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
02:30 PM
Leveraging standardized ‘omics datasets from The Great Lakes Atlas of Multi-omics Research (GLAMR) for harmful algal blooms monitoring and forecasting (9581)
Tutorial/Invited: Invited
Primary Presenter: Erik Kiledal, University of Michigan (kiledal@umich.edu)
Lake Erie, the shallowest and warmest of the Laurentian Great Lakes, experiences annual Microcystis-dominated harmful algal blooms. These blooms vary in timing, extent, and toxicity. Omics approaches have improved our understanding of bloom biology, and also serve as a powerful monitoring tool. However, omics datasets are often produced to serve the needs of individual studies and typically do not have the spatial or temporal coverage to adequately capture changes in lake biology, or facilitate modeling work. To this end we built the Great Lakes Atlas of Multi-omics Research (GLAMR), which aims to unite and standardize all Great Lakes omics datasets and associated metadata. While existing bloom models based on nutrient loading, weather, satellite imagery, and hydrodynamic models are reasonably able to forecast bloom extent, location, and seasonal severity, predicting production of the toxin microcystin has remained elusive. In this work, we leveraged omics datasets and paired water quality measurements from public omic datasets and long-term monitoring efforts to train and evaluate models of toxin production, highlighting the utility of ‘omics data standardization and re-use.
02:45 PM
MULTI’OMICS INDICATE DEPTH-DISCRETE PARTITIONING OF NITROGEN METABOLISM IN A TOXIC PLANKTOTHRIX RUBESCENS BLOOM IN THE WINTER WATER COLUMN (8956)
Primary Presenter: Brittany Zepernick, University of North Carolina at Chapel Hill (bnzeper95@gmail.com)
In this study, we conducted a metagenomic+metabolomic field study to address a community concern in our own back yard: What was causing Mead’s Quarry (Knoxville, TN) to turn pink? A case study was designed and implemented by graduate students at the University of Tennessee-Knoxville enrolled in the course-based authentic learning experience Advanced Techniques in Field Microbiology (Spring 2023). The team leveraged a $3,000 budget to conduct meaningful, depth-discrete multi ‘omics research. Metagenomic analyses and phylogenetic confirmations revealed the quarry was dominated by a bloom of the pink cyanobacterium Planktothrix rubescens. Physiochemical analyses indicated the bloom was concentrated in the cold, light-limited metalimnion, with microcystin-LR levels exceeding the U.S. EPA limit for recreational exposure. Untargeted metabolomics suggested P. rubescens communities were differentially partitioning nitrogen metabolism strategies by depth (0.5 m vs. 2.0 m). This work has revealed a previously underappreciated role of arginine biosynthesis and pyrimidine metabolism in the ecological success of P. rubescens. We subsequently provide these results as a novel ecophysiological hypothesis contributing to the proliferation of this harmful cyanobacterial bloom former in the light-limited metalimnion. Cumulatively, we reinforce the synergistic employment of multiple meta ’omics techniques is feasible on a small-scale while proving impactful on a larger-scale.
03:00 PM
eDNA AS A COMPLEMENTARY TOOL FOR OYSTER RESTORATION EFFORTS IN THE HAMPTON RIVER (9754)
Primary Presenter: Jeanette Davis, Hampton University (Jeanette.davis@hamptonu.edu)
The emerging science of eDNA can provide a continuous flow of data which is vital for protecting and managing aquatic resources, such as oyster reefs. Within the last decade, species detection from eDNA has shown exciting potential for routine species surveys. Oyster reef environments provide tremendous ecological, economic, and cultural value. Currently, oyster reefs of the Hampton River are heavily degraded and condemned for human consumption due to contamination and poor water quality. However, the oysters of the Hampton River continue to hold importance for the communities of Hampton Roads, particularly those that are historically underrepresented and there have been recent oyster restoration efforts. This project aims to use eDNA as a long-term tool to assess and monitor species biodiversity before, during and after oyster restoration efforts in the Hampton River. Three sites were selected to represent a natural oyster reef site, a planting oyster reef site and a control site that lacks oysters. It is important to set baseline of ecological data, such as community structure, species richness, and seasonal shift especially in a data-poor system such as of the Hampton River. We then aim to create a restoration site planning tool that uses eDNA data to identify leverage points where future habitat restoration would maximize biodiversity benefits.
03:15 PM
TAKING THE PULSE OF COASTAL ECOSYSTEMS THROUGH TRANSCRIPTOMICS: INSIGHTS FROM THE BLUE DAMSELFISH OF OKINAWA (9099)
Primary Presenter: Emma Gairin, Okinawa Institute of Science and Technology Graduate University (emma.gairin@hotmail.fr)
40% of humans live within 100 kilometres of the ocean, causing unprecedented degradation to coastal habitats. This is often monitored with water parameters or biological community surveys, which are not informative of the compounded impact of stressors on organisms. Transcriptomics offer a novel method to assess the impact of human activities on organisms by screening the expression level of all genes, revealing sublethal effects and acclimation limits to local conditions. We obtained the transcriptomes of adult and juvenile blue damselfish Chrysiptera cyanea in 18 coastal locations, from urban bays to isolated reefs, in Okinawa, Japan. The transcriptomic landscapes were influenced by urbanisation level at the level of all genes and for subsets of genes. Among these, marker genes for chemical pollution exposure were significantly upregulated in urban zones, in parallel with immune system impairment and potential endocrine disruption, with hyperthyroidic urban fish. As changes in energy metabolism were detected, an aquarium study of the impact of food availability (fed vs. non-fed) on C. cyanea’s transcriptome was conducted. Fish from urban zones clustered with the fed group and showed high lipid metabolism: human activities may provide ‘fast food’, with large quantities of low-quality nutrients. This study explored new methods for ecosystem assessment, combined aquarium and field ‘omics to refine interpretations, and revealed that urbanisation has a widespread effect on fish, with modifications in gene expression across biological processes.
03:30 PM
Investigating the microbial basis of resilience to stony coral tissue loss disease (8845)
Primary Presenter: Cynthia Becker, Ithaca College (cynthiabecker95@gmail.com)
Stony coral tissue loss disease (SCTLD) affects at least 22 species of reef-building coral in Florida and the Caribbean. Bacteria are implicated as a primary cause of SCTLD, but the community of bacteria and archaea within coral hosts is diverse and includes taxa that may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to host resistance to SCTLD, we sequenced metagenomes from 41 Orbicella faveolata colonies from two reefs in the Lower Florida Keys. Before and after tissue collection, we monitored disease prevalence and frequency of in situ amoxicillin treatments. In June 2021, 46.3% of the colonies presented with SCTLD, which increased to 63.4% after two years. Despite proximity to affected colonies, 28.8% of colonies were never diseased. Following in silico removal of coral host, algal symbiont, and other eukaryotic DNA sequences, we had on average 30 million reads per sample that were used for metagenome co-assembly and analysis. Variation in bacterial functions was explained by disease status at sampling, composition of the algal symbiont community, and colony fate within the monitoring period. We hypothesize that genes related to putatively beneficial functions such as nitrogen and sulfur cycling, and vitamin biosynthesis will be enriched in corals that were unaffected despite multiple years of proximity to SCTLD. Future efforts to integrate other ‘omics data collected from the same colonies may further reveal potential mechanisms by which microbes contribute to intraspecies differences in disease resistance.
03:45 PM
METAGENOMICS AND METATRANSCRIPTOMICS REVEAL CYANOTOXINS AS “STOPPERS” IN THE NITROGEN CYCLE (9806)
Primary Presenter: Daniel Roelke, Texas A&M University Galveston (droelke@tamu.edu)
We studied 20 lakes in the southcentral USA located across a strong precipitation gradient to understand better the relationships between hydraulic flushing, nutrient loading, cyanobacteria composition and activity, the presence and expression of cellular processes related to nitrogen and phosphorus, and the presence and activity of production pathways for multiple cyanotoxins. Using metagenomics and metatranscriptomics, we found that toxin-producing cyanobacteria and toxin-production pathways were more prevalent when hydraulic flushing and loading of total phosphorus and soluble reactive phosphorus were lower. We also found that NOX loading was associated with toxin-production pathways. Regarding the nitrogen cycle, we discovered that toxin-producing genes were negatively associated with denitrification and dissimilatory nitrate reduction and mostly negatively associated with nitrogen fixation. These same genes were positively associated with nitrification. As a whole, our findings suggest that during periods of drought, exacerbated by climate change in this region, the prevalence of toxin-producing cyanobacteria will increase and that the nitrogen cycle will be disrupted in a way that N2 gas exchanges with the atmosphere will be reduced, and in-lake nitrogen will accumulate. Furthermore, this nitrogen will accumulate as NO3, not NH4. Accumulation of nitrogen in these lakes will likely increase the ambient N:P, destabilizing cyanobacteria blooms that form when N:P is low and reinforcing cyanobacteria blooms that form when N:P is high. This also suggests that in the southcentral USA, climate change will make more pressing the issue of regulating nitrogen and phosphorus loading in managing cyanobacteria blooms.
SS08B - Integrating and developing ‘omics technologies in aquatic community ecology
Description
Time: 2:30 PM
Date: 31/3/2025
Room: W207CD