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Person: Thomas Schweder

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Published: April 24, 2017
eLife
Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
Authors: Donato Giovannelli, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani
C-DEBI Contribution Number: 368
Project Data
Last Modified: June 11, 2012
An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Publications >
eLife
Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans
Authors: Donato Giovannelli, Stefan M. Sievert, Michael Hügler, Stephanie Markert, Dörte Becher, Thomas Schweder, Costantino Vetriani
Published: April 24, 2017
C-DEBI Contribution Number: 368

Abstract

Anaerobic thermophiles inhabit relic environments that resemble the early Earth. However, the lineage of these modern organisms co-evolved with our planet. Hence, these organisms carry both ancestral and acquired genes and serve as models to reconstruct early metabolism. Based on comparative genomic and proteomic analyses, we identified two distinct groups of genes in Thermovibrio ammonificans: the first codes for enzymes that do not require oxygen and use substrates of geothermal origin; the second appears to be a more recent acquisition, and may reflect adaptations to cope with the rise of oxygen on Earth. We propose that the ancestor of the Aquificae was originally a hydrogen oxidizing, sulfur reducing bacterium that used a hybrid carbon fixation pathway for CO2fixation. With the gradual rise of oxygen in the atmosphere, more efficient terminal electron acceptors became available and this lineage acquired genes that increased its metabolic flexibility while retaining ancestral metabolic traits.
Source: http://dx.doi.org/10.7554/elife.18990

Related Items

Awards
Awards > Postdoctoral Fellowships
Award Dates: June 1, 2014 — May 31, 2016
Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere
Awardee: Donato Giovannelli (Rutgers University)
Current Placement: Research Fellow, National Research Council, Institute for Marine Science CNR-ISMAR Ancona
Degree: Ph.D. Applied Biology, Ecology and Microbiology, University of Naples (2013)
Advisor: Costantino Vetriani (Rutgers University)
Project Data
An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Project TitleAn Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
AcronymMicrobial Communities at Deep-Sea Vents
URLhttp://www.bco-dmo.org/project/2216
CreatedJune 11, 2012
ModifiedJune 11, 2012

Project Description

Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives: 1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities. 2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents. 3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents. 4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms.

Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts.

Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context.

Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)

Project Maintainers

NameAffiliationRoleContact
Stefan M. SievertWoods Hole Oceanographic Institution (WHOI)Lead Principal Investigator
Costantino VetrianiRutgers UniversityPrincipal Investigator
Dionysis I. FoustoukosCarnegie Institution for Science (CIS)Principal Investigator
Ramunas StepanauskasBigelow Laboratory for Ocean SciencesPrincipal Investigator
Craig TaylorWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Jeffrey S. SeewaldWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Nadine Le BrisLaboratoire d'Écogéochimie des Environnements Benthiques (LECOB)International Collaborator
Niculina MusatMax Planck Institute for Marine Microbiology (MPI)International Collaborator
Thomas SchwederUniversity of GreifswaldInternational Collaborator
Fengping WangShanghai Jiao Tong University (SJTU)International Collaborator

Related Items

Awards
Awards > Postdoctoral Fellowships
Award Dates: May 1, 2013 — April 30, 2015
Dissimilatory Fe(III) reduction metabolisms in high-pressure ocean crustal environments: An experimental case study of the archeaon Geoglobus acetivorans
Awardee: Ileana Pérez-Rodríguez (Carnegie Institute of Washington)
Current Placement: Assistant Professor, University of Pennsylvania
Degree: Ph.D. Microbial Ecology, Rutgers University
Advisors: Dionysis I. Foustoukos (Carnegie Institute of Washington), Andrew Steele (Carnegie Institute of Washington)
Awards > Research Grants
Award Dates: March 1, 2013 — September 30, 2014
Heterotrophy in deep-sea reducing environments: Physiology and metabolism of aerobic hydrocarbonoclastic bacteria
PI: Costantino Vetriani (Rutgers University)
Datasets
Last Modified: February 13, 2017
Instruments: Ion Chromatograph, Isobaric Gas-Tight Sampler
vent chemical composition-Crab Spa
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Dionysis I. Foustoukos, Nancy Copley
Last Modified: August 19, 2016
Instruments: Automated DNA Sequencer, ROV Jason, McLane Pump
Chemosynthetic biofilm diversity
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Costantino Vetriani, Nancy Copley, Nancy Copley
Last Modified: February 10, 2017
Instruments: ROV Jason, Automated DNA Sequencer, Optode, Chemiluminescence NOx Analyzer
Jason-II sample log
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Stefan M. Sievert, Craig Taylor, Heterotrophy in deep-sea reducing environments: Physiology and metabolism of aerobic hydrocarbonoclastic bacteria, Nancy Copley
Last Modified: February 13, 2017
Instruments: Isobaric Gas-Tight Sampler, Shipboard Incubator, Microscope-Optical, Microscope-Electron
Incubation in diffuse flow vent fluids - Crab Spa
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Dionysis I. Foustoukos, Nancy Copley
Last Modified: April 18, 2019
Instruments: ROV Jason, Automated DNA Sequencer, Isobaric Gas-Tight Sampler
Vent_CSP_SAG
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Ramunas Stepanauskas, Nancy Copley
Last Modified: July 24, 2017
Instruments: Isobaric Gas-Tight Sampler, Water Temperature Sensor, ROV Jason
Vent fluid chemistry: AT26-10 and AT26-23
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Heterotrophy in deep-sea reducing environments: Physiology and metabolism of aerobic hydrocarbonoclastic bacteria, Stefan M. Sievert, Nancy Copley
Last Modified: October 12, 2018
Instruments: Automated DNA Sequencer
16S rRNA sequence and collection data
Data Project: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Project Maintainers: Stefan M. Sievert, Costantino Vetriani, Dionysis I. Foustoukos, Ramunas Stepanauskas, Craig Taylor, Jeffrey S. Seewald, Nadine Le Bris, Niculina Musat, Thomas Schweder, Fengping Wang
Dataset Maintainers: Stefan M. Sievert, Nancy Copley

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