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Bente Aa Lomstein - One of the best experts on this subject based on the ideXlab platform.
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Endospore abundance and d l amino acid modeling of Bacterial turnover in holocene marine sediment aarhus bay
Geochimica et Cosmochimica Acta, 2012Co-Authors: Alice T Langerhuus, Mark A Lever, Yuki Morono, Fumio Inagaki, Bo Barker Jorgensen, Bente Aa LomsteinAbstract:Abstract In order to study Bacterial activity, and turnover times of Bacterial necromass and biomass in marine sediment, two stations from the Aarhus Bay, Denmark were analyzed. Sediment cores were up to 11 m deep and covered a timescale from the present to ∼11,000 years ago. Sediment was analyzed for total hydrolysable amino acids (THAA), total hydrolysable amino sugars, the Bacterial Endospore marker dipicolinic acid (DPA), and amino acid enantiomers ( l - and d -form) of aspartic acid. Turnover times of Bacterial necromass and vegetative cells, as well as carbon oxidation rates were estimated by use of the d : l -amino acid racemization model. Diagenetic indicators were applied to evaluate the diagenetic state of the sedimentary organic matter. The contribution of amino acids to total organic carbon, and the ratio between the amino acids aspartic acid and glutamic acid, and their respective non protein degradation products, β-alanine and γ-amino butyric acid, all indicated increasing degradation state of the organic matter with sediment depth and age. Quantification of DPA showed that Endospores were abundant, and increased with depth relative to vegetative cells. Most of the amino acids (97%) could be ascribed to microbial necromass, i.e. the remains of dead Bacterial cells. Model estimates showed that the turnover times of microbial necromass were in the range of 0.5–1 × 10 5 years, while turnover times of vegetative cells were in the range of tens to hundreds of years. The turnover time of the TOC pool increased with depth in the sediment, indicating that the TOC pool became progressively more refractory and unavailable to microorganisms with depth and age of the organic matter.
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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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.
James B Gillespie - One of the best experts on this subject based on the ideXlab platform.
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sensors for detection of calcium associated with Bacterial Endospore suspensions
Analytica Chimica Acta, 2001Co-Authors: Laura C Taylor, Mary Beth Tabacco, James B GillespieAbstract:Abstract We describe a method of detecting Bacterial Endospores via quantitation of calcium uniquely associated with spore suspensions. The sensor is created by combining a fluorescent calcium-sensitive indicator, calcein, in a viscous membrane on planar, silica glass coupons. The sensor coupon is affixed to the distal end of an optical fiber, which provides excitation light and collects the fluorescence emission. Aqueous micro-droplets of Bacterial spores are added to the sensor and the resulting increase in fluorescence intensity is monitored. This assay effectively exploits the high concentration of calcium ion found in the spore core and expressed on the surface, and fluorescence spectroscopy, as an indirect method to detect and quantify spore concentration. This sensor technology is applicable to near real-time detection of calcium in Bacterial spore suspensions without interference from light scattering or other ambient biological materials such as bacteria, pollen, viruses, and fungal spores.
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mitigating phosphate interference in Bacterial Endospore detection by tb dipicolinate photoluminescence
Analytica Chimica Acta, 2001Co-Authors: Nicholas F Fell, Paul M Pellegrino, James B GillespieAbstract:A new technique for the detection of Bacterial Endospores using terbium dipicolinate photoluminescence has been previously reported in the literature. The performance of this technique is adversely affected by the presence of substances that contain phosphate ions. This deficiency must be overcome before this method can be used as a viable means of detecting Bacterial Endospores. We have experimentally investigated methods for mitigating the phosphate problem and demonstrate that the addition of AlCl3 is a solution to the problem. Proper experimental procedures for this method are also presented.
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Bacterial Endospore detection using terbium dipicolinate photoluminescence in the presence of chemical and biological materials
Analytical Chemistry, 1998Co-Authors: Paul M Pellegrino, David L Rosen, Nicholas F Fell, James B GillespieAbstract:A determination of the viability of an Endospore detection technique using terbium dipicolinate photoluminescence in the presence of other chemical and biological materials was performed. The compounds and organisms examined, possible environmental constituents, covered three broad categories: organic compounds, inorganic compounds, and biological materials. Each substance was tested for a false positive, which occurs if the intrinsic terbium photoluminescence is enhanced in the absence of a Bacterial Endospore. The detection technique was also investigated for false negatives, which occur if a known positive Endospore signal is inhibited significantly. Although several materials may give rise to false negative signals, none caused a false positive signal to be observed.
Arthur J Spivack - One of the best experts on this subject based on the ideXlab platform.
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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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.
Charles P Moran - One of the best experts on this subject based on the ideXlab platform.
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a lytm domain dictates the localization of proteins to the mother cell forespore interface during Bacterial Endospore formation
Journal of Bacteriology, 2011Co-Authors: Jeffrey Meisner, Charles P MoranAbstract:A large number of proteins are known to reside at specific subcellular locations in Bacterial cells. However, the molecular mechanisms by which many of these proteins are anchored at these locations remains unclear. During Endospore formation in Bacillus subtilis, several integral membrane proteins are located specifically at the interface of the two adjacent cells of the developing sporangium, the mother cell and forespore. The mother cell membrane protein SpoIIIAH recognizes the cell-cell interface through an interaction with the forespore membrane protein SpoIIQ, and then the other proteins are positioned there by the SpoIIIAH-SpoIIQ complex. In this study, we investigated the molecular mechanisms underlying the formation of the SpoIIIAH-SpoIIQ complex. Using gel filtration chromatography and isothermal titration calorimetry, we measured the binding parameters that characterize the SpoIIIAH-SpoIIQ interaction in vitro. We also demonstrated that the interaction of SpoIIIAH and SpoIIQ is governed by their YscJ and degenerate LytM domains, respectively. Therefore, the LytM domain of SpoIIQ provides the positional cue that dictates the localization of mother cell membrane proteins to the mother cell-forespore interface.
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a channel connecting the mother cell and forespore during Bacterial Endospore formation
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: Jeffrey Meisner, Adriano O Henriques, Xin Wang, Monica Serrano, Charles P MoranAbstract:At an early stage during Bacillus subtilis Endospore development the bacterium divides asymmetrically to produce two daughter cells. The smaller cell (forespore) differentiates into the Endospore, while the larger cell (mother cell) becomes a terminally differentiated cell that nurtures the developing forespore. During development the mother cell engulfs the forespore to produce a protoplast, surrounded by two bilayer membranes, which separate it from the cytoplasm of the mother cell. The activation of σG, which drives late gene expression in the forespore, follows forespore engulfment and requires expression of the spoIIIA locus in the mother cell. One of the spoIIIA-encoded proteins SpoIIIAH is targeted specifically to the membrane surrounding the forespore, through an interaction of its C-terminal extracellular domain with the C-terminal extracellular domain of the forespore membrane protein SpoIIQ. We identified a homologous relationship between the C-terminal domain of SpoIIIAH and the YscJ/FliF protein family, members of which form multimeric rings involved in type III secretion systems and flagella. If SpoIIIAH forms a similar ring structure, it may also form a channel between the mother cell and forespore membranes. To test this hypothesis we developed a compartmentalized biotinylation assay, which we used to show that the C-terminal extracellular domain of SpoIIIAH is accessible to enzymatic modification from the forespore cytoplasm. These and other results lead us to suggest that SpoIIIAH forms part of a channel between the forespore and mother cell that is required for the activation of σG.
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structure and assembly of the Bacterial Endospore coat
Methods, 2000Co-Authors: Adriano O Henriques, Charles P MoranAbstract:Many biological processes are mediated through the action of multiprotein complexes, often assembled at specific cellular locations. Bacterial Endospores for example, are encased in a proteinaceous coat, which confers resistance to lysozyme and harsh chemicals and influences the spore response to germinants. In Bacillus subtilis, the coat is composed of more than 20 polypeptides, organized into three main layers: an amorphous undercoat; a lamellar, lightly staining inner structure; and closely apposed to it, a striated electron-dense outer coat. Synthesis of the coat proteins is temporally and spatially governed by a cascade of four mother cell-specific transcription factors. However, the order of assembly and final destination of the coat structural components may rely mainly on specific protein—protein interactions, as well as on the action of accessory morphogenetic proteins. Proteolytic events, protein—protein crosslinking, and protein glycosylation also play a role in the assembly process. These modifications are carried out by enzymes that may themselves be targeted to the coat layers. Coat genes have been identified by reverse genetics or, more recently, by screens for mother cellspecific promoters or for peptide sequences able to interact with certain bait proteins. A role for a given locus in coat assembly is established by a combination of regulatory, functional, morphological, and topological criteria. Because of the amenability of B. subtilis to genetic analysis (now facilitated by the knowledge of its genome sequence), coat formation has become an attractive model for the assembly of complex macromolecular structures during development. ' 2000 Academic Press
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structure and assembly of the Bacterial Endospore coat
Methods, 2000Co-Authors: Adriano O Henriques, Charles P MoranAbstract:Many biological processes are mediated through the action of multiprotein complexes, often assembled at specific cellular locations. Bacterial Endospores for example, are encased in a proteinaceous coat, which confers resistance to lysozyme and harsh chemicals and influences the spore response to germinants. In Bacillus subtilis, the coat is composed of more than 20 polypeptides, organized into three main layers: an amorphous undercoat; a lamellar, lightly staining inner structure; and closely apposed to it, a striated electron-dense outer coat. Synthesis of the coat proteins is temporally and spatially governed by a cascade of four mother cell-specific transcription factors. However, the order of assembly and final destination of the coat structural components may rely mainly on specific protein-protein interactions, as well as on the action of accessory morphogenetic proteins. Proteolytic events, protein-protein crosslinking, and protein glycosylation also play a role in the assembly process. These modifications are carried out by enzymes that may themselves be targeted to the coat layers. Coat genes have been identified by reverse genetics or, more recently, by screens for mother cell-specific promoters or for peptide sequences able to interact with certain bait proteins. A role for a given locus in coat assembly is established by a combination of regulatory, functional, morphological, and topological criteria. Because of the amenability of B. subtilis to genetic analysis (now facilitated by the knowledge of its genome sequence), coat formation has become an attractive model for the assembly of complex macromolecular structures during development.
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a bacillus subtilis secreted protein with a role in Endospore coat assembly and function
Journal of Bacteriology, 1999Co-Authors: Monica Serrano, Charles P Moran, Rita Zilhao, Ezio Ricca, Amanda J Ozin, Adriano O HenriquesAbstract:Bacterial Endospores are encased in a complex protein coat, which confers protection against noxious chemicals and influences the germination response. In Bacillus subtilis, over 20 polypeptides are organized into an amorphous undercoat, a lamellar lightly staining inner structure, and an electron-dense outer coat. Here we report on the identification of a polypeptide of about 30 kDa required for proper coat assembly, which was extracted from spores of a gerE mutant. The N-terminal sequence of this polypeptide matched the deduced product of the tasA gene, after removal of a putative 27-residue signal peptide, and TasA was immunologically detected in material extracted from purified spores. Remarkably, deletion of tasA results in the production of asymmetric spores that accumulate misassembled material in one pole and have a greatly expanded undercoat and an altered outer coat structure. Moreover, we found that tasA and gerE mutations act synergistically to decrease the efficiency of spore germination. We show that tasA is the most distal member of a three-gene operon, which also encodes the type I signal peptidase SipW. Expression of the tasA operon is enhanced 2 h after the onset of sporulation, under the control of ςH. When tasA transcription is uncoupled from sipW expression, a presumptive TasA precursor accumulates, suggesting that its maturation depends on SipW. Mature TasA is found in supernatants of sporulating cultures and intracellularly from 2 h of sporulation onward. We suggest that, at an early stage of sporulation, TasA is secreted to the septal compartment. Later, after engulfment of the prespore by the mother cell, TasA acts from the septal-proximal pole of the spore membranes to nucleate the organization of the undercoat region. TasA is the first example of a polypeptide involved in coat assembly whose production is not mother cell specific but rather precedes its formation. Our results implicate secretion as a mechanism to target individual proteins to specific cellular locations during the assembly of the Bacterial Endospore coat.
Alice T Langerhuus - One of the best experts on this subject based on the ideXlab platform.
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Endospore abundance and d l amino acid modeling of Bacterial turnover in holocene marine sediment aarhus bay
Geochimica et Cosmochimica Acta, 2012Co-Authors: Alice T Langerhuus, Mark A Lever, Yuki Morono, Fumio Inagaki, Bo Barker Jorgensen, Bente Aa LomsteinAbstract:Abstract In order to study Bacterial activity, and turnover times of Bacterial necromass and biomass in marine sediment, two stations from the Aarhus Bay, Denmark were analyzed. Sediment cores were up to 11 m deep and covered a timescale from the present to ∼11,000 years ago. Sediment was analyzed for total hydrolysable amino acids (THAA), total hydrolysable amino sugars, the Bacterial Endospore marker dipicolinic acid (DPA), and amino acid enantiomers ( l - and d -form) of aspartic acid. Turnover times of Bacterial necromass and vegetative cells, as well as carbon oxidation rates were estimated by use of the d : l -amino acid racemization model. Diagenetic indicators were applied to evaluate the diagenetic state of the sedimentary organic matter. The contribution of amino acids to total organic carbon, and the ratio between the amino acids aspartic acid and glutamic acid, and their respective non protein degradation products, β-alanine and γ-amino butyric acid, all indicated increasing degradation state of the organic matter with sediment depth and age. Quantification of DPA showed that Endospores were abundant, and increased with depth relative to vegetative cells. Most of the amino acids (97%) could be ascribed to microbial necromass, i.e. the remains of dead Bacterial cells. Model estimates showed that the turnover times of microbial necromass were in the range of 0.5–1 × 10 5 years, while turnover times of vegetative cells were in the range of tens to hundreds of years. The turnover time of the TOC pool increased with depth in the sediment, indicating that the TOC pool became progressively more refractory and unavailable to microorganisms with depth and age of the organic matter.
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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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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Endospore abundance microbial growth and necromass turnover in deep sub seafloor sediment
Nature, 2012Co-Authors: Bente Aa Lomstein, Alice T Langerhuus, Bo Barker Jorgensen, Steven Dhondt, Arthur J SpivackAbstract:A new approach, the d:l-amino-acid model, is used to quantify the distributions and turnover times of living microbial biomass, Endospores and microbial necromass, and to determine their role in the sub-seafloor carbon budget. Since the discovery of the deep marine biosphere, which includes microbial communities in deep sub-floor sediments that contribute perhaps one-tenth of all living biomass on Earth, microbiologists have been trying to explain how microorganisms utilize the extremely low supply of carbon and energy in this unpromising habitat. Lomstein et al. have quantified diagnostic microbial cell components in a deep-sea sediment drilling core from the continental shelf off Peru, and have used these data to calculate microbial biomass, the mass of dead microbes and the mass of Bacterial spores. They estimate that microbial biomass turnover occurs on a timescale of hundreds to thousands of years. 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 approach—the d:l-amino-acid model—to 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.