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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

2015 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
Substantial progress was made initiating work under this new approved project which began in December of 2014 and replaces project 2072-63000-003-00D, "Quantifying Habitat Utilization and Reducing Juvenile Oyster Mortality in Pacific Shellfish Production". These projects have related objectives, all of which fall under National Program 106, Component 4. Sustainable Production Systems. This project focuses on problem statement C – Develop shellfish systems to maximize productivity and environmental compatibility. The first objective concerns evaluating two species of burrowing shrimp, which are pests that cause substantial problems for the shellfish aquaculture industry in the Pacific Northwest. Annual surveys initiated under the previous project revealed that due to recent annual recruitment events in 2011-2013, populations of ghost shrimp have increased again in Willapa Bay, Washington following a decade long decline. No recruitment was observed in 2014 and new surveys were initiated in 2015 under sub-objective 1.1. of the new project, to compare densities of the 2011-2013 age classes of shrimp within and outside of oyster culture beds. A technique developed during the previous project to determine age of these shrimp using the pigment lipofuscin found in the shrimp’s neural tissues was confirmed using shrimp of known age. We also compared results with a second technique that utilizes counts of ring structures in the gastric mill, a hard toothed structure found in the shrimp’s digestive system that is retained when the shrimp grow and molt. Shrimp larvae hatch in the estuary but spend most of their larval period in the nearshore coastal ocean and then must recruit as post-larvae back to coastal estuaries. A re-examination of long term recruitment patterns suggests that while it varies widely from year to year and even amongst estuaries, the magnitude of recruitment is directly related to subsequent shrimp population size in these estuaries. Years with highest recruitment appear to be associated with weak northward transport of the larvae during the larval period. While shellfish growers may not be able to predict these conditions in advance, they should be able to use recruitment indices to predict when shellfish beds should be treated and may be able to more effectively and prescriptively treat small shrimp with shallow burrows. We are actively working with the integrated pest management coordinator hired by the shellfish industry to develop and test tools including small venturi pump samplers for tracking shrimp recruitment in order to establish an industry monitoring program. A new program to use the pesticide imadocloprid for shrimp control was approved by the regulatory agencies, but at least temporarily shelved in 2015 due to public perception and market issues, as well as some concern with efficacy of the chemical, which is influenced by local conditions including burrow depth, time of application and vegetative cover. There is renewed interest in a search for alternative control techniques and applying these towards integrated pest management, which takes into account shrimp pest ecology and population in order to sustain aquaculture activities in these estuaries. A tool for consistently measuring juvenile oyster survival and growth was developed and tested in Willapa Bay in the previous project and we are completing data collection in a second estuary under sub-objective 1.2 in the new project that now addresses reduced carbonate saturation states (ocean acidification) due to climate change as a source of reduced growth and mortality of juvenile oysters. We observed a gradient in both growth and mortality from the mouth to the head of the Wiilapa Bay estuary in the previous study and a significant difference between oysters deployed off and on-bottom, presumably due to siltation and predation. The new project is more directed at water chemistry as one source of mortality or altered growth and whether eelgrass can modify that chemistry and its effects on shellfish. Work under Objective two of the new project was also initiated. Results of the previous project suggest that most fish including juvenile English sole, shiner perch, and sculpins are found in greater abundance in structured intertidal habitats (both eelgrass and oyster aquaculture) than in open unstructured mudflat. Abundance is also higher during daytime flood tides. We finished similar work to assess use of clam aquaculture beds and the introduced eelgrass Zostera japonica and began work to modify and test underwater video techniques which will be used to quantify habitat use at the landscape scale. The spatial extent of both aquaculture and eelgrass habitats in Willapa Bay, Washington were quantified in the previous project which suggested that eelgrass is affected by oyster aquaculture at the scale of individual beds and by some harvest practices, but is not greatly impacted at the estuarine landscape scale from year to year. We began a similar assessment for Humboldt Bay, California and Netarts Bay in Oregon and completed a second analysis of the Willapa Bay data to model the effects of sea level rise due to climate change on eelgrass and its continued interaction with oyster aquaculture. Since eelgrass is widely viewed as essential nursery habitat for commercially valuable fish like English sole and salmon, this research will be useful for permitting decisions regarding both current and proposed expansion of sustainable aquaculture operations in West Coast estuaries.


Review Publications
Dumbauld, B.R., Mccoy, L.M. 2015. The effect of oyster aquaculture on seagrass (Zostera marina) at the estuarine landscape scale in Willapa Bay, Washington (USA). Aquaculture Environment Interactions. 7:29-47.