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Don A Cowan - One of the best experts on this subject based on the ideXlab platform.
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nutrient acquisition rather than stress response over diel cycles drives microbial transcription in a hyper arid namib desert soil
2019Co-Authors: Carlos Leonsobrino, Jean-baptiste Ramond, Gillian Maggskolling, Don A CowanAbstract:Hot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Data_Sheet_1_Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil.doc
2019Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil
2019Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network
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Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a dessicated Namib Desert soil
2018Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that most functions did not fluctuate on a diel basis, except for a eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
Botho Bowien - One of the best experts on this subject based on the ideXlab platform.
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JMMB Research Article mol Operon of R. eutropha 619 Involvement of an Unusual mol Operon in Molybdopterin Cofactor Biosynthesis
2013Co-Authors: Tanja Burgdorf, Dagmar Bömmer, Botho BowienAbstract:In contrast to its parent strain, transposon Tn5-Mob insertion mutant HB6 of the facultative Chemoautotroph Ralstonia eutropha was unable to grow organoautotrophically on formate and exhibited no activity of Mo-dependent, membrane-bound formate dehydrogenase (M-FDH) when cultivated mixotrophically on fructose plus formate. The activity of another molybdoenzyme, the soluble, NAD +-linked formate dehydrogenase which is the key enzyme of formate utilization in R. eutropha, was greatly diminished in the mutant. HB6 also lacked the W-dependent M-FDH activities that were newly discovered in organoautotrophically, lithoautotrophically, or mixotrophically grown wildtype cells. However, an additional W-dependent M-FDH activity, observed in heterotrophically grown stationary-phase cells, was present in the mutant although at a considerably reduced level. Sequence analyses of the complementing chromosomal wildtype and the corresponding mutant DNA fragment revealed the transposon insertion to be located in moeA, a gene involved in the biosynthesis of the molybdopterin cofactor (MoCo). Nevertheless, mutant HB6 was able to grow on xanthine as carbon and energy source and with nitrate as nitrogen source. The utilization of these substrates requires the function of the MoCo-containing enzymes xanthine dehydrogenase and assimilatory nitrate reductase, respectively, that were still active in the mutant. A moeA deletion mutant exhibited the same phenotype as that of HB6. The moeA gene belongs to an unusual mol operon consisting of four genes (moeA, moaD, moaE, and moaF) and being constitutively expressed at low level. Unlike MoeA, the large subunit of molybdopteri
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carbonic anhydrase is essential for growth of ralstonia eutropha at ambient co2 concentrations
2002Co-Authors: Bernhard Kusian, Dieter Sultemeyer, Botho BowienAbstract:Mutant strain 25-1 of the facultative Chemoautotroph Ralstonia eutropha H16 had previously been shown to exhibit an obligately high-CO2-requiring (HCR) phenotype. Although the requirement varied with the carbon and energy sources utilized, none of these conditions allowed growth at the air concentration of CO2. In the present study, a gene designated can and encoding a β-carbonic anhydrase (CA) was identified as the site altered in strain 25-1. The mutation caused a replacement of the highly conserved glycine residue 98 by aspartate in Can. A can deletion introduced into wild-type strain H16 generated mutant HB1, which showed the same HCR phenotype as mutant 25-1. Overexpression of can in Escherichia coli and mass spectrometric determination of CA activity demonstrated that can encodes a functional CA. The enzyme is inhibited by ethoxyzolamide and requires 40 mM MgSO4 for maximal activity. Low but significant CA activities were detected in wild-type H16 but not in mutant HB1, strongly suggesting that the CA activity of Can is essential for growth of the wild type in the presence of low CO2 concentrations. The HCR phenotype of HB1 was overcome by complementation with heterologous CA genes, indicating that growth of the organism at low CO2 concentrations requires sufficient CA activity rather than the specific function of Can. The metabolic function(s) depending on CA activity remains to be identified.
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genetics and control of co2 assimilation in the Chemoautotroph ralstonia eutropha
2002Co-Authors: Botho Bowien, Bernhard KusianAbstract:The nutritional versatility of facultative autotrophs requires efficient overall control of their metabolism. Most of these organisms are Proteobacteria that assimilate CO2 via the highly energy-demanding Calvin-Benson-Bassham reductive pentose-phosphate cycle. The enzymes of the cycle are encoded by cbb genes organized in cbb operons differing in size and composition, although conserved features are apparent. Transcription of the operons, which may form regulons, is strictly controlled, being induced during autotrophic but repressed to varying extents during heterotrophic growth of the bacteria. The Chemoautotroph Ralstonia eutropha is one of the organisms studied extensively for the mechanisms involved in the expression of cbb gene systems. CbbR is a LysR-type transcriptional regulator and the key activator protein of cbb operons. The cbbR gene is typically located adjacent and in divergent orientation to its cognate operon. The activating function of CbbR seems to be modulated by metabolites signaling the nutritional state of the cell to the cbb system. Phosphoenolpyruvate is such a signal metabolite acting as a negative effector of R. eutropha CbbR, whereas NADPH has been proposed to be a coactivator of the protein in two other Chemoautotrophs, Xanthobacter flavus and Hydrogenophilus thermoluteolus. There is evidence for the participation of additional regulators in cbb control. In the photoautotrophs Rhodobacter capsulatus and Rhodobacter sphaeroides, response regulator RegA of the global two-component signal transduction system RegBA serves this function. It is conceivable that specific variants of cbb control systems have evolved to ensure their optimal integration into regulatory networks operating in the diverse autotrophs characterized by different metabolic capabilities.
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genetics and control of co 2 assimilation in the Chemoautotroph ralstonia eutropha
2002Co-Authors: Botho Bowien, Bernhard KusianAbstract:The nutritional versatility of facultative autotrophs requires efficient overall control of their metabolism. Most of these organisms are Proteobacteria that assimilate CO2 via the highly energy-demanding Calvin-Benson-Bassham reductive pentose-phosphate cycle. The enzymes of the cycle are encoded by cbb genes organized in cbb operons differing in size and composition, although conserved features are apparent. Transcription of the operons, which may form regulons, is strictly controlled, being induced during autotrophic but repressed to varying extents during heterotrophic growth of the bacteria. The Chemoautotroph Ralstonia eutropha is one of the organisms studied extensively for the mechanisms involved in the expression of cbb gene systems. CbbR is a LysR-type transcriptional regulator and the key activator protein of cbb operons. The cbbR gene is typically located adjacent and in divergent orientation to its cognate operon. The activating function of CbbR seems to be modulated by metabolites signaling the nutritional state of the cell to the cbb system. Phosphoenolpyruvate is such a signal metabolite acting as a negative effector of R. eutropha CbbR, whereas NADPH has been proposed to be a coactivator of the protein in two other Chemoautotrophs, Xanthobacter flavus and Hydrogenophilus thermoluteolus. There is evidence for the participation of additional regulators in cbb control. In the photoautotrophs Rhodobacter capsulatus and Rhodobacter sphaeroides, response regulator RegA of the global two-component signal transduction system RegBA serves this function. It is conceivable that specific variants of cbb control systems have evolved to ensure their optimal integration into regulatory networks operating in the diverse autotrophs characterized by different metabolic capabilities.
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Bowien O. Identification of a novel gene, aut, involved in autotrophic growth of Alcaligenes eutrophus
1994Co-Authors: Andreas Freter, Botho BowienAbstract:The aerobic facultative Chemoautotroph Alcaligenes eutrophus was found to possess a novel gene, designated aut, required for both lithoautotrophic (hydrogen plus carbon dioxide) and organoautotrophic (formate) growth (Aut+ phenotype). Insertional mutagenesis by transposon TnS-Mob localized the gene on a chromo-somal 13-kbp EcoRI fragment. Physiological characterization of various Aut- mutants revealed pleiotropic effects caused by the transposon insertion. Heterotrophic growth of the mutants on substrates catabolized via the glycolytic pathway was slower than that of the parent strains, and the colony morphology of the mutants was altered when grown on nutrient agar. The heterotrophic derepression of the cbb operons encoding Calvin cycle enzymes was abolished, although their expression was still inducible in the presence of formate. Apparently, the mutation did not affect the cbb genes directly but impaired the autotrophic growth in a more general manner. The conjugally transferred wild-type EcoRI fragment allowed phenotypic in trans comple-mentation of the mutants. Further subcloning and sequencing identified a single open reading frame (aut) of 495 bp that was sufficient for complementation. The monocistronic aut gene was constitutively transcribed into a 0.65-kb mRNA. However, its expression appeared to be low. Heterologous expression of aut was achieved in Escherichia coli, resulting in overproduction of an 18-kDa protein. Database searches yielded weak partial sequence similarities of the deduced Aut protein sequence to some cytidylyltransferases, but no indication fo
Jean-baptiste Ramond - One of the best experts on this subject based on the ideXlab platform.
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nutrient acquisition rather than stress response over diel cycles drives microbial transcription in a hyper arid namib desert soil
2019Co-Authors: Carlos Leonsobrino, Jean-baptiste Ramond, Gillian Maggskolling, Don A CowanAbstract:Hot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Data_Sheet_1_Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil.doc
2019Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil
2019Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network
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Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a dessicated Namib Desert soil
2018Co-Authors: Carlos León-sobrino, Jean-baptiste Ramond, Gillian Maggs-kölling, Don A CowanAbstract:Hot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that most functions did not fluctuate on a diel basis, except for a eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
Carlos Leonsobrino - One of the best experts on this subject based on the ideXlab platform.
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nutrient acquisition rather than stress response over diel cycles drives microbial transcription in a hyper arid namib desert soil
2019Co-Authors: Carlos Leonsobrino, Jean-baptiste Ramond, Gillian Maggskolling, Don A CowanAbstract:Hot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of Chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that Chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
Josephine Z Rapp - One of the best experts on this subject based on the ideXlab platform.
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microbial ecology of the cryosphere sea ice and glacial habitats
2015Co-Authors: Antje Boetius, Alexandre M Anesio, Jody W Deming, Jill A Mikucki, Josephine Z RappAbstract:The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, Chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.
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microbial ecology of the cryosphere sea ice and glacial habitats
2015Co-Authors: Antje Boetius, Alexandre M Anesio, Jody W Deming, Jill A Mikucki, Josephine Z RappAbstract:In this Review, Boetiuset al. summarize our current knowledge of the microbial ecology of Earth's frozen realms, including sea ice and glacial habitats. They describe the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities. The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, Chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.