Recent Submissions

  • AquaDocs Guide for Collection Administrators, Version 1

    Simpson, Pauline; Taylor, Sally (UNESCO/IOC Project Office for IODEOostende, Belgium, 2021-07-22)
    This guide is for Collections Administrators who can edit items after they have been published in the repository.
  • AquaDocs Guide for Editors, Version 1

    Simpson, Pauline; Taylor, Sally (UNESCO/IOC Project Office for IODEOostende, Belgium, 2021-07-22)
    This document will guide Editors through the workflow stages and the process of approving, rejecting, or editing items submitted to AquaDocs.
  • AquaDocs Guide for Depositors, Version 1

    Simpson, Pauline; Taylor, Sally (UNESCO/IOC Project Office for IODEOostende, Belgium, 2021-07-22)
    This guide will walk depositors through the process of submitting a full text item into AquaDocs.
  • IODE-OceanDocs Policy Document 2018.

    Simpson, Pauline (UNESCO/IOC Project Office for IODEOostende, Belgium, 2018)
    OceanDocs is a secure, permanent open access repository for marine related institutes or marine related projects and is hosted by the Project Office for IODE of the Intergovernmental Oceanographic Commission (IOC) of Unesco. OceanDocs was created in 2007 to develop a distributed network of institutional, regional and national repositories. It started life as OdinPubAfrica, an open access repository1 developed by the Intergovernmental Oceanographic Commission, Ocean Data and Information Network (ODIN) Project, Marine Information Management Group, to contain the scientific literature from African marine science institutes. Other, ODIN groups were also interested in developing a similar repository project for their region. As a result the OdinPubAfrica repository was extended to accept other ODIN groups and was renamed OceanDocs (http://www.oceandocs.org). The implementation of the OceanDocs Network: - Makes scientific research of marine science institutes more quickly, and easily and freely accessible to the research and policy management community, - Makes local and regional grey literature available on a worldwide scale - Enhances the internal scientific communication - Facilitates publishing of research findings (e-journal as well as e-archive), specifically for scientists in Developing Countries thereby promoting their research and increasing their access to the international research forum.
  • MARSPLAN–BS - Case study 3 Burgas: Land-sea interactions

    Stancheva, M.; Stanchev, H.; Krastev, A.; Palazov, A.; Yankova, M.; Institute of Oceanology (Academic Publishing HouseVarna, Bulgaria, 2017)
    This report presents the results of Case Study 3 Burgas: land-sea interactions under the project Cross border maritime spatial planning in the Black Sea – Romania and Bulgaria (MARSPLAN–BS), Grant Agreement: EASME/EMFF/2014/1.2.1.5/2/SI2.707672 MSP LOT 1 /BLACK SEA/MARSPLAN–BS. The project is co-funded by the European Commission through the European Maritime and Fisheries Fund (EMFF), DG MARE: https://ec.europa.eu/maritimeaffairs/index_en. The case study was one of the case studies with major challenges carried out within the MARSPLAN–BS Project.
  • Preliminary review of the legal framework governing the use of chemicals in aquaculture in Asia

    Van Houtte, Annick Date published: 2000; Arthur, J.R. (Aquaculture Department, Southeast Asian Fisheries Development CenterTigbauan, Iloilo, Philippines, 2000)
    This preliminary review looks into legislation governing the use of chemicals in aquaculture in Asia. Brief assessments are made of the legislation relating to chemical contamination and the use of veterinary drugs and feed additives, a section is dedicated to trade in aquaculture products, and a few conclusions are then drawn. While mandatory measures of control are desirable and feasible, soft law instruments, such as codes of practice and conduct, allow an element of flexibility to be maintained while avoiding undue legislative restraints on scientific and technical progress.
  • Quantifying Recent Trends in Seagrass Cover and Biomass in a Stressed Environment, Pulau Semakau, Singapore

    Bramante, James F. (National University of Singapore, 2014)
    Globally, seagrass habitats have experienced sharp declines over the past century, with an annual loss of seagrass cover of 7%yr-1 since 1990. Despite the attention to seagrass this decline has brought, little research has been directed towards trends of seagrass habitats in Singapore. The research presented here developed and applied remote sensing methods to partially fill this gap, provide tools for more extensive monitoring in the future, and contribute to the global body of seagrass research. Satellite images from four different satellite sensors were used to estimate seagrass bed extent in Singapore’s second largest seagrass meadow, at Pulau Semakau, from 2001 to 2013. Statistical estimates of image signal-to-noise ratios were used to screen images for quality. Validation data collected in 2013 were used to estimate error for supervised classifications produced from each sensor. A novel method was explored to account for macroalgae blooms in the study area, but the resulting correction could not be validated and did not affect the overall trends in seagrass bed extent. In addition to the classification analysis, an empirical model linking remote sensing reflectance to above-ground biomass was constructed to examine the distribution of seagrass within the meadow. Applied to WV2 images from 2011 and 2013, this model produced estimates of above-ground biomass with root mean squared error (RMSE) of 54 gm-2 and 44.7 gm-2, respectively, within ranges of 0-288 gm-2 and 0-229 gm-2, respectively. A novel index to measure seagrass density non-destructively was developed to help conservation and monitoring efforts. This index, normalized canopy index (NCI), was estimated from satellite imagery more precisely than above-ground biomass, producing estimates from the 2013 WV2 image corresponding to field data with an R2 of 0.71 relative to the R2 of 0.39 produced by the above-ground biomass model. This index may be a promising, non-destructive alternative to above-ground biomass for remote sensing studies and should be pursued further in future research. Based on the time-series classification analysis, seagrass bed extent at Pulau Semakau declined from over 44.6 ha in April 2002 to 25.3 ha in June 2013. This decline occurred at an average of 5.1%yr-1 from 2001 to 2013, although this rate of decline slowed to 3.7%yr-1 in 2012. These declines are likely representative of other seagrass habitats in Singapore. Broader monitoring is required to determine to what extent Singapore’s seagrasses are disappearing. Although seagrass bed extent declined by 17% from April 2011 to June 2013, over the same time period total above-ground biomass in the seagrass meadow declined only 5%, from 41.6 Mg to 39.6 Mg. Two acute sedimentation events recorded over this time period corresponded to a large and permanent decrease in bed extent captured by WV2 imagery and a small and temporary decrease in bed extent captured by ALI imagery. I hypothesize that the discrepancy in decreases in extent and biomass, coupled with an increase in median biomass, is attributable to preferential survival and recolonization of dense-biomass seagrass species during these sedimentation events. Measurements of seagrass species abundance during this time period provide support for this hypothesis. This exercise demonstrates the advantages and limitations of monitoring seagrass bed extent and above-ground biomass. Bed extent provides a measure of overall viability of a seagrass meadow, but above-ground biomass provides a better index of spatially variable health and internal change. Coupled, these two measurements provide greater insight into complex seagrass bed processes and seagrass response to disturbance.
  • Crabbing into an uncertain future: the blue swimming crab fisher in coastal town of Eastern Philippines

    Cabrales, Pedro; Racuyal, Jesus; Mañoza, Alfredo (2015)
    This research project sought to find out the socio-economic status of the small-scale fishers of the blue swimming crab (Portunuspelagicus) in Samar, considering the diminishing volume of catch of the species in the recent years. Using a blend of quantitative and qualitative methods, the study employed an interview schedule, focus group discussion (FGD) and observation in collecting data not only from the fishers but also from other sectors directly involved in the blue swimming crab industry.
  • Transferable drug resistance plasmids in fish pathogenic bacteria.

    Aoki, Takashi; Arthur, J. Richard (Aquaculture Department, Southeast Asian Fisheries Development Center, 2000)
    Chemotherapeutic agents have been developed for treating bacterial infections and have been widely used for cultured fish for the last 30 years in Japan. The extensive use of chemotherapeutants has resulted in an increase in the occurrence of drug resistance in fish-pathogenic bacteria and also in the bacterial flora of the intestinal tract of cultured fish. The kinds of chemotherapeutants used are correlated with the occurrence of the corresponding drug-resistant genes in fish-pathogenic bacteria. Almost all multiple-drug resistant strains are carried on the transferable R plasmid, although resistance in fish pathogens to nitrofuran derivatives and pyridonecarboxylic acids is associated with a chromosomal gene. The DNA sequences of R plasmids generally differ depending on the species of fish pathogen. Exceptions are the R plasmids of Aeromonas hydrophila and A. salmonicida, which have the same resistance markers as chloramphenicol, streptomycin, and sulfonamides (SA); and the R plasmids of A. hydrophila and Edwardsiella tarda, which have the same resistance markers as SA and tetracycline. The fish pathogens A. hydrophila, A. salmonicida, E. tarda, Enterococcus seriolicida, Pasteurella piscicida, and Vibrio anguillarum are all widely distributed in fish farms in various areas, and within each species the R plasmid has an identical DNA sequence. The chloramphenicol resistance (cat) gene of the R plasmid from Gram-negative bacteria was classified into CAT I, II, III, and IV according to the DNA sequence. The cat gene of P. piscicida was classified as CAT I, those of A. salmonicida and E. tarda were classified as CAT II, and that of V. anguillarum was classified as CAT II or IV, depending on the time the strains were isolated. The tetracycline-resistance determinants (Tet), which occur in six classes (Tet A through Tet G), were class D in the R plasmids obtained from strains of V. anguillarum that were isolated from 1989 to 1991. The Tet for strains of V. anguillarum isolated from 1973 to 1977 was classified as Tet B, while for strains isolated from 1980 to 1983 it was classified as Tet G.
  • Socio-economic profile of the Philippine National Aquasilviculture Program (PNAP) beneficiaries in Jiabong, Samar, Philippines

    Enate, Rholyna; Diocton, Renato; Macopia, Janet (2013)
    A total of 37 beneficiaries under the Philippine National Aquasilviculture Program (PNAP) was interviewed using the structured survey questionnaire of Socioeconomic Monitoring Guidelines for Coastal Managers in Southeast Asia (SocMon SEA). Most of the members of the households are young and in-school. Household heads’ primary occupation is fishing, a shift from mussel farming- the town’s major industry in the past decades. Perceived threat by the beneficiaries is related to the environment specifically typhoon and the problems on waste disposal. It also identified law enforcement as weak leading to dwindling fish catch, mass mortality of mussel, red tide and other problems affecting their primary sources of income. However, they could not relate these phenomena to the most likely causes. The current occupation does not provide sufficient income for the family as they seek for alternative jobs. Garbage and poor implementation of laws are among the identified problems of the beneficiaries.
  • The use of chemicals in carp and shrimp aquaculture in Bangladesh, Cambodia, Lao PDR, Nepal, Pakistan, Sri Lanka and Viet Nam.

    Phillips, M (Aquaculture Department, Southeast Asian Fisheries Development Center.Tigbauan, Iloilo, Philippines, 2000)
    This paper provides an overview on the use of chemicals in seven countries in Asia (Bangladesh, Cambodia, Nepal, Laos PDR, Pakistan, Sri Lanka and Viet Nam), with an emphasis on coastal shrimp aquaculture and inland carp farming systems. The data come primarily from a recently completed survey of aquaculture farms in Asian countries conducted under the ADB/NACA Regional Study and Workshop on Aquaculture Sustainability and Environment. The issues discussed include the types and uses of chemicals in shrimp and carp culture, farm management practices and use of chemicals, hazards and adverse impacts associated with chemical use, alternative approaches to chemical use, and research recommendations. In inland carp farming, apart from lime and fertilizers, which are unlikely to give rise to any significant negative environmental impact, the overall use of chemicals is extremely low. Piscicides are used in some countries to control predators prior to stocking of ponds, but the use of antimicrobials and disease-control chemicals is limited to a small percentage (<5%) of producers. Most small-scale producers, who dominate aquaculture production in these countries, simply do not have the resources or need for such chemicals. The situation is similar in shrimp culture, with lime and fertilizers, followed by piscicides, being the most common chemicals used. The use of antimicrobials increases with intensification in shrimp culture, and these chemicals are mostly used in more intensive shrimp farming. In both shrimp and carp culture, promotion of “primary” health management practices probably offers greatest scope for prevention of aquatic animal disease outbreaks and the need for chemical use.
  • Government regulations concerning the use of chemicals in aquaculture in Japan

    Wilder, M.N.; Arthur, J.R.; Lavilla-Pitogo, C.R.; Subasinghe, R.P. (Aquaculture Department, Southeast Asian Fisheries Development Center, PhilippinesTigbauan, Iloilo, Philippines, 2000)
    In Japan, fisheries research activity is of a very diversified nature and is overseen by the national and prefectural governments. Regarding the use of chemicals in aquaculture, various regulations exist to protect the safety of cultured aquatic animals intended for human consumption. Under Japan’s Drug Laws, certain materials are designated as “medical products” for use in humans and animals, and their usage is strictly regulated. This paper introduces aspects of this legislation as relevant to the aquaculture industry and discusses how they are actually applied on the level of operation. Prefectural fish disease centers and extension services engage in the actual supervision of the use of such designated chemicals. In reference to government research structure, the Ministry of Agriculture, Forestry and Fisheries maintains 29 national research institutes, nine of which are fisheries institutes directly under the Fisheries Agency. The prevention and treatment of fish disease is an important research theme, and programs are being implemented, especially at the National Research Institute of Aquaculture. An auxiliary organ of the Fisheries Agency, the Japan Fisheries Resource Conservation Association operates educational and training programs for employees of prefectural centers and extension services whereby individuals receive certification as fish health specialists.
  • Traditional practices of fermenting small rock oysters (Sacosstrea sp.) 'Sisi'

    Patosa, Florabelle; Doncillo, Leonora; Diocton, Renato; Gomba, Felisa; Orale, Ronald (2014)
    The fermented product from small rock oyster (Sacosstrea sp.) locally known, 'Sisi' is an essential source of livelihood in Zumarraga, Samar. Key informant interviews, ocular observation and focus group discussion (FGD) were conducted to find out the traditional practices used in producing 'Sisi'. Salient findings showed that non-standardized processing of Sisi was practiced, thus limiting the revenues derived from this marginalized industry. Furthermore, 'Sisi' has high ash content with high microbial count which indicates that there are some colonies that grow in the mixture. Hence, there is a need to standardize the methods applied in producing fermented small rock oyster 'Sisi'.
  • The Use of Chemicals in Aquaculture in India

    Pathak, S.C.; Ghosh, S.K.; Palanisamy, K. (National Bank for Agriculture and Rural Development: IndiaNational Bank for Agriculture and Rural Development, 2000)
    A review of the use of chemotherapeutants and other chemicals and drugs in Indian aquaculture is presented. A large number of products are used for various purposes such as soil and water treatments, disinfectants, piscicides, herbicides, organic and inorganic fertilizers, feed additives, therapeutants, and anesthetics. Farm management techniques for the use of chemicals are discussed, as are the hazards posed by, and impacts resulting from chemical use. Other approaches to disease prevention (crop holiday, pond preparation, regulating stocking density, effluent treatment systems) are considered, and national regulations on the use of chemicals in aquaculture and current research being conducted in India are summarized. Recommendations for the improved use of chemicals in Indian aquaculture are provided for farmers, government and aquaculture institutions, the chemical industry, regional and international agencies, and research institutions.
  • The use of chemicals in aquaculture in India.

    Pathak, S.C.; Ghosh, S.K.; Palanisamy, K.; Arthur, J.R.; Lavilla-Pitogo, C.R.; Subasinghe, R.P. (Southeast Asian Fisheries Development CenterTigbauan, Iloilo, Philippines, 2000)
    A review of the use of chemotherapeutants and other chemicals and drugs in Indian aquaculture is presented. A large number of products are used for various purposes such as soil and water treatments, disinfectants, piscicides, herbicides, organic and inorganic fertilizers, feed additives, therapeutants, and anesthetics. Farm management techniques for the use of chemicals are discussed, as are the hazards posed by, and impacts resulting from chemical use. Other approaches to disease prevention (crop holiday, pond preparation, regulating stocking density, effluent treatment systems) are considered, and national regulations on the use of chemicals in aquaculture and current research being conducted in India are summarized. Recommendations for the improved use of chemicals in Indian aquaculture are provided for farmers, government and aquaculture institutions, the chemical industry, regional and international agencies, and research institutions.
  • The use of chemicals in aquaculture in the People's Republic of China.

    Jiang, Yulin; Arthur, J.R.; Lavilla-Pitogo, C.R.; Subasinghe, R.P. (Aquaculture Department, Southeast Asian Fisheries Development Center., 2000)
    Aquaculture in China has developed very rapidly in recent years. Chemicals have become important tools in the control of disease and prevention of losses in various culture systems. The occurrence of diseases stimulated the development and production of drugs for aquatic culture systems, and promoted research on chemicals and their applications. Meanwhile, there exist some problems in the application of chemicals; and there are some potential risks in their usage in aquaculture which should not be neglected. This paper describes the use of chemicals for the prevention and control of diseases in aquaculture in China. Their production, marketing, and usage, as well as associated problems and adverse impacts are also discussed. Approaches and practices to prevent diseases are also given. National regulations, on-going research and other aspects of the use of chemicals in aquaculture in China are also highlighted.
  • Latest research on acute hepatopancreatic necrosis disease (AHPND) of Penaeid shrimps

    Hirono, Ikuo; Pakingking, R. V., Jr. (Aquaculture Department, Southeast Asian Fisheries Development CenterTigbauan, Iloilo, Philippines, 2016)
    Acute hepatopancreatic necrosis disease (AHPND) is caused by unique strains of Vibrio parahaemolyticus (VPAHPND) and V. harveyi that have transferrable plasmid carrying the virulent PirAB-like toxin genes. The genomes of VPAHPND strains and V. harveyi from Thailand and Viet Nam, respectively, have been characterized by our group. The genome of VPAHPND strains from Mexico, Viet Nam, and China have also been studied by other groups. We have developed a conventional polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) methods for the detection of AHPND using a primer set that targets the PirAB-like toxin genes of VPAHPND. We have characterized the toxin genes of VPAHPND strains and also constructed a recombinant plasmid (broad host range) carrying PirAB-like toxin genes. Non-VPAHPND strain N7 which does not carry the plasmid and strain FP11 which is carrying a plasmid not coding for the toxin genes were transformed with the plasmid carrying PirAB-like toxin genes. As a result, the transformed N7 and FP11 strains became virulent and killed whiteleg shrimp (Penaeus vannamei) similar to or at par with the virulence of VPAHPND strain. We then fed the whiteleg shrimp with commercial feed containing the formalin-killed VPAHPND strain. After 2 days of feeding, all of the whiteleg shrimp died. These results clearly indicate that the PirAB-like toxin is the virulence factor of VPAHPND. We have been investigating the virulence mechanism of the PirAB-like toxin produced by VPAHPND strains. First, we calculated the copy number of plasmid encoding the PirAB-like toxin genes of several VPAHPND strains. The copy number of the plasmid varied, ranging from 1 to 36 copies. Interestingly, VPAHPND strains carrying low copy number of plasmid were more virulent than VPAHPND strains carrying high copy number of the plasmid. These results imply that the copy number of toxin genes is not an important factor responsible for the degree of virulence of the VPAHPND strains. We are also studying other factors associated with the virulence of PirAB-like toxin. Likewise, we are developing prevention methods against AHPND including the use of formalin-killed cell vaccine, IgY additive in feed, and nano-bubble treatment of rearing water. This paper summarizes the current R&D on the disease.
  • The Use of Chemicals in Aquaculture in Thailand

    Tonguthai, Kamonporn (Aquaculture DepartmentPhilippines, 2000)
    In Thailand, many chemicals are used to treat diseases of cultured aquatic animals and to improve water quality in culture facilities. Along with the intensification of aquaculture practices that has occurred in recent years in Thailand, chemical use has also increased, particularly in marine shrimp culture. This paper summarizes information on the types of chemotherapeutants commonly used in Thailand, their sources and costs, the treatment regimes used, the adverse impacts that have resulted and the hazards posed. Also included is information on national regulations, a summary of on-going research, and recommendations to aquaculturists, producers and suppliers of chemicals, government agencies and scientists. It is concluded that although chemicals and drugs will continue to play an important role in the development of Thai aquaculture, they must be used with caution to avoid adverse effects such as environmental damage and the development of resistant strains of pathogens. To minimize chemical usage, additional emphasis needs to be placed on developing good management practices for aquaculture systems.
  • The use of chemicals in carp and shrimp aquaculture in Bangladesh, Cambodia, Lao PDR, Nepal, Pakistan, Sri Lanka and Viet Nam.

    Phillips, Michael; Phillips, Michael (2000)
    This paper provides an overview on the use of chemicals in seven countries in Asia (Bangladesh, Cambodia, Nepal, Laos PDR, Pakistan, Sri Lanka and Viet Nam), with an emphasis on coastal shrimp aquaculture and inland carp farming systems. The data come primarily from a recently completed survey of aquaculture farms in Asian countries conducted under the ADB/NACA Regional Study and Workshop on Aquaculture Sustainability and Environment. The issues discussed include the types and uses of chemicals in shrimp and carp culture, farm management practices and use of chemicals, hazards and adverse impacts associated with chemical use, alternative approaches to chemical use, and research recommendations. In inland carp farming, apart from lime and fertilizers, which are unlikely to give rise to any significant negative environmental impact, the overall use of chemicals is extremely low. Piscicides are used in some countries to control predators prior to stocking of ponds, but the use of antimicrobials and disease-control chemicals is limited to a small percentage (<5%) of producers. Most small-scale producers, who dominate aquaculture production in these countries, simply do not have the resources or need for such chemicals. The situation is similar in shrimp culture, with lime and fertilizers, followed by piscicides, being the most common chemicals used. The use of antimicrobials increases with intensification in shrimp culture, and these chemicals are mostly used in more intensive shrimp farming. In both shrimp and carp culture, promotion of “primary” health management practices probably offers greatest scope for prevention of aquatic animal disease outbreaks and the need for chemical use.
  • OceanDocs Search Guide: Browse, Discover, Simple and Advanced Search.

    Simpson, Pauline (International Oceanographic Data and Information Exchange (IODE) of the Intergovernmental Oceanographic Commission (IOC)Oostende, Belgium, 2016)
    You can search OceanDocs without Login (ie you have registered) but there is some functionality that will not be available to you (Export; RSS Feed etc)

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