110 records found.
C-DEBI Contribution 105
June 1, 2011

Summary: The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

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C-DEBI Contribution 136
October 2, 2012

The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅1029 cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth’s total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth’s total number of microbes and total living biomass to be, respectively, 50–78% and 10–45% lower than previous estimates.

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C-DEBI Contribution 177
March 27, 2013

Half of the microbial cells in the Earth’s oceans are found in sediments1. Many of these cells are members of the Archaea2, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota3 and Aigarchaeota4, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.

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Number of Sequences8,915,670
C-DEBI Contribution 129
April 5, 2012

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood1, 2. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state3. Here we apply a new approachthe D:L-amino-acid modelto quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.

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C-DEBI Contribution 130
May 18, 2013

Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O2 liter−1 year−1 near the sediment-water interface to 0.001 micromoles of O2 liter−1 year−1 at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10−3 femtomoles of O2 cell−1 day−1 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux.

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Note that the oxygen fluxes at sites 8-11 are likely to be underestimated because the coarse spatial resolution conceals oxygen consumption in the top few cm. The volumetric oxygen consumption rates were calculated by dividing the surface oxygen flux by the oxygen penetration depth for the sites on the Equator and from modeling for Site 11. The O2 penetration at sites 9 to11 was deeper than the core obtained. The O2 profile at Site 9 was similar in shape to sites 10 and 11, but only 4 m was recovered. The volumetric oxygen consumption data for Site 11 represent the range calculated between 1m and 30m below sea floor.

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C-DEBI Contribution 110
September 23, 2011

Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discoveredZetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.

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C-DEBI Contribution 121
February 18, 2012

The genus of Marinobacter is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of Marinobacter aquaeolei VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many “opportunitrophic” genetic characteristics and strategies that M. aquaeolei has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of M. aquaeolei and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.

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C-DEBI Contribution 125
May 15, 2012

The permeable upper oceanic basement serves as a plausible habitat for a variety of microbial communities. There is growing evidence suggesting a substantial subseafloor biosphere. Here new time series data are presented on key inorganic species, methane, hydrogen and dissolved organic carbon (DOC) in ridge flank fluids obtained from subseafloor observatory CORKs (Circulation Obviation Retrofit Kits) at Integrated Ocean Drilling Program (IODP) boreholes 1301A and 1026B. These data show that the new sampling methods (Cowen et al., 2012) employed at 1301A result in lower contamination than earlier studies. Furthermore, sample collection methods permitted most chemical analyses to be performed from aliquots of single large volume samples, thereby allowing more direct comparison of the data. The low phosphate concentrations (0.06–0.2 μM) suggest that relative to carbon and nitrogen, phosphorus could be a limiting nutrient in the basement biosphere. Coexisting sulfate (17–18 mM), hydrogen sulfide (∼0.1 μM), hydrogen (0.3–0.7 μM) and methane (1.5–2 μM) indicates that the basement aquifer at 1301A either draws fluids from multiple flow paths with different redox histories or is a complex environment that is not thermodynamically controlled and may allow co-occurring metabolic pathways including sulfate reduction and methanogenesis. The low DOC concentrations (11–18 μM) confirm that ridge flank basement is a net DOC sink and ultimately a net carbon sink. Based on the net amounts of DOC, oxygen, nitrate and sulfate removed (∼30 μM, ∼80 μM, ∼40 μM and ∼10 mM, respectively) from entrained bottom seawater, organic carbon may be aerobically or anaerobically oxidized in biotic and/or abiotic processes.

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C-DEBI Contribution 115
May 1, 2012

Most ecosystems on Earth exist in permanent darkness, one or more steps removed from the light-driven surface world. This collection of dark habitats is the most poorly understood on Earth, in particular the size, function, and activity of these ecosystems and what influence they have on global biogeochemical processes. The vastest of these ecosystems constitute the “deep biosphere”—habitats physically located below the surface of continents and the bottom of the ocean. The deep biosphere has been the subject of considerable—and increasing—study and scrutiny in recent years. New deep biosphere realms are being explored from deep in mines in South Africa, to sediments in the middle of oceanic gyres—and beyond. New technologies are emerging, permitting researchers to do active, manipulable experimentation in situ within the subsurface. This review highlights recent history of the research and the exciting new directions this field of research is going in, and discusses some of the most active and interesting field realms currently under scrutiny by researchers examining this deep, dark, intraterrestrial life.

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C-DEBI Contribution 139
March 15, 2013

Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ13C- and δ34S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ13C signatures locally attenuated by heterotrophic metabolism.

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