Microbial biomarkers as an early warning system for Sudden Unusual Mortality Syndrome (SUMS) in oysters

Abstract

Sudden Unusual Mortality Syndrome (SUMS) is an existential threat to the off-bottom oyster aquaculture industry in the United States. The syndrome is characterized by rapid onset of mortalities that often exceed 50% in near-market size oysters. These deaths lead to devastating loss of cash flow and an inability to supply products to established customers. The cause of SUMS is unknown, but preliminary data points to a microbial (eukaryotic, bacterial, viral) component. The microbial communities, or microbiome, of an organism is directly linked to its health. Changes in microbiome structure can indicate condition of an animal prior to visible signs of disease, and we hypothesize that this is the case for SUMS. These microbial shifts can be identified and monitored to provide an early warning system that allow oyster growers to mitigate losses. However, recommended mitigation strategies have not been tested for their effectiveness. The purpose of this project is to use metagenomics to reveal microbial signatures related to syndrome onset and progression and provide science-based recommendations for oyster farmers to prevent mass mortalities. 

This will be accomplished through the following objectives: 1) to identify members of the oyster microbiome that are linked to SUMS events and develop a rapid diagnostic test based on these microbial biomarkers, and 2) to test mitigation strategies to reduce the impact of SUMS. Triploid oysters will be deployed to Portersville Bay and Dauphin Island, Alabama, and monitored for mortalities. Samples, including oyster tissues and fecal ribbons, will be collected every other week. Upon occurrence of SUMS, oyster tissues collected before, during, and after the event will be subjected to metagenomic analyses to characterize the eukaryotic, bacterial and viral organisms, as well as virulence and metabolic genes, that shift during these events. A PCR-based diagnostic test will be developed based on microbial biomarkers, which may be organisms or genes, that signal SUMS. The diagnostic test will be validated using tissues collected from a variety of SUMS events. Microbial biomarkers will be analyzed in fecal ribbons to determine if feces can replace tissues as a non-lethal monitoring strategy. Additionally, two mitigation techniques will be examined. In the fall, oysters will be deployed to mid-Mobile Bay to overwinter. These oysters will be returned to Portersville Bay in the early spring to determine the impacts of relocation on mortalities. For the second method, the stocking density of the oysters will be halved at the beginning of a SUMS event. Survival will be compared for both strategies. The use of metagenomics to characterize microbiome patterns will provide an early warning of SUMS onset, enabling the oyster industry to make informed decisions about whether to activate mitigation strategies with known effectiveness. These results will have beneficial long-term outcomes that reduce losses in oyster farming, resulting in greater returns that allow expansion of the industry and growth of the local economy and workforce. The ability to mitigate mortalities will benefit coastal ecosystems and increase the economic sustainability of the off-bottom oyster aquaculture industry.

Objectives

1. To identify members of the oyster microbiome that are linked to SUMS events and develop a rapid diagnostic test based on these microbial biomarkers.
2. To test mitigation strategies to reduce the impact of SUMS.

Methodology

To address Objective 1, triploid oysters will be deployed at two off-bottom oyster aquaculture sites that experience yearly SUMS events. Oysters will be monitored for mortality every other week. At each time point, triplicate fecal ribbons collected in trays place underneath floating cages and triplicate oyster tissues containing pooled gill and digestive tract will be collected. Water quality parameters will be measured. At the report of a SUMS event, ten oyster samples spanning before, during and after the event will be subjected to metagenomics sequencing to characterize the eukaryotic, bacterial and viral (DNA and RNA) communities of the oysters. Bioinformatics analysis will identify microbial biomarkers, which may include microbes and/or their genes, of SUMS. A rapid diagnostic test will be developed to detect the biomarkers. The test will be validated against a variety of samples collected from SUMS events. The test will also be used to determine if the biomarkers exist in the fecal ribbon samples.

To address Objective 2, triploid oysters will be deployed to three sites in coastal Alabama, one at a site that does not experience SUMS and two that do. One batch of oysters will be overwintered at the non-SUMS site and moved to one of the SUMS sites to test relocation as a mitigation strategy. Survival will be compared between the relocated oysters and those that overwintered at the SUMS site. The effect of reduced stocking density will be tested by cutting the density of oyster grow-out bags in half at the beginning of a SUMS event. Mortality will be compared between the two stocking densities. Relocation and stocking density reduction will also be analyzed against each other to determine if the mitigation strategies are effective and if one is more beneficial than the other.

Rationale

Sudden Unusual Mortality Syndrome (SUMS) describes mass mortality events in off-bottom eastern oyster aquaculture for which the cause is unknown. A large event on the U.S. Gulf coast in 2024 led to losses of more than 50% in near-market size oysters at several farms in Alabama and Mississippi. Due to the severity and unpredictability of SUMS, it is a significant threat to the oyster aquaculture industry. The cause remains unknown, but preliminary data suggests microbial involvement. Given the connections among the microbiome composition, environmental parameters and host health, oyster-associated microbial communities likely shift in composition prior to SUMS, offering predictive biomarkers.

The hypotheses of this proposal are (1) the oyster microbiome shifts prior to SUMS events, providing microbial indicators that enable early detection and (2) relocation and/or reduced stocking densities mitigate mortalities. We will test these hypotheses using metagenomic technologies to analyze the microbiome of oyster tissues to identify microbial signatures of SUMS. We will develop a rapid diagnostic test for SUMS biomarkers for early detection, which will allow farmers to initiate scientifically tested mitigation strategies prior to mortalities. We will also determine whether analysis of fecal ribbons can be used as a novel, non-lethal monitoring method. 

The project addresses the MASGC priority to “identify causes and develop management strategies to eliminate oyster aquaculture mass mortality events.” Metagenomic data will not allow for monitoring as an early warning system for SUMS but will also provide insight into potential causes of the syndrome. The outputs of this project will reduce losses at the farm level, improving the economic sustainability of the industry. Lower mortalities also mean less risk, encouraging growth of the off-bottom oyster aquaculture industry and benefitting local communities and economies.