Marine microbes have an outsized effect on global ocean ecosystem function and health. Advances in ‘omics’ have revolutionized our knowledge of the distribution, metabolic capacities, and activity of microbes within the biosphere. While the power of individual ‘omic tools is great, there is immense promise if we can successfully integrate across tools to learn more about connections between the diversity of genes, proteins, and molecules. This promise comes with the challenge of matching different data types that have unique taxonomic specificity, biological regulation, and numerical meaning. This session invites contributions that utilize multi-omic approaches which inform on microbial resiliency in the oceans. We encourage submissions that explicitly tackle the challenges of merging multiple ‘omics’ datasets in new ways, those which explore spatial and temporal dynamics, and/or reveal new insights into plasticity and redundancy within microbial communities.
Lead Organizer: Matthew Harke, Gloucester Marine Genomics Institute (matthew.harke@gmgi.org)
Co-organizers:
Kevin Becker, GEOMAR Helmholtz Centre for Ocean Research Kiel (kbecker@geomar.de)
Angela Boysen, Pacific Lutheran University (aboysen@plu.edu)
Benjamin Pontiller, GEOMAR Helmholtz Centre for Ocean Research Kiel (bpontiller@geomar.de)
Presentations
08:30 AM
Introducing Epithemia: A Rhopalodiaceae diatom-diazotroph symbiosis isolated from the North Pacific Subtropical Gyre (6997)
Primary Presenter: Sam Wilson, University (sam.wilson@newcastle.ac.uk)
Two new species of pennate Rhopalodiaceae diatoms (Epithemia pelagica and Epithemia catenata) were recently isolated from North Pacific Subtropical Gyre. The diatoms are unique as they contain nitrogen-fixing endosymbionts that have historically been characterized as independent unicellular cyanobacteria. Laboratory based culture measurements demonstrated that the evolutionary transition from a free-living cell to an endosymbiont has meant that nitrogen fixation is longer restricted to the night and can occur during both day and night. Analysis of global ocean sequence databases revealed Epithemia is widespread through the tropical and subtropical oceans. To learn more about the endosymbiosis, the host and symbiont genomes were recently sequenced as part of the Aquatic Symbiosis Genomics Project. Until now, the marine Rhopalodiaceae-diazotroph symbioses have been overlooked but their ubiquitous presence in the marine environment and their potential as cultured model organisms for the study of organelle evolution provides new insights into nitrogen fixation at the cellular and ecosystem scale.
08:45 AM
MICROBIAL DYNAMICS OF VITAMIN B1 (THIAMIN) IN DANISH COASTAL WATERS (5639)
Primary Presenter: Meriel Bittner, University of Copenhagen (meriel.bittner@bio.ku.dk)
The essential micronutrient vitamin B1 (thiamin, B1) can periodically limit microbial communities and bulk productivity, thereby affecting biogeochemical fluxes. In addition, low environmental concentrations of B1 can cause deficiencies in organisms at higher trophic levels. Previous research has shown that the inability to synthesize B1 (auxotrophy) is widespread among prokaryotes and phytoplankton. However, knowledge about B1 bioavailability and microbial physiology related to B1 is limited. To address this, samples were collected from Danish coastal water masses at a seasonal or diurnal temporal resolution. We combined metagenomics, metatranscriptomics and targeted metabolomics to elucidate the detailed cycling of this micronutrient among microbial communities. Genomic and transcriptomic analyses indicated that 80% of the microbial community was auxotrophic for B1. To overcome B1 auxotrophy, prokaryotes expressed specific transporters or enzymes to use B1 related compounds and salvage B1. In some cases, concentrations of B1 or related compounds could be linked to microbial populations or environmental conditions. Overall, only few microbial populations synthesized B1 in Danish coastal waters, these populations varied depending on time or water mass sampled. The combination of multiple ‘omics-based’ datasets allowed a more in depth understanding of B1 dynamics within microbial communities, and how and which microorganisms contribute to the ecosystem function of B1 synthesis.
09:00 AM
Sifting through the ‘omics’ to uncover the hidden roles of marine microbes (5574)
Primary Presenter: Maggie Sogin, University of California at Merced (esogin@ucmerced.edu)
The protection and conservation of ocean habitats hinges on our understanding of the role marine microbes play in maintaining ecosystem health in the face of environmental change. One strategy towards defining these roles is to leverage ‘omics’ technologies to capture microbial responses to changes in their environment. In this talk, I will highlight our work focused on leveraging emerging ‘-omics’ techniques to undercovering the hidden role of marine microbes across coastal habitats. First, I will provide insights from our ‘omic observations that allowed us to show that sucrose is piling up to mM concentrations underneath seagrass meadows. Specifically, we used a combination of metagenomic, metatranscriptomic and metabolomic analyses, and in situ incubation experiments, to show that sucrose persists in Posidonia oceanica rhizospheres because aromatic-rich dissolved organic matter (DOM) produced by the seagrass inhibits microbial metabolism under low oxygen conditions. I will then outline our current approach towards leveraging ‘omics methods to determine microbial function with host-associated microbiomes. Overall, our work demonstrates the power of ‘omic analysis in furthering our understanding of microbial ecosystem dynamics across ocean regions.
09:15 AM
Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton (4685)
Primary Presenter: Robert Lampe, Scripps Institution of Oceanography (rlampe@ucsd.edu)
Coastal upwelling regions are among the most biologically productive ecosystems in the ocean but may be threatened by amplified ocean acidification from rising atmospheric CO2. Increased acidification is hypothesized to reduce iron bioavailability for marine phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that iron-stressed phytoplankton in an upwelling region respond to short-term acidification exposure with a multitude of iron uptake pathways and strategies that reduce cellular iron demand. A multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2 for up to four days. Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification in conjunction with reductions in cellular iron utilization. Meanwhile, phytoplankton growth, nutrient uptake, and community compositions remained unchanged suggesting that these mechanisms may confer short-term resistance to acidification. By extrapolating these short-term results, we speculate that longer-term exposure to acidification without increased iron inputs may result in increased iron stress for phytoplankton communities.
09:30 AM
Metabolites accumulating within regions of net nutrient regeneration in the California Current Ecosystem (6986)
Primary Presenter: Ralph Torres, University of California, San Diego (rrtorres@ucsd.edu)
The turnover of organic nitrogen is a key process in maintaining marine productivity. In coastal regions, remineralization associated with the enhanced export of organic matter can lead to the accumulation of reduced nitrogen, notably at the primary nitrite maximum. Particle remineralization likely alters the surrounding water in other ways, by adding dissolved organic matter (DOM) that can contribute to nutrient cycling and microbial productivity. An investigation of the dissolved metabolites accumulating at these depths may reveal the role of DOM in driving the microbial ecology of this environment. Here, we measured nutrients, particulate organic matter, bacterial abundance, microbial dynamics via 16S rRNA sequencing and metabolites via solid phase extracted non-targeted metabolomics across multiple Lagrangian-based research cruises within the California Current Ecosystem Long Term Ecological Research program. We observe depth-dependent and diel trends in in-situ nitrite and ammonium concentrations, which we used as proxies to isolate the potential impact of particle remineralization on extracellular metabolite composition by mining non-targeted metabolomics datasets that showed similar trends. Molecular networking conjoined with in-silico annotation tools revealed metabolites and compound classes enriched in nitrogen and sulfur unique to these depths of elevated nitrite and ammonium. Microbe-metabolite correlations further yield information towards understanding the metabolic processes occurring in the water column at elevated recycled nitrogen concentrations.
09:45 AM
Comparing microeukaryote metatranscriptomes and metaproteomes captured using an autonomous underwater vehicle (4742)
Primary Presenter: Natalie Cohen, University of Georgia (cohen@uga.edu)
Marine microeukaryotes can be characterized metabolically and taxonomically through transcripts and proteins, but it is unclear to what extent these biochemical pools are concordant in natural communities. Using an autonomous underwater vehicle, the microbial communities were vertically sampled along the western North Atlantic Ocean. Taxonomy and function were examined using a paired metatranscriptomic and metaproteomic approach. Only protein pools demonstrated strong shifts in vertical structure at the supergroup level, with foraminifera, radiolaria, picozoa, and discoba enriched below 200m, and fungi enriched in seawater collected from below 3,000m. Relatively few haptophyte transcripts were observed in surface waters, yet they were a substantial fraction of the eukaryotic protein pool. We furthermore observed a difference in taxonomic annotations, with on average 38% of eukaryotic proteins unable to be confidently annotated below the supergroup level compared to 21% of transcripts. These proteins were functionally enriched in cytoskeletal components and may represent abundant, evolutionarily conserved proteins. Possible explanations for discrepancies between biochemical pools include lineage-specific loss of protein or RNA during lab processing, differences in RNA/protein composition and ratios among taxonomic groups, growth rate effects, and/or cell lysis during in situ filtration. These findings underscore the utility of paired omics for comprehensively reconstructing microbial community dynamics.
SS060 Omics Ocean Observations to Reveal Microbial Ecosystem Dynamics and Resilience
Description
Time: 8:30 AM
Date: 5/6/2023
Room: Sala Santa Catalina