MBARI procedures for automated nutrient analyses using a modified Alpkem Series 300 Rapid Flow Analyzer

This report documents the methods used at the Monterey Bay Aquarium Research Institute (MBARI) for analyzing seawater nutrient samples with an Alpkem Series 300 Rapid Flow Analyzer (RFA) system. The methods have been optimized for the particular requirements of this laboratory. The RFA system has been used to analyze approximately 20,000 samples during the past two years. The methods have been optimized to run nutrient analyses in a routine manner with a detection limit of better than -±1% and a within run precision of -±1% of the full scale concentration range. The normal concentration ranges are 0-200 ~M silicate, 0-5 ~M phosphate, 0-50 ~M nitrate, 0-3 ~M nitrite, and 0-10 ~M ammonium. The memorandum is designed to be used in a loose-leaf binder format. Each page is dated and as revisions are made, they should be inserted into the binder. The revisions should be added into the binder. Retain the old versions in order to maintain a historical record of the procedures. (88 pages)

An Easy-to-Construct Automated Winkler Titration System

The instrument described in this report is an updated version of the high precision, automated Winkler titration system described by Friederich et al.(1984). The original instrument was based on the work of Bryan et al. (1976) who developed a colorimetric endpoint detector and on the work of Williams and Jenkinson (1982) who produced an automated system that used this detector. The goals of our updated version of the device described by Friederich et al. (1984) were as follows: 1) Move control of the system to the MS-DOS environment because HP-85 computers are no longer in production and because more user-friendly programs could be written using the IBM XT or AT computers that control the new device. 2) Use more "off the shelf" components and reduce the parts count in the new system so that it could be easily constructed and maintained. This report describes how to construct and use the new automated Winkler titration device. It also includes information on the chemistry of the Winkler titration, and detailed instructions on how to prepare reagents, collect samples, standardize and perform the titrations (Appendix I: Codispoti, L.A. 1991 On the determination of dissolved oxygen in sea water, 15pp.). A disk containing the program needed to operate the new device is also included. (pdf contains 33 pages)

Adsorptive Media Investigations and Testing for Improved Performance of Stormwater Treatment Systems in the Tahoe Basin

Retrofit activities, such as improving hydrology and incorporating more advanced treatment methods into systems where feasible, may improve phosphorus (P) removal performance of current Best Management Practices (BMPs). In the recent past, chemical treatment systems such as chemical dosing and the use of adsorptive media have become more prevalent for treating stormwater and hold promise for improving the P removal performance of stormwater treatment BMPs (Bachand et al., 2005; Patel et al., 2005). Our primary objective for this project has been to investigate whether adsorptive media hold any promise for improving P removal performance of stormwater basins and treatment wetlands at Lake Tahoe.... (PDF contains 99 pages)

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example, management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things a description of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Tracking Pacific bluefin tuna (Thunnus thynnus orientalis) in the northeastern Pacific with an automated algorithm that estimates latitude by matching sea-surface-temperature data from satellites with temperature data from tags on fish

Data recovered from 11 popup satellite archival tags and 3 surgically implanted archival tags were used to analyze the movement patterns of juvenile northern bluefin tuna (Thunnus thynnus orientalis) in the eastern Pacific. The light sensors on archival and pop-up satellite transmitting archival tags (PSATs) provide data on the time of sunrise and sunset, allowing the calculation of an approximate geographic position of the animal. Light-based estimates of longitude are relatively robust but latitude estimates are prone to large degrees of error, particularly near the times of the equinoxes and when the tag is at low latitudes. Estimating latitude remains a problem for researchers using light-based geolocation algorithms and it has been suggested that sea surface temperature data from satellites may be a useful tool for refining latitude estimates. Tag data from bluefin tuna were subjected to a newly developed algorithm, called “PSAT Tracker,” which automatically matches sea surface temperature data from the tags with sea surface temperatures recorded by satellites. The results of this algorithm compared favorably to the estimates of latitude calculated with the lightbased algorithms and allowed for estimation of fish positions during times of the year when the lightbased algorithms failed. Three near one-year tracks produced by PSAT tracker showed that the fish range from the California−Oregon border to southern Baja California, Mexico, and that the majority of time is spent off the coast of central Baja Mexico. A seasonal movement pattern was evident; the fish spend winter and spring off central Baja California, and summer through fall is spent moving northward to Oregon and returning to Baja California.

Classification of Coastal Communities Reporting Commercial Fish Landings in the U.S. Northeast Region: Developing and Testing a Methodology

The National Marine Fisheries Service is required by law to conduct social impact assessments of communities impacted by fishery management plans. To facilitate this process, we developed a technique for grouping communities based on common sociocultural attributes. Multivariate data reduction techniques (e.g. principal component analyses, cluster analyses) were used to classify Northeast U.S. fishing communities based on census and fisheries data. The comparisons indicate that the clusters represent real groupings that can be verified with the profiles. We then selected communities representative of different values on these multivariate dimensions for in-depth analysis. The derived clusters are then compared based on more detailed data from fishing community profiles. Ground-truthing (e.g. visiting the communities and collecting primary information) a sample of communities from three clusters (two overlapping geographically) indicates that the more remote techniques are sufficient for typing the communities for further in-depth analyses. The in-depth analyses provide additional important information which we contend is representative of all communities within the cluster.

Testing a Device to Exclude Ovigerous Blue Crabs, Callinectes sapidus, from Commercial Pots

North Carolina fishery managers are considering methods to offer greater protection to the blue crab, Callinectes sapidus, spawning stock while maintaining a viable commercial fishery for female blue crabs in high salinity estuaries. We tested how effectively wire rectangles, or excluders, of two internal sizes, 45x80 mm and 45x90 mm, would prevent entry of ovigerous female (sponge) crabs into pots relative to control pots (without excluders) while maintaining sizes and catch rates of male and nonsponged female hard crabs. Field sampling among three pot designs (two excluder sizes and control pots) was conducted in Core Sound, N.C., during 2004–06. Median sizes (carapace widths) of mature female crabs were not different among the three pot types. However, median sizes of male crabs and sponge crabs were greater in control pots than pots with either size of excluder. Catch rates of mature female crabs from control pots were greater than from pots with 45x85 mm excluders. Catch rates of legal male and sponge crabs from control pots were greater than from pots with either size of excluder. Results indicate that using excluders involves a tradeoff between reducing catches and sizes of sponge crabs while also reducing sizes and catches of legally harvestable nonsponge crabs; moreover, the reduction in total catch and sizes would be greater for legal male crabs than for legal nonsponged female crabs. In high salinity waters close to North Carolina’s existing no-harvest blue crab sanctuaries, where females typically dominate catches of hard crabs, the benefit of using excluders to prevent entry of sponge crabs may outweigh a potentially modest decrease in landings of nonsponged females.

A general framework for integrating environmental time series into stock assessment models: model description, simulation testing, and example

We present a method to integrate environmental time series into stock assessment models and to test the significance of correlations between population processes and the environmental time series. Parameters that relate the environmental time series to population processes are included in the stock assessment model, and likelihood ratio tests are used to determine if the parameters improve the fit to the data significantly. Two approaches are considered to integrate the environmental relationship. In the environmental model, the population dynamics process (e.g. recruitment) is proportional to the environmental variable, whereas in the environmental model with process error it is proportional to the environmental variable, but the model allows an additional temporal variation (process error) constrained by a log-normal distribution. The methods are tested by using simulation analysis and compared to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. In the traditional method, the estimates of recruitment were provided by a model that allowed the recruitment only to have a temporal variation constrained by a log-normal distribution. We illustrate the methods by applying them to test the statistical significance of the correlation between sea-surface temperature (SST) and recruitment to the snapper (Pagrus auratus) stock in the Hauraki Gulf–Bay of Plenty, New Zealand. Simulation analyses indicated that the integrated approach with additional process error is superior to the traditional method of correlating model estimates with environmental variables outside the estimation procedure. The results suggest that, for the snapper stock, recruitment is positively correlated with SST at the time of spawning.

Sequential analysis for testing quality standard of fish ham and sausage

Fish sausages are finely ground fish flesh, either of a single species or mixed, homogenised with starch, sugar, fat, spices and preservatives, generally filled in cylindrical synthetic or natural casings and pasteurised. Similar products containing small pieces of quality fish and lard are termed "fish ham". They are highly relished products in Japan, annual consumption exceeding 2 lakh tones. Preliminary studies have shown that they can catch a lucrative market in our country. However, being a pasteurised product which is often consumed as such without any further cooking, strict quality control measures have to be enforced so as to avoid food poisoning hazards. Besides physical characteristics like absence of damages, pin-holes, curliness and air pockets as well as jelly strength, texture and flavour, chemical characteristics like pH and acid values, moisture, carbohydrate and fat contents and volatile bases have to be assessed. A very important test that has to be carried out along with the above, before passing a lot for free distribution is the bacteriological examination to avoid the presence of pathogenic organisms.