Thraustochytrids - lightly-pigmented estuarine and marine microheterotrophs, taxonomically aligned with heterokont algae - are of great biotechnological interest because they produce substantial amounts of polyunsaturated fatty acids (PUFAs) especially docosahexaenoic acid (DHA:6n3). In this study, twenty-seven strains, isolated from twenty mangrove areas in the Philippine archipelago, were mass-produced in axenic flask cultures using high-glucose medium with continuous agitation. Polymorphic loci of thraustochytrid genomes, determined using four arbitrary primers (OPC02, OPC05, OPC07 and OPC08) in PCR analysis, were randomly amplified as molecular markers for genetic fingerprinting. Electrophoretic banding patterns of DNA amplicons, recognized based on nucleic acid size, were scored on data matrix and analyzed using Jaccard's coefficient and single-linkage hierarchical clustering to characterize degree of genetic relatedness among thraustochytrids. Conclusively, nearest-neighbor dendrogram of randomly amplified polymorphic DNAs (RAPDs) markers classify the strains into two monophenetic clades, representing the two major genera: Schizochytrium and Thraustochytrium.

This paper presents some of the preliminary results and findings of an ongoing study, jointly conducted by the Southeast Asian Fisheries Development Center (SEAFDEC AQD) and Philippine Institute for Development Studies (PIDS), which assesses the current state of aquaculture in Laguna de Bay. The study uses primary and secondary data. The primary data were gathered through interviews with key informants and a cross-section survey of fishpen and fishcage operators and their operations in Laguna de Bay conducted in 2007. The secondary data were gathered from the published statistical indices of institutional sources and other relevant literature. The results of the study indicate that aquaculture in Laguna de Bay is a vibrant industry that includes not only fishpen and fishcage operators but also various participants in its input and product markets. Furthermore, they show that aquaculture contributes significantly to fish production in the lake as well as to national aquaculture and fisheries production. The results of the study also indicate that while aquaculture in Laguna de Bay has been an important economic contributor locally and nationally, it has been facing numerous problems over time that constrain its development. Of these, environment-related problems, lack of access to cheap capital, obstruction of navigational lanes by fishpens, existence of illegal fishpens, poaching and overall limited support from the government were considered very serious by aquaculture operators. These problems, therefore, may be the ones needing the most attention.

All three countries experienced major progress in intensive shrimp farming at different ties. Intensive farming of monodon shrimp (Penaeus monodon, an indigenous species) was first launched by the Philippines, followed by Thailand, then by Peninsular Malaysia. The survey was conducted from 2000-2005. The disease-causing bacterial that seiously damaged monodon culture were luminous bacteria in the Philippines and white spot virus in Thailand and Malaysia. Production decreased because of these diseases in the mid-1990s in the Philippines and after 2000 in Thailand and Malaysia. In 1998, the Green Water System (hereinafter referred to as GWS) was developed, and a proportion of culture ponds introduced it and resumed monodon culture using the intensive method. In Thailand, the vannamei shrimp (Penaeus vannamei, an exotic species from South America) has now replaced monodon previously raised using the extensive method. In Malaysia, monodon is cultured using only the intensive method, and some culture pond enterprises started to culture vannamei instead of monodon in 2004. In the Philippines, companies engaging in monodon culture have many ponds and lower stocking density because they culture large-size shrimp, but are exposed to high running costs such as fuels and probiotics. On the other hand, in Thailand, individuals engaging in monodon culture have few ponds and higher stocking density since they culture small-scale shrimp. Labor costs are low because most of the work is done by family member.

Orange-spotted grouper, Epinephelus coioides, is a valuable commodity in the Philippines. In 2001, mass mortality occurred in the grouper larvae at Aquaculture Department, Southeast Asian Fisheries Development Center (SEAFDEC/AQD) and the disease was identified as viral nervous necrosis (VNN). Since then, the disease has been observed every year and the grouper hatcheries have been devastated. In this paper, recent studies of VNN which were conducted at the SEAFDEC/AQD from 2001 to 2006 are reviewed. 1) Susceptibility to the VNN virus was tested among fish species that were cultured in mangrove brackish are. Five representative cultured fish species including orange-spotted grouper, Asian sea bass (Lates calcarifer), mangrove red snapper (Lutjanus argentimaculatus), milkfish (Chanos chanos) and rabbitfish (Siganus guttatus) were used in the test where the virus was intraperitoneally injected into the juveniles. Although low or no mortality occurred in the challenge test, histopathological changes were observed in the brain and retina where the virus was re-isolated. The results were the same among the species except for rabbitfish which had no evidence for the infection. It was verified that the virus has a wide host range. 2) To estimate the possible risk of viral spread by vertical transmission, virus distribution was determined in asymptomatic groupers including 7 broodstock and 17 juveniles with body weights ranging from 4 to 12 kg and 2 to 9 respectively. The virus was detected by PCR method. The highest detection rate was in the brain, and the virus was also detectable in other organs such as the gills, heart, spleen, kidney, blood, esophagus, stomach, intestine, liver, gonad, swim bladder and/or skin. 3) As a possible VNN vaccine, a DNA p;asmid encoding the capsid protein of the virus was evaluated. After the challenge, the mortalities between the native and DNA-injected fish appeared significantly different (P<0.05).

To address its mandate to develop environment-friendly culture techniques, the Southeast Asian Fisheries Development Center, Aquaculture Department (SEAFDEC/AQD) is trying to establish a culture system in mangroves for commercially important aquaculture species. Recently, SEAFDEC/AQD has successfully produced sandfish, Holothuria scabra, in the hatchery. Using hatchery-bred juveniles, monoculture and co-culture trials are being conducted in ponds, pens and cages. This study investigated the feasibility of the co-culture of black tiger shrimp, Penaeus monodon, and H. scabra in the mangroves by comparing growth and survival in monoculture and co-culture conditions. Water and sediment quality were compared between treatments. Results showed that growth and survival of P. monodon (P. monodon only = 48.8±4.9%; P. monodon + H. scabra = 46.1±7.4%) and H. scabra (H. scabra only = 13.1±6.1%; P. monodon + H. scabra = 12.3±6.2%) grown together or separately did not significantly differ. P. monodon survivial was positively correlated while growth negatiely correlated with temperature. Feed input significantly increased sulfide levels in both treatments (P. monodon; P. monodon + H. scabra) and sulfide significantly differed between treatments with the highest concentration in P. monodon only, then P. monodon + H. scabra and H. scabra only. Ammonia concentrations followed the same trend as sulfide but did not significantly differ among treatments. P. monodon cultured in mangroves were not affected by the white spot syndrome virus which affected neighboring culture ponds. Results of these initial trials may not be conclusive yet but show a promising culture system for P. monodon that may be integrated with the mangroves.

Shrimps like all invertebrates are believed to lack true adaptive immunity but recent evidence indicate that they can be protected against pathogenic organisms by priming their immune system with immunostimulatory substances. Here, we describe results of investigation aimed to strengthen shrimp immunity as a preventive strategy against white spot syndrome virus (WSSV) infection. Oligodeoxynucleotides (ODNs) with and without Cytosine-Guanine (CpG) motifs, and Vibrio harveyi genomic DNA (VHD) were administered by intramuscular injection and shrimp responses were assessed by ex vivo assays and experimental infection trials. Results showed that CpG ODN significantly increased ex-vivo immunity indices such as total hemocyte count (THC), plasma agglutination titer (PAT) and hemocyte lysate agglutination titer (HLAT). VHD significantly increased immune indices such as THC, plasma total protein (PTP) and HLAT. Reverse (GpC) motifs increased THC only. At a lower viral challenge dose, both CpG and GpC motifs, and VHD, were able to reduce shrimp mortality significantly but only CpG and VHD did so at a higher challenge dose. Strengthening shrimp immunity by the use of immunostimulatory nucleotides and bacterial genomic DNA could be a feasible preventive approach in the management of WSSV infections in shrimp.

The fish assemblage of a small, open access mangrove creek highly influenced by aquaculture farms, was studied for the first time in the Philippines as a baseline of such system as well as examining the degree of ecological disturbance among fish habitats, as basis for the necessity to rehabilitate mangrove resources aiming to balance human activities and mangrove functioning. In total, 475 fishes (total weight = 3875 g) were captured and 50 species representing 32 families were identified. Thirty two species were represented by small numbers (< 5 individuals). Commercial species was considerably high (~23 species) but majority were low grade commercial species. Total species, species diversity and fish abundance consistently showed a decreasing pattern from outside creek to inner creek. Fish habitats exhibited substantial differences following a distinct spatial segregation of fish communities, a dominance of non-shared species and a minimal species overlapping inside the creek, which is attributable to the existing mangrove fragmentation associated with aquaculture ponds in the area. Increasing levels of disturbances were observed within the creek indicating ‘stress’ as a result of overutilization of mangroves by aquaculture farms. Our results confirmed the need to rehabilitate mangrove resources in this area. The development of mangrove resources through reforestation, coupled by strict regulation of fishing activities and aquaculture ponds will reduce ecological stress in the area and regain gradually a robust mangrove functioning that will improve fish diversity, fisheries and productivity of adjacent coastal systems by creating a suitable fish nursery, feeding ground and refuge habitat.

Unwarranted accumulation of halogenated compounds in the rivers and streams has in recent years emerged due to the widespread use agricultural pesticides. The presence of these halogenated compounds in the water does not only suppress the immune system of fish but adversely induce serious morbidity and mortality among cultured stocks. Importantly, gradual accumulation of these compounds in the system of cultured and wild freshwater fish species cultured in ponds and floating net-cages in dams and rivers, respectively, poses some risks to humans, the end users. In this study, we attempted to isolate bacteria from the gut of pond-reared rohu (Labeo rohita) in Myanmar, screened the isolated bacteria for dehalogenase gene using molecular technique and tested the ability of these bacteria to degrade halogenated compounds in vitro. The eight bacterial strains studied were identified as Enterobacter mori strain MK-121001, Enterobacter cloacae strains MK121003, MK-121004, MK121010, Ralstonia solanacearum strain 121002, Acinetobacter baumannii strain MK121007, Chromobacterium violaceum strain MK121009 and Pantoea vagans strain 121011. Only three bacterial strains (MK121002, MK121007 and MK121009) were capable of degrading 2,2-dichloropropionic acid (2,2-DCP) as the sole carbon source up to a final substrate concentration of 20 mM. Their mean growth doubling time ranging from 6 - 23 hours with the maximum of chloride ion released of 85%. PCR amplification with oligonucleotide primers designed from group I dehalogenase revealed the presence of dehalogenase genes in all isolates suggesting dehalogenase gene in strains 121001, 121003, 121004, 121010 and 121011 were silenced. In contrast, group II dehalogenase primers did not show any PCR amplification. These results suggest that MK121002, MK121007 and MK121009 only encode a group I dehalogenase and its non-stereoselectivity is in agreement with previoulsly described group I haloacid dehalogenase. The partial gene sequences were blasted but no significant sequence identity was observed. Therefore, it suggests the 2-haloacid dehalogenase of MK121002, MK12-1007 and MK- 121009 might be a novel group I 2-haloacid dehalogenase. The results indicated a broad distribution of dehalogenation genes in many microbial genomes that harbor dehalogenase(s) due to the exposure of the microorganisms to the naturally occurring or man-made halogenated compounds in the environmental systems. So far, microorganisms capable of producing dehalogenases were mainly isolated from soil and scarcely from aquatic animals and their environments. To the authors’ knowledge, this is the first report on the isolation of dehalogenase-producing bacteria from the gut of pond-reared freshwater fish, Labeo rohita, in Myanmar.

The SS-type rotifer Brachionus rotundiformis is a common initial food for rearing fish larvae with a small mouth. However, there are commercially important fish species whose mouth sizes are too small to feed on SS-type rotifers. In 2004, we isolated a small (body length = 82.7 ± 10.9 μm; body width 40.5 ± 6.4 μm), flexible, and iloricate rotifer, Proales similis from an estuary in Okinawa, Japan. Under laboratory conditions (25 °C, 2–25 ppt) P. similis produced its first offspring on 2.5 to 2.8 days after hatching, and produced 4.3 to 7.8 offspring within 4.0 to 4.7 days life span. Batch cultured P. similis fed Nannochloropsis oculata suspension at 28.8 μg dry weight ml^{− 1} and cultured at 25 °C, 25 ppt filtered seawater, increased exponentially from 25 to 2400 ind ml^{− 1} after 11 days of culture with an overall intrinsic rate of natural increase (r) of 0.42 day^{− 1}. The growth rate of P. similis was not significantly different when fed fresh N. oculata and super fresh Chlorella vulgaris-V12®. Total lipid per wet weight of P. similis fed by N. oculata and C. vulgaris were 2.4 and 2.6%, respectively. The compositions of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and arachidonic acid (ARA) of P. similis fed N. oculata were 23.2, 0.0 and 5.3%, respectively, while these were 11.0, 17.5 and 0.5% respectively, when fed C. vulgaris. The use of P. similis to feed small mouth fish including seven-band grouper Epinephelus septemfasciatus, rusty angelfish Centropyge ferrugata, and humphead wrasse Cheilinus undulatus showed that it is an excellent starter food for these species because of their high selectivity index and improved survival. In addition, P. similis was ingested by Japanese eel Anguilla japonica larvae with a complicated digestive system. The use of P. similis as starter feed for small mouth fish larvae is highly recommended.