Advancements in ‘omics tools, such as metagenomics, metatranscriptomics, metabolomics, proteomics, and lipidomics, have revolutionized our understanding of aquatic ecosystems and produced immense amounts of data. Often, different ‘omics data types are interrelated, therefore connecting them has the potential to make research efforts more robust. If we remain siloed, we may miss potentially important components of aquatic systems that could provide insight into important ecological processes in this changing world. However, dealing with “big data” is computationally challenging, and the tools and expertise to glean biological information lags behind abilities to produce the data. Furthermore, there is currently no standardization of practices for collection, processing, or bioinformatic analyses, but there exist many protocols and frameworks that are commonly used within the community. Therefore, better standardizing tools and creating workflows for the integration of different ‘omics data may advance our understanding of aquatic biodiversity, function, and environmental change.
This session aims to highlight research that develops, integrates, and applies ‘omics data to take the pulse of aquatic biodiversity, function, and ecosystem change. For example, studies that couple metagenomics and metabolomics data, or work that focuses on tools to standardize or visualize different types of ‘omics data, would be ideal additions to this session. We invite talks across ecosystems, target organisms, and omic disciplines that highlight how novel omics practices can be leveraged to answer fundamental questions in aquatic ecology, evolutionary biology, and biogeochemistry. Our goal is for this session to stimulate a discussion around best practices in omics and to bring together scientists from diverse disciplines so that we may better leverage and integrate these tools in the coming years.
Lead Organizer: Cynthia Becker, Ithaca College (cynthiabecker95@gmail.com)
Co-organizers:
Alicia Reigel, Washington and Lee University (areigel@wlu.edu)
Jeanne Bloomberg, Woods Hole Oceanographic Institution (jeanne.bloomberg@whoi.edu)
Natalie Cohen, University of Georgia (cohen@uga.edu)
Adrian Marchetti, University of North Carolina Chapel Hill (amarchet@email.unc.edu)
Presentations
09:00 AM
A COMMUNITY-WIDE INTERCOMPARISON OF METATRANSCRIPTOMIC METHODS FOR CHARACTERIZING MICROBIAL EUKARYOTE CONTRIBUTIONS TO THE BIOLOGICAL CARBON PUMP (9118)
Tutorial/Invited: Invited
Primary Presenter: Harriet Alexander, Woods Hole Oceanographic Institution (halexander@whoi.edu)
Microeukaryotes are central players in the biological carbon pump, driving primary production, carbon export, and trophic transfer within the marine food web. Metatranscriptomics, or the sequencing of the total expressed mRNA within a community, has become a broadly used approach in biological oceanography to observe marine assemblages, including their metabolism and ecological functioning. However, critical gaps exist in our understanding of how methodological choices and practices influence downstream biological interpretations, including estimates of community composition and metabolic function. We coordinated a metatranscriptomic intercomparison exercise across a group of 13 labs located in the United States to examine the impact of extraction methods, library preparation, sequencing depth, and bioinformatic approaches on the biological interpretation of marine metatranscriptomic data. Large-volume filters were collected in the deep chlorophyll maximum from the Costa Rica Upwelling Zone and distributed among the labs for extraction and sequencing, resulting in 29 sequenced samples, which varied in extraction methodology and sequencing coverage (from 2 to 113 gigabase pairs). The number of assembled transcripts varied, as did the content of proteins predicted from recovered transcripts. This type of community-led intercomparison effort is a first step in assessing how meta-omic data might be influenced by methodological choices both in the lab and in silico, but work remains to discern sources of variability and improve data interoperability.
09:15 AM
APPROPRIATE REFERENCE DATASETS ARE CRUCIAL FOR PROPER INTERPRETATION OF META-OMICS DATASETS (8976)
Primary Presenter: Shiri Graff van Creveld, University of Washington (shirig@uw.edu)
Marine food webs are primarily built upon diverse unicellular phytoplankton. Analysis of phytoplankton community structure using environmental ‘omics methods depend on comparisons to reference datasets. Therefore, our understanding of the taxonomy and function of a natural community depends on the quality and relevance of the reference datasets. Although the Pacific Ocean is the largest ecosystem on Earth, open ocean Pacific phytoplankton are woefully underrepresented in algal culture collections and sequencing datasets. Here I demonstrate how the addition of newly sequenced isolates in reference datasets alters our understanding of in situ microbial communities and their environmental adaptations. Using a metatranscriptomic analysis of flavodoxin expression in Pacific diatoms across environmental gradients and on-deck incubations in the North Pacific, I show the impact of these additions. Additionally, I isolated and characterized dozens of novel open-ocean Pacific phytoplankton strains[1] that we are currently sequencing and adding to the next version of our Marine Functional EukaRyotic Reference Taxa (MarFERReT) dataset[2]. We hope that ongoing community contribution to the MarFERReT dataset through its Github repository[3] will enhance future analysis of phytoplankton’s data from diverse environments. References: [1] Graff van Creveld, S., et al. (2024). Journal of Phycology. [2] Groussman, R. D., et al (2023). Scientific Data, 10(1), 926. [3] https://github.com/armbrustlab/marferret
09:30 AM
DEVELOPMENT AND APPLICATION OF A LARGE-SCALE PANGENOMIC FRAMEWORK FOR THE STUDY OF CYANOHAB TAXON MICROCYSTIS (9422)
Primary Presenter: Chris McLimans, University of Oklahoma (cmclimans@ou.edu)
Cyanobacterial harmful algal blooms of species, such as the common and often toxigenic Microcystis, are predicted to increase in frequency and magnitude as nutrient loading and global warming impact freshwater system, this negatively affecting food webs, ecosystem function, and fresh water access globally. Historically, ecological characterization and managing risks[JEB1] associated with this problematic taxon has been clouded by cryptic morphological and genetic diversity. Morphology of Microcystis may shift with environmental conditions, while genetic classification (e.g., 16S) indicates a single species with multiple ecotypes. Leveraging large-scale pangenome analyses that integrate hundreds of genomes, we established a robust framework that resolves previously hidden biodiversity in Microcystis. We identified 26 genome clusters, 16 of which qualify for species demarcation, that serve as the basis for examining functional trait variation between species. For example, this framework enabled resolution of 4 species with the toxin trait, containing all 10 genes required for microcystin synthesis, while 11 species lacked all microcystin synthesis genes. Interestingly, we resolved a single species containing both toxic and non-toxic genotypes which may reflect loss of the trait in a single species. Similar analyses for other ecotype characteristics are underway. Overall, we describe a valuable framework to integrate large datasets to resolve historical discrepancies in the classification of aquatic taxa and its application to improve the study of a globally problematic taxon.
09:45 AM
Developing Quantitative Understanding of Marine Microbiology Using Nutrient Colimitation Observations in Escherichia coli (9490)
Primary Presenter: Mia Franks, University of Southern California (mgfranks@usc.edu)
Marine microbes are integral to biogeochemical cycling. In turn, micro- and macro- nutrients are known to limit their spatial distribution, growth yields, and growth rates. Previous research on nutrient limitation states that the lowest relative bio-necessary nutrient required for growth, is the main limiter of primary production. However, both laboratory and field experiments show unexpected deviations, suggesting that multiple nutrients can limit growth (colimitation). This implies that different nutrient limitations are not mutually exclusive. Despite these observations, research is lacking on how multiple nutrients simultaneously affect growth rates and cellular mechanisms. I present proteomic biomarkers from the model organism Escherichia coli reflecting the cellular biology in carbon and nitrogen colimitation. I will use these preliminary biomarkers to determine the (co)limitation state for microbes at the San Pedro Ocean Time Series, a proxy for the oligotrophic ocean local to Los Angeles. At this location, we push the lower limits of high quality metaproteomic volumes, and I present on the ability of smaller sample volumes to represent microbial communities, despite environmental heterogeneity. Developing a quantitative understanding of microbial interactions with environmental nutrient concentrations will deepen our understanding of microbial thinking and increase our ability to predict microbial responses to changing environmental conditions.
10:00 AM
Tracking the cycling of organic osmolytes in the ocean (9517)
Primary Presenter: Winifred Johnson, University of North Carolina Wilmington (johnsonwm@uncw.edu)
In the ocean, around 50% of fixed carbon is cycled through the microbial food web each day, representing a large flux of energy and matter. A sizable portion of this flux is likely comprised of organic osmolytes, which are small molecules that are either synthesized or transported into cells to maintain osmotic balance across cell membranes. These molecules are small, polar and structurally diverse encompassing a variety of sugars, amino acids and derivatives, and sulfur-containing metabolites. Due to this structural complexity, these molecules have primarily been studied individually or as part of their structural classes rather than as a functional group. We are adapting analytical and metabolomics tools to study this group of molecules in culture and across marine and coastal gradients. Here, we will discuss differences in osmolyte composition in phytoplankton cultures, in a variety of coastal aquatic environments, and the potential implications for biogeochemical processes.
10:15 AM
A spatially resolved subcellular proteome map provides insight into protein function and trace metal distribution in Thalassiosira pseudonana (9731)
Primary Presenter: Loay Jabre, Woods Hole Oceanographic Institution (loay.jabre@whoi.edu)
Thousands of chemical reactions take place simultaneously within each phytoplankton cell. These reactions—collectively, metabolism—depend on specific molecular machinery (proteins) and specific subcellular conditions to occur. Eukaryotic phytoplankton compartmentalize these reactions within organelles, where the necessary conditions and proteins are maintained. Understanding the subcellular locations of proteins and their proximity to other proteins and cofactors (such as metals) is therefore essential for understanding phytoplankton metabolism. We developed a "spatial omics" method that uses precise cell lysis followed by ultracentrifugation to separate intact and viable organelles into several distinct fractions. We then applied a combination of untargeted mass spectrometry-based proteomics, metalloproteomics, and enzyme rate measurements to study these organellar fractions in detail. With this approach, we constructed a spatially resolved subcellular proteome map of the diatom Thalassiosira pseudonana, which we used to probe the subcellular locations of thousands of proteins in a single experiment. This enabled us to gain deeper insight into protein function and protein resource allocation in phytoplankton. Further, by integrating trace metal and metabolic rate measurements into these subcellular proteome maps, we can examine the elemental distribution within phytoplankton cells, the roles of metals in metabolism, and the potential impact of shifts in chemical gradients on ocean metabolism and ultimately biogeochemistry.
SS08A - Integrating and developing ‘omics technologies in aquatic community ecology
Description
Time: 9:00 AM
Date: 31/3/2025
Room: W207CD