Fred Conte's Programs

Finfish Production, Broodstock Development, and Aquatic Animal Welfare

California has the most diverse aquaculture finfish industry in the United States. The various topographies and microclimates produce a wide range of water temperatures and over twenty-five species of finfish are in production. Products include food, recreational, and ornamental species. California does not have a major aquaculture finfish processing industry. Of the food species, most are live-hauled to larger metropolitan areas where they are retailed as a live product. Secondary food species, used in the recreational fishing industry, support a multi-billion-dollar-a-year recreational sports industry. The major species produced are channel catfish, rainbow trout, trout eggs, largemouth bass, striped bass, hybrid striped bass, lesser sunfish, multiple species of bait fish, tilapia, sturgeon, carp, ornamental Koi, aquarium fish and aquarium feeder fish. Because of the large number of finfish species, University resources are more often directed toward discipline studies such as reproduction and pathology.

Extension outreach activities in finfish aquaculture are conducted by the campus-based Extension Specialist working independently, or in concert with other University departmental faculty who also have some outreach responsibility. This cooperative effort expands the outreach capabilities of the aquaculture program and allows greater utilization of University resources. Major outreach programs being conducted in freshwater aquaculture include channel catfish production, trout, aquaponics, farm pond aquaculture, aquaculture system design and management, water quality management, finfish species physiology and biological requirements, finfish disease management, production site selection and pond facility construction, and aquaculture permit process and regulations. Major commitments include sturgeon broodstock development and caviar production; and outreach projects associated with larval marine finfish diets.

Animal welfare is a major concern of California's general population and an issue addressed within the University of California. Animal welfare means the humane treatment of animals managed by humans. In the case of food production animals, this means that the animals are maintained under "best management practices" throughout their life, and humanely slaughtered before processing. Well-designed best management practices for aquatic animals are designed to reduce damage through handling, stress and disease. In support of these efforts, programs have been established with the aquaculture industry to develop animal welfare positions within the industry and to develop best management practices for holding farm-raised aquatic species, including humane slaughter.

California sturgeon are rendered unconscious using a club to administer a blow to the head prior to bleeding and slaughter. My program, in cooperation with Sterling Caviar, has conducted studies that demonstrated the effective use of Cash Specials and Cash CPK2 captive bolt guns to administer the appropriate stun in large fish (40+ kgs). Saggital sections of the sturgeon head revealing the brain were used to determine where to administer the stun, and later to assess the effects of the stun. External head morphology related to internal brain structures was used to standardize positioning of the captive bolt, and external anatomical responses were identified to determine if the stun was successful. BUNZL Processing Division of Omaha, Nebraska used the results and sent them to Accles & Shelvoke, Ltd. in the U.K. for the design of a prototype pneumatic-operated captive bolt stunning system that will be appropriate for use on meat and caviar sturgeon. This information and technology was also extended to the Louisiana alligator industry.

Oyster Production And Shellfish Sanitation

Oyster aquaculture is California's oldest aquaculture industry. What began in the early 1850's as a transplant seed industry is today a valuable asset to the state's economy, traditions and a guardian of our natural resources. Current production is primarily in Humboldt Bay, Drakes Estero, Tomales Bay, Morro Bay and Agua Hedionda Lagoon in Carlsbad. The industry grows a variety of species, including Pacific and Kumamoto oysters. The demand for oyster products far exceeds the state's production level and the majority of shellfish products consumed in the state are imported from the Pacific Northwest and, to a lesser extent, the Atlantic and Gulf states. The California product is considered prime and the production areas are among the best in the country.

The California Department of Public Health in cooperative programs with the shellfish industry conducts regular certification programs and shellfish monitoring programs to assure food quality. Two essential programs are the monitoring of the bays for indications of contamination by human sewage and for the occurrence of natural biotoxins, such as paralytic shellfish poison, produced by toxic phytoplankton. These two monitoring programs provide a safe product for the consumer and provide an early warning system for people sport-harvesting shellfish in noncommercial areas. One of the strongest arguments for a strong shellfish industry is its position as the "canary in the mine." As long as the shellfish industry exists, the bays and other shellfish- growing areas will be monitored for water quality to assure human health safety. The monitoring programs include coliform, chemical, and biotoxin analysis. These activities are one of the greatest deterrents to resource exploitation by any group using the coastal zone, including the shellfish industry itself.

A significant completed project was programs to assess the positive and negative environmental impacts of shellfish culture on bay environments, and mitigation efforts to alleviate negative impacts. These were cooperative efforts with industry, state and federal agencies, which led to the transition of the oyster industry in Humboldt Bay from bottom culture to off-bottom culture in a nine-year program. With the completion of that project, emphasis was switched to shellfish sanitation.

In recent years, my shellfish program has emphasized research into computer applications, focused on development of shellfish sanitation simulation and analytical models in a cooperative program with the California Department of Public Health (CDPH). The models are incorporated into software used by shellfish regulators and the commercial industry. My colleague and programmer is Dr. Abbas Ahmadi of the Department of Animal Science.

Our first model and software’ Aquarius version 1.0, resulted in adaptation of new rainfall closure regulations for two growing areas in Humboldt Bay. The oysters companies were able harvest oysters for an increased number of days, which translated into additional income of about 1.2 million dollars. Meetings were held at the Pacific Rim Shellfish Conference where State and Federal Shellfish regulators were asked what improvements they would like to see in an improved model. Regulators expressed enthusiasm for an expanded program, and identified twelve additional components that they considered essential to a fully mature program that could be used as a decision-making tool in their processes. A grant was obtained from the Western Regional Aquaculture Center (WRAC) to help defray a portion of the cost of producing Aquarius version 2.0. A core development team including University and CDHS personnel guided the software’s development. The University’s responsibility was to design and build the program, and the agency responsibility was to Beta-test the program using real data, and cross-check the accuracy of the program against their own statistical analysis and procedures.

Aquarius v.2.0 is a more powerful tool than its predecessor. The program is written in the Visual FoxPro database programming language and uses the Visual Basic for Application (VBA) codes for communicating with Microsoft Excel. To accommodate the needs of public health agencies, major upgrades were incorporated in version 2.0, to include two statistical sample size programs, improved data filtration options, and the inclusion of additional parametric and non-parametric statistical analyses that increase the reliability of the decision making process necessary for public health objectives. We were also asked to expand the program to meet federal and state sanitation requirements by including additional, mandated options, including rainfall data that can show cumulative daily, 6- hourly, hourly and Tip-data format (tip containers); and options for Three-Tube Test, Five-Tube Test, 12-Tube Test, Membrane Filter (MF); and Restricted 3-, 5-, and 12- Tube Test. To meet a specific public health challenge in measuring conditions in saturated watersheds, an option was incorporated to use data from Wet Antecedent Conditions only, and options to define these conditions. Options for statistical parameters include choices of Alpha and Beta Level for Statistics, with options to apply either the standard NSSP method to meet the NSSP criteria, in which the Geometric Mean must be less than 14 and the Estimated 90th percentile must be less than 49 for 3- tube Test, or a NSSP-CI method in which CI stands for Confidence Interval. The second choice is a more sensitive option in which the NSSP method is modified by using the upper limit of the 95% confidence interval, which is used only for compliance sampling when challenging the adequacy of sample sizes.

The Aquarius software has had major impact on how CDPH collects water samples for testing, and has influenced CDPH to switch their method of statistical analysis from regression analysis to T-test. We found while examining CDPH data, that their use of regression analysis revealed inadequacy in sample sizes taken late in the closure period that resulted in low P-values, which required extrapolation of data, and a high degree of subjective interpretation of results. We also found that by switching to the statistical T-test, a critical period could be identified in which the site was closed under the old regulation, but open under a proposed new regulation. Not only could the T-test determine if significant differences existed between the two rules, but additional statistics to determine proper sample size could be performed. This was a radical departure from the way the agency evaluated data in the past. After extensive beta-testing of the program, Aquarius v2.0 with the new statistical features was finalized and adopted by the CDPH as a tool in January 2009.

A second software program, Processing Program (RPP, was developed as a direct spin-off of Aquarius v2.0. The CDPH spends numerous hours converting databases by hand to formats that could be used in analytical spreadsheets and/or software. The primary problems were human error caused by duplicate data, the need to reverse data entries without error, and conversion of tip rainfall data to cumulative rainfall data, without error. The RPP program is composed of four modules designed to prepare databases for use in any analytical rainfall program, and has specific application to Aquarius v2.0.

The Dup module removes duplicated data in any dataset. The Rev module reverses the sorting order of rainfall data, and the Sum module calculates cumulative Tip (from tip containers) rainfall data from hourly rainfall data; and the Tip module is designed to calculate the hourly rainfall data from cumulative or non-cumulative tip rainfall data. The resolution of the input data file can focus down to multiple tips per hour, and even multiple tips per minute. The RPP program was beta tested and adopted by the CDPH in February 2009. Based on the successful adoption of Aquarius v2.0 and the Rainfall Processing Program by the CDPH, regional industry and agency workshops were held in California and Washington demonstrating the various models applications.

I have since obtained an additional grant from WRAC to begin development of Aquarius v.3.0. The original computer model will be reconfigured to incorporate tidal activities into the sanitation analysis, a parameter that has not been accomplished before because of the sheer magnitude of the datasets and associated analyses. Additional analytical features will also be incorporated. This is a regional research project involving multiple state inputs over a three-year period.

Internet and Social Media

A major portion of my program is directed toward use of the Internet and “New Media” for the dissemination of aquaculture information. The hub of the system is my website California Aquaculture.  California Aquaculture is a regional web site for the western United States, but has national and international audiences. The website is a storehouse of aquaculture information, with links to other aquaculture resources, including institutions, government agencies, and publications. A special section of the website, the News link, provides announcements of meeting and conferences, and contains articles and editorials on aquaculture subjects. A major feature of the website is the library of .pdf publications covering all aspects of aquaculture and operates by an internal program, Outreach Web. Outreach Web, created using a grant from the Western Regional Aquaculture Center (WRAC), allows the user to search for publications by keyword, author, or title. Major feature of the website are Podcasts, accessed directly from the site, but are also available as free educational Podcasts on iTunes. The site also features Flash videos of aquaculture subjects.

We have established California Aquaculture Facebook in our efforts to reach additional audiences. Our CA Facebook is designed to highlight rapidly developing stories and to redirect the reader to the original source of the information, or an expanded article on the California Aquaculture website under the News link. In 2011, we initiated a Twitter function as part of our information delivery system