skip to main content

This content will become publicly available on June 29, 2023

Title: Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound
ABSTRACT The Olympia oyster ( Ostrea lurida ) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass ( Zostera marina ) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, and surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after 2 months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated more » with oyster physiology and survival rates. IMPORTANCE This is the first exploration of the microbial colonizers of the Olympia oyster, a native oyster species to the West Coast, which is a focus of restoration efforts. The patterns of differential microbial colonization by location reveal microscale characteristics of potential restoration sites which are not typically considered. These microbial dynamics can provide a more holistic perspective on the factors that may influence oyster performance. « less
; ; ; ; ;
Kormas, Konstantinos Aristomenis
Award ID(s):
Publication Date:
Journal Name:
Microbiology Spectrum
Sponsoring Org:
National Science Foundation
More Like this
  1. Established non-native species can have significant impacts on native biodiversity without any possibility of complete eradication. In such cases, one management approach is functional eradication, the reduction of introduced species density below levels that cause unacceptable effects on the native community. Functional eradication may be particularly effective for species with reduced dispersal ability, which may limit rates of reinvasion from distant populations. Here, we evaluate the potential for functional eradication of introduced predatory oyster drills (Urosalpinx cinerea) using a community science approach in San Francisco Bay. We combined observational surveys, targeted removals, and a caging experiment to evaluate the effectiveness of this approach in mitigating the mortality of prey Olympia oysters (Ostrea lurida), a conservation and restoration priority species. Despite the efforts of over 300 volunteers that removed over 30,000 oyster drills, we report limited success. We also found a strong negative relationship between oyster drills and oysters, showing virtually no coexistence across eight sites. At experimental sites, there was no effect of oyster drill removal on oyster survival in a caging experiment, but strong effects of caging treatment on oyster survival (0 and 1.6% survival in open and partial cage treatments, as compared to 89.1% in predator exclusion treatments).more »We conclude that functional eradication of this species requires significantly greater effort and may not be a viable management strategy in this system. We discuss several possible mechanisms for this result with relevance to management for this and other introduced species. Oyster restoration efforts should not be undertaken where Urosalpinx is established or is likely to invade.« less
  2. Abstract Background

    The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.


    We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes ofmore »the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.


    Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome.

    « less
  3. Abstract

    The eastern oyster, Crassostrea virginica, forms reefs that provide critical services to the surrounding ecosystem. These reefs are at risk from climate change, in part because altered rainfall patterns may amplify local fluctuations in salinity, impacting oyster recruitment, survival, and growth. As in other marine organisms, warming water temperatures might interact with these changes in salinity to synergistically influence oyster physiology. In this study, we used comparative transcriptomics, measurements of physiology, and a field assessment to investigate what phenotypic changes C. virginica uses to cope with combined temperature and salinity stress in the Gulf of Mexico. Oysters from a historically low salinity site (Sister Lake, LA) were exposed to fully crossed temperature (20°C and 30°C) and salinity (25, 15, and 7 PSU) treatments. Using comparative transcriptomics on oyster gill tissue, we identified a greater number of genes that were differentially expressed (DE) in response to low salinity at warmer temperatures. Functional enrichment analysis showed low overlap between genes DE in response to thermal stress compared with hypoosmotic stress and identified enrichment for gene ontologies associated with cell adhesion, transmembrane transport, and microtubule-based process. Experiments also showed that oysters changed their physiology at elevated temperatures and lowered salinity, with significantlymore »increased respiration rates between 20°C and 30°C. However, despite the higher energetic demands, oysters did not increase their feeding rate. To investigate transcriptional differences between populations in situ, we collected gill tissue from three locations and two time points across the Louisiana Gulf coast and used quantitative PCR to measure the expression levels of seven target genes. We found an upregulation of genes that function in osmolyte transport, oxidative stress mediation, apoptosis, and protein synthesis at our low salinity site and sampling time point. In summary, oysters altered their phenotype more in response to low salinity at higher temperatures as evidenced by a higher number of DE genes during laboratory exposure, increased respiration (higher energetic demands), and in situ differential expression by season and location. These synergistic effects of hypoosmotic stress and increased temperature suggest that climate change will exacerbate the negative effects of low salinity exposure on eastern oysters.

    « less
  4. Oysters are described as estuarine ecosystem engineers because their reef structures provide habitat for a variety of flora and fauna, alter hydrodynamics, and affect sediment composition. To what spatial extent oyster reefs influence surrounding infauna and sediment composition remains uncertain. We sampled sediment and infauna across 8 intertidal mudflats at distances up to 100 m from oyster reefs within coastal bays of Virginia, USA, to determine if distance from reefs and physical site characteristics (reef elevation, local hydrodynamics, and oyster cover) explain the spatial distributions of infauna and sediment. Total infauna density increased with distance away from reefs; however, the opposite was observed for predatory crustaceans (primarily crabs). Our results indicate a halo surrounding the reefs of approximately 40 m (using an increase in ~25% of observance as the halo criterion). At 90 m from reefs, bivalves and gastropods were 70% more likely to be found (probability of observance), while there was an approximate 4-fold decrease for large crustaceans compared to locations adjacent to reefs. Increases in percent oyster reef cover and/or mean reef area did not statistically alter infauna densities but showed a statistical correlation with smaller sediment grain size, increased organic matter, and reduced flow rates. Weaker flowmore »conditions within the surrounding mudflats were also associated with smaller grain sizes and higher organic matter content, suggesting multiple drivers on the spatial distribution of sediment composition. This study emphasizes the complexity of bio-physical couplings and the considerable spatial extent over which oyster reefs engineer intertidal communities.« less
  5. Abstract Background

    Understanding the factors that influence microbes’ environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, “specificity” is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao’s (Theor Popul Biol, 1982., Sankhya A, 2010. ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.


    We present our R packagespecificityfor performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity tomore »the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.


    specificityis well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers usingspecificity’s companion package,specificity.shiny.

    « less