Characterizing Salt Marsh Microbial Communities in Sediments of Varying Depth
Duck Harbor, Wellfleet, Massachusetts
Salt marshes are vital ecosystems that serve a variety of roles in an environment; they filter nutrients and act as habitats for numerous species and as carbon sponges (Barbier et al. 2011). During wash-over events, water levels increase enough to rush over these marshes’ natural barriers, such as dunes, flooding the lower-lying areas with water and sediment (Castagno et al. 2025). Frequent wash-over events, which often occur during storms, can change the ecosystem by altering soil composition and plant life, leading to changes in marsh structure.
Because salt marshes sequester carbon at higher rates than large, terrestrial forests, they are integral to lowering the increasing carbon levels in the atmosphere (Bulseco et al. 2024). Carbon storage and nutrient filtration can be attributed to the microbes that inhabit these marshes and their anaerobic respiration below the surface. The goal of this study, funded in part by an Undergraduate Research Award (URA) from the Hamel Center for Undergraduate Research, was to investigate how frequent wash-over events alter microbial communities over time as sediments become buried in the salt marsh subsurface. By matching DNA from soil samples to the known DNA of different microbes, we can get a full picture of the community in a salt marsh, which in turn can help guide future marsh restoration efforts.
Research Methods
To measure this, Dr. Ashley Bulseco and her team collected three different two-meter-deep sediment core samples in August 2024 from Duck Harbor, a salt marsh that transitioned from a salt marsh to a forest and is transitioning back to a marsh, in Wellfleet, Massachusetts. In the mid-1900s, large dunes cut off the marsh’s access to seawater, resulting in a pitch pine forest growing over time (Button 2025). In early 2021, incredibly high tides caused seawater to flood the forest, leading to a slow shift in soil and plant composition. Duck Harbor experiences these wash-over events on an almost monthly basis during spring tides. Unlike most wash-over events, these occur on a regular basis regardless of weather, which is unusual, considering most wash-overs are an effect of larger storms. This has also caused the marsh to transition from freshwater to saltwater, which can have a strong effect on the resident microbial communities (Morrissey et al. 2013).
The author in the lab.
The sediment core was sectioned at 10-centimeter intervals, and 2-centimeter sections of the sediment were collected individually and flash-frozen by my mentor, Dr. Ashley Bulesco, in summer 2024. My goal in the lab was to work through these soil samples, extracting DNA from each, which could then be used for polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene. This gene allows for the taxonomic identification of bacterial and archaeal communities. My work was the continuation of a former undergraduate researcher, with whom I frequently partnered in the lab. I extracted ~70% of the total number of samples, meticulously recording them in a master spreadsheet.
To do this, I homogenized the frozen samples and subsampled approximately 250–500 micrograms of the soil for each extraction. Using the ZymoBIOMICS DNA Miniprep Kit, I extracted genomic DNA from these samples following the manufacturer’s instructions. To do so, the samples were placed in small tubes containing tiny beads that, when centrifuged, collide and disrupt microbial cell walls, allowing DNA products to spill out. After separating these cell walls, I added DNA-binding agents and washed away PCR inhibitors that may have been present in each sample. These were filtered and continuously centrifuged until only the microbial DNA remained. Currently, I am conducting PCR to amplify the 16S rRNA sequence of each sample. Using R, a statistical data analysis and graphic software, I will run published bioinformatic pipelines to evaluate differences in microbial communities by depth as sediment was buried. To obtain a comprehensive snapshot of the microbial community, sequences will be processed with DADA2 (Callahan et al. 2016) and visualized with Phyloseq (McMurdie and Holmes 2013), packages within R that use Illumina amplicon sequencing data to decipher the community.
Preliminary Results
Preliminary results exist from my colleague’s effort in spring 2025 that will be fully explored in conjunction with the new sequence data being produced this spring. Using the small amount of the samples collected, it was determined that there was an overall decrease in microbial diversity as depth increased along each of the three location cores. (Figures 1 and 2) The observed communities shared some of the same microbial makeup throughout the depths, but there was no consistent composition. From this, we can infer that the different soil types deposited by wash-overs contain variable organic matter characteristics, resulting in very different habitats for microorganisms. Ideally, the newly sequenced DNA I worked with will shed more light on the microbial communities and exactly what microbes are shared throughout the depths, and when combined with organic matter data, might explain their patterns over time.
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Figure 1 (left). Percent organic matter and microbial diversity. Figure 2 (right). Differences among samples by depth.
This research is important because determining which microbial communities exist in a rapidly changing salt marsh can provide insight for future restoration efforts. Determining the ideal composition of the microbes as the ecosystem transitions into a marsh can allow more of a focus on supporting beneficial microbial interactions through inoculation of new plants and soils. Further, this shows how wash-over events can change not only the landscape but the entire ecological community. Effort should be put into preventing these wash-over events, because it is unknown how changing the microbial community will affect the marsh’s carbon storage and nutrient filtration abilities. Though the frequent wash-overs in Duck Harbor are irregular compared with most wash-overs, that might change as sea level elevation rises and larger storms become more common in the New England area. Low-lying marshes and other coastal ecosystems could be at risk.
Next Steps
This project is far from finished, and much can be learned from this unique salt marsh. This spring, I am using PCR to amplify each of the remaining samples in order to obtain sequencing data of the 16S rRNA gene. I am continuing to learn R, which will assist with cataloguing the microbial communities, giving us a snapshot of the microbial community at each depth, and allowing us to compare microbial structure and diversity. The next steps for this project may also consist of metagenomics, which can offer information on the different functional potentials of the observed microbes. Further, these samples may undergo RNA extraction rather than DNA extraction, which will show the active soil microbiome, rather than all present microbes. DNA extractions can pick up trace DNA that is left in the soil from past microbes or viruses, whereas RNA will show only living microbes, because it is actively constructed only by live microorganisms. I plan to present my eventual findings at UNH’s 2026 Undergraduate Research Conference.
Overall, I have grown as a scientist and as a person through this project, and my experience doing undergraduate research has been nothing short of amazing. I have been able to combine two of my passions, genetic studies and environmental conservation, into a project that I am immensely proud of. In my home state of Rhode Island, I grew up down the road from a salt marsh. I played in it as a child, and later taught children in it through a nature camp. I have always had a deep connection with these ecosystems, and being able to dig deep and study microbial health is extremely rewarding.
Thank you to Mr. Dana Hamel for providing funding for this research through an Undergraduate Research Award (URA). I am so grateful for the opportunity to conduct paid research as an undergraduate, and I have grown in many ways throughout this semester. I am especially thankful for my mentor, Dr. Ashley Bulseco, for everything she has taught me. With her help, I mastered the laboratory skills of my field that I would need in any professional lab and learned how to communicate as a scientist through lab meetings and research presentations. I became an expert in extracting DNA from soil samples and learned how to conduct PCR experiments. I found my note-taking, organizational, and presentation skills growing, as well as my scientific curiosity. This project has made me excited to dive deeper into this subject and continue my research.
References
Barbier, E. B., S. D. Hacker, C. Kennedy, E. W. Koch, A. C. Stier, and B. R. Silliman. 2011. The value of estuarine and coastal ecosystem services. Ecological Monographs 81: 169–193. [doi.org/10.1890/10-1510.1].
Bulseco, A. N., A. E. Murphy, A. E. Giblin, J. Tucker, J. Sanderman, J. L. Bowen. 2024. Marsh sediments chronically exposed to nitrogen enrichment contain degraded organic matter that is less vulnerable to decomposition via nitrate reduction, Science of The Total Environment 915: 169681, ISSN 0048-9697. [doi.org/10.1016/j.scitotenv.2023.169681].
Button, K. 2025. Study of macroinvertebrates finds emerging resilience after massive coastal breach. Park Science 39: 2. www.nps.gov/articles/000/psv39n2_study-of-macroinvertebrates-finds-emerging-resilience-after-massive-coastal-breach.htm.
Callahan, B., P. McMurdie, M. Rosen, et al. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13: 581–583. [doi.org/10.1038/nmeth.3869].
Castagno, K. A., E. J. Fitzgerald, K. Button, P. Zu?iga, T. Tucker, T. Smith, M. Borrelli. 2025. Washover fan deposits resulting from perigean spring tides: An example from Cape Cod, Massachusetts, USA. Geomorphology 470: 109536, ISSN 0169-555X. [doi.org/10.1016/j.geomorph.2024.109536].
McMurdie, P. J., and S. Holmes. 2013. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLOS ONE 8: 4, e61217. [doi.org/10.1371/journal.pone.0061217].
Morrissey, E. M., J. L. Gillespie, J. C. Morina, and R. B. Franklin. 2013. Salinity affects microbial activity and soil organic matter content in tidal wetlands. Global Change Biology 20: 1351–1362. [doi.org/10.1111/gcb.12431].
Author and Mentor Bios
Seren Davies is a sophomore genetics major at the University of New Hampshire. Originally from Bristol, Rhode Island, she has worked with Dr. Ashley Bulseco’s MicroEco lab for over a year. During this time, she has pursued research regarding the microbial communities within salt marshes and the ways these are altered by the changing environment. In addition, she serves as a student ambassador for the Hamel Center for Undergraduate Research, an executive member for UNH’s Alpha Phi Omega, an employee of the Audubon Society of Rhode Island, and a member of the UNH Honors College.
Ashley Bulseco is an assistant professor in the Department of Biological Sciences at the University of New Hampshire. Her research focuses on understanding the microbial response to human-driven disturbances in wetland, estuarine, and marine ecosystems. She is particularly interested in whether shifts in the microbial community translate to changes in ecosystem function, especially in relation to carbon and nitrogen cycling. Dr. Bulseco’s work often takes a multifaceted approach to address these questions, applying a range of interdisciplinary techniques that combine fieldwork, controlled laboratory experiments, biogeochemical measurements, sequencing, and bioinformatics. Before coming to UNH, she taught environmental science and oceanography at the high school level, and she plans to continue exploring her passion for innovative and inclusive pedagogical practices in STEM.
Copyright 2026 ? Seren Davies
