Characterizing genetic and ecological consequences of shellfish aquaculture

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2024

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Abstract

Coastal ecosystems are made up of habitats that provide critical ecosystem services, including saltmarshes, seagrasses, mangroves, and oyster reefs. However, they are also some of the most threatened and are vulnerable to anthropogenic and environmental stressors. Oyster reefs have been harvested within a fraction of their historical abundance, resulting in the loss of the goods and services that they provide to the people and surrounding ecosystems. In this dissertation, I explore how shellfish aquaculture can serve to supplement those services. In Chapter 1, I address the limited availability of specialized stock for environmental conditions. North Carolina’s aquaculture industry has been growing. However, there is no commercial oyster hatchery operating out of North Carolina, and most hatchery-stocked oysters in the state come from non-local lines. The UNC Wilmington Shellfish Research Hatchery, however, has been working on developing North Carolina oyster lines, derived from populations of oysters collected from across the state coastline and kept in isolated populations. In Chapter 1, I grow three of these lines in a common environment and determine that there is no influence of genetic line on final size, but there may be a connection to recovery from stress. I then use a genome-wide scan to assess the population structure within and between the lines. From this, I found that the three lines were genetically distinct from each other and had limited inbreeding. Our study contributes to the broader literature on the impact of population history on performance and emphasizes the difficulty of maintaining genetic diversity in highly fecund marine species in hatchery environments. Understanding the genetic fitness of these stocks and the conditions they thrive in will improve the pipeline of hatchery production as well as downstream use, as oysters are often spread widely from commercial hatcheries to seed aquaculture and restoration alike. A consequence of the increase in aquaculture has been the addition of complex hard substrate into unstructured areas. Overharvesting and loss of oysters has resulted in bare or otherwise unstructured substrate and thus loss of habitat for many organisms that used oyster reefs for habitat, nurseries, and foraging grounds. The addition of complex structure, then, may also be supplementing those needs and returning habitat to the area. Because oyster reefs host a diverse range of taxa, many of which are transient users, to measure a broad swathe of the community with a traditional sampling scheme would involve multiple survey strategies and taxonomists and have minimal temporal resolution. Environmental DNA (eDNA), on the other hand, is a non-invasive, relatively low-manpower, taxonomically broad methodology that does not require taxonomic experts. Through collecting and sequencing DNA from cells naturally shed by living organisms into their environment, this survey strategy can be used in a range of environments and is particularly useful to record cryptic and transitory taxa. However, high sequencing and library preparation costs associated with this method are barriers to widespread implementation. In Chapter 2, I develop methods to sequence and analyse environmental DNA using the Oxford Nanopore GridION sequencing platform. While eDNA has great potential as a biomonitoring tool, one barrier to adoption is the high cost and lead time for sequencing and library preparation. Oxford Nanopore Technology (ONT) systems have been increasingly of interest as a lower upfront cost alternative to second generation sequencing, but there has been little work benchmarking expectations of the platform when using mixed and low-quality DNA samples, such as eDNA. In Chapter 2, I use a stepwise process to establish bioinformatic and technological limitations of the ONT platform that would influence eDNA analysis. During this process, I show that by clustering sequences based on similarity, error correction against other sequences in the cluster, and strict taxonomic assignment cutoff thresholds, Oxford Nanopore sequencing can be used to accurately perform eDNA sequencing with samples amplified with broad-spectrum PCR primers. However, the tradeoff to these steps is lower taxonomic resolution and lower sequencing depth. In Chapter 3, I assess the habitat value of small-scale aquaculture facilities and how it compares to that of intertidal oyster reefs by comparing the biological communities associated with oyster aquaculture and oyster reefs using environmental DNA and the methodology developed in Chapter 2. I find that a wide variety of taxa made use of oyster aquaculture, many of which were also found at oyster reefs. This included generalists like mud snails and polychetes as well as specialist fauna like blennies and mobile, higher trophic level taxa like drum and mullet. Although the taxa were widely shared, the community composition between the two habitats differed. Vertebrate taxa were recorded more often at oyster reefs, while most of the aquaculture community at a given time was composed of benthic and planktonic fauna. These findings illustrate that an expansive host of organisms can be found around oyster aquaculture, many of which are shared with oyster reefs, indicating that the structure provided by aquaculture gear has the potential to provide habitat provisioning services like that of oyster reefs. There is great potential for shellfish aquaculture to contribute positive services to the environment, but it is important to understand the benefits that are possible and the risks and negative impacts that may occur. This will allow for incorporating environmental impact into farm design and siting, and improve the long-term sustainability of aquaculture. The findings in this dissertation contribute towards understanding and improving the services provided by oyster aquaculture, including through contributing towards understanding the effect of hatchery selection and genotype-by-environment interactions on oyster stocks, improving accessibility of biomonitoring tools by developing an eDNA analysis pipeline using the Oxford Nanopore Technology sequencing platform, and examining habitat provisioning services of aquaculture gear.

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Givens, Laura (2024). Characterizing genetic and ecological consequences of shellfish aquaculture. Dissertation, Duke University. Retrieved from https://hdl.handle.net/10161/31876.

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