scholarly journals Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer

2019 ◽  
Author(s):  
L.M. Seyler ◽  
W.J. Brazelton ◽  
C. McLean ◽  
L.I. Putman ◽  
A. Hyer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dissolved Inorganic Carbon ◽  
Sequence Data ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Carbon Assimilation ◽  
Mass Spectrometry Data ◽  
Physiological Adaptation ◽  
Coast Range ◽  
Coast Range Ophiolite

AbstractSerpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. These reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry of microbial populations that inhabit these environments are understudied and are complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of twelve wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we determined that several carbon assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl-CoA pathway, and methylotrophy are used by the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggests that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.ImportanceThis study describes the metabolic pathways by which microbial communities in a serpentinite-influenced aquifer may produce biomass from the products of serpentinization. Serpentinization is a widespread geochemical process, taking place over large regions of the seafloor, particularly in slow-spreading mid ocean ridge and subduction zone environments. The serpentinization process is implicated in the origin of life on Earth and as a possible environment for the discovery of life on other worlds in our solar system. Because of the difficulty in delineating abiotic and biotic processes in these environments, major questions remain related to microbial contributions to the carbon cycle and physiological adaptation to serpentinite habitats. This research explores multiple mechanisms of carbon assimilation in serpentinite-hosted microbial communities.

scholarly journals Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Lauren M. Seyler ◽  
William J. Brazelton ◽  
Craig McLean ◽  
Lindsay I. Putman ◽  
Alex Hyer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Sequence Data ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Mass Spectrometry Data ◽  
Physiological Adaptation ◽  
Coast Range ◽  
Coast Range Ophiolite

ABSTRACT Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable. IMPORTANCE This study describes the potential metabolic pathways by which microbial communities in a serpentinite-influenced aquifer may produce biomass from the products of serpentinization. Serpentinization is a widespread geochemical process, taking place over large regions of the seafloor and at continental margins, where ancient seafloor has accreted onto the continents. Because of the difficulty in delineating abiotic and biotic processes in these environments, major questions remain related to microbial contributions to the carbon cycle and physiological adaptation to serpentinite habitats. This research explores multiple mechanisms of carbon fixation and assimilation in serpentinite-hosted microbial communities.

scholarly journals Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

2016 ◽  
Author(s):  
Martin E. Nowak ◽  
Valérie F. Schwab ◽  
Cassandre S. Lazar ◽  
Thomas Behrendt ◽  
Bernd Kohlhepp ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Carbon Isotopes ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Carbon Sources ◽  
Oxygen Depletion ◽  
C Isotopes ◽  
Abiotic Controls ◽  
Upper Aquifer

Abstract. Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e. carbonate equilibria) and biotic factors influence δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the geochemical modelling program NETPATH, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate dramatically different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes of 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13C and 14C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface derived carbon sources.

scholarly journals Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

2017 ◽  
Vol 21 (9) ◽  
pp. 4283-4300 ◽  
Author(s):  
Martin E. Nowak ◽  
Valérie F. Schwab ◽  
Cassandre S. Lazar ◽  
Thomas Behrendt ◽  
Bernd Kohlhepp ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Carbon Isotopes ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Geochemical Modeling ◽  
Carbon Sources ◽  
Oxygen Depletion ◽  
C Isotopes ◽  
Upper Aquifer

Abstract. Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria) and biotic factors influence the δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in the δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes in 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water–rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13C and 14C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface-derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface-derived carbon sources.

scholarly journals Microaerophilic Cooperation of Reductive and Oxidative Pathways Allows Maximal Photosynthetic Membrane Biosynthesis in Rhodospirillum rubrum

2003 ◽  
Vol 69 (11) ◽  
pp. 6577-6586 ◽  
Author(s):  
Hartmut Grammel ◽  
Ernst-Dieter Gilles ◽  
Robin Ghosh
Keyword(s):  
Rhodospirillum Rubrum ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Pyridine Nucleotide ◽  
Tricarboxylic Acid ◽  
Physiological Adaptation ◽  
Marker Enzyme ◽  
Photosynthetic Membrane ◽  
Acid Cycle ◽  
Microaerophilic Conditions

ABSTRACT The purple nonsulfur bacterium Rhodospirillum rubrum has been employed to study physiological adaptation to limiting oxygen tensions (microaerophilic conditions). R. rubrum produces maximal levels of photosynthetic membranes when grown with both succinate and fructose as carbon sources under microaerophilic conditions in comparison to the level (only about 20% of the maximum) seen in the absence of fructose. Employing a unique partial O2 pressure (pO2) control strategy to reliably adjust the oxygen tension to values below 0.5%, we have used bioreactor cultures to investigate the metabolic rationale for this effect. A metabolic profile of the central carbon metabolism of these cultures was obtained by determination of key enzyme activities under microaerophilic as well as aerobic and anaerobic phototrophic conditions. Under aerobic conditions succinate and fructose were consumed simultaneously, whereas oxygen-limiting conditions provoked the preferential breakdown of fructose. Fructose was utilized via the Embden-Meyerhof-Parnas pathway. High levels of pyrophosphate-dependent phosphofructokinase activity were found to be specific for oxygen-limited cultures. No glucose-6-phosphate dehydrogenase activity was detected under any conditions. We demonstrate that NADPH is supplied mainly by the pyridine-nucleotide transhydrogenase under oxygen-limiting conditions. The tricarboxylic acid cycle enzymes are present at significant levels during microaerophilic growth, albeit at lower levels than those seen under fully aerobic growth conditions. Levels of the reductive tricarboxylic acid cycle marker enzyme fumarate reductase were also high under microaerophilic conditions. We propose a model by which the primary “switching” of oxidative and reductive metabolism is performed at the level of the tricarboxylic acid cycle and suggest how this might affect redox signaling and gene expression in R. rubrum.

scholarly journals Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Andrew Oliver ◽  
Brandon LaMere ◽  
Claudia Weihe ◽  
Stephen Wandro ◽  
Karen L. Lindsay ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Reproductive Health ◽  
Microbial Communities ◽  
Carbon Sources ◽  
Amplicon Sequencing ◽  
Vaginal Microbiome ◽  
Content Type ◽  
Healthy Women ◽  
Healthy Pregnancy ◽  
Tof Ms

ABSTRACT Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well-adapted microbes which are able to survive in a narrow pH range and are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. We characterized the cervicovaginal microbiomes of 16 healthy women throughout the three trimesters of pregnancy. Additionally, we analyzed saliva and urine metabolomes using gas chromatography-time of flight mass spectrometry (GC-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) lipidomics approaches for samples from mothers and their infants through the first year of life. Amplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF MS and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus have high mannitol levels, which is unexpected given the characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Overall, using a multi-“omic” approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition. IMPORTANCE Humans have a unique vaginal microbiome compared to other mammals, characterized by low diversity and often dominated by Lactobacillus spp. Dramatic shifts in vaginal microbial communities sometimes contribute to the presence of a polymicrobial overgrowth condition called bacterial vaginosis (BV). However, many healthy women lacking BV symptoms have vaginal microbiomes dominated by microbes associated with BV, resulting in debate about the definition of a healthy vaginal microbiome. Despite substantial evidence that the reproductive health of a woman depends on the vaginal microbiota, future therapies that may improve reproductive health outcomes are stalled due to limited understanding surrounding the ecology of the vaginal microbiome. Here, we use sequencing and metabolomic techniques to show novel associations between vaginal microbes and metabolites during healthy pregnancy. We speculate these associations underlie microbiome dynamics and may contribute to a better understanding of transitions between alternative vaginal microbiome compositions.

scholarly journals MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 726
Author(s):  
Mike W.C. Thang ◽  
Xin-Yi Chua ◽  
Gareth Price ◽  
Dominique Gorse ◽  
Matt A. Field
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Differential Analysis ◽  
Biomedical Sciences ◽  
Metagenomic Sequence ◽  
Differential Abundance ◽  
Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences.  While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs.  Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics.  MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

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