, when he was 18 years old.  He, subsequently, adopted it in 1801 to calculate the orbit of the newly discovered planet Ceres.  Gauss published his way of looking at the least-squares approach in 1809 and gave several hints that the least-squares algorithm was a minimum variance linear estimator and that it was derivable from maximum likelihood considerations.  Laplace wrote a very substantial chapter about the method in his fundamental treatise on probability theory published in 1812.  Surprisingly, there still remains an unexplored aspect of the least-squares method: since the traditional formulation is stated as minimizing the sum of squared deviations subject to the linear (or nonlinear) specification of a regression model, this mathematical programming problem must have a dual counterpart.  This note fills this gap and shows that the least-squares estimates of unknown parameters and deviations can be obtained by maximizing the net value of sample information.

First record of a freshwater cave sponge (Porifera, unknown gen. and sp.) in a cave inhabited by Astyanax cavefish in the Sierra de El Abra, San Luis Potosí, Mexico

The karstic cave, la Cueva de Los Sabinos, located in the Sierra de El Abra in the state of San Luis Potosí, Mexico, is mostly known for hosting a population of blind, depigmented Astyanax mexicanus cavefish. Herein, we report the discovery of a non-pigmented sponge (Porifera) in the final sump of this cave. No genus or species name could be attributed because we did not collect any specimen. Up to now, the sponge distribution seems restricted to a single pool in la Cueva de Los Sabinos, but further careful exploration of other pools of the cave as well as closely related cavities is warranted. To our knowledge, this observation constitutes the fourth report of a freshwater, white, cave-adapted sponge in the world and the first for Mexico and North America. It is also the eleventh troglobite species encountered in Los Sabinos. Our discovery confirms the exceptionally rich biodiversity of this cave ecosystem

Vertical distribution of pH in the top ~10 m of deep-ocean sediments: Analysis of a unique dataset

We analyze, for the first time in the oceanographic literature, pH over the top ~10 m of the sediment (down to 11.9 m) in a deep-sea environment, together with the oxidation/reduction potential and concentrations of solid organic carbon (OC) and CaCO3. A total of 1157 sediment cores were collected from years 2000 to 2011 over >300,000 km2 in the South China Sea, at water depths up to 3702 m. We found that there were marked downward pH increases in the upper 2 m of the sediment (first 20-40 ka, corresponding to the geochemically active period). In deeper, older sediment (up to 200 ka), pH was generally less variable with depth but not uniform, and solid OC may have been consumed down to ≥10 m depth. This reflected interactions between in situ geochemical diagenetic processes, which tended to create vertical variations, and vertical diffusion of ions, which tended to even out vertical variability. In other words, there were slow diagenetic geochemical processes in the sediment layer below 2 m, and the effects of these in situ processes were partly offset by vertical diffusion. Overall, our study identified a previously unknown consistent pH difference between the upper 2 m of the sediment and the underlying layer down to ≥10 m, and suggested combinations of geochemical diagenetic processes and vertical diffusion of ions in the porewater to explain it. These results provide a framework for further studies of pH in the top multi-meter layer of the sediment in the World Ocean

Estimates of Water-Column Nutrient Concentrations and Carbonate System Parameters in the Global Ocean: A Novel Approach Based on Neural Networks

A neural network-based method (CANYON: CArbonate system and Nutrients concentration from hYdrological properties and Oxygen using a Neural-network) was developed to estimate water-column (i.e., from surface to 8,000 m depth) biogeochemically relevant variables in the Global Ocean. These are the concentrations of three nutrients [nitrate (NO3−), phosphate (PO43−), and silicate (Si(OH)4)] and four carbonate system parameters [total alkalinity (AT), dissolved inorganic carbon (CT), pH (pHT), and partial pressure of CO2 (pCO2)], which are estimated from concurrent in situ measurements of temperature, salinity, hydrostatic pressure, and oxygen (O2) together with sampling latitude, longitude, and date. Seven neural-networks were developed using the GLODAPv2 database, which is largely representative of the diversity of open-ocean conditions, hence making CANYON potentially applicable to most oceanic environments. For each variable, CANYON was trained using 80 % randomly chosen data from the whole database (after eight 10° × 10° zones removed providing an “independent data-set” for additional validation), the remaining 20 % data were used for the neural-network test of validation. Overall, CANYON retrieved the variables with high accuracies (RMSE): 1.04 μmol kg−1 (NO3−), 0.074 μmol kg−1 (PO43−), 3.2 μmol kg−1 (Si(OH)4), 0.020 (pHT), 9 μmol kg−1 (AT), 11 μmol kg−1 (CT) and 7.6 % (pCO2) (30 μatm at 400 μatm). This was confirmed for the eight independent zones not included in the training process. CANYON was also applied to the Hawaiian Time Series site to produce a 22 years long simulated time series for the above seven variables. Comparison of modeled and measured data was also very satisfactory (RMSE in the order of magnitude of RMSE from validation test). CANYON is thus a promising method to derive distributions of key biogeochemical variables. It could be used for a variety of global and regional applications ranging from data quality control to the production of datasets of variables required for initialization and validation of biogeochemical models that are difficult to obtain. In particular, combining the increased coverage of the global Biogeochemical-Argo program, where O2 is one of the core variables now very accurately measured, with the CANYON approach offers the fascinating perspective of obtaining large-scale estimates of key biogeochemical variables with unprecedented spatial and temporal resolutions. The Matlab and R codes of the proposed algorithms are provided as Supplementary Material

Bile acids destabilise HIF-1a and promote anti-tumour phenotypes in cancer cell models.

BACKGROUND: The role of the microbiome has become synonymous with human health and disease. Bile acids, as essential components of the microbiome, have gained sustained credibility as potential modulators of cancer progression in several disease models. At physiological concentrations, bile acids appear to influence cancer phenotypes, although conflicting data surrounds their precise physiological mechanism of action. Previously, we demonstrated bile acids destabilised the HIF-1a subunit of the Hypoxic-Inducible Factor-1 (HIF-1) transcription factor. HIF-1 overexpression is an early biomarker of tumour metastasis and is associated with tumour resistance to conventional therapies, and poor prognosis in a range of different cancers. METHODS: Here we investigated the effects of bile acids on the cancer growth and migratory potential of cell lines where HIF-1a is known to be active under hypoxic conditions. HIF-1a status was investigated in A-549 lung, DU-145 prostate and MCF-7 breast cancer cell lines exposed to bile acids (CDCA and DCA). Cell adhesion, invasion, migration was assessed in DU-145 cells while clonogenic growth was assessed in all cell lines. RESULTS: Intracellular HIF-1a was destabilised in the presence of bile acids in all cell lines tested. Bile acids were not cytotoxic but exhibited greatly reduced clonogenic potential in two out of three cell lines. In the migratory prostate cancer cell line DU-145, bile acids impaired cell adhesion, migration and invasion. CDCA and DCA destabilised HIF-1a in all cells and significantly suppressed key cancer progression associated phenotypes; clonogenic growth, invasion and migration in DU-145 cells. CONCLUSIONS: These findings suggest previously unobserved roles for bile acids as physiologically relevant molecules targeting hypoxic tumour progression

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island

10.3389/fmicb.2017.00197Frontiers in Microbiology8FEB19