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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

2016 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 on this project which falls 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 the evaluation of two species of burrowing shrimp, which are pests that cause substantial problems for the shellfish aquaculture industry in the Pacific Northwest. Annual surveys conducted since 2004 revealed that populations of ghost shrimp have increased again in Willapa Bay, Washington following a decade long decline. Shrimp larvae hatch in the estuary, but spend most of their larval period in the nearshore coastal ocean and then must recruit annually as small post-larvae back to coastal estuaries. An examination of long term patterns suggests that while this recruitment varies widely from year to year and amongst estuaries, the magnitude of recruitment is directly related to subsequent shrimp population size in these estuaries. No recruitment was observed at a long term monitoring location in Willapa Bay from 2004–2010, but occurred again from 2011-2013 and again in 2015. We observed shrimp recruitment to all four estuaries surveyed in 2015. This is of concern to the shellfish industry because a program developed to use the pesticide imadocloprid for shrimp control in Washington State was canceled in 2015 due to public perception and market issues. Growers currently have no means of controlling shrimp on their aquaculture leases and beds. We conducted surveys within and outside of some of these beds that were supposed to be treated in 2015 to determine whether shrimp present on these beds were the result of recent recruitment events. A technique developed to determine age of these shrimp using the pigment lipofuscin found in the shrimp’s neural tissues was confirmed using shrimp of known age which we held in tanks for four years. The effect of temperature on pigment accumulation was also explored in the laboratory and found to be non-significant for temperatures that these shrimp normally experience in the field. We developed a theoretical cohort-based model to explore population dynamics of ghost shrimp in Yaquina Bay, Oregon and found that the natural mortality rate was high, but consistent among older age cohorts over this four year period. We are currently using this technique to evaluate the age of shrimp found on shellfish beds in Willapa Bay in 2015 and for the previous four years, in order to apply this model to shrimp populations there. This is important because while shellfish growers may not be able to predict recruitment in advance, they should be able to use annual assessments of recruitment to predict when shrimp populations on shellfish beds have exceeded a threshold and treatment should be considered. We are actively working with collaborators and the shellfish industry to develop and test tools including a small venturi pump sampler for tracking shrimp recruitment, establish an industry monitoring program, and re-examine potential alternative control techniques for these newly recruited shrimp in order to sustain aquaculture activities in these estuaries. We measured juvenile oyster survival and growth in Netarts Bay, Oregon to examine the effect of reduced carbonate saturation states (ocean acidification) due to climate change. We are especially interested in whether eelgrass, an estuarine plant, can modify that water chemistry and its effects on shellfish via photosynthesis and C02 uptake. Project collaborators demonstrated that eelgrass increased both growth and survival of oyster spat at two locations and that observed patterns might be due to compensatory growth during daily low-CO2 periods associated with the seagrass growing season. We are currently examining whether there is also a concurrent gradient in the effect of eelgrass and water chemistry on oyster growth and mortality from the mouth to the head of the estuary as we have previously observed in Willapa Bay, Washington. Work under the second project objective was initiated. We finished analyses of previous underwater video conducted in Willapa Bay, Washington where Japanese eelgrass, an introduced species, has expanded its distribution and is being actively controlled in clam aquaculture beds. Fish and invertebrate community composition was not significantly different between introduced and native eelgrass habitats in this estuary, but there was an effect of removal of non-native eelgrass with some fish species preferring the open habitat created and others more abundant in eelgrass. We modified this sampling technique and used underwater video cameras to quantify habitat use by fish and invertebrates at the landscape scale in four estuaries from Samish Bay, Washington to Humboldt Bay, California. We deployed cameras within oyster longline aquaculture, along the edge of this culture and in eelgrass habitats in each of these estuaries. We also gathered data on the spatial extent of aquaculture in Humboldt Bay, California and Tillamook Bay, Oregon in order to build spatial models to compare eelgrass distribution within and outside of oyster aquaculture areas. 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 aquaculture in west coast estuaries.

1. Models of burrowing shrimp population dynamics can be used to advance integrated pest management. Burrowing shrimp are a problem for the U.S. West Coast shellfish aquaculture industry because they cause oysters to sink under the surface of the sediment and die. ARS scientists in Newport, Oregon monitored shrimp populations, quantified annual patterns of shrimp recruitment to West Coast estuaries and built an age based population dynamics model for these shrimp by quantifying the amount of lipofuscin, a pigment in their brains. Though recruitment of small young-of-the year shrimp varies widely from year to year and from estuary to estuary, the age based model suggested that there was also consistent and relatively high natural mortality of older shrimp after recruitment. Though the chemical treatment program in Washington State continues to be difficult to permit, developing a good monitoring plan that includes recruitment indices may focus efforts on developing an integrated pest management program with alternative treatments for shrimp recruits with shallow burrows and allow the industry to control them before they become a significant issue.