Year: 2021
Type: article
Abstract: Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus strains and their transcripts were more abundant than others in individual vent sites, and among the genes differentiating the Methanothermococcus SAGs were those related to nitrogen fixation and the CRISPR/Cas immune system. SAGs possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
Source: Frontiers in Microbiology
Institutions: Carleton College, Finch Therapeutics (United States), Centre National de la Recherche Scientifique, Université de Montpellier, Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Institut de Recherche pour le Développement, Marine Biological Laboratory, Bigelow Laboratory for Ocean Sciences, Woods Hole Oceanographic Institution
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,950
Awards: VIRUSES ARE UBIQUITOUS IN THE WORLDS OCEANS PLAYING AN ESSENTIAL ROLE IN BIOGEOCHEMICAL PROCESSES WHILE REPRESENTING A VAST SOURCE OF GENETIC DIVERSITY. YET WE STILL KNOW LITTLE ABOUT NATURAL VIRAL COMMUNITIES. HYDROTHERMAL SYSTEMS HAVE BEEN PREVALENT ON EARTH SINCE THE PLANET WAS FORMED AND ITS HYPOTHESIZED THAT LIFE MAY HAVE ORIGINATED AND EVOLVED NEAR DEEP-SEA HYDROTHERMAL VENTS MAKING THEM THE MOST ANCIENT CONTINUOUSLY INHABITED ECOSYSTEMS ON THE PLANET. EXTANT ORGANISMS LIVING IN THESE ANALOGUES OF EARLY HABITATS MAY STILL HARBOR GENETIC AND METABOLIC CHARACTERISTICS OF EARLY LIFE. VIRUSES PLAY A CRITICAL ROLE IN THE ULTIMATE SURVIVAL OF MICROBES BY MEDIATING HOST FUNCTIONAL DIVERSIFICATION AND ENHANCING ADAPTABILITY VIA HORIZONTAL GENE TRANSFER AND LYSOGENY A REPLICATION STRATEGY ENABLING THE VIRUS TO INCORPORATE ITS GENOME INTO THEIR HOSTS (PROPHAGE). IN THIS PROJECT WE WILL EXAMINE THE LIFESTYLE AND IMPACT OF VIRUSES ON MICROBIAL COMMUNITIES IN THE SUBSEAFLOOR OF DEEP-SEA HYDROTHERMAL VENTS. WE WILL INVESTIGATE DNA AND RNA VIRUSES THE LATTER COMPRISING THE MOST ANCIENT GROUP OF VIRUSES ON OUR PLANET. OUR RESEARCH PLAN WILL DETERMINE INFECTION DYNAMICS AND INTERROGATE HOST ASSOCIATIONS BOTH OF WHICH ARE KNOWN TO LEAD TO PHYSIOLOGICAL ALTERATIONS AND WIDE-RANGING EVOLUTIONARY TRAJECTORIES. SPECIFIC GOALS WE PLAN TO ADDRESS INCLUDE I) DETERMINE PHAGE HOST RANGE AND SPECIFICITY TO DIVERSE MICROBIAL HOST ISOLATES FROM DEEP-SEA HYDROTHERMAL VENTS II) DETERMINE ROLE OF VENT VIRUSES IN MICROBIAL HOST EVOLUTION AND ECOLOGY AT DEEPSEA HYDROTHERMAL VENTS III) IDENTIFY NOVEL RNA VIRUSES FROM DEEP-SEA HYDROTHERMAL VENTS. ELUCIDATION OF THESE GOALS WILL ALLOW US TO BETTER CONSTRAIN THE IMPACT OF VIRAL COMMUNITIES IN THE SUBSEAFLOOR AND EXAMINE THE NATURE OF VIRUS-HOST INTERACTIONS AS MODELS FOR UNDERSTANDING EARLY LIFE. WE WILL USE VIRAL INFECTION STUDIES TO EXPERIMENTALLY INVESTIGATE ISOLATES FROM A PHYLOGENETICALLY DIVERSE COLLECTION OF CULTURED VENT MICROBES INCLUDING BOTH BACTERIA AND ARCHAEA. THE EXISTING CULTURE COLLECTION WILL FACILITATE TESTING HOST-RANGES OF VIRAL ISOLATES INDICATING POSSIBLE EVOLUTIONARY BREAKPOINTS OF VIRAL TRANSFER. CULTURED ISOLATES WILL BE INTERROGATED USING PROPHAGE INDUCTION ASSAYS AND CHALLENGE EXPERIMENTS FOLLOWED BY SEQUENCING AND MICROSCOPY. TO IDENTIFY THE HOST RANGE/SPECIFICITY OF PHAGE ISOLATED PHAGE WILL BE MIXED WITHIN AND BETWEEN RELATED HOST MICROBIAL GENERA. INCREASES IN PHAGE TITERS WILL BE MEASURED TO EVALUATE AMPLIFICATION DURING INFECTION. GENOMIC-BASED TECHNOLOGIES OF VIRUSES AND MICROBES WILL BE LEVERAGED TO INTERROGATE VIRUSES THEIR HOSTS AND INTERACTIONS. WE WILL COMPUTATIONALLY INTERROGATE OMICS INFORMATION FOR EVIDENCE OF VIRAL-MEDIATED CELLULAR GENE TRANSFER AND LYSOGENIC CONVERSION AND HOST IMMUNITY MARKERS RESULTING FROM PAST INFECTION. FINALLY RNA VIRUSES INCLUDING RETROVIRUSES WILL BE CHARACTERIZED VIA HOMOLOGY BINNING AND PHYLOGENETICS FROM COMMUNITY METAGENOMIC TRANSCRIPTOMIC DATA. THE STUDY OF EXTREMOPHILIC ORGANISMS AND THEIR METABOLIC PATHWAYS HABITATS AND DISTRIBUTION IS ESSENTIAL TO UNDERSTANDING THE ORIGIN AND EVOLUTION OF LIFE ON EARTH THE MAIN GOAL OF NASAS EXOBIOLOGY AND EVOLUTIONARY BIOLOGY PROGRAM. VIRUSES ARE IMPORTANT EVOLUTIONARY DRIVERS OF NATURAL MICROBIAL COMMUNITIES AND EXAMINATIONS OF VIRAL COMMUNITIES IN THE ROCK-HOSTED OCEANIC SUBSEAFLOOR ARE JUST BEGINNING THAT HOLD GREAT PROMISE FOR REVEALING NEW INFORMATION ABOUT REMOTE LIFE ON EARTH AND THE POSSIBILITIES FOR LIFE ON OTHER PLANETARY BODIES. OUTREACH ACTIVITIES INCLUDE TRAINING UNDERGRADUATE STUDENTS AT A SMALL LIBERAL ARTS COLLEGE IN CUTTING-EDGE GENOMICS AND BIOINFORMATICS TECHNIQUES AND DEVELOPING AN EXTREME VIRUS MODULE FOR ELEMENTARY SCHOOL STUDENTS, Collaborative Research: Venting Outside the Box - Extending the Known Limits to Seafloor Hydrothermal Circulation and the Chemosynthetic Life it Supports, G1758054977, G2696920255, RII Track-2 FEC: Single Cell Genome-to-Phenome: Integrating Genome and Phenome Analyses of Individual Microbial Cells in Complex Microbiomes, G4104088580, G5974128683, Dimensions: Collaborative Research: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents, G8866926934
OpenAlex ID: W3193419291