Uttam Kumar Sarkar

Conservation of freshwater fish resources of India: new approaches, assessment and challenges

The freshwater resources of India are currently experiencing an alarming decline in fish biodiversity due to several factors and as a result, a sizeable portion of fresh water fishes have been categorized as threatened. This emphasizes an immediate need for initiating research and actions for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater ecosystem from numerous threats is the creation of freshwater aquatic sanctuary (FAS) within protected area network. Though similar conservation practices are well established in the terrestrial and marine ecosystem, however, the work on freshwater systems has been very slow and negligible. In the present communication we conceptualized the need and approach for developing FAS within the protected area network based on our observations in the water bodies of the selected wildlife sanctuaries in Northern India as well as success stories of some other countries. In this study we assessed the fish diversity in the selected protected areas of Northern India. The assessment indicated that these sanctuaries harbor 28.26–31.13% of freshwater fishes, which are threatened in other areas. Apart from Indian Major Carps, Tor putitora, Chitala chitala, Pangasius pangasius, Clupisoma gerua, Ailia coila, Aorichthys aor, Wallago attu, Rhinomugil corsula, Ompok pabda, Ombok pabo etc. were the important species encountered in the protected waters. The various issues related to FAS including objectives, approach, potential tools, implementation and management are discussed towards saving endangered fish germplasm resources. Approaches, tools and modus operandi proposed in this communication could be utilized by other developing countries in the region.

Captive breeding of endangered fish Chitala chitala (Hamilton-Buchanan) for species conservation and sustainable utilization

Over the last few decades wild population of Chitala chitala (HamiltonBuchanan) has been declined more than 50% due to various reasons and is presently listed under endangered (EN) category due to reduced abundance. In the present communication wild C. chitala were collected from natural habitats and induced to spawn under captivity during July 2002 by injecting three different doses of synthetic hormone Ovaprim. Intramuscular injections were administered to fishes using three different doses (1.5, 1.0 and 0.5 ml/kg body weight). Artificial breeding pool was prepared for each set by encircling area (20 × 5 m) with mosquito net, where wooden country boat (8 × 4 × 2.5 feet with surface area 48.5 sq. feet) was placed inside the breeding pool. Distinct spawning behavior was noticed in the experimental sets with different hormonal dose whereas no spawning activity was noticed in control set. The fertilization rate varied from 48.8680.2% and total numbers of spawned eggs in two sets of experiments were estimated to be 81,034. The average number of eggs deposited 15 ± 2.1/square inches. The fertilized eggs were large in size (4.5 ± 0.05 mm), adhesive and attached to the hard substratum. The eggs hatch out between 168192 h after fertilization and about 33,639 hatchlings were produced. Newly hatched larvae measured 10.23 ± 0.03 mm and 0.031± 0.008 gm in weight and the mean diameter of yolk sac was 4.1 ± 0.08 mm. The yolk sac remains attached up to a week. The percentage survival of hatchlings varied from 42.2 to 65.60. Statistical analysis was worked out to determine the relation between the hormone dosage with different breeding parameters like latency period, fertilization rate, egg output, hatching rate and hatchling production.

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.

BackgroundMicrosatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.DescriptionFishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview.ConclusionsFishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies

White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7–VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as interaction between both the biological counterparts that crafts a micro-environment feasible for entry of virus into the shrimp is still unknown. In the present study, we applied molecular modeling (MM), molecular dynamics (MD) and docking to compute surface mapping of infective amino acid residues between interacting proteins. Our result showed that α-helix of PmRab7 (encompassing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) interacts with β-sheets of VP28 (containing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) and Arg69-Ser74, Val75-Ile143, Leu73-Ile143, Arg79-Asn144, Ala198-Ala182 bonds contributed in the formation of PmRab7–VP28 complex. Further studies on the amino acid residues and bonds may open new possibilities for preventing PmRab7–VP28 complex formation, thus reducing chances of WSD. The quantitative predictions provide a scope for experimental testing in future as well as endow with a straightforward evidence to comprehend cellular mechanisms underlying the disease.

Application of Probiotics in Shrimp Aquaculture: Importance, Mechanisms of Action, and Methods of Administration

ABSTRACT Shrimp aquaculture is the fastest growing animal food producing sectors in the world due to its high demand in developed countries; however, they are affected by diseases mainly caused by opportunistic pathogens results in huge economic losses. Today preventive and management measures are central concern to overcome such outbreak of diseases. The adverse effect of chemotherapeutics in shrimp farming has drawn attention for the development of non-antibiotic and environment friendly agents, which is one of the key factors for health management in shrimp aquaculture. In recent years, application of probiotics against virus and bacteria in shrimp farming had been a novel and safe approach since they promote the innate immune response. Probiotics for bacterial diseases like vibriosis is well reported, but for viral diseases, the authentic strains still need research. Apart from the discovery of new or better formulations, improvement in the probiotic benefits may be helpful. Thus, better and economic production methods, administration ways or combination with other preventive/therapeutic measures are welcomed. Further studies are still necessary to increase the knowledge about use of probiotics to control bacterial infections in shrimp but much more efforts are needed in the case of viral diseases. In this review, potential application of probiotics in shrimp aquaculture: importance, mechanisms of action and methods of administration are being focused. The article also explains the limitations and prospects of probiotics in sustainable and ecofriendly shrimp culture to augment the total shrimp aquaculture production.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes.

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics. Availability The database is available for free at http://mail.nbfgr.res.in/fbis/

Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene.

Abstract Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.

Benchmarking pre-spawning fitness, climate preferendum of some catfishes from river Ganga and its proposed utility in climate research

The concept of threshold condition factor (Fulton), beyond which more than 50% of the female fish population may attain readiness for spawning coined as pre-spawning fitness (Kspawn50), has been proposed in the present article and has been estimated by applying the non-parametric Kaplan-Meier method for fitting survival function. A binary coding strategy of gonadal maturity stages was used to classify whether a female fish is “ready to spawn” or not. The proposed Kspawn50 has been generated for female Mystus tengara (1.13–1.21xa0units), M. cavasius (0.846–0.945xa0units), and Eutropiichthys vacha (0.716–0.799xa0units). Information on the range of egg parameters (fecundity, egg weight, egg diameter) expected at the pre-spawning stage was also generated. Additional information on species-specific thermal and precipitation window (climate preferendum) within which Kspawn50 is attained was also generated through the LOESS smoothing technique. Water temperatures between 31 and 36xa0°C (M. tengara), 30 and 32xa0°C (M. cavasius), and 29.5 and 31xa0°C (E. vacha) and monthly rainfall between 200 and 325xa0mm (M. tengara), >u2009250xa0mm (M. cavasius), and around 50xa0mm and between 350 and 850xa0mm (E. vacha) were found to be optimum for attainment of Kspawn50. The importance of parameterization and benchmarking of Kspawn50 in addition to other conventional reproductive biology parameters has been discussed in the present article. The purposes of the present study were fulfilled by generating baseline information and similar information may be generated for other species replicating the innovative methodology used in this study.

Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation

A total of 1671 ESTs of Labeo rohita were retrieved from dbEST database and analysed for functional annotation using various computational approaches. The result indicated 1387 non-redundant (184 contigs and 1203 singletons) putative transcripts with an average length of 542 bp. These 1387 transcript sequences were matched with Refseq_RNA, UniGene and Swiss-Prot on high threshold cut-off for functional annotation along with help of gene ontology and SSRs markers. We developed extensive Perl programming based modules for processing all alignment files, comparing and extracting common hits from all files on a threshold, evaluating statistics for alignment results and assigning gene ontology terms. In this study, 92 putative transcripts predicted as orthologous genes and among those, 44 putative transcripts were annotated with gene ontology terms. The annotated orthologous gene of our result associated with some very important proteins of L. rohita involved in biotic and abiotic stresses and glucose metabolism of spermatogenic cells etc. The unidentified transcripts, if found important in expression profiling can be vital resource after re-sequencing. The predicted genes can further be used for enhancing productivity and controlling disease of L. rohita.

Flood plain wetland fisheries of India: with special reference to impact of climate change

Floodplain wetlands of India are biologically rich sensitive ecosystem that support unique aquatic biodiversity and play vital role in providing livelihood and nutritional security to a large section of the population of the country. Besides contributing to the environmental sustainability through Carbon sequestration, flood plain wetlands also serve as source for harvesting flood and rain water. Covering around 5.5xa0Lakhxa0ha area, the flood plain wetlands of India are one of the major sources for fish production of the country, offering vast potential for capture as well as culture based fisheries. Degradation and shrinkage of the floodplain wetlands have been recorded due to several natural and anthropogenic reasons. In addition to that, the change in the climatic condition may have a far more devastating impact on these natural resources. Substantial change in climate with increasing temperature trend (0.60xa0°C during last 112xa0years) as well as changing pattern and intensity of rainfall have been reported in India. It is projected that extreme climate changes may have profound impact on wetlands, mediated through several direct or indirect pathways. Attention is urgently required at different levels for conservation and revamping of these resources along with coping up and mitigation strategies to address the impending challenges. However, there is dearth of scientific information specific to the flood plain wetlands of India. This paper reviews the present status and importance of the flood plain wetlands of India with special reference to impact of climate change along with coping-up and mitigation measures.