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H M Jonkers - One of the best experts on this subject based on the ideXlab platform.
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two dimensional mapping of photopigment distribution and activity of chloroflexus like bacteria in a hypersaline Microbial Mat
FEMS Microbiology Ecology, 2008Co-Authors: Ami Bachar, Dirk De Beer, Lubos Polerecky, H M Jonkers, Jan Fischer, Kyriakos VamvakopoulosAbstract:Pigment analysis in an intact hypersaline Microbial Mat by hyperspectral imaging revealed very patchy and spatially uncorrelated distributions of photopigments Chl a and BChl a/c, which are characteristic photopigments for oxygenic (diatoms and cyanobacteria) and anoxygenic phototrophs (Chloroflexaceae). This finding is in contrast to the expectation that these biomarker pigments should be spatially correlated, as oxygenic phototrophs are thought to supply the Chloroflexaceae members with organic substrates for growth. We suggest that the heterogeneous occurrence is possibly due to sulfide, whose production by sulfate-reducing bacteria may be spatially heterogeneous in the partially oxic photic zone of the Mat. We furthermore mapped the near-infra-red-light controlled respiration of Chloroflexaceae under light and dark conditions and found that Chloroflexaceae are responsible for a major part of oxygen consumption at the lower part of the oxic zone in the Mat. The presence of Chloroflexaceae was further confirmed by FISH probe and 16S rRNA gene clone library analysis. We assume that species related to the genera Oscillochloris and 'Candidatus Chlorothrix', in contrast to those related to Chloroflexus and Roseiflexus, depend less on excreted photosynthates but more on the presence of free sulfide, which may explain their presence in deeper parts of the Mat.
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contribution of chloroflexus respiration to oxygen cycling in a hypersaline Microbial Mat from lake chiprana spain
Environmental Microbiology, 2007Co-Authors: Lubos Polerecky, Dirk De Beer, Ami Bachar, Raphaela Schoon, Mor Grinstein, Bo Barker Jorgensen, H M JonkersAbstract:In dense stratified systems such as Microbial Mats, photosynthesis and respiration are coupled due to a tight spatial overlap between oxygen-producing and -consuming microorganisms. We combined microsensors and a membrane inlet mass spectrometer with two independent light sources emitting in the visible (VIS) and near infrared (NIR) regions to study this coupling in more detail. Using this novel approach, we separately quantified the activity of the major players in the oxygen cycle in a hypersaline Microbial Mat: gross photosynthesis of cyanobacteria, NIR light-dependent respiration of Chloroflexus-like bacteria (CLB) and respiration of aerobic heterotrophs. Illumination by VIS light induced oxygen production in the top approxiMately 1 mm of the Mat. In this zone CLB were found responsible for all respiration, while the contribution of the aerobic heterotrophs was negligible. Additional illumination of the Mat with saturating NIR light completely switched off CLB respiration, resulting in zero respiration in the photosynthetically active zone. We demonstrate that microsensor-based quantification of gross and net photosyntheses in dense stratified systems should carefully consider the NIR light-dependent behaviour of CLB and other anoxygenic phototrophic groups.
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diversity and function of chloroflexus like bacteria in a hypersaline Microbial Mat phylogenetic characterization and impact on aerobic respiration
Applied and Environmental Microbiology, 2007Co-Authors: Ami Bachar, H M Jonkers, Enoma O Omoregie, Rutger De WitAbstract:We studied the diversity of Chloroflexus-like bacteria (CLB) in a hypersaline phototrophic Microbial Mat and assayed their near-infrared (NIR) light-dependent oxygen respiration rates. PCR with primers that were reported to specifically target the 16S rRNA gene from members of the phylum Chloroflexi resulted in the recovery of 49 sequences and 16 phylotypes (sequences of the same phylotype share more than 96% similarity), and 10 of the sequences (four phylotypes) appeared to be related to filamentous anoxygenic phototrophic members of the family Chloroflexaceae. Photopigment analysis revealed the presence of bacteriochlorophyll c (BChlc), BChld, and γ-carotene, pigments known to be produced by phototrophic CLB. Oxygen microsensor measurements for intact Mats revealed a NIR (710 to 770 nm) light-dependent decrease in aerobic respiration, a phenomenon that we also observed in an axenic culture of Chloroflexus aurantiacus. The metabolic ability of phototrophic CLB to switch from anoxygenic photosynthesis under NIR illumination to aerobic respiration under non-NIR illumination was further used to estiMate the contribution of these organisms to Mat community respiration. Steady-state oxygen profiles under dark conditions and in the presence of visible (VIS) light (400 to 700 nm), NIR light (710 to 770 nm), and VIS light plus NIR light were compared. NIR light illumination led to a substantial increase in the oxygen concentration in the Mat. The observed impact on oxygen dynamics shows that CLB play a significant role in the cycling of carbon in this hypersaline Microbial Mat ecosystem. This study further demonstrates that the method applied, a combination of microsensor techniques and VIS and NIR illumination, allows rapid establishment of the presence and significance of CLB in environmental samples.
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photosynthesis controlled calcification in a hypersaline Microbial Mat
Limnology and Oceanography, 2005Co-Authors: Rebecca Ludwig, Dirk De Beer, Fuad A Alhorani, H M JonkersAbstract:We investigated the hypothesis that sulfate reduction rather than oxygenic photosynthesis promotes calcification in a hypersaline Microbial Mat by increasing the ion concentration product: ICP 5 [Ca 21 ] 3 [CO ]. Pore-water 22 3 calcium concentration profiles directly measured with microsensors show that calcium concentration in the photic zone decreased in illuminated Mats and increased slightly in dark Mats. High pH values in the photic zone of illuminated Mats resulted in higher carbonate concentrations (2.25 mmol L 21 ) than in dark Mats (0.75 mmol L 21 ), although the dissolved inorganic carbon (DIC) pore-water concentration in the former was much lower (5.9 mmol L 21 ) than in the latter (9.9 mmol L 21 ). The pH-induced rise in carbonate concentration in the light was the main factor influencing the ICP, while changes in Ca 21 concentration played a subsidiary role. Sulfate reduction did not result in a net pH increase in these Mats, as rates in the photic zone were comparable between illuminated and dark Mats (4 and 5 nmol cm 22 h 21 , respectively), and pH increased in illuminated Mats but not in dark Mats. Calcium carbonate precipitation in the photic zone of these hypersaline Mats is primarily controlled by photosynthesisinduced pH and carbonate concentration increases. However, heterotrophic bacteria, including sulfate reducers, play an important complementary role in calcification because they maintain high concentrations of DIC in the Mat pore water.
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structural and functional analysis of a Microbial Mat ecosystem from a unique permanent hypersaline inland lake la salada de chiprana ne spain
FEMS Microbiology Ecology, 2003Co-Authors: H M Jonkers, Olivier Pringault, Rutger De Wit, Rebecca Ludwig, Gerard Muyzer, Niko Finke, Helge Niemann, Dirk De BeerAbstract:The benthic Microbial Mat community of the only permanent hypersaline natural inland lake of Western Europe, ‘La Salada de Chiprana’, northeastern Spain, was structurally and functionally analyzed. The ionic composition of the lake water is characterized by high concentrations of magnesium and sulfate, which were respectively 0.35 and 0.5 M at the time of sampling while the total salinity was 78 g l−1. Community composition was analyzed by microscopy, high-performance liquid chroMatography (HPLC) pigment analyses and by studying culturable bacteria from different functional groups. Therefore, denaturing gradient gel electrophoresis (DGGE) was applied on most probable number (MPN) dilution cultures. Microscopy revealed that a thin layer of Chloroflexus-like bacteria overlaid various cyanobacteria-dominated layers each characterized by different morphotypes. DGGE analysis of MPN dilution cultures from distinct Mat layers showed that various phylotypes of anoxygenic phototrophic, aerobic heterotrophic, colorless sulfur-, and sulfate-reducing bacteria were present. The Mats were furthermore functionally studied and attention was focussed on the relationship between oxygenic primary production and the flow of carbon through the Microbial community. Microsensor techniques, porewater and sediment photopigment analysis were applied in order to estiMate oxygenic photosynthetic rates, daily dynamics of (in)organic carbon porewater concentration and migration behavior of phototrophs. Chiprana Microbial Mats produced dissolved organic carbon (DOC) both during the day and night. It was estiMated that 14% of the Mats gross photosynthetic production and 49% of the Mats net photosynthetic production diffused out of the Mat in the form of low molecular mass fatty acids, although these compounds made up only 2% of the total DOC pool. The high flux of dissolved fatty acids from the Microbial Mat to the water column may explain why in this system Chloroflexus-like bacteria proliferate on top of the cyanobacterial layers since these photoheterotrophic bacteria grow preferably on organic phototrophic exudates. Furthermore it may also explain why high numbers of viable sulfate-reducing bacteria were found in the fully oxygenated sediment surface layers. These organisms apparently do not have to compete with aerobic heterotrophic community members due to the ample availability of organic substrates. Moreover, the high production of DOC strongly indicates that the Mat community was nutrient limited in its growth. Photopigment analysis revealed furthermore that chlorophyll a (Chla) and three of its allomeres had a complementary depth distribution what suggests that the Chla allomeres are functional adaptations to differences in light quality and/or quantity and may be species specific.
Aude Fourçans - One of the best experts on this subject based on the ideXlab platform.
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Molecular analysis of the spatio-temporal distribution of sulfate-reducing bacteria (SRB) in Camargue (France) hypersaline Microbial Mat
Microbial Ecology, 2008Co-Authors: Aude Fourçans, Anthony Ranchou-peyruse, Pierre Caumette, Robert DuranAbstract:The spatio-temporal distribution of sulfate-reducing bacteria (SRB) in the Microbial Mat of Camargue (Salins-de-Giraud, France) was investigated by molecular approaches at both microscale spatial resolution and different taxonomic organization levels. The vertical distribution of the SRB populations was correlated with oxygen and sulfide microgradient fluctuations. Comparisons of Terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed distinct locations of some operational taxonomic units at daytime and at night (4:00 or 15:00 hours) revealing important differences on the structures of the bacterial communities. When oxygen penetrates the Mat, SRB migration was observed either downward to reach deeper anoxic zones to escape oxygen or upward to reach oxic surface zones. When no migration was observed, both metabolism switches and aggregate forMations were suspected. These behaviors allowed the aerotolerant SRB to deal with oxygen. The analysis of the Desulfococcus-Desulfonema-Desulfosarcina T-RFLP profiles revealed up-migrating populations related to both Desulfonema sp. and Desulfosarcina variabilis. T-RFLP profiles combined with 16S ribosomal ribonucleic acid gene library analysis of the Desulfobacter group revealed two distinct populations: a population related to the recently described Desulfotignum genus migrating upward during the night and a population of a new species of the Desulfobacter uniformly located throughout the Mat independent of the period. Thus, the identification of the new oxygen-tolerant SRB will provide the basis for understanding the physiological adaptations to oxygen.
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seasonal and diel distributions of denitrifying and bacterial communities in a hypersaline Microbial Mat camargue france
Water Research, 2007Co-Authors: Christelle Desnues, Aude Fourçans, Robert Duran, Valerie Michotey, Andrea Wieland, Cui Zhizang, Patricia BoninAbstract:Changes in spatio-temporal distribution of bacterial and denitrifying communities were qualitatively studied in a Microbial Mat from Camargue (France). During a diel and a seasonal cycle, patterns of 16S rRNA and nitrite reductase genes (nirS and nirK) were compared by denaturing gradient gel electrophoresis (DGGE). Statistical analysis of DGGE profiles showed a significant seasonal shift in the community structure of the nirS-containing bacteria with a winter superficial population that extended in summer, whereas the nirK-containing bacteria seemed more affected by vertical gradients rather than by month-to month-changes. Denitrifying activities remained stable during these sampling times. The bacterial community at the surface of the Mat also changed according to season, but appeared stable over a day. Finally, during a diel cycle nirK populations were localized in zones with large fluctuations of environmental parameters (oxygen, pH, and sulfur levels) while nirS populations seemed more restricted to the permanent anoxic layer of the Microbial Mat.
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Vertical migration of phototrophic bacterial populations in a hypersaline Microbial Mat from Salins-de-Giraud (Camargue, France)
FEMS Microbiology Ecology, 2006Co-Authors: Aude Fourçans, Anthony Ranchou-peyruse, Pierre Caumette, A. Solé, E. Diestra, I. Esteve, R. DuranAbstract:The spatio-temporal distribution of phototrophic communities of the hypersaline photosynthetic Camarguc Microbial Mat (Salins-de-Giraud, France) was investigated over a diel cycle by combining microscopic and molecular approaches. Microcoleus chthonoplastes and Halomicronema excentricum, the dominant cyanobacteria of this oxyphotrophic community, were observed with confocal laser scanning microscopy to determine their biomass profiles. Both bacteria have similar vertical distributions, varying from a homogenous distribution through the Mat during the night, to a specific localization in the upper oxic zone of 1.5 mm during the day. Terminal restriction fragment length polymorphism of PCR-amplified pufM gene fragments revealed three groups of anoxyphototrophic populations, which varied according to the two opposite periods of the diel cycle under study. They were either specifically detected in only one period, or homogenously distributed through the Mat in all periods, or located in specific zones of the Mat depending on the period considered. Oxygen concentrations, pH and biomass of the major filamentous cyanobacteria were the determinative factors in the distribution of these anoxyphototrophs across the Mat. Thus, vertical migration, cell-cell aggregate forMation and metabolic switches were the most evident defence of the photosynthetic populations against the adverse effects of sulfide and oxygen fluxes during a diel cycle.
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Characterization of functional bacterial groups in a hypersaline Microbial Mat community (Salins-de-Giraud, Camargue, France)
FEMS Microbiology Ecology, 2004Co-Authors: Aude Fourçans, M. Kühl, T.g. De Oteyza, A. Wieland, A. Solé, E. Diestra, J. Van Bleijswijk, J.o. Grimalt, I. Esteve, G. MuyzerAbstract:A photosynthetic Microbial Mat was investigated in a large pond of a Mediterranean saltern (Salins-de-Giraud, Camargue, France) having water salinity from 70‰ to 150‰ (w/v). Analysis of characteristic biomarkers (e.g., major Microbial fatty acids, hydrocarbons, alcohols and alkenones) revealed that cyanobacteria were the major component of the pond, in addition to diatoms and other algae. Functional bacterial groups involved in the sulfur cycle could be correlated to these biomarkers, i.e. sulfate-reducing, sulfur-oxidizing and anoxygenic phototrophic bacteria. In the first 0.5 mm of the Mat, a high rate of photosynthesis showed the activity of oxygenic phototrophs in the surface layer. Ten different cyanobacterial populations were detected with confocal laser scanning microscopy: six filamentous species, with Microcoleus chthonoplastes and Halomicronema excentricum as dominant (73% of total counts); and four unicellular types affiliated to Microcystis, Chroococcus, Gloeocapsa, and Synechocystis (27% of total counts). Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments confirmed the presence of Microcoleus, Oscillatoria, and Leptolyngbya strains (Halomicronema was not detected here) and revealed additional presence of Phormidium, Pleurocapsa and Calotrix types. Spectral scalar irradiance measurements did not reveal a particular zonation of cyanobacteria, purple or green bacteria in the first millimeter of the Mat. Terminal-restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA gene fragments of bacteria depicted the community composition and a fine-scale depth-distribution of at least five different populations of anoxygenic phototrophs and at least three types of sulfate-reducing bacteria along the microgradients of oxygen and light inside the Microbial Mat.
Michael Kuhl - One of the best experts on this subject based on the ideXlab platform.
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in situ hydrogen dynamics in a hot spring Microbial Mat during a diel cycle
Applied and Environmental Microbiology, 2016Co-Authors: Niels Peter Revsbech, Michael Kuhl, David M Ward, Erik Trampe, Mads LichtenbergAbstract:ABSTRACT Microbes can produce molecular hydrogen (H2) via fermentation, dinitrogen fixation, or direct photolysis, yet the H2 dynamics in cyanobacterial communities has only been explored in a few natural systems and mostly in the laboratory. In this study, we investigated the diel in situ H2 dynamics in a hot spring Microbial Mat, where various ecotypes of unicellular cyanobacteria (Synechococcus sp.) are the only oxygenic phototrophs. In the evening, H2 accumulated rapidly after the onset of darkness, reaching peak values of up to 30 μmol H2 liter−1 at about 1-mm depth below the Mat surface, slowly decreasing to about 11 μmol H2 liter−1 just before sunrise. Another pulse of H2 production, reaching a peak concentration of 46 μmol H2 liter−1, was found in the early morning under dim light conditions too low to induce accumulation of O2 in the Mat. The light stimulation of H2 accumulation indicated that nitrogenase activity was an important source of H2 during the morning. This is in accordance with earlier findings of a distinct early morning peak in N2 fixation and expression of Synechococcus nitrogenase genes in Mat samples from the same location. Fermentation might have contributed to the forMation of H2 during the night, where accumulation of other fermentation products lowered the pH in the Mat to less than pH 6 compared to a spring source pH of 8.3. IMPORTANCE Hydrogen is a key intermediate in anaerobic metabolism, and with the development of a sulfide-insensitive microsensor for H2, it is now possible to study the microdistribution of H2 in stratified Microbial communities such as the photosynthetic Microbial Mat investigated here. The ability to measure H2 profiles within the Mat compared to previous measurements of H2 emission gives much more detailed inforMation about the sources and sinks of H2 in such communities, and it was demonstrated that the high rates of H2 forMation in the early morning when the Mat was exposed to low light intensities might be explained by nitrogen fixation, where H2 is formed as a by-product.
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Systems Biology and Ecology of Microbial Mat Communities - Systems biology and ecology of Microbial Mat communities
Frontiers Research Topics, 2016Co-Authors: Martin G. Klotz, Donald A. Bryant, James K. Fredrickson, William P. Inskeep, Michael KuhlAbstract:Microbial Mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial Mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial Mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of Microbial populations that can be studied in situ under stable conditions for many years. Consequently, Microbial Mat communities are ideal natural laboratories and represent excellent model systems for studying Microbial community structure and function, Microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, Microbial Mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of Microbial Mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of Microbial Mats and the complex interplay among individual populations and their physicochemical environment. These processes ultiMately control the biogeochemical cycling of energy and/or nutrients in Microbial systems. Similarities in Microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding Microbial community dynamics and the ecological role of specific Microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex Microbial communities.
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diel metabolomics analysis of a hot spring chlorophototrophic Microbial Mat leads to new hypotheses of community member metabolisms
Frontiers in Microbiology, 2015Co-Authors: Youngmo Kim, Shane Nowack, Millie T Olsen, Eric D Becraft, Jason M Wood, Vera Thiel, Isaac Klapper, Michael KuhlAbstract:Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic Microbial Mats, requiring adaptive and accliMative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic Microbial Mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the Mat, which were hypothesized to occur in major Mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the Mat responding to temporal differences in their niches
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temporal metatranscriptomic patterning in phototrophic chloroflexi inhabiting a Microbial Mat in a geothermal spring
The ISME Journal, 2013Co-Authors: Michael Kuhl, Donald A. Bryant, Zhenfeng Liu, Christian G Klatt, Marcus Ludwig, Sheila Ingemann Jensen, David M WardAbstract:Filamentous anoxygenic phototrophs (FAPs) are abundant members of Microbial Mat communities inhabiting neutral and alkaline geothermal springs. Natural populations of FAPs related to Chloroflexus spp. and Roseiflexus spp. have been well characterized in Mushroom Spring, where they occur with unicellular cyanobacteria related to Synechococcus spp. strains A and B′. Metatranscriptomic sequencing was applied to the Microbial community to determine how FAPs regulate their gene expression in response to fluctuating environmental conditions and resource availability over a diel period. Transcripts for genes involved in the biosynthesis of bacteriochlorophylls (BChls) and photosynthetic reaction centers were much more abundant at night. Both Roseiflexus spp. and Chloroflexus spp. expressed key genes involved in the 3-hydroxypropionate (3-OHP) carbon dioxide fixation bi-cycle during the day, when these FAPs have been thought to perform primarily photoheterotrophic and/or aerobic chemoorganotrophic metabolism. The expression of genes for the synthesis and degradation of storage polymers, including glycogen, polyhydroxyalkanoates and wax esters, suggests that FAPs produce and utilize these compounds at different times during the diel cycle. We summarize these results in a proposed conceptual model for temporal changes in central carbon metabolism and energy production of FAPs living in a natural environment. The model proposes that, at night, Chloroflexus spp. and Roseiflexus spp. synthesize BChl, components of the photosynthetic apparatus, polyhydroxyalkanoates and wax esters in concert with fermentation of glycogen. It further proposes that, in daytime, polyhydroxyalkanoates and wax esters are degraded and used as carbon and electron reserves to support photomixotrophy via the 3-OHP bi-cycle.
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conversion and conservation of light energy in a photosynthetic Microbial Mat ecosystem
The ISME Journal, 2010Co-Authors: Mohammad A A Alnajjar, Dirk De Beer, Michael Kuhl, Bo Barker Jorgensen, Lubos PolereckyAbstract:Here we present, to the best of our knowledge, the first balanced light energy budget for a benthic Microbial Mat ecosystem, and show how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (Jabs). Our approach uses microscale measurements of the rates of heat dissipation, gross photosynthesis and light absorption in the system, and a model describing light propagation and conversion in a scattering–absorbing medium. The energy budget was dominated by heat dissipation on the expense of photosynthesis: in light-limiting conditions, 95.5% of the absorbed light energy dissipated as heat and 4.5% was channeled into photosynthesis. This energy disproportionation changed in favor of heat dissipation at increasing irradiance, with >99% of the absorbed light energy being dissipated as heat and 700 μmol photon m−2 s−1 (>150 J m−2 s−1). Maximum photosynthetic efficiencies varied with depth in the euphotic zone between 0.014−0.047 O2 per photon. Owing to steep light gradients, photosynthetic efficiencies varied differently with increasing irradiances at different depths in the euphotic zone; for example, at Jabs>700 μmol photon m−2 s−1, they reached around 10% of the maximum values at depths 0−0.3 mm and progressively increased toward 100% below 0.3 mm. This study provides the base for addressing, in much more detail, the photobiology of densely populated photosynthetic systems with intense absorption and scattering. Furthermore, our analysis has promising applications in other areas of photosynthesis research, such as plant biology and biotechnology.
David A Stahl - One of the best experts on this subject based on the ideXlab platform.
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spatial and temporal variability in a stratified hypersaline Microbial Mat community
FEMS Microbiology Ecology, 2009Co-Authors: Jesse G Dillon, Scott R Miller, Brad M Bebout, Meredith Hullar, Nicolais Pinel, David A StahlAbstract:Hypersaline Microbial Mat communities have recently been shown to be more diverse than once thought. The variability in community composition of hypersaline Mats, both in terms of spatial and temporal dimensions, is still poorly understood. Because this inforMation is essential to understanding the complex biotic and abiotic interactions within these communities, terminal restriction fragment analysis and 16S rRNA gene sequencing were used to characterize the near-surface community of a hypersaline Microbial Mat in Guerrero Negro, Mexico. Core samples were analyzed to assay community variability over large regional scales (centimeter to kilometer) and to track depth-related changes in population distribution at 250-μm intervals over a diel period. Significant changes in total species diversity were observed at increasing distances across the Mat surface; however, key species (e.g. Microcoleus sp.) were identified throughout the Mat. The vertical position and abundance of >50% of the 60 peaks detected varied draMatically over a diel cycle, including Beggiatoa sp., cyanobacteria, Chloroflexus sp., HalochroMatium sp., Bacteroidetes sp. and several as-yet-identified bacteria. Many of these migrations correlated strongly with diel changes in redox conditions within the Mat, contributing to strong day–night community structure differences.
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high rates of sulfate reduction in a low sulfate hot spring Microbial Mat are driven by a low level of diversity of sulfate respiring microorganisms
Applied and Environmental Microbiology, 2007Co-Authors: Jesse G Dillon, Scott R Miller, Brad M Bebout, Susan Fishbain, Kirsten Silvia Habicht, Samuel M Webb, David A StahlAbstract:The importance of sulfate respiration in the Microbial Mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this Mat community was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the Mat late in the day when photosynthetic oxygen production ceased and were associated with a Thermodesulfovibrio-like population. Reduced activity at greater depths was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation.
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diversity of sulfate reducing bacteria in oxic and anoxic regions of a Microbial Mat characterized by comparative analysis of dissimilatory sulfite reductase genes
Applied and Environmental Microbiology, 1999Co-Authors: Dror Minz, Jodi Flax, Stefan J Green, Gerard Muyzer, Yehuda Cohen, Michael Wagner, Bruce E Rittmann, David A StahlAbstract:Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline Microbial Mat and to evaluate their distribution in relation to levels of oxygen. The most highly diverse DSR sequences, most related to those of the Desulfonema-like organisms within the δ-proteobacteria, were recovered from oxic regions of the Mat. This observation extends those of previous studies by us and others associating Desulfonema-like organisms with oxic habitats.
Subir Sarkar - One of the best experts on this subject based on the ideXlab platform.
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Microbial Mat structures in profile: The Neoproterozoic Sonia Sandstone, Rajasthan, India
Journal of Asian Earth Sciences, 2011Co-Authors: Pradip Samanta, Soumik Mukhopadhyay, Anudeb Mondal, Subir SarkarAbstract:Abstract Ubiquitous microorganisms, especially cyanobacteria preferably grow on the sediment surface thereby producing Microbial Mats. In the absence of grazers and bioturbators, Microbial Mat is a unique feature of the Proterozoic. Most of the papers so far published described a wide variety of bed surface Microbial Mat structures with rare illustrations from sections perpendicular to bedding. Nonetheless, bed surface exposures are relatively rare in rock records. This limitation of bed surface exposures in rock records suggest that a study of Microbial Mats in bed-across sections is needed. The 60 m thick coastal marine interval of the Sonia Sandstone ForMation is bounded between two terrestrial intervals, a transgressive lag at the base and an unconformity at the top, and has been chosen for exploration of Microbial Mat structures in bed-across sections. A wide variety of Microbial Mat-induced structures in bed-across sections are preserved within the coastal interval of the Sonia Sandstone. Though many of these structures are similar in some aspects with bed surface structures, some of those presented here are new. The palaeogeographic range of these Microbial structures extends from supralittoral to neritic. Diagenetic alterations of Microbial Mats produce pyrite and those zones are suitable for the preservation of Microbial remains. SEM and EDAX analyses show fossil preservation of filamentous Microbial remains that confirm the presence of Microbial Mats within the coastal interval of the Sonia Sandstone. Effects of proliferation of Microbial Mats in the siliciclastic depositional setting are numerous. The Mat-cover on sediment surfaces hinders reworking and/or erosion of the sediments thereby increases the net sedimentation rate. Successive deposition and preservation of thick Microbial Mat layer under reducing environments should have a great potential for hydrocarbon production and preservation and therefore these Proterozoic forMations could be a target for exploration.
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Microbial Mat mediated structures in the ediacaran sonia sandstone rajasthan india and their implications for proterozoic sedimentation
Precambrian Research, 2008Co-Authors: Subir Sarkar, Pradip Samanta, Pradip K Bose, Pratip Sengupta, P G ErikssonAbstract:Abstract A strong influence of Microbial Mats on the physics of Neoproterozoic sedimentation is explored within a 60 m-thick stratigraphic interval within the Sonia Sandstone, Jodhpur Group, western India. This marine interval is bounded by two terrestrial units, its base being marked by a transgressive lag and the top by an unconformity. Progradation from upper neritic, above fair-weather wave base to supralittoral settings was later terminated by a transgression; deposits of lower shoreface-upper shoreface transition thus overlie supralittoral aeolian sandstones, the basal contact of the former deposits being marked by another transgressive lag. A wide spectrum and abundant examples of Microbial Mat or Mat-derived structures supports unusual cohesiveness within granular sand deposited in a high-energy marine environment. The cohesiveness is manifested in abundant preservation of several delicate primary structures and also in their replication in overlying beds, even after they were subjected to high-energy currents. A low rate of sedimentation and severely restricted sediment reworking resulted from prolific Mat growth, and consequent depletion in the sediment budget was manifested in bedform migration and evolution. These factors could also have influenced the sequence-building pattern in a distinctive way, as is already reported from several Meso- and Neoproterozoic successions. Ubiquitous Mat growth thus had the potential to impart significant distinctions to Proterozoic clastic sedimentary successions.
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atlas of Microbial Mat features preserved within the siliciclastic rock record
2007Co-Authors: Juergen Schieber, Subir Sarkar, Pradip K Bose, P G Eriksson, Santanu Banerjee, Wladyslaw Altermann, Octavian CatuneanuAbstract:Drawing on a combination of modern occurrences and likely ancient counterparts, this atlas is a treatise of Mat-related sedimentary features that one may expect to see in ancient terrigenous clastic sedimentary successions. By combining modern and ancient examples, the connection is made to likely forMative processes and the utilization of these features in the interpretation of ancient sedimentary rocks. * The first full compilation of Microbial Mat features/structures preserved in the sliciclastic rock record * High quality, full color photographs fully support the text * Modern and ancient examples connect the forMative processes and utilization of Mat-related features in the interpretation of sedimentary rocks
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Microbial Mat control on siliciclastic precambrian sequence stratigraphic architecture examples from india
Sedimentary Geology, 2005Co-Authors: Subir Sarkar, P G Eriksson, Santanu Banerjee, Octavian CatuneanuAbstract:Abstract An attempt has been made to understand, within a cause-and-effect framework, the sequence-building pattern in Proterozoic time that witnessed non-uniformiteranean Microbial Mat growth and epeiric sea development. Marine or marginal marine successions in three Neoproterozoic forMations, the Sonia Sandstone in western India, and the Sirbu Shale and Upper Bhander Sandstone in central India have been examined here for this purpose. The strikingly common feature of all three forMations is vertical stacking of highstand systems tracts without intervention of any significant transgressive deposits. In one instance only, the transgressive systems tract is represented by a thin granular transgressive lag, and in all other cases the evidence of transgression is simply marked by the presence of marine flooding surfaces. The absence of transgressive strata relates to the low sea floor gradients, which facilitated rapid transgressions, combined with a generally low sediment supply. Aggradation under normal regressive highstand conditions, in spite of the low sediment supply, was promoted by the prolific growth of Microbial Mats, which reduced the effects of wave and current reworking by organic binding of clastic particles.