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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

2017 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
Objective 1 concerns the evaluation of two sources of juvenile shellfish mortality that cause substantial problems for the shellfish aquaculture industry in the Pacific Northwest. Burrowing shrimp are pests that cause shellfish to sink under the surface of the sediment and die and reduced carbonate saturation states known as ocean acidification (OA) causes larval oysters in particular to have problems forming/secreting their shells. 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 coastal estuaries. An examination of long-term records suggests that while the absolute numbers of shrimp recruiting vary widely from year to year and amongst estuaries, trends in relative abundance are similar amongst the four estuaries that we have been monitoring. No recruitment was observed at a long-term monitoring location in Willapa Bay from 2004–2010, but recruitment re-occurred from 2011-2016. We observed shrimp recruitment to all four estuaries surveyed in 2015-16. We developed simple models to demonstrate that recruitment is also directly related to shrimp population size in subsequent years. 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 are approaching a threshold and treatment should be considered. The recent increase in recruitment is therefore of concern to the shellfish industry because a program developed to use the pesticide imidacloprid for shrimp control in Washington State was suspended in 2015 due to public perception and market issues. While a group of growers has re-applied for a new permit to use this pesticide in 2018, currently the industry more broadly has no means of controlling shrimp on their aquaculture leases and beds at the same time that shrimp populations are increasing. We held a joint workshop with Washington State University in April 2017 to present these research results directly to industry stakeholders along with suggested monitoring techniques for use in integrated pest management of these shrimp on shellfish beds. 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, to establish an industry monitoring program, and to re-examine potential alternative control techniques – in particular those that may work for these newly recruited shrimp in order to sustain shellfish aquaculture in these estuaries. Most documented effects of OA have been shown to occur in the larval phase when oysters are initially forming their shell and/or at metamorphosis when they settle to become small juveniles (spat) and the U.S. West coast aquaculture industry has adapted by buffering and changing water chemistry in shellfish hatcheries. We are especially interested, however, in what happens to oyster spat once they are deployed in the estuary and whether eelgrass, an estuarine plant, can modify that water chemistry and its effects on these spat via photosynthesis and carbon dioxide (C02) uptake. We measured juvenile oyster survival and growth in Netarts Bay, Oregon to examine the effect of reduced carbonate saturation states in 2015. Project collaborators demonstrated that eelgrass increased both growth and survival of oyster spat in the estuary and this might be due to compensatory growth during daily low-CO2 periods associated with the seagrass growing season. Due to the complex nature of estuarine water chemistry measurements and the need to monitor changes on a continuous basis over several months, this data analysis is still ongoing and we are currently evaluating whether a concurrent gradient in the effect of eelgrass and water chemistry on oyster growth and mortality from the mouth to the head of the Netarts Bay also occurred. We are planning a second field experiment in 2018. Objective 2 is designed to examine use of intertidal estuarine habitats including oyster aquaculture by fish and crab. We analyzed data collected using underwater video cameras in four estuaries from Samish Bay, Washington to Humboldt Bay, California. Cameras were deployed within oyster longline aquaculture, along the edge of this culture and in eelgrass habitats at several sites in each of these estuaries in 2016 and sampled again with a slightly modified design in 2017. Most of the fish in both eelgrass and aquaculture habitats seemed to be transiting and not foraging or using the structure provided as refuge. The two most common species of fish observed were shiner perch and staghorn sculpin in all four estuaries. Preliminary results suggest that perch were more frequently observed in longline aquaculture than in eelgrass and sculpins along the edge than in either separate habitat. We also gathered data on the relative strength of predation in these habitats using small pieces of bait tethered to poles and found the highest predation to occur in Tillamook Bay, Oregon, but no differences in baits consumed amongst habitats. 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 like English sole and salmon. They do not consider aquaculture as habitat and instead simply minimize its potential effect on eelgrass. The oyster aquaculture industry has at least in part shifted culture operations where oysters are planted directly on the bottom to using off-bottom structures (longlines, floating bags) in order to minimize these impacts. Our research is one of the first evaluations of these off-bottom culture structures as potential fish habitat. We also gathered data on the spatial extent of aquaculture in Humboldt Bay, California and Tillamook Bay, Oregon and are building models to compare eelgrass distribution within and outside of oyster aquaculture areas in these estuaries. This research will be useful for permitting decisions regarding both current and proposed expansion of aquaculture in U.S. west coast estuaries.

1. Underwater video platform to quantify fish and crab use of intertidal longline oyster aquaculture beds. Regulations developed by management agencies currently constrain new or expanded shellfish aquaculture operations because they are designed to protect eelgrass as valuable estuarine habitat for fish and crab. They do not consider aquaculture as habitat and instead simply minimize its potential effect on eelgrass. The shellfish aquaculture industry has at least in part shifted from on-bottom culture operations to using off-bottom structures (longlines, floating bags) in order to minimize impacts to eelgrass. Off-bottom culture structures are impossible to sample for mobile fish and crab with most traditional sampling methods which use nets. USDA-ARS researchers in Newport, Oregon and project collaborators at the Pacific Shellfish Institute designed underwater video assessment methods to evaluate the functional value of this off-bottom culture as habitat and compare it to that for adjacent eelgrass. Examination of video allowed for behavioral observations (e.g feeding, taking refuge) which can be used to examine the function of these habitats for these organisms.