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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

2019 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
Progress was made addressing both objectives and their sub-objectives, all of which fall under National Program 106, Component 4, Develop Shellfish Systems to Maximize Productivity and Environmental Compatibility. Research addressing Objective 1 is concerned with the evaluation of two sources of juvenile shellfish mortality that cause substantial problems for the shellfish aquaculture industry in the Pacific Northwest. Sub-objectives focus on: 1) burrowing shrimp, pests that cause shellfish to sink under the surface of the sediment and die, and 2) reduced carbonate saturation states, known as ocean acidification (OA), which cause larval oysters in particular to have problems forming/secreting their shells. Progress towards Sub-objective 1.1 in 2019 included an annual survey of burrowing shrimp populations in several estuaries. These annual surveys conducted since 2004 revealed that populations of burrowing shrimp have increased again in Willapa Bay, Washington, following a decade-long decline. 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 was observed at a long-term monitoring location in Willapa Bay from 2004–2010, but recruitment re-occurred beginning in 2011 with highest values from 2015-2017. Shrimp recruitment occurred in all four estuaries surveyed in these three years, but ARS researchers documented slightly lower recruitment in summer and fall 2018. Increased levels of recruitment are of concern to the shellfish industry because of a lack of control methods. Progress in 2019 also included updating simple models and a more detailed age-cohort population dynamics model used to demonstrate that recruitment is directly related to shrimp population size in subsequent years. These models suggest that mortality of new recruits and older shrimp is fairly high so that recent recruitment may not yet be approaching a threshold necessitating treatment as part of an integrated pest management approach. Sub-objective 1.2 focuses on juvenile oyster mortality due to OA and other water chemistry parameters, including the presence of food for juvenile oysters deployed as seed (spat) in the estuary. 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 began a new experiment in Willapa Bay during the summer of 2018 to test whether eelgrass, an estuarine plant, can modify water chemistry and 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. Data collected by ARS researchers in 2015 with oysters deployed at a broader array of stations along the estuary axis, however, suggested that this effect 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. Data collected in Willapa Bay during the summer of 2018 also displayed this strong estuarine gradient and a new experiment was deployed to evaluate in both estuaries in 2019. Research to address Sub-objective 2.1 included finalizing geographic information system (GIS) layers of both aquaculture and eelgrass habitats for Willapa, Humboldt and Tillamook 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 will be useful for permitting decisions regarding both current and proposed expansion of aquaculture in U.S. west coast estuaries. Research for Sub-objective 2.2 concerns the use of intertidal estuarine habitats including oyster aquaculture by fish and crab. Progress in 2019 included final analysis of data collected using underwater video cameras and fish traps in four estuaries from Samish Bay, Washington, to Humboldt Bay, California, in 2016 and again primarily in Willapa Bay in 2017, to compare off-bottom longline culture with on-bottom oyster culture as habitat. Cameras and traps were deployed within oyster culture beds, along the edge of the culture and in adjacent eelgrass habitats. Results suggest that 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. Few distinct edge effects were observed, except perhaps reduced abundance and lower foraging behavior for sculpins along edges.


Review Publications
Bosley, K.M., Wainwright, T., Dumbauld, B.R. 2019. Application of the extractable lipofuscin aging method to estimate mortality and population dynamics of the burrowing shrimp, Neotrypaea californiensis. Estuarine, Coastal and Shelf Science. 219:33-44.
Borin, J., Moser, M., Hansen, A., Beauchamp, D., Corbett, S., Dumbauld, B.R., Pruitt, C., Ruesink, J., Donoghue, C. 2017. Energetic requirements of green sturgeon (Acipenser medirostris) feeding on burrowing shrimp (Neotrypaea californiensis) in estuaries: importance of temperature, reproductive investment, and residence time. Environmental Biology of Fishes. 100:1561-1573.