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Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

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One of the major challenges in any sustainable aquaculture production systems is the accumulation of nitrogenous waste such as ammonia and its biological nitrification products viz nitrite and nitrate. Considering the bio-security issues, amelioration of these wastes without water exchange can be accomplished only by way of establishing in situ nitrification and denitrification through biofilters/ bioreactors activated with nitrifying/denitrifying bioaugmentors. In such systems, coexistence of aerobic denitrifiers, anaerobic ammonia oxidizers (Anammox) and complete ammonia oxidizers (Comammox) together with the autotrophic nitrifiers enhance the coupled nitrification-denitrification. This promotes total nitrogen removal without external carbon supplements or additional anerobic compartment in the system. Various recirculating aquaculture systems (RAS) comprise diverse nitrifying community in biofilters/bioreactors thereby imparting distinctive nitrogen conversion in the system. Meanwhile, the structure and population dynamics of the nitrifying/denitrifying consortia are influenced by the environmental factors forming the decisive factors of the success of the processes. Accordingly, understanding the complexity of nitrifying/denitrifying community composition turns out to be a requirement to facilitate its improvised performance. In this context, the review addresses different biological nitrogen removal systems, significance of nitrification-denitrification in RAS, genetic diversity of the key players in RAS, methods of analysis of their community structure, current application and prospects of the processes in RAS.

Surveys for bacteriological analysis of larval samples to isolate the associated vibrios were carried out during 1985^1992, 2001 and 2002 in three di¡erent hatcheries located on the southwest coast of India. Vibrio isolates were examined for their species diversity, virulence based on haemolysis in prawn blood agar, lipolysis, proteolysis and chitinolysis and antibiotic sensitivity.Vibrio cholerae was the predominant species in the apparently healthy larval samples, whereas V. alginolyticus and V. vulni¢cus dominated during disease and morbidity. No correlation was found between the hydrolytic properties and haemolytic activity of the vibrios associated with the larvae. All isolates were resistant to erythromycin and resistance to oxytetracycline, ampicillin and streptomycin sulphate was prevalent among the larger section of the Vibrio population. This suggested that antibiotic application may not be of much use to protect the larvae from vibriosis. This is the ¢rst report on the diversity of Vibrio species associated with Macrobrachium rosenbergii larvae and their virulence characteristics based on haemolysis in prawn blood agar.

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Recirculation aquaculture systems (RAS) depend on nitrifying biofilters for the maintenance of water quality, increased biosecurity and environmental sustainability. To satisfy these requirements a packed bed bioreactor (PBBR) activated with indigenous nitrifying bacterial consortia has been developed and commercialized for operation under different salinities for instant nitrification in shrimp and prawn hatchery systems. In the present study the nitrification efficiency of the bioreactor was tested in a laboratory level recirculating aquaculture system for the rearing of Penaeus monodon for a period of two months under higher feeding rates and no water exchange. Rapid setting up of nitrification was observed during the operation, as the volumetric total ammonia nitrogen removal rates (VTR) increased with total ammonia nitrogen (TAN) production in the system. The average Volumetric TAN Removal Rates (VTR) at the feeding rate of 160 g/day from 54-60th days of culture was 0.1533+/-0.0045 kg TAN/m(3)/day. The regression between VTR and TAN explained 86% variability in VTR (P<0.001). The laboratory level RAS demonstrated here showed high performance both in terms of shrimp biomass yield and nitrification and environmental quality maintenance. Fluorescent in-situ Hybridization analysis of the reactor biofilm ensured the presence of autotrophic nitrifier groups such as Nitrosococcus mobilis lineage, Nitrobacter spp and phylum Nitrospira, the constituent members present in the original consortia used for activating the reactors. This showed the stability of the consortia on long term operation.

a b s t r a c tThe addition of commercial nitrifying bacterial products has resulted in significant improvement of nitrification efficiency in recirculating aquaculture systems (RAS). We developed two nitrifying bacterial consortia (NBC) from marine and brackish water as start up cultures for immobilizing commercialized nitrifying bioreactors for RAS. In the present study, the community compositions of the NBC were analyzed by universal 16S rRNA gene and bacterial amoA gene sequencing and fluorescence in situ hybridization (FISH). This study demonstrated that both the consortia involved autotrophic nitrifiers, denitrifiers as well as heterotrophs. Abundant taxa of the brackish water heterotrophic bacterial isolates were Paenibacillus and Beijerinckia spp. whereas in the marine consortia they were Flavobacterium, Cytophaga and Gramella species. The bacterial amoA clones were clustered together with high similarity to Nitrosomonas sp. and uncultured beta Proteobacteria. FISH analysis detected ammonia oxidizers belonging to b subclass of proteobacteria and Nitrosospira sp. in both the consortia, and Nitrosococcus mobilis lineage only in the brackish water consortium and the halophilic Nitrosomonas sp. only in the marine consortium. However, nitrite oxidizers, Nitrobacter sp. and phylum Nitrospira were detected in both the consortia. The metabolites from nitrifiers might have been used by heterotrophs as carbon and energy sources making the consortia a stable biofilm.