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Microbial Diversity in the Indian Ocean Sediments: An Insight into the Distribution and Associated Factors.
Ambati, M, Kumar, MS
Current microbiology. 2022;(4):115
Abstract
Indian Ocean is the third largest oceanic division of the world and shelter to a huge microbial diversity. These microbes play an important role in the metabolism of carbon, sulfur, nitrogen, and phosphorus in the ocean water. They are also major contributors of carbon fixing and sequestration, as much as terrestrial plants to achieve CO2 emissions reduction. The prokaryotic community in the East Indian Ocean primarily comprises of heterotrophic bacteria like Alphaproteobacteria and Gammaproteobacteria, followed by Firmicutes and Actinobacteria. The Arabian Sea and the Bay of Bengal are typically characterized by presence of vast areas of oxygen minimum zones (OMZs) and have been witnessing a shift in the microbial diversity due to the changing conditions in the ocean water. Several canonical correspondence analyses reveal temperature, salinity, and phosphate levels as crucial environmental factors in propelling the distribution of diazotrophs. The viral consortia are dominated by the Caudovirales, an order of tailed bacteriophages. Due to the rapid change in the environmental factors such as topography, temperature, and sunlight contributing toward climate change, their role in sustaining the chemical composition of the ocean can be drastically affected especially with the evidence of several bacterial and fungal communities responding to latitudinal and temperature change. Therefore, we aim to critically review the status of microbial diversity in Indian Ocean to predict their response toward climate change as they are the sentinels of change in marine life and to understand the dynamics of microbial communities in the various locations of Indian Ocean.
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2.
The Complexity of Spills: The Fate of the Deepwater Horizon Oil.
Passow, U, Overton, EB
Annual review of marine science. 2021;:109-136
Abstract
The Deepwater Horizon oil spill was the largest, longest-lasting, and deepest oil accident to date in US waters. As oil and natural gas jetted from release points at 1,500-m depth in the northern Gulf of Mexico, entrainment of the surrounding ocean water into a buoyant plume, rich in soluble hydrocarbons and dispersed microdroplets of oil, created a deep (1,000-m) intrusion layer. Larger droplets of liquid oil rose to the surface, forming a slick of mostly insoluble, hydrocarbon-type compounds. A variety of physical, chemical, and biological mechanisms helped to transform, remove, and redisperse the oil and gas that was released. Biodegradation removed up to 60% of the oil in the intrusion layer but was less efficient in the surface slick, due to nutrient limitation. Photochemical processes altered up to 50% (by mass) of the floating oil. The surface oil expression changed daily due to wind and currents, whereas the intrusion layer flowed southwestward. A portion of the weathered surface oil stranded along shorelines. Oil from both surface and intrusion layers were deposited onto the seafloor via sinking marine oil snow. The biodegradation rates of stranded or sedimented oil were low, with resuspension and redistribution transiently increasing biodegradation. The subsequent research efforts increased our understanding of the fate of spilled oil immensely, with novel insights focusing on the importance of photooxidation, the microbial communities driving biodegradation, and the formation of marine oil snow that transports oil to the seafloor.
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3.
New Microbial Biodiversity in Marine Sediments.
Baker, BJ, Appler, KE, Gong, X
Annual review of marine science. 2021;:161-175
Abstract
Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.
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4.
Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea.
Jørgensen, BB, Andrén, T, Marshall, IPG
Environmental microbiology. 2020;(5):1688-1706
Abstract
The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.
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5.
Physiological limits to life in anoxic subseafloor sediment.
Orsi, WD, Schink, B, Buckel, W, Martin, WF
FEMS microbiology reviews. 2020;(2):219-231
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Abstract
In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?' from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life-death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life.
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6.
Methods for extracting 'omes from microbialites.
Gómez-Acata, ES, Centeno, CM, Falcón, LI
Journal of microbiological methods. 2019;:1-10
Abstract
Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.
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7.
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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8.
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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9.
Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems.
Liang, L, Wang, Y, Sivan, O, Wang, F
Science China. Life sciences. 2019;(10):1287-1295
Abstract
Anaerobic oxidation of methane (AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized, researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.
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10.
Organic geochemical approaches to understanding early life.
Alleon, J, Summons, RE
Free radical biology & medicine. 2019;:103-112
Abstract
Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.