NASA Exobiology (with D. Foustoukos): Physiological adaptations in hydrogenotrophic bacteria at extreme pressures. January 1, 2021 - December 31, 2023.
Summary: This project aims to constrain: i) the physiological adaptation of extremophiles to the pressure and nutrient levels found at deep-sea hydrothermal vents, and ii) phage-host interactions and coevolution. In task 1 we ask: How do piezophiles adapt to pressure gradients present at deep-sea and subsurface environments? We hypothesize that the membrane lipids saturation in piezophilic Epsilonprotebacteria decreases as the hydrostatic pressure increases. We will determine the changes in the membrane lipid composition (fatty acids and polar lipids) of these bacteria during growth at different pressures. In task 2 we ask: What is the role of environmental DNA uptake as an adaptation mechanism to pressure and nutrient-limitation stresses? We hypothesize that low and/or high pressure and nutrient availability regimes differentially affect the expression of DNA uptake genes in piezophilic Epsilonprotebacteria when exposed to exogenous DNA. We propose experiments to assess the level of expression of competence-related genes during the uptake of free DNA in these bacteria. In task 3 we hypothesize that the life cycle of the prophage hosted in a piezophilic Epsilonprotebacterium is affected by pressure and nutrient conditions that differ from those for optimum growth. We aim to: (i) investigate the pressure adaptation that triggers the lytic cycle of the bacteriophage; (ii) identify the nutrient regimes that trigger its lytic cycle; and (iii) investigate the ability of this bacteriophage to infect closely related strains.

NSF Division of Integrative Organismal Systems, Integrative Ecological Physiology Program: Collaborative research (with D. Foustoukos). Microbial hydrogen oxidation at high pressure: Role of hydrogenases and interspecies hydrogen transfer. National Science Foundation. May 1, 2020 – April 30, 2023.
Summary: A large fraction of Earth’s biosphere lives in the deep ocean and within the oceanic subsurface. This deep biosphere thrives under conditions of high hydrostatic pressures (>10 MPa, 1000 meter depth) and often high-temperatures and is adapted not only to pressure, but also to sharp temperature and redox gradients. Considering the contribution of these thermopiezophilic microbial communities to the Earth’s microbiome, their role in linking the geological and biological element cycles in the deep-ocean, and their relevance for the evolution of early life on Earth, it is striking how little we know about the function and physiological responses of thermopiezophiles to the physical and chemical conditions they encounter in their habitats. This project aims to gain insight into the adaptation mechanisms of thermopiezophilic, hydrogen-oxidizing bacteria to different pressure and hydrogen concentration regimes. The model organism is Nautilia sp. strain PV-1, a deep-sea vent thermopiezophilic, anaerobic chemolithoautotroph that couples H2 oxidation to either to NO3- or S0 reduction, and whose genome has been sequenced. This project will investigate the expression of the different hydrogenases of strain PV-1 in response to pressures up to 40 MPa, and to limiting and non-limiting concentration of hydrogen. This project will also expolre synthrophic growth by interspecies hydrogen transfer between Marinitoga piezophila, a fermentative, hydrogen-producing thermopiezophile and the hydrogen consuming strain PV-1. Novel continuous culture techniques will be used to simulate the deep-sea physical (temperature, pressure) and chemical (hydrogen concentration) conditions.

NSF Biological Oceanography: Collaborative research (with L. Mullineaux and S. Arellano). The predictive nature of microbial biofilms for cuing larval settlement at deep-sea hydrothermal vents. National Science Foundation. May 1, 2020 – April 30, 2023. Read more about the Biofilms4Larvae project.
Summary: Decades of research at hydrothermal vents have shown that larvae of endemic vent animals disperse effectively between vents, yet we don't know how they complete the journey by locating and settling in suitable habitat. This question remains one of the key unresolved puzzles in the ecology of deep-sea hydrothermal vents. We suggest that microbial biofilms are a good signpost for larval settlement at vents because they integrate temporal variability in abiotic and biotic features of vent habitats. To test our overarching hypothesis that microbial biofilms cue the larval settlement of vent animals, we will employ a field program of short-term settlement experiments combined with cutting-edge microbial ‘omics’ work, followed by shipboard settlement experiments that leverage our unique expertise in hydrothermal-vent larvae and microbial biofilm culture. This approach allows us to use our field experiments to statistically model the factors that best predict larval settlement in the field, then test those predictions with shipboard experiments that decouple covarying conditions. We will produce a science-in-action documentary filled with ocean science and exploration intended for television distribution and museum screenings. We will use footage of the deep-sea vents, shipboard and diving operations, and laboratory work to create a documentary that highlights the foundation of scientific research: hypothesis-driven research, the application of the scientific method, and the importance of critical thinking.

NASA Topical Workshops, Symposia, and Conferences (with D. Giovannelli): Bridging the US and European Astrobiology community: supporting US scientist attendance to Extremophiles 2018 Conference. June 11, 2018 - June 10, 2019.

Center for Dark Energy Biosphere Investigations (C-DEBI; with D. Foustoukos): Synthrophic growth of piezophilic deep-sea vent bacteria. 2018-2019.
Summary: The goal of this proposal is to gain insight into the metabolic and molecular adaptations of deep-sea and subseafloor bacteria exposed to crustal pressures (200-500 atm). The model organism will be an anaerobic nitrate-reducing bacterium (Nautilia sp. strain PV-1) isolated from subseafloor fluids discharged from an active vent at the East Pacific Rise (2500 m depth). We will investigate the rates of carbon fixation and anaerobic respiration of PV-1 by using our high-pressure chemostat. Further, we propose to investigate the synthrophic growth kinetics of a co-culture composed of the fermentative, hydrogen-producing piezophile, Marinitoga piezophila, and the hydrogenotrophic Nautilia strain PV-1. We anticipate that understanding the pressure adaptations of this strain PV-1, as well as its interactions with heterotrophic bacteria with whom it shares its ecological niche, will provide a unique opportunity to define the spatial and temporal variability of the subseafloor biosphere in the Earth's oceanic crust. Watch our video on the high pressure/high temperature chemostat.

Vertex Pharmaceuticals VOICE Project Phase II (with R. Lutz): Deep-sea drug discovery from hydrothermal vents. December 1, 2015 - March 15, 2017. Watch our video on anaerobic microbiology.

NSF-MCB: Collaborative Research (with D. Giovannelli and D. Foustoukos): Evolution of early metabolism: Carbon fixation, anaerobic respiration and ROS detoxification in the anaerobic vent bacterium, Thermovibrio ammonificans. National Science Foundation. August 15, 2015 - August 14, 2018. Watch our video on the high pressure/high temperature chemostat.
Summary: Bacteria that can live without oxygen (anaerobes) and survive in hot environments (thermophiles) inhabit extreme environments such as deep-sea hydrothermal vents that resemble the early Earth. These modern-day bacteria co-evolved with our planet, and as a result, these organisms carry both ancestral and more recently acquired genes and can be used as models to reconstruct the evolution of microbial processes, including how these bacteria obtained energy and the carbon needed to grow. To gain insight into these processes Thermovibrio ammonificans, an organism that inhabits deep-sea hydrothermal vents, will be studied. Integrated into these studies will be outreach activities for middle and high school students. Lesson plans will be developed and used in after-school programs, in professional training programs for K-12 educators, and informal activities such as the 4-H Summer Science Program.

NASA Exobiology (with F. Robb): Sentinel Microbes that Utilize Carbon Monoxide as Energy and Carbon Source. July 30, 2015 - July 29, 2018.
Summary: Chemoautotrophy—which is the anchor that embeds the biosphere within geochemistry— is grounded on carbon-fixation, the transformation of C1 compounds into small organic molecules and hence into the large array of organic compounds that constitute metabolism. Carbon monoxide (CO) is the most abundant C source in the cosmic gas phase, and follows after hydrogen as the most common gas in the universe. This proposal seeks to model the evolution of metabolism for carbon fixation into early life forms and we consider utilization of CO an excellent candidate for the carbon and energy source in the first life forms.

Vertex Pharmaceuticals VOICE Project Phase I (with R. Lutz): Deep-sea drug discovery from hydrothermal vents. May 29, 2015 - November 30, 2015.

Center for Dark Energy Biosphere Investigations (C-DEBI): Heterotrophy in deep-sea reducing environments: Physiology and metabolism of aerobic hydrocarbonoclastic bacteria. March 1, 2013 - February 28, 2014.

NSF Dimensions of Biodiversity: Collaborative Research (with S. Sievert and D. Foustoukos): An integrated study of energy metabolism, carbon fixation, and colonization mechanisms in chemosynthetic microbial communities at deep-sea vents. National Science Foundation. October 1, 2011 - September 30, 2014. Read more about the EPR project or watch our R/V Atlantis cruise video.
Summary: We propose a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, we 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.

NSF Biological Oceanography: Collaborative Research (with S. Sievert and D. Foustoukos): Autotrophic carbon fixation at a shallow-water hydrothermal system: Constraining microbial activity, isotopic and geochemical regimes. National Science Foundation. October 1, 2011 - September 30, 2013. Read more about the Milos project.
Summary: We propose a research program that employs a powerful combination of cutting-edge research tools aiming to improve our understanding of autotrophic carbon fixation and its chemical and isotopic signature along environmental gradients in the shallow water hydrothermal system of Milos island, Greece.

NSF Supplement to NSF MCB Transcriptional analysis of the deep-sea vent Epsilonproteobacterium, Caminibacter mediatlanticus, in response to different growth conditions. July18, 2011 - June 30, 2012.

InterRidge Student Fellowship to support Italian graduate student Donato Giovannelli, 2011 - 2012.

NSF RIDGE: Collaborative Research (with R. Lutz, G. Luther and T. Shank): Integrating geological, chemical, and biological processes: Implications for ecological succession on the East Pacific Rise. National Science Foundation. September 1, 2009 – August 31, 2010.
Summary: We propose to characterize the pre- and post-eruption environmental context of chemical, microbial and metazoan colonization over time, with the additional goal of identifying the relevant scales of integration and synthesis of our ecological observations and experiments for future investigations of community dynamics at hydrothermal vents.

NSF-MCB (Metabolic Biochemistry, with E. Bini): Transcriptional analysis of the deep-sea vent Epsilonproteobacterium, Caminibacter mediatlanticus, in response to different growth conditions. March 15, 2009 - March 31, 2012.
Summary: This project combines physiological experiments, carried out using batch, continuous cultures, and in-situ incubations, with the quantification of the expression of specific genes (by qRT-PCR) in the deep-sea vent bacterium Caminibacter mediatlanticus, using information derived from the genome sequence of this organism. The significance of the proposed study rest in the fact that gene expression in C. mediatlanticus will be investigated under growth conditions that reflect, in terms of concentrations of nutrients, those encountered by this organism in its natural environment. Such genome-enabled studies are critical to acquire fundamental information on gene expression in organisms that are ecologically relevant in their natural habitat, and to bridge the gap between laboratory-based investigations of pure cultures and environmental studies of natural microbial communities.

NSF Center for Environmental and BioInorganic Chemistry (CEBIC - P.I.: Dr. F. Morel, Princeton University): Alkane Oxidation in Pure Cultures and Natural Microbial Communities from Deep-Sea Hydrothermal Vents: Linking Diversity and Function. October 1, 2005 - September 30, 2006. Subcontract.
Summary: The proposed work focuses on alkane-oxiding bacteria, a group of organisms which has not been investigated in detail in marine geothermal environments, but which we are showing to be relevant at deep-sea hydrothermal vents. Our work will specifically investigate the link between diversity and function in this class of organisms by targeting the alkB gene, which encodes for the alkane hydroxylase, a key enzyme in the oxidation of n-alkanes.

NSF MIP Collaborative Research (with K. Casciotti and S. Sievert): Physiology and Molecular Ecology of Thermophilic Nitrate-Reducing Microorganisms at Deep-Sea Hydrothermal Vents. June 15, 2005 - May 31, 2008. No cost extension to May 31, 2009.
Summary: This study will investigate the physiology and ecology of thermophilic, nitrate-reducing microorganisms at deep-sea hydrothermal vents. Since the microbial contribution to the nitrogen cycle at deep-sea hydrothermal vents remains largely unknown, this study is designed to fill this gap. Recent studies revealed the occurrence of novel thermophilic microorganisms that couple the reduction of nitrate with autotrophic CO2 fixation in marine geothermal environments. The ecological significance of such a microbial community at deep-sea vents is twofold: 1) these organisms contribute to the primary productivity by fixing CO2, and 2) their nitrate respiratory metabolism (namely, the reduction of NO3- to NO2-, N2, or NH4+) implicate that nitrogen is conserved within the vent system and is recycled into the vent nitrogen cycle. This research will integrate novel cultivation and molecular techniques with stable isotope analyses to explore the physiology of nitrate-reducing microorganisms, and to assess their functional diversity and activity. By establishing a link between physiology, phylogeny and activity, this study will contribute to our understanding of the ecological relevance of nitrate-reducing organisms at deep-sea vents, as well as their contribution to both the carbon and nitrogen cycling. This research will also contribute to the expansion of the database of genes relevant to CO2 fixation and NO3- reduction, allowing for the improvement of detection tool for monitoring these microbial processes in the environment. This project will offer training opportunities to one graduate student and several undergraduate students, and it will support educational and outreach activities associated with several NSF-sponsored programs (e.g., the Mid-Atlantic Center for Ocean Science Education Excellence and the Student Experiments at Sea).

NSF REU Supplement to NSF MCB Microbial Interactions and Processes: Physiology and molecular ecology of thermophilic nitrate-reducing microorgansisms at deep-sea hydrothermal vents. June 15, 2006 - May 31, 2007. Vetriani, C.

NSF RIDGE Collaborative Research (with R. Lutz, G. Luther and T. Shank): Integrated Studies of Biological Community Structure at Deep-Sea Hydrothermal Vents. October 1, 2003 - September 30, 2007. Supplement and extension to March 31, 2009.
Summary: Our proposed studies represent an integrated program designed to assess factors responsible for biological community structure at hydrothermal vents in the area between 9°49.61' and 9°50.36'N (known as the Biologic-Geologic Transect) along the crest of the East Pacific Rise (EPR). The objective of this multi-disciplinary effort is to gain a fundamental new understanding of the biological, chemical, and physical characteristics, variability, and processes affecting organism community structure (from microbes to megafauna) in deep-sea vent systems. We have selected study sites which we feel are optimal for building upon the extensive recent data sets obtained in, or in close proximity to, the 9°50'N EPR region, an area heavily impacted by an April 1991 volcanic eruption along the ridge crest. These are also sites that should maximize integration with a variety of envisioned geophysical (e.g., seismic) and geochemical (e.g., major element) studies envisioned as being conducted by other workers.
Our proposed studies are designed to address the following broad hypotheses:
(1) Dramatic changes in biological community structure at vents are correlated with seismic, tectonic and/or volcanic activity within the region.
(2) Vent fluid chemistry (principally sulfide speciation and concentration) is the predominant factor controlling the structure of vent communities.
(3) The structure of microbial communities associated with diffuse flows varies with time, temperature, and in response to differences in oxygen, iron, manganese and sulfur speciation.

NSF Biocomplexity: EREUPT (with P. Falkowski, A. Knoll, O. Schofield and K. Miller): The Evolution and Radiation of Eucaryotic Phytoplankton. September 1, 2000 - August 31, 2005.

Joint Genome Institute: Metagenomes of chemosynthetic microbial biofilms from deep-sea hydrothermal vents.

Deep-Sea Microbiology Lab/Molecular Research LP/Rutgers Biological Mass Spectrometry Facility: Metagenomes and metaproteomes of microbial biofilms and sediments from shallow-water gas vents.

Deep-Sea Microbiology Lab/MicrobesNG, Biotechnology and Biological Sciences Research Council, England/Rutgers Biological Mass Spectrometry Facility: Genome and proteome of the piezophilic Epsilonproteobacterium, Nautilia sp.strain PV-1.

Deep-Sea Microbiology Lab/MicrobesNG, Biotechnology and Biological Sciences Research Council, England: Genomes of new bacterial genera and species isolated in the DSML.

Deep-Sea Microbiology Lab/Bigelow Laboratory for Ocean Sciences: Metatranscriptomes of chemosynthetic microbial biofilms from deep-sea hydrothermal vents.

Deep-Sea Microbiology Lab/Rutgers Biological Mass Spectrometry Facility/University Greifswald, Germany: Proteome of Thermovibrio ammonificans.

Department of Energy/Joint Genome Institute: Genome of Thermovibrio ammonificans DSM 15698.

Gordon and Betty Moore Foundation: Genome of Caminibacter mediatlanticus DSM 16658.

Rutgers University, Research Council Grant “DNA uptake in bacteria from marine geothermal habitats”. 2020-2021.

Rutgers University, Research Council Grant “Phage induction of lysogenic bacterial isolates from deep-sea hydrothermal vents”. 2012 - 2013.

Rutgers University, Research Council Grant “Analysis of functional gene transcripts in microbial chemosynthetic biofilms from deep-sea hydrothermal vents ”. 2011 - 2012.

Rutgers University, Research Council Grant “Development of a system for the genetic manipulation of the deep-sea vent Epsiloproteobacterium, Caminibacter mediatlanticus”. 2008 - 2009.

Rutgers Undergraduate Research Fellow Program. “Application of Fluorescent In-Situ Hybridization (FISH) for the Quantitative Detection of Nitrate-Reducing Bacteria from Deep-Sea Hydrothermal Vents". 2004– 2005.

Department of Agriculture and NJAES: “Discovery and Biotechnological Applications of Novel Microorganisms from High Temperature Environments”. 2001-2004.

Rutgers University, Basic Research Grant "Assessment of the Ecological Relevance of Nitrate-Ammonifiyng Microorganisms from Deep-Sea Vents". 2004.

Rutgers University, Research Council Grant “Isolation of Anaerobic Thermophilic Bacteria from Hydrothermal Vents”. 2003 - 2004.

Rutgers Undergraduate Research Fellow Program. “Isolation of Thermophilic, Chemolithotrophic, Nitrate-Reducing Bacteria from Deep-Sea Hydrothermal vents. 2003 – 2004.

Institute of Marine and Coastal Sciences/Rutgers University Summer Research Program “Microbial Oxidation of n-Alkanes: Isolation of Organisms from Deep-Sea Vents and Cold Seeps, and Identification of Alkane Hydroxylase Genes”. 2003.