A sea-bottom sampler that collects both water and sediment simultaneously

A simple sampler, assembled mainly from commercially available eq uipment, is described. It simultaneously collects water samples at 1, 2, 3, 4, 5, and 6 m above the sea floor and takes a short core at the same location

Daily patterns of fluorescence in vivo in the central equatorial Pacific

A daily cycle of fluorescence in vivo was strikingly apparent in surface waters of the central equatorial Pacific between latitudes 4N and 10S, but not in waters to the north or south of this zone. These changes in fluorescence did not represent changes in chlorophyll-a concentration, but rather a photoinhibition of fluorescence by ambient light. Higher nutrient and chlorophyll-a concentrations were found in the region where cycling occurred...

Interdisciplinary study of warm core ring physics, chemistry, and biology

We are conducting an interdisciplinary study of the structure and dynamics of Gulf Stream \Warm Core Rings by a time series investigation of selected rings. This program consists of highly integrated components which include physical, chemical, and biological investigation and modeling studies. These components are designed to provide information on the structure of rings and exchange mechanisms at ring boundaries, on their marine chemistry, and on the environmental controls of biological activity of selected constituents associated with Warm Core Rings. This research is being conducted by approximately two dozen investigators from thirteen marine institutions. An interdisciplinary program of the scope proposed is required in order to understand the interdependence among biological, chemical, and physical processes in the ocean. This study of the structure and evolution of Warm Core Rings will enhance the understanding of fundamental oceanic processes and the role of rings in the region where they occur

A stable genetic polymorphism underpinning microbial syntrophy

Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms and they remain a topic of active investigation. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions