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
04:30 PM
UNRAVELING THE INFECTION DYNAMICS AND BIOGEOCHEMICAL EFFECTS OF PARASITIC MARINE PROTISTS USING A MULTI-OMICS APPROACH (9148)
Primary Presenter: Sean Anderson, University of New Hampshire (seanceltics34@gmail.com)
Parasitic protists in the alveolate group, Syndiniales, are highly diverse and prevalent in global marine and freshwater habitats. However, Syndiniales parasite-host infection dynamics remain unclear, including strain-level variability and the influence of parasitism on carbon cycling and bacterial consumption of labile dissolved organic matter (DOM). Here, we used multiple ‘omics methods to explore infection of the same dinoflagellate host, Scrippsiella acuminata, by two Syndiniales strains (4401 and 4390). Untargeted metabolomics revealed significant differences in the composition of extracellular metabolites between parasite strains, time over the infection cycle, and infected vs. host (and spore-only) controls. Specific features were significantly elevated (log2 fold) in infected treatments, representing compounds of interest that may indicate infection. Strain-level physiological differences were also observed, namely higher infection success (38% infected) for 4401 compared to 4390 (12%). Lastly, we performed an inoculation experiment with 4401 filtrate to examine bacterial responses via metabarcoding and metatranscriptomics. Initial results confirmed the rapid response of natural bacterial communities to labile DOM (6 hours) and revealed a shift in composition after 24-48 hours that favored copiotrophic taxa (e.g., Cytophagales). This work provides new insights into the strain-level infection dynamics and biogeochemistry of marine parasitic protists and reinforces the importance of integrating multiple ‘omics tools to better define parasitism in microbial food webs.
04:45 PM
HYPOXIA DISRUPTS METABOLISM IN CORAL AND SEA ANEMONE LARVAE (8917)
Primary Presenter: Benjamin Glass, University of Pennsylvania (benglass@sas.upenn.edu)
Anthropogenic environmental inputs are driving seawater hypoxia in tropical coral reefs and temperate estuaries. Little is known regarding how the larvae of reef-building corals and estuarine sea anemones are impacted by hypoxia, yet this knowledge is critical for predicting species’ trajectories. To explore this key question, we exposed stage-matched larvae (planulae) of the reef-building corals Galaxea fascicularis and Porites astreoides and the sea anemone Nematostella vectensis to a simulated hypoxic event (6 h at 2 mg dissolved oxygen L-1). Interestingly, larvae of all three species decreased swimming following hypoxia, while only the coral larvae showed declines in aerobic respiration rates. These responses were correlated with changes in metabolite abundances quantified via liquid chromatography-mass spectrometry. Specifically, larvae exposed to hypoxia showed decreases in aerobic pathways including fatty acid oxidation and oxidative phosphorylation, instead relying on glycolysis, ketone body usage, the citric acid cycle, and branched-chain amino acid metabolism to produce cellular energy. While these metabolic adjustments likely promoted short-term survival, all three species still displayed decreases in long-term performance (e.g., growth). Thus, metabolic acclimation was insufficient to protect larvae from the negative effects of hypoxia. Overall, these findings demonstrate that hypoxia presents a significant threat to coral and sea anemone early life stages, emphasizing the need to limit the drivers of ocean deoxygenation for their persistence.
05:00 PM
Intra- and extracellular metabolomics reveal new dimensions of Prochlorococcus activity over diel light/dark cycles (9494)
Primary Presenter: Kathryn Halloran, Woods Hole Oceanographic Institution (khhalloran@gmail.com)
Prochlorococcus, the dominant phytoplankton in oligotrophic oceans, synchronizes with daily changes in light availability and thus displays diel rhythmicity in its cell cycle, transcriptome, and proteome. This synchronization has significant implications for downstream ecosystem function and carbon cycling, as heterotrophic organisms respond to daily fluctuations in fixed organic carbon. However, exudation and cross-feeding are difficult to predict from sequence-based data, and diel rhythms of exudation have not been characterized in Prochlorococcus. To address this gap, we took a metabolomics approach to characterizing Prochlorococcus (strain MIT9301) cultures grown under a diel light/dark cycle. We sampled for intra- and extracellular metabolites, and made use of multiple new methods (aniline and benzoyl chloride derivatization) for measuring previously unquantified extracellular metabolites. We found that both intracellular and extracellular metabolite concentrations displayed diel rhythmicity, allowing us to make molecule-specific and temporally resolved connections between Prochlorococcus activity and released labile carbon. We also found evidence that Prochlorococcus reassimilates metabolites which it previously released into solution. This reassimilation may be a means of retaining nutrients like nitrogen or phosphorous, and could generate competition between Prochlorococcus and co-occurring heterotrophic microbes for released Prochlorococcus metabolites. Together this work expands our understanding of Prochlorococcus physiology and marine carbon cycling.
05:15 PM
INTERROGATION OF METABOLIC CONTROL AND GENE REGULATORY MECHANISMS DURING STRESS IN THE PICOPHYTOPLANKTON PICOCHLORUM CELERI USING MULTIOMICS (9247)
Primary Presenter: Bishoy Kamel, Lawrence Berkeley National Laboratory (bskamel@lbl.gov)
As an important constituent of the marine picophytoplankton, photosynthetic eukaryotes such as Picholorum celeri play an important role in the global carbon cycle and primary productivity in coastal ecosystems. In addition, small cell size and high growth rates make them ideal candidates for biomass production and potential applications in the mitigation of CO2 emissions. Using multiomics data from a multi-factorial-design experiment and modeling approaches, we integrated proteomics, metabolomics, and transcriptomics into a systems biology model to probe the complex interactions between metabolism, rhythmicity, cell-cycle, and stress. We employed state of the art methods such as DNA affinity purification sequencing (Dap-seq), to build a regulatory network that, when combined with the metabolic model of P. celeri, provided a mechanistic understanding of the cellular processes at the interplay between metabolism and gene regulation. The results highlighted key adaptations of P. celeri to high salinity and temperature, and the ability to shift carbon fixation strategies accordingly through the orchestration of multiple molecular pathways in concert with key rhythmic cellular processes. The research framework established in this study underscores the critical role of multiomics integration in exploring non-model organisms and expanding our foundational understanding of molecular pathways in algae across various ecosystems.
05:30 PM
TRANSCRIPTIONAL MARKERS OF ORGANIC SUBSTRATE AVAILABILITY IN A COASTAL MARINE BACTERIUM (8812)
Primary Presenter: Samantha Cerda, University of North Carolina at Chapel Hill (samanth@email.unc.edu)
The marine carbon pool is a complex source of nutrients for microbes, which is found within the context of highly complex microbial community, making it difficult to identify which carbon substrates are supporting which microbes in the ocean. One approach to identifying which substrates are driving the marine carbon cycle is to use bacterial cells as a biosensor of the labile substrates available to the community using transcriptomics. To determine if transcriptomics could be used as a reliable indicator of substrate availability, a batch culture approach was taken with the heterotrophic bacterium Rugeria Pomeroyi (DSS-3)- a common and abundant bacteria in coastal oceans. DSS-3 was grown in a glucose and carbon substrate mix including succinate, DMSP, TMAO, leucine, glycerol, and benzoate. RNA was sequenced at the exponential phase of growth and differential gene expression for each treatment was quantified. We are able to see strong correlations between carbon substrate availability and gene expression, specifically in transporter genes and genes at the beginning of these various metabolic pathways. Overall, we were able to identify several genes in metabolic pathways enriched for DSS-3 that can be applied to environmental metatranscriptomic datasets, offering an avenue to identify carbon substrates present without a need for complex chemical analyses. This work is providing insights into the relationship between carbon substrate availability and an organisms physiological and metabolic responses, generating insights into microbial roles in ocean carbon cycling.
05:45 PM
Understanding niche partitioning among microbial taxa in the Central Pacific using Metaproteomics (9275)
Primary Presenter: Huck Bagby, University of Georgia (hcb07500@uga.edu)
Analyzing the distribution of microbial functional roles can provide much needed context for understanding microbial communities in the Central Pacific. This presentation is focused on an analysis of variation among integral proteins along multiple scales. The main two points of emphasis are the variance of key substrate binding transport system proteins in Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, Actinobacteria, and Euryarchaeota and photosynthetic proteins in Prochlorococcus and Synechococcus. Metaproteomics data, from the 2016 ProteOMZ expedition, was analyzed to study spatial variation among bacterial community composition and the differences in function over space. The cruise sampled sites across 5,000 km through parts of the North Pacific Subtropical Gyre, Eastern Tropical North Pacific, and the equatorial upwelling zone. The first emphasis focuses on how substrate preference by heterotrophic prokaryotes varies along vertical scales by analyzing substrate binding transport proteins of carbon substrates. The second emphasis addresses challenges in light harvesting, photoinhibition, and iron stress experienced by picocyanobacteria by focusing on variance in photosynthetic protein distributions. Both Prochlorococcus and Synechococcus have unique responses to these issues and tracking the associated proteins can provide insight into the environmental challenges they face. The main takeaways for each emphasis are a definitive stratification of metabolic transporters and contrasting niche strategies between picocyanobacterial taxa.
SS08C - Integrating and developing ‘omics technologies in aquatic community ecology
Description
Time: 4:30 PM
Date: 31/3/2025
Room: W207CD