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

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

DATA AVAILABILITY : The DNA sequencing data for the C. nodosa genome assembly have been deposited in the NCBI database under BioProject PRJNA1041560 via the link https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1041560. All assemblies and annotations for all seagrass species discussed in the current paper can be found at https://bioinformatics.psb.ugent.be/gdb/seagrasses/. The transcriptome data (including raw data and clean data) and sequencing QC reports for C. nodosa can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Cymnodnscriptome_2, the transcriptome data and sequencing QC reports for P. oceanica can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Posocenscriptome_2, the transcriptome data and sequencing QC reports for T. testudinum can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Thatesnscriptome_4 and the transcriptome data for Z. marina are from ref. 15. For the public databases, the RFAM database v.14.7 can be downloaded at https://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/, the UniProt database can be accessed from the web at http://www.uniprot.org and downloaded from http://www.uniprot.org/downloads and the NCBI nucleotide database can be accessed via https://www.ncbi.nlm.nih.gov/.We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the ‘savannahs of the sea’ are of major concern in times of climate change and loss of biodiversity.The DOE, JGI, Berkeley, California, USA, under the Community Sequencing Program 2018; the European Research Council under the European Union’s Horizon 2020 research and innovation programme ; Ghent University (Methusalem funding); the Deutsche Forschungsgemeinschaft (German Research Foundation); the Helmholtz School for Marine Data Science; partially supported by the project Marine Hazard, PON03PE_00203_1 (MUR, Italian Ministry of University and Research) and by the National Biodiversity Future Centre Program, Italian Ministry of University and Research, PNRR, Missione 4 Componente 2 Investimento 1.4; and Universiti Malaysia Terengganu.https://www.nature.com/nplants2024-07-26hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-14:Life below wate

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