DSpace @ SEAFDEC/AQD
Southeast Asian Fisheries Development Center, Aquaculture Department Institutional Repository (SAIR) is the official digital repository of scholarly and research information of the department. This is to enable the effective dissemination of AQD researchers' in-house and external publications for free and online. The repository uses DSpace, an open source software, developed at Massachusetts Institute of Technology (MIT) Libraries. It is an Open Archives Initiative (OAI)-compliant.
Initially, the repository shall contain preprints, full-texts or abstracts of journal articles, books and conference proceedings written by SEAFDEC/AQD scientists and researchers. The aim is to promote these publications especially those published in international peer-reviewed journals and generate higher citation through increased visibility.
It will also provide free access to all in-house publications of SEAFDEC/AQD. Full-text digitized copies of fishfarmer-friendly materials like books, handbooks, policy guidebooks, conference proceedings, extension manuals, institutional reports, annual reports (AQD Highlights), and newsletters (SEAFDEC Asian Aquaculture, Aqua Farm News, AquaDept News and AQD Matters) can be retrieved and downloaded.
In the future, SAIR will expand its collection to include images, presentations, audios, and videos among others.
The objectives of the repository are to: (1) to provide reliable means for SEAFDEC/AQD researchers to store, preserve and share their research outputs and (2) to provide easy access and increase the visibility of SEAFDEC/AQD scientific publications
SAIR also aims to encourage SEAFDEC/AQD researchers for self-archiving and submitting pre-prints from which metadata will be screened and approved by the library staff.
Total volume of 3D small patch reefs reflected in aerial photographs can predict total species richness of coral reef damselfish assemblages on a shallow back reef -
Ecological Research, 2015 - Springer VerlagBecause fish have a high dispersal ability, an understanding coral reef fish metacommunity structure is vital for effective conservation. Coral reefs provide patchy habitat of various sizes and scales. We examined the species–area relationship (SAR) of damselfish (Pomacentridae) assemblages over 81 environmentally homogenous patch reefs ranging 0.07–45.4 m2 with low coral cover. Patch reefs were located in the shallow back reef (<2.5 m deep) off Ishigaki Island, Japan. Reef area was measured by performing image analysis of enlarged sections of a high-resolution (>1/2500) color aerial photograph used as a fine-scale seascape map. To assess the effects of three-dimensional meso-scale rugosity on species richness, we assumed that all reefs had a cylindrical shape and examined species by volume (area × height) relationships (SVR). Patch reef volume was a better determinant of species richness than area, and the regression functions of SVR provided better estimates of patch reef species richness. Neither the observed SVRs nor SARs, however, could be explained by a random placement model alone. Our results suggest that several small reefs are likely to have higher species richness than a single large reef of equivalent area in the shallow back reef where large patch reefs are flat. Thus, total patch reef volume (area × height) better reflects meso-scale rugosity and is a useful indicator of total species richness relative to the total amount of essential habitat in shallow back reefs.
Communities in SAIR
Select a community to browse its collections.
Abdominal segment deformity syndrome (asds) and fused body segment deformity (fbsd) in cultured Penaeus indicus -
Aquaculture, 2017 - ElsevierThe abdominal segment deformity disease (ASDD) is a new shrimp disease reported only in cultured Penaeus vannamei in Thailand. Shrimp with ASDD have deformed abdominal segment, jagged gut line and bumpy surfaces. Similar signs were observed in cultured P. indicus in the Philippines. However, aside from the signs described for ASDD, some P. indicus showing abdominal segment deformity syndrome (ASDS) had more severe deformities up to the extent that the number of body segments was reduced due to fusion. Shrimp with fused body segment deformity (FBSD) had four instead of five pairs of legs. To account the prevalence of the deformities in P. indicus, shrimp were classified into grossly normal shrimp (NS), shrimp with abdominal segment deformity syndrome (ASDS) and shrimp with fused segments (FBSD). Out of the shrimp sampled, 83.4 ± 5.4% was NS, 10.9 ± 6.2% was ASDS and 5.7 ± 3.0% was FBSD. Morphometric characteristics of the shrimp were measured. There was no significant difference in body weight (BW) among male and female NS, ASDS and FBSD. In both sexes, total length (TL) of FBSD was significantly shorter compared to NS and ASDS. Shrimp samples were also screened to be negative for known infectious viral diseases including white spot syndrome virus (WSSV), infectious hypodermal and haematopoietic necrosis virus (IHHNV), infectious myonecrosis virus (IMNV), P. vannamei nodavirus (PvNV), Macrobrachium rosenbergii nodavirus (MrNV) and Taura syndrome virus (TSV). Occurrence of ASDS and FBSD in post-larvae (PL) produced from captive and wild spawners were also determined. Based on a tank experiment, no significant difference was detected between the percentages of ASDS in PL produced from wild or captive spawners but FBSD was only noted in PL produced from the latter. Deformities generally did not affect the size of P. indicus except for the reduced length of shrimp with FBSD which when coupled with missing pleopods could lead to major economic loss for shrimp farmers if not addressed properly.
Conference paper- In RV Pakingking Jr., EGT de Jesus-Ayson & BO Acosta (Eds.), Addressing Acute Hepatopancreatic Necrosis Disease (AHPND) and Other Transboundary Diseases for Improved Aquatic … Diseases for Improved Aquatic Animal Health in Southeast Asia, 22-24 February 2016, Makati City, Philippines, 2016 - Aquaculture Department, Southeast Asian Fisheries Development CenterThe farming of penaeid shrimps in Cambodia began in 1989 and has significantly expanded since 1991. Shrimp cultivation has been carried out in the four coastal provinces, i.e. Kampot, Kep, Preah Sihanouk Ville, and Koh Kong. Black tiger shrimp (Penaeus monodon) and whiteleg shrimp (P. vannamei) are the main species being cultured extensively and intensively in brackishwater ponds in Kampot, Kep, and Preah Sihanouk Ville, and Koh Kong, respectively. Extensive shrimp ponds were constructed close to the mangrove areas with some containing mangroves within the pond and stocking density ranging from 5,000 to 20,000 postlarvae/ha. However, the productivity remains low at >100 kg/ ha/ year. On the contrary, intensive culture has a stocking density ranging from 300,000 to 500,000 postlarvae/ha. While high cost of investment for farm establishment, pond construction and farm operation are required, productions of newly established farms have reached 7 to 8 metric tons (MT) /ha per crop. The occurrence of white spot disease, monodon baculovirus disease, and yellow head disease was first reported in 1999 among cultured P. monodon in Koh Kong province causing a number of farmers to stop the intensive cultivation of black tiger shrimp. To date, only a small proportion of shrimp farmers have ventured into extensive shrimp farming with approximately 10 ha of shrimp areas currently in operation. To mitigate the negative impacts of shrimp diseases and promote the expansion of the shrimp industry in Cambodia, development of a national reporting system for aquatic animal diseases; capacity building for detection, monitoring and disease surveillance; creation of National Guidelines On Good Shrimp Aquaculture Practices; establishment of subresearch centers and concomitant funding support for marine aquaculture development and extension services; establishment of local shrimp hatcheries and provision of hands-on trainings for farmers; and strengthening collaborations among provincial officers, researchers and farmers network should be accordingly instituted.
Status of acute hepatopancreatic necrosis disease (AHPND) and other emerging diseases of penaeid shrimps in Viet Nam - In RV Pakingking Jr., EGT de Jesus-Ayson & BO Acosta (Eds.), Addressing Acute Hepatopancreatic Necrosis Disease (AHPND) and Other Transboundary Diseases for Improved Aquatic … Diseases for Improved Aquatic Animal Health in Southeast Asia, 22-24 February 2016, Makati City, Philippines, 2016 - Aquaculture Department, Southeast Asian Fisheries Development CenterAcute hepatopancreatic necrosis disease (AHPND), formerly called early mortality syndrome (EMS), was first reported in 2010 among penaeid shrimps cultivated in the Mekong Delta Region of Viet Nam albeit without any laboratory confirmation. The disease subsequently spread to a wide range of shrimp production areas in the same region (Soc Trang: 1,719 ha; Bac Lieu: 346 ha; and Ca Mau: 3,493 ha), so that the Government of Viet Nam requested for technical assistance from the Food and Agriculture Organization (FAO) of the United Nations in 2011. In 2012, FAO supported Viet Nam through the project TCP/VIE/3304 Emergency assistance to control the spread of an unknown disease affecting shrimps in Viet Nam, under which the Department of Animal Health of Viet Nam (DAH) collaborated with the University of Arizona and FAO experts to carry out indepth studies to identify the etiologic agent of the disease. As a result, unique isolates of Vibrio parahaemolyticus was identified as the causative agent of AHPND in 2013. Viet Nam has been vigilant and transparent with regard to aquatic animal diseases through official notifications to the World Organization for Animal Health (OIE) and the Network of Aquaculture Centres in Asia-Pacific (NACA). AHPND outbreaks have no clear temporal pattern with black tiger (Penaeus monodon) and whiteleg (P. vannamei) shrimps showing similar incidence risk. The disease occurs at any stage of shrimp cultivation, i.e. on average about 35 days after stocking. To date, unwarranted outbreaks of AHPND in major shrimp-producing provinces in Viet Nam have been apparently regulated. Aside from AHPND, white spot disease (WSD) has also been a persistent problem responsible for serious economic losses in many shrimp-producing areas in Viet Nam. To prevent and control the further spread of infectious diseases of shrimps including AHPND and WSD, multiple control measures have been implemented including guidance of farmers to improve production conditions, facilities and biosecurity application, active surveillance of shrimp production areas for early warning, screening of broodstock and postlarvae for any OIE listed diseases, regulation on movement of stocks, and collaboration with regional and international organizations in carrying out in-depth epidemiological studies that will be needed in the formulation of pragmatic and holistic disease interventions.
Community-based stock enhancement of abalone, Haliotis asinina in Sagay marine reserve: Achievements, limitations and directions - In K Hajime, T Iwata, Y Theparoonrat, N Manajit & VT Sulit (Eds.), Consolidating the Strategies for Fishery Resources Enhancement in Southeast Asia. Proceedings of the Symposium … Strategy for Fisheries Resources Enhancement in the Southeast Asian Region, Pattaya, Thailand, 27-30 July 2015, 2016 - Training Department, Southeast Asian Fisheries Development CenterThe Sagay Marine Reserve (SMR) under the National Integrated Protected Area System (NIPAS) is one of the many reef areas in the Visayan Sea in the central part of the Philippine archipelago. The SMR covers 32,000 ha or 59% of coastal waters north of the mainland Sagay City. Donkey’s ear abalone is one of the most sought mollusks traded by small-scale fishers in Molocaboc Island located within the SMR. High buying prices in local and international markets compared with other fish catch motivated fishers to target abalone and caused its overfishing. SEAFDEC/AQD, with support from the Government of Japan Trust Fund (JTF), conducted a community-based stock enhancement through a tri-party collaboration between the fisherfolks of Molocaboc Island, the Sagay local government at the village and city levels, and SEAFDEC/AQD. The study showed that the decision and implementation of stock enhancement and the definition of its objectives and relevance involves the strong engagement with stakeholders. For over a period of eight years (2007-2014), we learned that stock enhancement necessarily involve high financial investments and enormous transaction cost over a long period of time which are often not affordable to local governments of coastal communities in Southeast Asia. Thus, community-based collaborations may help achieve enhancement and restocking goals.
Conference paper- In RV Pakingking Jr., EGT de Jesus-Ayson & BO Acosta (Eds.), Addressing Acute Hepatopancreatic Necrosis Disease (AHPND) and Other Transboundary Diseases for Improved Aquatic … Diseases for Improved Aquatic Animal Health in Southeast Asia, 22-24 February 2016, Makati City, Philippines, 2016 - Aquaculture Department, Southeast Asian Fisheries Development CenterAcute 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.