Random amplification polymorphic DNA-PCR (RAPD) analysis of Vib rio algin oly tic u s strains isolated from green mussels ( Perna viridis ) in Marudu Bay, Sabah

Vibrio alginolyticus infection is common in aquatic species. The species has been isolated from infected green mussels (Perna viridis) cultivated at Marudu Bay, Sabah. The infection of V. alginolyticus was prevalent since 2009 and caused more than 60% mortality of the mollusc. This study was conducted on V. alginolyticus isolated from clinically infected P. viridis at cultivation area in Marudu Bay from 2013. Twenty isolates were randomly selected and subjected to RAPD-PCR analysis using 20 sets of RAPD primers. Results showed that the most suitable primers were OPA 3, OPA 5, OPA 9, OPA 10 and OPA 12 where the significant bands ranging from 100-2500 bp. Genetic variability among the isolates as revealed by these primers indicated that RAPD-PCR method has good discriminative ability and can be used as a rapid typing method of differentiating V. alginolyticus strains isolated from infected green mussels for epidemiological investigation

Construction and Analysis of Metagenome Library from Bacterial Community Associated with Toxic Dinoflagellate <em>Alexandrium tamiyavanichii</em>

Previous studies have suggested that a specific community of bacteria coexists within the phycosphere of marine dinoflagellates. In order to better understand the dinoflagellate-bacteria relationships, a fosmid clone library was constructed from the metagenome DNA and analyzed. Some of the fosmid clones were end-sequenced. A total of 1501 fosmid clones with insert sizes of 30–40 Kbp were produced. End sequencing of 238 clones showed that 55% of the genes had known functions, 11% were of putative function and 34% were genes of unknown function or had no match in Genbank. There were approximately 14% sequences with no classification and could potentially represent novel genes. Analysis of these partial sequences also revealed some promising enzymes that possess various potential industrial applications such as chitinases, kinases, agarases and oxygenases. The results also showed that the bacterial flora of the Alexandrium tamiyavanichii culture was dominated by the Alpha-proteobacteria, followed by Bacteroidetes and Gamma-proteobacteria. The findings in this study suggested that the bacterial community may play various role in the association with dinoflagellate. This study had also shown that dinoflagellate-associated bacterial community is a valuable source for discovery of novel genes and gene products

PROBIOTICS BACTERIA AS QUORUM SENSING DEGRADER CONTROL Aeromonas hydrophila PATHOGENICITY IN CULTURED RED HYBRID TILAPIA

Quorum sensing (QS) is the interaction of bacteria cell-to-cell to regulate various bacterial functions, including bacterial virulence. It has been suggested that QS interruption is an anti-infective strategy to combat diseases in aquaculture. This research was conducted to isolate the potential probiotics bacteria as QS degrader from the fish gut and investigate its efficiency in reducing Aeromonas hydrophila pathogenicity by in vitro and in vivo assay. In this study, three isolates from the fish gut were able to degrade N-acyl homoserine lactone (AHL), one of the QS signals of A. hydrophila. Based on 16S rDNA sequence analysis, isolate CPi12 was identified as Klebsiella sp., CBa5 and CBa7 were identified as Enterobacter tabaci. These isolates were co-cultured with A.hydrophila for five days. Results revealed that all isolates could decrease the AHL production of A. hydrophila but did not affect the growth of the pathogen. In vivo assay results showed that isolate CPi12 reduced the pathogenicity of A.hydrophila against tilapia with a significantly higher survival rate (p&lt;0.05) of fish in the CPi12-fed group than the control group. Meanwhile, isolate CBa7 was significant (p&lt;0.05) for growth performance, including specific growth rate (SGR), weight gain (WG), feed conversion ratio (FCR), mean weight gain (MWG), and average daily growth (ADG) among whole treatment and control group. These results displayed that the probiotics bacteria as QS degrader isolated from the fish gut could control the pathogenicity of Aeromonas hydrophila. It has been proposed that QS degrader bacteria might be an alternative solution for disease control

Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review

Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts

Biodiversity and functional metagenomic profiling of microbial communities in Tasik Kenyir, Terengganu

Tasik Kenyir located in the state of Terengganu is the largest artificial lake in Southeast Asia with mean-depth of 37 m. This lake plays an important role in maintaining the biodiversity in the surrounding environment. Microbial communities in the lake are important, as most of the nutrients are recycled through the “microbial loop”. Thus, understanding the connection between the diversity composition and functional role of aquatic microbial community is crucial for proper lake management. This study aims to determine the diversity and functions of microbial assemblages in Tasik Kenyir by means of shotgun metagenomics analysis. Briefly, water samples were collected from pristine and disturbed areas. Metagenome DNA were then extracted directly and subjected to clone-independent sequencing. Data sequences of all samples were analyzed and functional annotated using bioinformatics software MEGAN6. Analysis showed up to 41 phyla that had been detected from the water samples with the presence of dominant bacterial populations of more than 90% in all samples. Proteobacteria was the most dominant phylum, representing more than 70% of the microbiome in all samples. Other taxa such as Bacteriodetes, Terrabacteria group, Verrucomicrobia, Planctomycetes and Chloroflexi were also found as part of the microbial communities. The first sample from the disturbed area, TKSA1 had 3% of total contigs read assigned to genera Pseudomonas while the other samples appeared to be more homogeneous. The lake also appeared to contain a mixture of autotrophs and heterotrophs capable of performing main biogeochemical cycles. Findings of the present study has provided us valuable information on the microbial diversity structures and their functions in the nutrient processing pathways that occurred in the Tasik Kenyir environment and thus sheds light on the importance of freshwater microbial communities for ecosystem and human health

Microbiota composition data for wild and captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839

The Labroides dimidiatus is known as the “doctor fish” because of its role in removing parasites and infectious pathogens from the body of other fishes. This important role played both in wild and captive conditions could represent a novel form of parasitic transmission process mediated by the cleaning activity of the fish. Yet, there is a paucity of data on the microflora associated with this fish which is important for tracking disease infection and generally monitoring the health status of the fish. This article, therefore, represents the first dataset for the microbiota composition of wild and captive L. dimidiatus. Wild fish samples and carriage water were gotten in Terengganu Malaysia around the corals of the Karah Island. The captive sample, however, was obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Thereafter, bacteria present on the skin, in the stomach and the aquarium water were enumerated using culture-independent approaches and Next Generation Sequencing (NGS) technology. Data obtained from the three metagenomic libraries using NGS analysis gave 1,426,740 amplicon sequence reads which are composed of 508 operational taxonomic units (OTUs) for wild samples and 3,238,564 valid reads and 828 OTUs for captive samples. All sequence reads were deposited in the GeneBank (Accession numbers SAMN14260247, SAMN14260248, SAMN14260249, SAMN14260250, SAMN14260251, and SAMN14260252). The dataset presented is associated with the research article “16S rDNA-Based Metagenomic Analysis of Microbial Communities Associated with Wild Labroides dimidiatus From Karah Island, Terengganu, Malaysia”. The microbiota data presented in this article can be used to monitor the health and wellbeing of the ornamental fish, especially under captivity, hence preventing possible cross-infectio

Draft genome sequence of Mameliella alba strain UMTAT08 isolated from clonal culture of toxic dinoflagellate Alexandrium tamiyavanichii

Mameliella alba strain UMTAT08 was isolated from clonal culture of paralytic shellfish toxin producing dinoflagellate, Alexandrium tamiyavanichii. Genome of the strain UMTAT08 was sequenced in order to gain insights into the dinoflagellate-bacteria interactions. The draft genome sequence of strain UMTAT08 contains 5.84Mbp with an estimated G + C content of 65%, 5717 open reading frames, 5 rRNAs and 49 tRNAs. It contains genes related to nutrients uptake, quorum sensing and environmental tolerance related genes. Gene clusters for the biosynthesis of type 1 polyketide synthase, bacteriocin, microcin, terpene and ectoine were also identified. This is suggesting that the bacterium possesses diverse adaptation strategy to survive within the dinoflagellate phycosphere. The draft genome sequence and annotation have been deposited at DDBJ/EMBL/GenBank under the accession number JSUQ00000000

Hidden genetic diversity in snakeskin gourami, Trichopodus pectoralis (Perciformes, Osphronemidae), inferred from the mitochondrial DNA CO1 gene

Eighty-four specimens collected from 13 populations from Malaysia, Thailand, and Vietnam were analysed, revealing 21 putative haplotypes with overall estimated haplotype and nucleotide diversities of 0.79 and 0.0079, respectively. High levels of diversity and an absence of founder effects were observed among populations in peninsular Malaysia. In contrast, populations from Sarawak exhibited low genetic diversity, which is a typical sign of colonies introduced from a single source. Historical translocation of Trichopodus pectoralis from Thailand to Malaysia, as well as to the Philippines, Indonesia, and Myanmar was apparent. Historical introduction of T. pectoralis from Vietnam was also detected in peninsular Malaysia

Non-lethal heat shock increased Hsp70 and immune protein transcripts but not Vibrio tolerance in the white-leg shrimp.

Non-lethal heat shock boosts bacterial and viral disease tolerance in shrimp, possibly due to increases in endogenous heat shock protein 70 (Hsp70) and/or immune proteins. To further understand the mechanisms protecting shrimp against infection, Hsp70 and the mRNAs encoding the immune-related proteins prophenoloxidase (proPO), peroxinectin, penaeidin, crustin and hemocyanin were studied in post-larvae of the white-leg shrimp Litopenaeus vannamei, following a non-lethal heat shock. As indicated by RT-qPCR, a 30 min abrupt heat shock increased Hsp70 mRNA in comparison to non-heated animals. Immunoprobing of western blots and quantification by ELISA revealed that Hsp70 production after heat shock was correlated with enhanced Hsp70 mRNA. proPO and hemocyanin mRNA levels were augmented, whereas peroxinectin and crustin mRNA levels were unchanged following non-lethal heat shock. Penaeidin mRNA was decreased by all heat shock treatments. Thirty min abrupt heat shock failed to improve survival of post-larvae in a standardized challenge test with Vibrio harveyi, indicating that under the conditions of this study, L. vannamei tolerance to Vibrio infection was influenced neither by Hsp70 accumulation nor the changes in the immune-related proteins, observations dissimilar to other shrimp species examined

Cyst viability and stress tolerance upon heat shock protein 70 knockdown in the brine shrimp Artemia franciscana

Females of the brine shrimp Artemia franciscana produce either free-swimming nauplii via ovoviviparous pathway of reproduction or encysted embryos, known as cysts, via oviparous pathway, in which biological processes are arrested. While previous study has shown a crucial role of ATP-dependent molecular chaperone, heat shock protein 70 (Hsp70) in protecting A. franciscana nauplii against various abiotic and abiotic stressors, the function of this protein in diapausing embryos and cyst development, however, remains unknown. RNA interference (RNAi) was applied in this study to examine the role of Hsp70 in cyst development and stress tolerance, with the latter performed by desiccation and freezing, a common method used for diapause termination in Artemia cysts. Hsp70 knockdown was apparent in cysts released from females that were injected with Hsp70 dsRNA. The loss of Hsp70 affected neither the development nor morphology of the cysts. The time between fertilization and cyst release from Artemia females injected with Hsp70 dsRNA was delayed slightly, but the differences were not significant when compared to the controls. However, the hatching percentage of cysts which lacks Hsp70 were reduced following desiccation and freezing. Taken together, these results indicated that Hsp70 possibly plays a role in the stress tolerance but not in the development of diapause-destined embryos of Artemia. This research makes fundamental contributions to our understanding of the role molecular chaperone Hsp70 plays in Artemia, an excellent model organism for diapause studies of the crustaceans