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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

2018 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
Research addressing 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. Two sub-objectives focus on burrowing shrimp, pests that cause shellfish to sink under the surface of the sediment and die, and reducing carbonate saturation states, known as ocean acidification (OA), which cause 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 ARS researchers have been monitoring. Little to no recruitment was observed at a long-term monitoring location in Willapa Bay from 2004–2010, but recruitment re-occurred from 2011-2017. Shrimp recruitment occurred in all four estuaries surveyed in the last three years and this increase is 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 re-applied for a new permit to use this pesticide in 2018, this permit was denied, so the industry in Washington and elsewhere has no means of controlling shrimp on their aquaculture leases and beds at the same time that shrimp populations are increasing. Simple models were used to demonstrate that recruitment is directly related to shrimp population size in subsequent years and a more detailed age-cohort population dynamics model was developed, which suggests that mortality of older shrimp is fairly high. 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 and a simplified model to predict when shrimp populations on shellfish beds are approaching a threshold when they would either need to implement control or no longer be able to grow shellfish. An active program is being developed in collaboration with other researchers and the shellfish industry to monitor recruitment, test these models with data collected on shellfish beds, and 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 affect oyster larvae during initial shell formation or at metamorphosis when they settle to become small juveniles (spat). The U.S. West Coast aquaculture industry has adapted by buffering and changing water chemistry in shellfish hatcheries. The second project Sub-objective focuses instead on juvenile oyster mortality once they have metamorphosed into spat and are deployed in the estuary. The question is whether eelgrass, an estuarine plant, can modify that water chemistry and its effects on these spat via photosynthesis and carbon dioxide (C02) uptake. The possible importance of eelgrass was demonstrated by experiments conducted in Netarts Bay, Oregon in 2015. In these experiments project collaborators demonstrated that more oyster spat survived when placed in eelgrass and that oysters on average grew faster. Data collected by ARS researchers with oysters deployed at a broader array of stations along the estuary axis, however, suggested that this effect may be site-specific and not as clear for individual spat by the end of the first growing season. It is also apparent 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. Research for Objective 2 is designed to examine use of intertidal estuarine habitats including oyster aquaculture by fish and crab. Data were collected using underwater video cameras in four estuaries from Samish Bay, Washington, to Humboldt Bay, California, in each of these estuaries in 2016 and again primarily in Willapa Bay in 2017, to compare off-bottom longline culture with on-bottom oyster culture as habitat. Cameras were deployed within oyster culture beds, along the edge of the culture and in adjacent eelgrass habitats. Results suggest that structures created by off-bottom oyster culture is similar to that created by eelgrass and attracts similar fish and invertebrates, particularly shiner surf perch. Most of the fish in both eelgrass and aquaculture habitats seemed to be transiting and not foraging or using the structure provided as refuge. Data was also gathered on the relative strength of predation in these habitats using small pieces of bait tethered to poles and showed the highest predation to occur in Tillamook Bay, Oregon, but no differences in baits consumed amongst habitats. Predation was also higher in off-bottom longline culture than in on-bottom oyster culture and seems to be attributable to higher abundance of staghorn sculpin in this habitat. Few distinct edge effects were observed except, perhaps, reduced abundance and lower foraging behavior for sculpins along this edge. Mesocosms (small tanks with bottoms removed so they could be deployed over these habitats in the field) were designed in 2018 and will be used to more directly quantify predation effects on juvenile Dungeness crab and English sole in these habitats in 2019. 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. This is one of the first evaluations of these off-bottom culture structures as potential fish habitat. Data gathered on the spatial extent of aquaculture in Humboldt Bay, Tillamook Bay, and Willapa Bay, will be used to construct models to compare eelgrass distribution and fish utilization 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.


Review Publications
Dumbauld, B.R., Bosley, K. 2018. Recruitment ecology of burrowing shrimps in US Pacific coast estuaries. Estuaries and Coasts - Journal of the Estuarine Research Federation.
Bosley, K., Copeman, L., Dumbauld, B.R., Bosley, K. 2017. Identification of burrowing shrimp food sources along an estuarine gradient using fatty acid analysis and stable isotope ratios. Estuaries and Coasts - Journal of the Estuarine Research Federation. 40:1113-1130.