Student prepares niskin bottle on boat.

Maine-eDNA
Research Symposium

Thursday, June 20 2024

Join us for the Maine-eDNA Research Symposium on Thursday, June 20 at the Portland Gateway at 300 Fore St. in Portland, Maine. 

Hear from leading researchers in sessions on aquaculture, ecosystem restoration, harmful algal blooms, and range shifts and how Maine-eDNA is informing our understanding of them.

Meet keynote speaker Katy Klymus Ph.D., a Research Biologist at the Columbia Environmental Research Center, and learn about the development of eDNA standards, READInet, how U.S. agencies are applying eDNA to their work, and her research on eDNA ecology. 

Join us for the symposium’s student poster session showcasing research from across the state on diverse research topics. Meet and talk to students and learn how they are using eDNA technologies to better understand Maine’s aquatic environments.

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Agenda

9:00: Refreshments and Sign-In

9:30: Welcoming Remarks and Introduction to Maine-eDNA

  • Kody Varahramyan (UMaine, Vice President for Research and Dean of the Graduate School)

9:45: Aquaculture: Approaches to tracking changes in natural and commercial sites

  • Nichole Price (Senior Research Scientist, Bigelow Laboratory)
  • Phoebe Jekielek (Maine-eDNA Ph.D. Candidate, UMaine)
  • David Ernst (Postdoctoral Fellow, Bigelow Laboratory)
  • Aaron Whitman (Senior Research Associate, Gulf of Maine Research Institute & Maine-eDNA Masters Student, UMaine)
  • Cara Blaine (Cultivation Specialist, Atlantic Sea Farms)

10:45: Break

11:00: Range Shifts: Understanding species on the move in a changing climate

  • David Emerson (Senior Research Scientist, Bigelow Laboratory)
  • Emily Lancaster (Maine-eDNA Ph.D. Graduate, UMaine)
  • Dara Yiu (Maine-eDNA Ph.D. Candidate, UMaine)
  • Kyle Oliveira (Maine-eDNA Ph.D. Candidate, UMaine)

12:00: Networking Lunch

12:45: Keynote Speaker: Katy Klymus, Ph.D., Research Biologist, Columbia Environmental Research Center

1:45: Ecosystem Restoration: Understanding past and present changes in freshwater and marine systems under fisheries and restoration management

  • Michael Kinnison (Professor of Evolutionary Applications, UMaine)
  • Julia Sunnarborg (Maine-eDNA Ph.D. Candidate, UMaine)
  • Sharon Mann (Maine-eDNA Ph.D. Candidate, UMaine)
  • Grayson Huston (Maine-eDNA Ph.D. Candidate, UMaine)

2:45: Break

3:00: Harmful Algal Blooms: Monitoring, detecting, and understanding marine and freshwater algal blooms

  • Peter Countway (Senior Research Scientist, Bigelow Laboratory)
  • Robin Sleith (Postdoctoral Scientist, Bigelow Laboratory)
  • Sydney Greenlee (Maine-eDNA Ph.D. Candidate, UMaine)
  • Avery Lamb (Ph.D. Candidate, UMaine)

4:00: Poster Session

5:00: Symposium Close

Student Poster Abstracts

Abstract: Blue crabs (Callinectes sapidus) historically ranged from Cape Cod to Uruguay, though in recent years have had an increased presence within the Gulf of Maine. Understanding this natural range expansion is crucial for getting a glimpse into how marine crustaceans may respond to the impacts of ongoing anthropogenic climate change, particularly in regards to their complex, multi-step life cycles. Reports of blue crabs within the Gulf of Maine date back to the 1860s, primarily during warmer years, though from 2016 onward, their presence in southern Maine has been more consistent. This project seeks to understand the temporal dynamics and trophic impacts of blue crabs within this novel environment. To understand blue crab temporal dynamics, we are using both environmental DNA (eDNA) and traditional survey methods in southern Maine. To understand trophic impacts, we are using DNA-based gut content analysis to understand whether these crabs are likely to impact key shellfish species (e.g., softshell clams, lobsters), and stable isotopes to characterize their trophic niche. This presentation will demonstrate the methods used for understanding this ongoing range expansion, determine likely impacts of blue crabs on key Gulf of Maine shellfish, and what long term outcomes could arise from a warming world for marine crustaceans.

Abstract: Despite the importance of fishes to human livelihood, culture, and industry in coastal Maine, fish assemblages on rocky reefs are an understudied component of the ecosystem. We conducted visual surveys for fishes and simultaneously collected eDNA on 11 reefs that span 250 km of Maine’s coast for three consecutive years. Here, I will discuss the process of using 12S metabarcoding of the eDNA samples to characterize and assess spatial variation in fish assemblages, using rigorous laboratory replication and data processing methods designed to balance maximal detection of rare species with reducing erroneous species in the dataset. I will also show the first results of this data, on which I am currently working!

Abstract: Environmental DNA (eDNA) is increasingly being used to detect species in low density in a variety of habitats. Invertebrate animals pose challenges to eDNA sampling due to their varied bauplans which may affect eDNA shedding rates. In a two year time series with accompanying lab experiments, we look at the efficacy of eDNA sampling to detect changes in invasive invertebrate abundance over time. We found that while eDNA works well to detect some species, other species haphazardly shed eDNA in a manor that does not suit species detection or abundance measures. Following this research, we strongly recommend validation of eDNA methods to ensure that the meaning of the molecular signal is clear.

Abstract: The recovery of DNA from lake sediments (sedDNA) has the potential to provide both short- and long-term data on a wide range of biological groups, advancing our understanding of how aquatic communities have changed over time. However, significant challenges remain regarding the recovery of genetic material from fish species, especially anadromous species only present for a portion of the year. Here, we investigate the spatial- and temporal-dynamics of fish environmental and sedimentary DNA to better characterize how anadromous alewife detection and total fish communities vary between sample location (littoral or pelagic), season (summer or winter), and type (sediment or water) in Walker Pond, Maine. Early metabarcoding analyses reveal clustering of both aqueous and sedimentary eDNA samples by season, with aqueous eDNA samples consistently detecting more taxa. Quantitative PCR of the summer samples indicate a similar trend, with aqueous eDNA having higher DNA concentrations and greater detection probabilities than sedDNA, regardless of sample location. Independently, sedDNA samples indicate their own spatial pattern, with greater alewife detection in deeper pelagic waters. Alewife DNA was not detected in any winter water samples, but was detected in one sediment sample, highlighting the long-term preservation potential of sedDNA. Though further exploration into the degradation and preservation rates of fish sedDNA is needed, these early results help elucidate some of the unknowns from this emerging field.

Abstract: Bridges and roads impeding salt marsh creeks are known as salt marsh restrictions. These restrictions are important components of salt marsh management strategies in the Northeast because of the degradation that can occur as a result of shifting hydrology. This degradation is based in microbial activity which causes remineralization of organic matter. As an initial exploration into how eDNA might be used to assess hydrologic restoration potential within these ecosystems, we present data on physicochemical soil quality parameters and16s amplicon sequencing along a 500 meter salinity gradient at 7 different tidal creeks each with a varying degree of hydrologic restriction.

Abstract: “Visual communication is recognized as an important aspect of scientific communication. The process of making media can be time consuming, may require additional collaborators, and in some cases requires expertise to operate image-making equipment such as an underwater drone or remotely operated vehicle (ROV). Research is limited about the dynamics and dimensions of collaborative image-making in the field or in the lab and the possibilities this engagement offers. This study reports on the possibilities and constraints of conducting collaborative digital media-making with an ROV within the Maine-eDNA (environmental DNA) project. Through an engaged, ethnographic research design, our communication research seeks to learn what kinds of conversations, questions, and co-produced knowledge may be generated through the collaborative process. We share insights drawn from field experiences, focus group discussions, and collaborative image-making events with ROV “Drolene.” For example, our analysis identified connections to communication concepts of embodiment through the participant’s physical experiences and perceptions that occur while using the drone, especially while using the ROV’s active headset. We also identified engagement with the ROV as a collaborative space for storytelling, sharing, and relationship building; care for the material environment through perceptions of the ROV’s potential for harm and spreading invasive species; and focal shifts during collaborative image-making activities, where data visualizations became a priority in fieldwork and ancillary in image-making events. Paying attention to these communication practices furthers our understanding of how communication shapes our Maine-eDNA transdisciplinary collaboration.”

Abstract: Population genetics has become an important tool in marine resource management, but the collection of genetic data for marine mammals can be physically invasive and logistically challenging. Environmental DNA (eDNA) provides a non-invasive method of monitoring the presence of marine mammals, but effective methodology is hindered by gaps in our knowledge about how eDNA behaves in the marine environment, and the utility of this method for population genetics has yet to be fully established. Here, we test the application of this new method to gray seals in the Northwest Atlantic, a population that is experiencing growth after a long history of bounties and exploitation. This investigation addresses two primary goals: to quantify gray seal eDNA spatially around haulout sites, and to test the ability of eDNA sampling to detect haplotypes at the mitochondrial control region. Gray seal DNA was consistently detected 50 meters from seal haulouts, with the highest quantity obtained at the shoreline. A single water sample was found to detect up to 14 different haplotypes. When compared to haplotypes identified from concurrently collected fecal samples, our eDNA sampling did not detect every haplotype present at a haulout. However, we found a positive correlation between the frequency of haplotypes present in our eDNA sampling and the frequency of those haplotypes in the population, as determined by previous tissue sampling, suggesting the possible utility of eDNA sampling for approximating population-scale allele frequencies. This work demonstrates the ability of eDNA sampling to capture genetic material from seals at haulout sites, with important nuances to consider for future use. Continued development of eDNA methodology will support future integration of this method into marine mammal management practices and increase our capacity to monitor protected species while minimizing impacts on individuals.

Abstract: As an apex predator in most of the environments it occupies, the presence of white sharks, Carcharodon carcharias, is vital to understanding how the species will impact ecosystem health and how we as humans may interact with the species. Utilizing environmental covariate data, modeled prey distribution layers, presence points for C. carcharias compiled from multiple data sources, and downscaled ocean climate projections, we create a presence-only model that projects habitat suitability likelihood of white sharks in the northwest Atlantic. Prior to the reveal of the forecast, we poll audience members to draw a forecast of their own given the future covariate data presented. The “human forecast” offers a unique opportunity to compare the maximum entropy (MaxEnt) model to human perspectives on covariate impact on habitat suitability. Using the MaxEnt ecological forecast, we can then identify areas that may be suitable habitat for C. carcharias. The projections created offer valuable insight into where we can expect white shark distribution to change in the coming decades, as well as how different sources of data influence these predictions. Thus, providing data to bring forward to interested parties and policy makers to prepare for a compatible future between humans and C. carcharias. With intensifying climate change altering the ocean and adjacent communities, understanding whether an apex predator will reoccupy a region can be vital information for those who depend on lower trophic levels for sustenance and livelihood.

Abstract: Kelp forests are important marine ecosystems that thrive in the cold, nutrient-rich waters of temperate regions around the world, including along the coast of Maine. Climate change is diminishing the function and resilience of kelp forests through the loss of forests at their trailing edges as well as the arrival of new species that can be detrimental to kelp health. Lacy bryozoan is colony forming, encrusting epiphytic bryozoan that settles on the fronds of Laminariales, and is a prime example of a species that has been introduced to the region as a direct result of climate change. Its presence on the kelp fronds is detrimental to the health and survival of the kelp forests in both direct and indirect ways, including diminishing the photosynthetic ability of kelps and causing brittle and broken fronds. Despite the fact that it is known how harmful lacy bryozoan can be to kelp forests, the distribution and presence along the coast of Maine is not well characterized. The goals of this project are to address; (1) When and where is lacy bryozoan present, and what is its distribution through space and time, as inferred by environmental DNA (eDNA)? (2) Does lacy bryozoan present seasonal dynamics along the coast of Maine? (3) What biotic and abiotic drivers explain the distribution of lacy bryozoan through space and time, including seasons and years?

Abstract: There has been growing interest in recent years in exploring the potential of sinking farmed kelp for marine carbon dioxide removal purposes. Given that long-term carbon sequestration requires incorporation into marine sediments, better tools to quantify and trace kelp biomass in such systems is required, as well as a better understanding of its degradation dynamics.

We conducted a sixteen-week anaerobic degradation experiment using sediment slurries amended with two treatment types: sugar kelp, or a mix of eight common regional coastal marine plant taxa used to represent generalized marine plant organic matter. To examine the potential for environmental DNA to serve as a quantitative biomarker of biomass, we used a sugar kelp-specific quantitative polymerase chain reaction assay as a proxy for kelp biomass, for comparison with more traditional analytical methods like total organic carbon analysis. We also sequenced samples for 16S and 18S ribosomal RNA to characterize changes in the associated sediment microbial communities, and to quantify changes in relative read counts of the added marine plant taxa over time.

Throughout the course of our experiment, kelp eDNA declined rapidly over the span of several weeks before stabilizing at readily detectable levels, indicating preservation of kelp biomass under anaerobic conditions in the absence of physical disturbance.

Bacterial communities showed strong shifts in community composition due to organic matter addition, with different shifts depending on the added material (kelp or mixed plant), indicating specific bacterial communities developed due to kelp biomass addition. Microbiomes in the kelp treatment showed enrichment in taxa associated with degradation of compounds rich in kelp biomass, such as sulphated polysaccharides.

Abstract: Alewife (Alosa pseudoharengus) are sea-run fishes which spend their adult lives in marine systems and return to their natural nursery habitats in freshwater to spawn. Juvenile alewives impact freshwater systems during their brief residency- they influence lower trophic levels by controlling primary production through the selective grazing of large-bodied zooplankton, they provide sustenance to wildlife, and they can improve water quality by transporting phosphorus as they migrate to marine systems. Due to the impacts juvenile alewife have on freshwater systems, natural resource managers and water quality monitors alike are interested in quantifying alewife densities. Currently, juvenile densities are derived from in-lake purse seine-survey methods- a laborious effort which must be done after dark and multiple seine hauls must be deployed for accuracy. Given the importance of juvenile alewife in freshwater systems and the logistical demands of current sampling techniques, there is a need for alternative sampling strategies that are accessible to a broad range of stakeholders such as alewife harvesters, restorationists, and resource managers. Collecting environmental DNA (eDNA), genetic information left by an organism in its environment, may provide a less labor intensive alternative to estimate juvenile alewife density in lakes. However, there are many factors: abiotic (water chemistry, temperature, sunlight, and dilution), biological (age and behavioral differences in shedding rate), and sampling strategies (replication, location, and timing) that may influence eDNA concentrations. This study investigates the potential drivers of eDNA heterogeneity in 7 lakes using estimated values for juvenile alewife density and biomass derived from purse seine sampling. Our research objectives were to investigate (1) heterogeneity of eDNA in nearby water samples, (2) drivers of heterogeneity in eDNA water samples with known juvenile alewife density and biomass, (3) temporal changes affecting juvenile alewife eDNA concentration (4) accumulation of eDNA over the course of a sampling period, (5) difference in mean eDNA concentration between samples collected during the day and at night, and (6) the efficacy of eDNA in predicting juvenile alewife density. We demonstrate a strong linear relationship between juvenile dentistry and eDNA concentration (R2=0.82) and found evidence that timing of water sample collection (R2=0.31) and water depth (R2=0.30) influence the predictable relationship between fish density and eDNA concentration. Our results provide guidance on sampling strategies to optimize targeted eDNA sampling to quantify juvenile alewife densities in lakes.

Abstract: The ability to model the ecological relationships between species within aquatic biomes provides important information for the purpose of understanding and preserving biodiversity in bodies of water. Our long-term goal is to understand interactions between organismal communities using network models. Network models use nodes to represent a given organism, and edges are used to represent an interaction between them. Interactions may be predator/prey relations or even just co-abundance. The usage of eDNA allows for the ability to infer detection of potentially large numbers of species in a water sample. This can be combined with using time-series data of eDNA relative abundances and network inference methods, Spearmans, SparCC, and others, to infer co-abundance networks which predict species-species relationships. An important remaining question in this field is whether functional relationships between organisms can be determined by examining network topology resulting from such methods. In regards to this, one approach is to leverage inferences with additional sources of data to refine results. Here we examine the effect of creating inferred networks from both eDNA as well as trawl data, with the expectation that highly significant and non-random relationships will be overlapped in both datasets. Utilizing a New Jersey coast study containing simultaneous eDNA and trawl data, network inference of the two datasets displayed high similarity in relationship type (positive correlated or negatively correlated) for overlapped predicted relationships, indicating the possibility such relationships might be significant or conserved between these two datasets. Future work will involve examining more datasets and including additional network inference tools, including exploring gene regulatory inference tools such as Genie3 or Netact, to continue to evaluate how eDNA and trawl data can be leveraged together to produce better predictions.

Environmental DNA (eDNA) can offer a non-invasive, cost-effective and efficient method for monitoring aquaculture and commercial fisheries populations to inform sustainable fisheries management practices. However, eDNA tools must be thoroughly groundtruthed to determine best practices for their appropriate application. While quantitative eDNA assays for sea scallops (Placopecten magellanicus) have been developed and calibrated for sperm and dockside conditions, we lack quantification rates of scallop eDNA generation and degradation, calibration for other life stages, e.g., eggs and larvae, and evaluation of field applications. These challenges are addressed through a combination of laboratory experiments and field observations. Using a controlled mesocosm experiment, the eDNA generation and degradation rates of scallops at different biomass densities over a 48-hour period are quantified. Positive linear relationships between eDNA generation rates and biomass and a negative linear relationships between eDNA degradation rates and biomass over time are expected. Using a vertically-stratified sampling design above a wild scallop bed, the spatial and temporal variability in scallop eDNA presence over a 6-month period is evaluated. During spawning and larval transport seasons, the eDNA signal is expected to be distributed throughout the water column. Outside of these seasons, the eDNA signal is expected to be limited to the benthos. Results from this work may inform the use of carefully constructed sampling designs to conduct adult stock assessments or to estimate recruitment potential and will identify benefits and shortcomings of eDNA as a tool for assessing commercially important species.

Many Pseudo-nitzschia spp. diatoms are capable of producing the potent neurotoxin domoic acid, responsible for amnesic shellfish poisoning. Pseudo-nitzschia australis has been reported to produce over 100pg of domoic acid per cell, the highest concentration reported in the genus, making it a species of high concern for resource managers. However, Pseudo-nitzschia species cannot easily be distinguished by morphology. We designed a real-time quantitative PCR assay for rapid and accurate detection and quantification of Pn. australis in environmental DNA samples. To relate qPCR data to cell count estimations, we determined the rbcS gene copy number experimentally in Pn. australis cultures. The limit of detection for this assay was determined to be equivalent to an estimated 1.2 cells per liter. We applied this novel assay to eDNA water samples collected in the Casco Bay region of the Gulf of Maine to detect and quantify Pn. australis from 2021-2023, revealing a peak in estimated abundance from mid-September to early December each year, though the signal in 2023 was an order of magnitude lower than the prior years. This study demonstrates how eDNA can be utilized for the early detection of a harmful algal bloom species, how qPCR can be calibrated with cell cultures, and provides a new tool for marine resource managers.