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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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2.
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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3.
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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4.
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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5.
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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6.
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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7.
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.
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8.
A review on mercury biogeochemistry in mangrove sediments: Hotspots of methylmercury production?
Lei, P, Zhong, H, Duan, D, Pan, K
The Science of the total environment. 2019;:140-150
Abstract
Wetlands are highly productive and biologically diverse environments that provide numerous ecosystem services, but can also be sources of methylmercury (MeHg) production and export. Mangrove wetlands contribute up to 15% of the coastal sediment carbon storage and ~10% of the particulate terrestrial carbon exported to the ocean. Thus, mercury (Hg) methylation in mangrove sediments and subsequent MeHg output to adjacent waters could have a great impact on global Hg cycling. In this review, we provide a comprehensive analysis of the literature on worldwide Hg concentrations in mangrove ecosystems, and the results reveal that a large range of total Hg (THg) and MeHg concentrations is detected in mangrove systems. Then, we discuss the potential roles of organic matter (OM) in controlling the Hg biogeochemistry in mangrove sediments. The intense OM decomposition by anoxic reduction (e.g., sulfate reduction) drastically affects sediment chemistries, such as redox potential, pH, and sulfur speciation, all of which may have a great impact on MeHg production. While the outwelling of carbon from mangroves has been extensively examined, little is known about their roles in exporting MeHg to adjacent waters. Our understanding of Hg biogeochemical processes in mangrove systems is constrained by the limited MeHg data and a lack of in-depth studies on the Hg methylation potential in this ecologically important environment. More efforts are needed to gain better insights into the contributions mangrove wetlands to the global Hg cycle.
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9.
Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite.
Nijenhuis, I, Stollberg, R, Lechner, U
FEMS microbiology ecology. 2018;(4)
Abstract
The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.
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10.
Ecology and evolution of seafloor and subseafloor microbial communities.
Orsi, WD
Nature reviews. Microbiology. 2018;(11):671-683
Abstract
Vast regions of the dark ocean have ultra-slow rates of organic matter sedimentation, and their sediments are oxygenated to great depths yet have low levels of organic matter and cells. Primary production in the oxic seabed is supported by ammonia-oxidizing archaea, whereas in anoxic sediments, novel, uncultivated groups have the potential to produce H2 and CH4, which fuel anaerobic carbon fixation. Subseafloor bacteria have very low mutation rates, and their evolution is likely dominated by selection of different pre-adapted subseafloor taxa under oxic and anoxic conditions. In addition, the abundance and activity of viruses indicate that they affect the size, structure and selection of subseafloor communities. This Review highlights how microbial communities survive in the unique, nutrient-poor and energy-starved environment of the seabed, where they have the potential to influence global biochemical cycles.