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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Research Project #428121

Research Project: Developing Methods to Improve Survival and Maximize Productivity and Sustainability of Pacific Shellfish Aquaculture

Location: Forage Seed and Cereal Research Unit

2020 Annual Report

This research will develop an improved understanding of the ecology of bivalve shellfish aquaculture in the estuarine environment in order to increase production by reducing mortality while ensuring that culture practices are sustainable and environmentally compatible. Mortality of bivales during this rearing process can be high resulting in low harvest and production. This project addresses two sources of juvenile mortality and attempts to quantify them at the estuarine landscape scale. Burrowing shrimp act as pests causing oysters to sink under the surface of the sediment and die. Shrimp have pelagic larvae that settle and recruit annually to the benthic population on estuarine tidelands where shellfish are grown. Recruitment will be modeled to develop improved control strategies for the industry. Juvenile shellfish are also subject to changing water chemistry due in part to anthropogenic carbon dioxide release and reduced carbonate saturation states which cause problems with shell formation and growth. This problem will also be examined to seek strategies that could mitigate effects at the estuarine landscape scale. Shellfish production is also constrained by regulatory actions regarding siting shellfish farms in the estuarine environment. The estuarine landscape includes a number of habitats including beds of submerged aquatic vegetation, open mudflat and shellfish. This project seeks to quantify these habitats, describe the interaction between shellfish culture production and aquatic vegetation and describe the functional value of these habitats for fish and invertebrates at the estuarine landscape scale. Objective 1: Quantify and model burrowing shrimp and ocean acidification as sources of juvenile shellfish mortality that constrain oyster aquaculture production in the West Coast estuaries. Sub-objective 1.1. Quantify how annual recruitment patterns affect population dynamics of burrowing shrimp in the estuaries. Model this at the landscape scale and develop control strategies for sustainable shellfish culture. Sub-objective 1.2. Determine whether reduced carbonate saturation states are a source of reduced growth and increased mortality of juvenile oysters after they leave the hatchery. Quantify juvenile oyster growth and mortality at a landscape scale in estuaries comparing habitats and locations as potential mitigating factors. Objective 2: Quantify the influence of shellfish aquaculture practices on existing estuarine habitats and quantify utilization of these habitats, including shellfish aquaculture, by fish and invertebrates at the estuarine landscape scale. Subobjective 2.1. Quantify the effects of oyster aquaculture on aquatic vegetation and utilize habitat maps to examine this interaction at the estuarine landscape scale and over inter-annual time frames. Subobjective 2.2. Quantify fish and invertebrate use of intertidal habitats including oyster aquaculture in Willapa Bay; evaluate the functional value of these habitats for fish and invertebrates.

This research addresses two current problems that constrain the shellfish aquaculture industry: 1) a lack of understanding about and the ability to eliminate or at least mitigate the effects of early mortality of juveniles caused by changing ocean conditions and pests such as burrowing shrimp and 2) environmental regulations concerning the impact of shellfish farming practices on the estuarine environment. Long term records of burrowing shrimp populations and new collections of animals from shellfish beds and control areas will be used to quantify the contribution of annual recruitment to shrimp population dynamics. Shrimp will be aged using the pigment lipofuscin and data used to develop a predictive index and define a threshold at which treatment to control these pests is necessary. Shellfish growers have observed the effects of changing ocean conditions (high PC02, acidic water) on larvae in the hatchery and potential effects on juvenile oyster seed in some growing areas. Field experiments will be conducted to verify oyster mortality due to poor water quality and track growth and survival over time along estuarine gradients. The effect of eelgrass which can potentially mitigate the effect of poor water chemistry via photosynthesis will also be investigated to suggest potential best management practices. Shellfish aquaculture modifies the estuarine environment and habitat including the presence of seagrass utilized by fish and invertebrates at the local scale. The known role of seagrasses as valuable estuarine nursery habitat for fish and invertebrates and existing no-net-loss provisions in federal and state regulations has resulted in a very precautionary approach by managers that avoids any direct impacts or damage to seagrass. The Army Corps of Engineers nationwide permits for shellfish aquaculture require notification prior to any shellfish activity in seagrass and a buffer zone between shellfish culture and seagrass, yet little scientific guidance exists regarding the functional value of either seagrass and especially aquaculture for species of concern at the estuarine landscape scale. During the next five years we will expand on prior research addressing effects of shellfish at mostly experimental scales using surveys and maps created from aerial photography for three west coast estuaries to examine effects on the estuarine landscape. Use of landscape scale features like the native eelgrass corridors, meadows and habitat edges as well as shellfish aquaculture beds and edges will also be evaluated utilizing underwater video and other trapping techniques. Habitat function will be assessed by conducting field microcosm and tethering experiments with juvenile Dungeness crab and English sole. This research will quantify disturbance to eelgrass by shellfish aquaculture at the landscape scale and define functional value of both habitats for species of concern providing a common understanding and a model decision tree for stakeholders making management decisions at individual locations.

Progress Report
This is the final report for project 2072-63000-004-00D, "Developing Methods to Improve Survival and Maximize Productivity and Sustainability of Pacific Shellfish Aquaculture," which terminated in December 2019. This project was merged with project 2072-31000-005-00D and replaced by new project 2072-63000-005-00D, "Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries." See the new project report for additional details. Substantial results were realized over the life of this project, which addressed two current problems that constrain the shellfish aquaculture industry: 1) a lack of understanding about and the ability to eliminate or at least mitigate the effects of early mortality of juveniles caused by changing ocean conditions and pests such as burrowing shrimp, and 2) environmental regulations concerning the impact of shellfish farming practices on the estuarine environment. ARS researchers in Newport, Oregon, continued to document the abundance of two species of burrowing shrimp that are pests to the shellfish aquaculture industry because they cause shellfish to sink under the surface of the sediment and die. The work advances Sub-objective 1.1. Annual surveys conducted in four estuaries along the U.S. West Coast revealed that populations of one species of shrimp, the ghost shrimp, have increased again following a long decline from about 1996–2010 while those of a second species, the blue mud shrimp, have collapsed due to large infestations of an introduced parasite that severely limits this shrimp’s ability to reproduce. Shrimp larvae hatch in the estuary, but spend most of their eight week larval period in the nearshore coastal ocean and then must return or “recruit” as small post-larvae back to these estuaries. Little to no recruitment of ghost shrimp was observed at a long-term monitoring location in Willapa Bay, Washington, from 2004–2010, but recruitment re-occurred beginning in 2011 with highest values observed from 2015-2017. Researchers created a simple model that showed that the magnitude and frequency of shrimp recruitment is directly related to subsequent shrimp population size in these estuaries. Scientists used the pigment lipofuscin, found in these shrimp’s brains, to age shrimp and built an age-based model which showed that there was consistent and relatively high natural mortality of larger shrimp after recruitment, most likely due to predation by crab and fish, including sturgeon. This is important because it suggests that this high natural mortality rate likely results in relatively low densities of large shrimp on most shellfish beds except during periods of repeated strong recruitment events. These models can be used in an Integrated Pest Management Program by the shellfish industry to predict when shrimp density is likely to become a problem for them. Public perception continues to make the chemical treatment program for these shrimp in Washington State difficult to permit. Scientists continue to work with the industry to develop a good monitoring plan that includes recruitment indices which may focus efforts on developing alternative treatments for these small young-of-the year shrimp with shallow burrows and potentially allow the industry to control them before they become a significant issue. A second research effort (Sub-objective 1.2) focused on juvenile oyster mortality due to ocean acidification (OA) and other water chemistry parameters including the presence of food for juvenile oysters deployed as seed (spat) in U.S. West Coast estuaries. Most documented effects of OA have been shown to affect oyster larvae during initial shell formation or at metamorphosis when they settle to become seed. The U.S. West Coast aquaculture industry has adapted to this problem by buffering and changing water chemistry in shellfish hatcheries, but seed may still be vulnerable and ARS researchers initiated experiments to test whether eelgrass, an estuarine plant, can modify water chemistry and assess its effects on these spat via photosynthesis and carbon dioxide uptake. The possible importance of eelgrass was demonstrated by experiments conducted in Netarts Bay, Oregon, in 2015 in which project collaborators demonstrated that more oyster spat survived when placed in eelgrass and that oysters on average grew faster in eelgrass. ARS researchers deployed oysters at a broader array of stations along the estuary axis and results suggested that the effect of eelgrass on growth over the summer might be site-specific and that factors other than water chemistry such as food concentration and co-occurring effects of eelgrass presence on fouling organisms like barnacles that compete with oysters for space, are important considerations. Results from an additional experiment conducted in Willapa Bay during the summer of 2018 also documented a significant estuarine gradient in spat survival with faster growth near the estuary mouth especially within eelgrass, but a reversed trend with either no difference or faster growth outside eelgrass further inside the estuary. Other factors like height above bottom and seed source were not significant, but a new experiment to further evaluate these gradients in both estuaries was deployed in 2019. Research to address Objective 2 in this project included completing maps of both aquaculture and eelgrass habitats for Willapa Bay, Washington, Humboldt Bay, California, and Tillamook Bay, Oregon, estuaries to evaluate their interaction at the landscape scale. This is important because regulations developed by management agencies currently constrain new or expanded shellfish aquaculture operations in order to protect eelgrass as valuable essential nursery habitat for commercially valuable fish. These regulations do not currently consider aquaculture as habitat and instead simply minimize its potential effect on eelgrass. This research continues to be used for permitting decisions regarding both current and proposed expansion of shellfish aquaculture in U.S. West Coast estuaries. ARS researchers and collaborators deployed underwater video cameras and fish traps within oyster culture beds, along the edge of the culture and in adjacent eelgrass habitats in four estuaries from Samish Bay, Washington, to Humboldt Bay, California, in 2016 and again primarily in Willapa Bay in 2017, to compare fish and crab use of off-bottom longline oyster culture with traditional on-bottom oyster culture. Results suggest that the structure created by off-bottom oyster culture is similar to that created by eelgrass and attracts similar fish and invertebrates, particularly shiner surf perch. Data gathered on the relative strength of predation in these habitats using small pieces of bait tethered to poles revealed differences in predation by estuary, but no differences in baits consumed amongst habitats. Predation was higher in off-bottom longline culture than in on-bottom oyster culture and most differences were attributable to higher abundance of staghorn sculpin, one important fish that utilizes these estuaries. Few distinct edge effects were observed except, perhaps, reduced abundance and lower foraging behavior for sculpins along edges.


Review Publications
Bosley, K.M., Coleman, N., Dumbauld, B.R. 2019. Verification of ageing methods for the burrowing shrimp, Neotrypaea californiensis, using extractable lipofuscin and gastric mill cuticular features. Journal of the Marine Biological Association of the United Kingdom. 99(7):1627-1638.