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Full-Text Articles in Life Sciences
Predominant Archaea In Marine Sediments Degrade Detrital Proteins, Karen Lloyd, Lars Schreiber, Dorthe G. Petersen, Kasper U. Kjeldsen, Mark A. Lever, Andrew D. Steen, Ramunus Stepanauskas, Michael Richter, Sara Kleindienst, Sabine Lenk, Andreas Schramm, Bo Barker Jørgensen
Predominant Archaea In Marine Sediments Degrade Detrital Proteins, Karen Lloyd, Lars Schreiber, Dorthe G. Petersen, Kasper U. Kjeldsen, Mark A. Lever, Andrew D. Steen, Ramunus Stepanauskas, Michael Richter, Sara Kleindienst, Sabine Lenk, Andreas Schramm, Bo Barker Jørgensen
Karen Lloyd
Half of the microbial cells in the Earth’s oceans are found in sediments. Many of these cells are members of the Archaea, singlecelled 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 …
Anaerobic Oxidation Of Methane At Different Temperature Regimes In Guaymas Basin Hydrothermal Sediments, Jennifer F. Biddle, Zena Cardman, Howard Mendlovitz, Daniel B. Albert, Karen G. Lloyd, Karen Lloyd, Antje Boetius, Andreas Teske
Anaerobic Oxidation Of Methane At Different Temperature Regimes In Guaymas Basin Hydrothermal Sediments, Jennifer F. Biddle, Zena Cardman, Howard Mendlovitz, Daniel B. Albert, Karen G. Lloyd, Karen Lloyd, Antje Boetius, Andreas Teske
Karen Lloyd
Anaerobic oxidation of methane (AOM) was investigated in hydrothermal sediments of Guaymas Basin based on d13C signatures of CH4, dissolved inorganic carbon and porewater concentration profiles of CH4 and sulfate. Cool, warm and hot in-situ temperature regimes (15–20 1C, 30–35 1C and 70–95 1C) were selected from hydrothermal locations in Guaymas Basin to compare AOM geochemistry and 16S ribosomal RNA (rRNA), mcrA and dsrAB genes of the microbial communities. 16S rRNA gene clone libraries from the cool and hot AOM cores yielded similar archaeal types such as Miscellaneous Crenarchaeotal Group, Thermoproteales and anaerobic methane-oxidizing archaea (ANME)-1; some of the ANME-1 …
Archaea Of The Miscellaneous Crenarchaeotal Group (Mcg) Are Abundant, Diverse, And Widespread In Marine Sediments, Kyoko Kubo, Karen Lloyd, Jennifer F. Biddle, Rudolf Amann, Andreas Teske, Katrin Knittel
Archaea Of The Miscellaneous Crenarchaeotal Group (Mcg) Are Abundant, Diverse, And Widespread In Marine Sediments, Kyoko Kubo, Karen Lloyd, Jennifer F. Biddle, Rudolf Amann, Andreas Teske, Katrin Knittel
Karen Lloyd
Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 lm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P¼0.06 for slot blot and P¼0.05 for qPCR). …
Environmental Evidence For Net Methane Production And Oxidation In Putative Anaerobic Methanotrophic (Anme) Archaeaemi_, Karen Lloyd, Marc J. Alperin, Andreas Teske
Environmental Evidence For Net Methane Production And Oxidation In Putative Anaerobic Methanotrophic (Anme) Archaeaemi_, Karen Lloyd, Marc J. Alperin, Andreas Teske
Karen Lloyd
Uncultured ANaerobic MEthanotrophic (ANME) archaea are often assumed to be obligate methanotrophs that are incapable of net methanogenesis, and are therefore used as proxies for anaerobic methane oxidation in many environments in spite of uncertainty regarding their metabolic capabilities. Anaerobic methane oxidation regulates methane emissions in marine sediments and appears to occur through a reversal of a methane-producing metabolism. We tested the assumption that ANME are obligate methanotrophs by detecting and quantifying gene transcription of ANME-1 across zones of methane oxidation versus methane production in sediments from the White Oak River estuary, North Carolina. ANME-1 consistently transcribe 16S rRNA and …
Quantitativepcrmethods Forrna Anddnainmarine Sediments: Maximizing Yieldwhile Overcoming Inhibition, Karen Lloyd, Barbara J. Macgregor, Andreas Teske
Quantitativepcrmethods Forrna Anddnainmarine Sediments: Maximizing Yieldwhile Overcoming Inhibition, Karen Lloyd, Barbara J. Macgregor, Andreas Teske
Karen Lloyd
For accurate quantification of DNA and RNA from environmental samples, yield loss during nucleic acid purification has to be minimized. Quantitative PCR (qPCR) and reverse transcription (RT)-qPCR require a trade-off between maximizing yield and removing inhibitors. We compared DNA and RNA yield and suitability for quantitative SYBR Green PCR and RT-PCR using the UltraClean and PowerSoil extraction kits and a bead-beating protocol with phenol/chloroform extraction steps. Purification methods included silica-column-based procedures from the MoBio kits, RNeasy MinElute, WizardPlus miniprep columns, and an acrylamide gel extraction. DNA and RNA purification with WizardPlus and RNeasy, respectively, led to significant losses of nucleic …
Spatial Structure And Activity Of Sedimentary Microbial Communities Underlying A Beggiatoa Spp. Mat In A Gulf Of Mexico Hydrocarbon Seep, Karen Lloyd, Daniel B. Albert, Jennifer F. Biddle, Jeffrey P. Chanton, Oscar Pizarro, Andreas Teske
Spatial Structure And Activity Of Sedimentary Microbial Communities Underlying A Beggiatoa Spp. Mat In A Gulf Of Mexico Hydrocarbon Seep, Karen Lloyd, Daniel B. Albert, Jennifer F. Biddle, Jeffrey P. Chanton, Oscar Pizarro, Andreas Teske
Karen Lloyd
Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the …
Metabolic Variability In Seafloor Brines Revealed By Carbon And Sulphur Dynamics, Samantha B. Joye, Vladimir A. Samarkin, Beth! N. Orcutt, Ian R. Macdonald, Kai-Uwe Hinrichs, Marcus Elvert, Andreas P. Teske, Karen Lloyd, Mark A. Lever, Joseph P. Montoya, Christof D. Meile
Metabolic Variability In Seafloor Brines Revealed By Carbon And Sulphur Dynamics, Samantha B. Joye, Vladimir A. Samarkin, Beth! N. Orcutt, Ian R. Macdonald, Kai-Uwe Hinrichs, Marcus Elvert, Andreas P. Teske, Karen Lloyd, Mark A. Lever, Joseph P. Montoya, Christof D. Meile
Karen Lloyd
Brine fluids that upwell from deep, hot reservoirs below the sea bed supply the sea floor with energy-rich substrates and nutrients that are used by diverse microbial ecosystems. Contemporary hypersaline environments formed by brine seeps may provide insights into the metabolism and distribution of microorganisms on the early Earth or on extraterrestrial bodies. Here we use geochemical and genetic analyses to characterize microbial community composition and metabolism in two seafloor brines in the Gulf of Mexico: an active mud volcano and a quiescent brine pool. Both brine environments are anoxic and hypersaline. However, rates of sulphate reduction and acetate production …
An Anaerobic Methane Oxidizing Community Of Anme-1b Archaea In Hypersaline Gulf Of Mexico Sediments, Karen Lloyd, Laura Lapham, Andreas Teske
An Anaerobic Methane Oxidizing Community Of Anme-1b Archaea In Hypersaline Gulf Of Mexico Sediments, Karen Lloyd, Laura Lapham, Andreas Teske
Karen Lloyd
Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as mcrA gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no archaea of other ANME subgroups were found with general and group-specific PCR primers. The ANME-1b community was found in the sulfate-methane interface, where undersaturated methane concentrations of ca. 100 to 250 _M coexist with sulfate concentrations around 10 mM. Clone libraries of …
Survival And Growth Of Two Heterotrophic Hydrothermal Vent Archaea, Pyrococcus Strain Gb-D And Thermococcus Fumicolans, Under Low Ph And High Sulfide Concentrations In Combination With High Temperature And Pressure Regimes, Virginia P. Edgcomb, Stephen J. Molyneaux, Simone Böer, Carl O. Wirsen, Mark Saito, Michael S. Atkins, Karen Lloyd, Andreas Teske
Survival And Growth Of Two Heterotrophic Hydrothermal Vent Archaea, Pyrococcus Strain Gb-D And Thermococcus Fumicolans, Under Low Ph And High Sulfide Concentrations In Combination With High Temperature And Pressure Regimes, Virginia P. Edgcomb, Stephen J. Molyneaux, Simone Böer, Carl O. Wirsen, Mark Saito, Michael S. Atkins, Karen Lloyd, Andreas Teske
Karen Lloyd
Growth and survival of hyperthermophilic archaea in their extreme hydrothermal vent and subsurface environments are controlled by chemical and physical key parameters. This study examined the effects of elevated sulfide concentrations, temperature, and acidic pH on growth and survival of two hydrothermal vent archaea (Pyrococcus strain GB-D and Thermococcus fumicolans) under high temperature and pressure regimes. These two strains are members of the Thermococcales, a family of hyperthermophilic, heterotrophic, sulfur-reducing archaea that occur in high densities at vent sites. As actively growing cells, these two strains tolerated regimes of pH, pressure, and temperature that were in most cases not tolerated …
Heterotrophic Archaea Dominate Sedimentary Subsurface Ecosystems Off Peru, Jennifer F. Biddle, Julius S. Lipp, Karen Lloyd, Ketil B. Sørensen, Rika Anderson, Helen F. Fredericks, Marcus Elvert, Timothy J. Kelly, Daniel P. Schrag, Mitchell L. Sogin, Jean E. Brenchley, Andreas Teske, Christopher H. House, Kaw-Uwe Hinrichs
Heterotrophic Archaea Dominate Sedimentary Subsurface Ecosystems Off Peru, Jennifer F. Biddle, Julius S. Lipp, Karen Lloyd, Ketil B. Sørensen, Rika Anderson, Helen F. Fredericks, Marcus Elvert, Timothy J. Kelly, Daniel P. Schrag, Mitchell L. Sogin, Jean E. Brenchley, Andreas Teske, Christopher H. House, Kaw-Uwe Hinrichs
Karen Lloyd
Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that …
Methanogen Diversity Evidenced By Molecular Characterization Of Methyl Coenzyme M Reductase A (Mcra) Genes In Hydrothermal Sediments Of The Guaymas Basin, Ashita Dhillon, Mark Lever, Karen Lloyd, Daniel B. Albert, Mitchell L. Sogin, Andreas Teske
Methanogen Diversity Evidenced By Molecular Characterization Of Methyl Coenzyme M Reductase A (Mcra) Genes In Hydrothermal Sediments Of The Guaymas Basin, Ashita Dhillon, Mark Lever, Karen Lloyd, Daniel B. Albert, Mitchell L. Sogin, Andreas Teske
Karen Lloyd
The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H2/CO2- and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile …
Effects Of Dissolved Sulfide, Ph, And Temperature On Growth And Survival Of Marine Hyperthermophilic Archaea, Karen Lloyd, Virginia P. Edgcomb, Stephen J. Molyneaux, Simone Böer, Carl O. Wirsen, Michael S. Atkins, Andreas Teske
Effects Of Dissolved Sulfide, Ph, And Temperature On Growth And Survival Of Marine Hyperthermophilic Archaea, Karen Lloyd, Virginia P. Edgcomb, Stephen J. Molyneaux, Simone Böer, Carl O. Wirsen, Michael S. Atkins, Andreas Teske
Karen Lloyd
The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms, Methanocaldococcus jannaschii, Archaeoglobus profundus, Thermococcus fumicolans, and Pyrococcus sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of Pyrococcus strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature …
Sulfide Ameliorates Metal Toxicity For Deep-Sea Hydrothermal Vent Archaea, Virginia P. Edgcomb, Stephen J. Molyneaux, Mak A. Saito, Karen Lloyd, Simone Böer, Carl O. Wirsen, Michael S. Atkins, Andreas Teske
Sulfide Ameliorates Metal Toxicity For Deep-Sea Hydrothermal Vent Archaea, Virginia P. Edgcomb, Stephen J. Molyneaux, Mak A. Saito, Karen Lloyd, Simone Böer, Carl O. Wirsen, Michael S. Atkins, Andreas Teske
Karen Lloyd
The chemical stress factors for microbial life at deep-sea hydrothermal vents include high concentrations of heavy metals and sulfide. Three hyperthermophilic vent archaea, the sulfur-reducing heterotrophs Thermococcus fumicolans and Pyrococcus strain GB-D and the chemolithoautotrophic methanogen Methanocaldococcus jannaschii, were tested for survival tolerance to heavy metals (Zn, Co, and Cu) and sulfide. The sulfide addition consistently ameliorated the high toxicity of free metal cations by the formation of dissolved metal-sulfide complexes as well as solid precipitates. Thus, chemical speciation of heavy metals with sulfide allows hydrothermal vent archaea to tolerate otherwise toxic metal concentrations in their natural environment. DOI: 10.1128/AEM.70.4.2551–2555.2004