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1.
The Formation and Distribution of Modern Ooids on Great Bahama Bank.
Harris, PM, Diaz, MR, Eberli, GP
Annual review of marine science. 2019;:491-516
Abstract
Great Bahama Bank (GBB) is the principal location of the formation and accumulation of ooids (concentrically coated, sand-size carbonate grains) in the world today, and as such has been the focus of studies on all aspects of ooids for more than half a century. Our view from a close look at this vast body of literature coupled with our continuing interests stresses that biological mechanisms (microbially mediated organomineralization) are very important in the formation of ooids, whereas the controlling factor for the distribution and size of ooid sand bodies is the physical energy. Mapping and coring studies of the modern ooid sand bodies on GBB provide insight into the rock record from different perspectives. An important consequence of the dual influence of ooid formation and distribution is that the geochemical signature of ooids is not in equilibrium with the seawater in which ooids form; therefore, extracting the paleophysical energy record from oolitic deposits is potentially more accurate than doing so for the paleochemical record.
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Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities.
Stal, LJ, Bolhuis, H, Cretoiu, MS
Environmental microbiology. 2019;(5):1529-1551
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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3.
Sulfur metabolites in the pelagic ocean.
Moran, MA, Durham, BP
Nature reviews. Microbiology. 2019;(11):665-678
Abstract
Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.
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4.
Modelling the marine eutrophication: A review.
Ménesguen, A, Lacroix, G
The Science of the total environment. 2018;:339-354
Abstract
In the frame of a national, joint scientific appraisal, 45 scientific French-speaking experts have been mandated in 2015-2016 by the French ministries of Environment and Agriculture to perform a global review of scientific literature dealing with the eutrophication phenomenon, in freshwater as well as in marine waters. This paper summarizes the main results of this review restricted to a sub-domain, the modelling approach of the marine eutrophication. After recalling the different aims pursued, an overview is given on the historical time course of this modelling effort, its world distribution and the various tools used. Then, the main results obtained are examined, highlighting the specific strengths and weaknesses of the present models. Needs for future improvement are then listed.
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5.
Microbial ecology of deep-sea hypersaline anoxic basins.
Merlino, G, Barozzi, A, Michoud, G, Ngugi, DK, Daffonchio, D
FEMS microbiology ecology. 2018;(7)
Abstract
Deep hypersaline anoxic basins (DHABs) are unique water bodies occurring within fractures at the bottom of the sea, where the dissolution of anciently buried evaporites created dense anoxic brines that are separated by a chemocline/pycnocline from the overlying oxygenated deep-seawater column. DHABs have been described in the Gulf of Mexico, the Mediterranean Sea, the Black Sea and the Red Sea. They are characterized by prolonged historical separation of the brines from the upper water column due to lack of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization of the different taxa in the brine-seawater transition zone coupled with the metabolic interactions and niche adaptations determine the metabolic functioning and biogeochemistry of DHABs. In particular, inherent metabolic strategies accompanied by genetic adaptations have provided insights on how prokaryotic communities can adapt to salt-saturated conditions. Here, we review the current knowledge of the diversity, genomics, metabolisms and ecology of prokaryotes in DHABs.
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6.
Iron-oxidizing bacteria in marine environments: recent progresses and future directions.
Makita, H
World journal of microbiology & biotechnology. 2018;(8):110
Abstract
Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.
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7.
Vibrio vulnificus infection: a persistent threat to public health.
Yun, NR, Kim, DM
The Korean journal of internal medicine. 2018;(6):1070-1078
Abstract
Vibrio vulnificus is a gram-negative bacterium that can cause serious, potentially fatal infections. V. vulnificus causes three distinct syndromes: an overwhelming primary septicemia caused by consuming contaminated seafood, wound infections acquired when an open wound is exposed to contaminated warm seawater, and gastrointestinal tract-limited infections. Case-fatality rates are higher than 50% for primary septicemia, and death typically occurs within 72 hours of hospitalization. Risk factors for V. vulnificus infection include chronic liver disease, alcoholism, and hematological disorders. When V. vulnificus infection is suspected, appropriate antibiotic treatment and surgical interventions should be performed immediately. Third-generation cephalosporin with doxycycline, or quinolone with or without third-generation cephalosporin, may be potential treatment options for patients with V. vulnificus infection.
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8.
Patterns of deoxygenation: sensitivity to natural and anthropogenic drivers.
Oschlies, A, Duteil, O, Getzlaff, J, Koeve, W, Landolfi, A, Schmidtko, S
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 2017;(2102)
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Abstract
Observational estimates and numerical models both indicate a significant overall decline in marine oxygen levels over the past few decades. Spatial patterns of oxygen change, however, differ considerably between observed and modelled estimates. Particularly in the tropical thermocline that hosts open-ocean oxygen minimum zones, observations indicate a general oxygen decline, whereas most of the state-of-the-art models simulate increasing oxygen levels. Possible reasons for the apparent model-data discrepancies are examined. In order to attribute observed historical variations in oxygen levels, we here study mechanisms of changes in oxygen supply and consumption with sensitivity model simulations. Specifically, the role of equatorial jets, of lateral and diapycnal mixing processes, of changes in the wind-driven circulation and atmospheric nutrient supply, and of some poorly constrained biogeochemical processes are investigated. Predominantly wind-driven changes in the low-latitude oceanic ventilation are identified as a possible factor contributing to observed oxygen changes in the low-latitude thermocline during the past decades, while the potential role of biogeochemical processes remains difficult to constrain. We discuss implications for the attribution of observed oxygen changes to anthropogenic impacts and research priorities that may help to improve our mechanistic understanding of oxygen changes and the quality of projections into a changing future.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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9.
Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms.
Mapelli, F, Scoma, A, Michoud, G, Aulenta, F, Boon, N, Borin, S, Kalogerakis, N, Daffonchio, D
Trends in biotechnology. 2017;(9):860-870
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Abstract
The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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10.
Microorganisms and ocean global change.
Hutchins, DA, Fu, F
Nature microbiology. 2017;:17058
Abstract
The prokaryotic and eukaryotic microorganisms that drive the pelagic ocean's biogeochemical cycles are currently facing an unprecedented set of comprehensive anthropogenic changes. Nearly every important control on marine microbial physiology is currently in flux, including seawater pH, pCO2, temperature, redox chemistry, irradiance and nutrient availability. Here, we examine how microorganisms with key roles in the ocean carbon and nitrogen cycles may respond to these changes in the Earth's largest ecosystem. Some functional groups such as nitrogen-fixing cyanobacteria and denitrifiers may be net beneficiaries of these changes, while others such as calcifiers and nitrifiers may be negatively impacted. Other groups, such as heterotrophic bacteria, may be relatively resilient to changing conditions. The challenge for marine microbiologists will be to predict how these divergent future responses of marine microorganisms to complex multiple variable interactions will be expressed through changing biogeography, community structure and adaptive evolution, and ultimately through large-scale alterations of the ocean's carbon and nutrient cycles.