A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation and marker discovery

The striped catfish (Pangasianodon hypophthalmus) culture industry in the Mekong Delta in Vietnam has developed rapidly over the past decade. The culture industry now however, faces some significant challenges, especially related to climate change impacts notably from predicted extensive saltwater intrusion into many low topographical coastal provinces across the Mekong Delta. This problem highlights a need for development of culture stocks that can tolerate more saline culture environments as a response to expansion of saline water-intruded land. While a traditional artificial selection program can potentially address this need, understanding the genomic basis of salinity tolerance can assist development of more productive culture lines. The current study applied a transcriptomic approach using Ion PGM technology to generate expressed sequence tag (EST) resources from the intestine and swim bladder from striped catfish reared at a salinity level of 9 ppt which showed best growth performance. Total sequence data generated was 467.8 Mbp, consisting of 4,116,424 reads with an average length of 112 bp. De novo assembly was employed that generated 51,188 contigs, and allowed identification of 16,116 putative genes based on the GenBank non-redundant database. GO annotation, KEGG pathway mapping, and functional annotation of the EST sequences recovered with a wide diversity of biological functions and processes. In addition, more than 11,600 simple sequence repeats were also detected. This is the first comprehensive analysis of a striped catfish transcriptome, and provides a valuable genomic resource for future selective breeding programs and functional or evolutionary studies of genes that influence salinity tolerance in this important culture species.

An evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypopthalmus) using an RNA-SEQ approach

The project investigated the molecular response of Tra catfish (Pangasianodon hypophthalmus) to elevated salinity conditions. We employed Next generation sequencing platform to evaluate differential gene expression profiles of key genes under two salinity conditions. Results of the current project can form the basis for further studies to confirm the functional roles of specific genes that influence salinity tolerance in the target species and more broadly in other freshwater teleost fishes. Ultimately, the approach can contribute to developing superior culture stocks of the target species.

The life cycle and genetic structure of the red alga Furcellaria lumbricalis on a salinity gradient

The life cycle and genetic diversity of the red alga Furcellaria lumbricalis (Hudson) Lamouroux were investigated in 15 populations in northern Europe. The occurrence of different life cycle phases and seasonality of reproduction were studied in four brackish populations in the northern Baltic Sea. Furthermore, a new method, based on genome screening with ISSR markers combined with a restriction-ligation method, was developed to discover microsatellite markers for population genetic analyses. The mitochondrial DNA cox2-3 spacer sequence and four microsatellite markers were used to examine the genetic diversity and differentiation of red algal populations in northern Europe. In addition, clonality and small-scale genetic structure of one Irish and four Baltic Sea populations were studied with microsatellite markers. It was discovered that at the low salinities of the northern Baltic Sea, only tetrasporophytes and males were present in the populations of F. lumbricalis and that winter was the main season for tetrasporangial production. Furthermore, the population occurring at the lowest salinity (3.6 practical salinity units, psu) did not produce spores. The size of the tetraspores was smaller in the Baltic Sea populations than that in the Irish population, and there were more deformed spores in the Baltic Sea populations than in the Irish populations. Studies with microsatellite markers indicated that clonality is a common phenomenon in the Baltic Sea populations of F. lumbricalis, although the proportion of clonal individuals varied among populations. Some genetic divergence occurred within locations both in Ireland and in the northern Baltic Sea. Even though no carpogonia were detected in the field samples during the study, the microsatellite data indicated that sexual reproduction occurs at least occasionally in the northern Baltic Sea. The genetic diversity of F. lumbricalis was highest in Brittany, France. Since no variation was discovered in the mtDNA cox2-3 spacer sequence, which is generally regarded as an informative phylogeographic marker in red algae, it can be assumed that the studied populations probably share the same origin.

Parametric Studies on Saltwater Intrusion into Coastal Aquifers for Anticipate Sea Level Rise

Saltwater intrusion into coastal aquifers is a global issue, exacerbated by increasing demands for freshwater in coastal regions. This study investigates into the parametric analysis on saltwater intrusion in a conceptual, coastal, unconfined aquifer considering wide range of freshwater draft and anticipated sea level rise. The saltwater intrusion under various circumstances is simulated through parametric studies using MODFLOW, MT3DMS and SEAWAT. The MODFLOW is used to simulate the groundwater flow system under changing hydro-dynamics in coastal aquifer. To simulate solute transport MT3DMS and SEAWAT is used. The saltwater intrusion process has direct bearing on hydraulic conductivity and inversely related to porosity. It may also be noted that increase in recharge rate considered in the study does not have much influence on saltwater intrusion. Effect of freshwater draft at locations beyond half of the width of the aquifer considered has marginal effect and hence can be considered as safe zone for freshwater withdrawals. Due to the climate change effect, the anticipated rise in sea level of 0.88 m over a century is considered in the investigation. This causes increase in salinity intrusion by about 25%. The combined effect of sea level rise and freshwater draft (C) 2015 The Authors. Published by Elsevier B.V.

Studies on the condition factor of the Sierra Leone mangrove oyster (Crassostrea tulipa)

Sierra Leone is a tropical country where water temperatures are high throughout the year. Consequently the local oysters tend to spawn the year round, with one or two spawning peaks. The condition of such tropical oysters may not be as high as those oyesters in temperate countries since the stored glycogen is regularly utilized to form gonads. A high condition factor value indicates that the oysters have accumulated glycogen and or gonads, whereas a low condition factor value indicates that the oysters have spawned and are in the process of accumulating glycogen, which may later be utilized for gonad development. In oyster culture, condition factor studies may be supported by plankton and oyster spat settlement studies in the culture area. These studies give an indication of when oyster larvae and spat settlement are at their peak values. In Sierra Leone studies of the plankton and spat settlement are undertaken every week throughout the year. Conditions factor is obtained from the ratio weight of dry (oyster) meat x 1000/internal volume. Detailed condition factor values are shown in relation to salinity at two stations. Condition factor declines with reducing salinity, which principally occurs during the rainy season. The best times to collect spat are May to June and September to October

Studies on the occurrence and growth rates of two intertidal fouling bryozoans in the Mattancherry channel of Cochin harbour, south-west coast of India

Occurrence and growth rates of two species of intertidal fouling bryozoans namely Electra bengalensis (Stoliczka) and Electra crustulanta (Pallas) are presented in this paper. The former was a typically marine form, settling on panels only during the high saline conditions of the pre-monsoon period and were absent during the low salinity conditions of the monsoon period, while the latter appeared to be a typical brackish water form settling on panels during the low saline conditions existing during the monsoon and post-monsoon periods and were totally absent during the pre-monsoon months. Regression co-efficient of the former was higher than that of the latter suggesting more pronounced growth in Electra bengalensis. Maximum growth for this species was noticed during March, April and May (pre-monsoon) while for the other species growth was more or less similar during monsoon and post-monsoon months (June-January) showing that the species was at home in oligohaline and mesohaline waters.

Studies on diversity of Hara's Laft-Khamir and Sout Beaches of the Gheshm polychaete

One of the most important marine ecologic phenomenon , is the study of animal community among the bed or benthic fauna. Macrobenthoses are the graet part of the benthic faune , that are more biomasses than meiofauna and microfauna. To study polychaetes diversity of Mangroves, located in Khoore-Khooran , sampling was conducted on a bimonthly and carried out from December 2001 to October 2002. Bottom samples were collected by Van Veen grab (0.025 m2)at 6 station from 2 transect Insitu measurement of temperature , pH , Do and salinity were done . Atotal of polychaetes werw identified within study 32 Family and 43 Genus . Cirriphormia and Nephtys were the most dominant genus in the studies . The range fomumerical abundance of polychaets was between 3006 per m2 in the station A3 to 559individual per mein the station A1 and the variation was done to different bottom , texture the variable environment conditions govrtneng the different parts of each creeks as well as within creeks . Application of diversity indices (Shannon H') on the dominant polychates assambladges has higher H' in the Azar and lower 1-1/ in the Mehr . and the stations B3 has the highest H' and the station A2 has the lowest H' Application of diversity and Richness, Evennes were studied and showed that the station A3 has the lowest evenness and the most individual , and station A1 has the middle pollution.

Studies on distribution, diversity and production of macrobenthic fauna in the Chahbahar Bay

The population density, distribution, diversity and secondry production of macrobenthic fauna of the inner Chahbahar Bay were studied through bi-monthly sampling from April 1995 to March 1996. Samples were collected from water near the bottom and sediment at 14 stations inside the Bay and one reference station located outside at the entrance to the Bay. The environmental parameters Such as temperature, water depth, salinity, pH and dissolved oxygen as well as percentage silt-clay and total organic matter of the sediment were measured. The faunal population density and their distribution is discussed in relation to the environmental changes. results obtained indicated both spatial and temporal heterogeneity in faunal distribution of the Chahbahar Bay. The total of 18 groups of macrofauna were identified in all samples. Amphipods formed the dominant group (21%) followed by polychaetes (19%), gastropods (15.7%) bivalves (10.6%) and all other groups (33.7%). Seasonal changes in faunal density is shown in relation to Indian Ocean southwest monsoon,the result of which indicated lower population density during monsoon (June to September) than that of the premonsoon (February to May) and post monsoon (October to January) periods. The numerical abundance of macrobenthos varied from 10260.m2 before monsoon to 5190 m2 during monsoon season. Three dominant groups of macrofauna including polychaetes, gastropods, and bivalves were identified in all collected samples. Indices of diversity, richness and evenness were calculated for these three dominant groups. The Shannon-Weaver information index was used to describe the spatially and temporally variation in diversity of these three major faunal groups. The results exhibited lower faunal diversity during monsoon period. The annual production of two dominant macrofauna species including a species of bivalve, Nuculana acuta and a species of Cephalochordata, Branchiostoma lanceolatum were measured by using age group determination. Furthermore the mean biomass and total annual production of macrobenthic fauna were estimated for the whole studied area. The potential yield of demersal fishery resources (fish and crustacean) then estimated and worked out to be 15360 tons/year asuming 10% ecological efficiency of hypothetical pyramid from 3rd to 4th marine trophic level. Accordingly the annual exploitable demersal fishery resources for the entire Chahbahar Bay was estimated to be 7600 to 8500 tons/year by taking 50 to 55% of the total estimated potential in to account.

Temperature- and salinity-dependent development of a Nordic strain of Ichthyophthirius multifiliis from rainbow trout

During the twentieth century evidence was presented which suggested the presence of various strains and races of the parasite Ichthyophthirius multifiliis Fouquet. However, ecological profiles of various parasite isolates from different climatic zones are sparse. Such stringent characterizations of parasite development at defined abiotic conditions could provide valuable criteria for the different races: profile comparison from various localities is one way to differentiate these strains. Baseline investigations were therefore performed on the associations between abiotic factors (temperature/salinity) and the development of theronts in tomocysts of I. multifiliis isolated from rainbow trout in a Danish trout farm. It was shown that tomocyst formation and theront development took place between 5 and 30degreesC. Development rates and sizes of theronts were clearly affected by temperature: theronts escaped tomocysts already after 16-27 h at 25degreesC and 30degreesC, whereas this process took 8-9 days at 5degreesC. Likewise, theront size decreased steadily from a maximum of 57.4 x 28.6 mum at 5degreesC to 28.6 x 20.0 mum at 30degreesC. This size variation was only partly associated with the number of theronts that appeared at different temperatures. The lowest number of theronts escaping from one tomocyst was indeed found at 5-7degreesC (mean 329-413). At 11.6, 17.0 and 21degreesC. the highest number of theronts appeared (mean 546-642). However, at 25 and 30degreesC, the number decreased (458 and 424, respectively). Additional studies on the salinity dependent development of the parasite (at 11.6degreesC) showed that salinities above 5 p.p.t. totally inhibited development. Even at 5 p.p.t. the developmental time significantly increased and the number of theronts produced from one tomocyst decreased.

Effects of mixture of nanoparticles under different salinity in the clams Ruditapes philippinarum and Ruditapes decussatus

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidadde do Algarve, 2015

Chemical Oceanographic Studies of the Coastal Waters of Cochin

The present study is an attempt to understand some of the chemical oceanographic processes of the coastal water and the backwaters of Cochin. The importance of this study lies in the fact that there has been an increasing concern on the environmental degradation of Cochin backwaters with respect to water and sediments due to various anthropogenic activities. The study comprises the results and discussion of the hydro chemical parameters of coastal waters of Cochin during different seasons with statistical analysis. The parameters dealt with are salinity, temperature, pH, dissolved oxygen, nitrite-N, nitrate-N, ammonia-N, Silicate-Si, phosphate-P, chlorophyll ‘a’ and suspended solids, dissolved trace metals and sediment characteristics including sediment metals

Ecological and Biochemical Studies On Cyanobacteria of Cochin Estuary and Their Application as Source of Antioxidants

The main objectives of the present investigation were to evaluate the qualitative and quantitative distribution of natural cyanobacterial population and their ecobiological properties along the Cochin estuary and their application in aquaculture systems as a nutritional supplement due to their nutrient-rich biochemical composition and antioxidant potential. This thesis presents a detailed account of the distribution of cyanobacteria in Cochin estuary, an assessment of physico-chemical parameters and the nutrients of the study site, an evaluation of the effect of physico-chemical parameters on cyanobacterial distribution and abundance, isolation, identification and culturing of cyanobacteria, the biochemical composition an productivity of cyanobacteria, and an evaluation of the potential of the selected cyanobacteria as antioxidants against ethanol induced lipid peroxidation. The pH, salinity and nutritional requirements were optimized for low-cost production of the selected cyanobacterial strains. The present study provides an insight into the distribution, abundance, diversity and ecology of cyanobacteria of Cochin estuary. From the results, it is evident that the ecological conditions of Cochin estuary support a rich cyanobacterial growth.

STUDIES ON TAXONOMY, DISTRIBUTION, ECOLOGY AND REPRODUCTIVE POTENTIAL OF ROTIFERS FROM SELECTED CENTRES IN COCHIN BACKWATER SYSTEM, KERALA

The studies were conducted in nine stations with varying ecological characteristics along Cochin backwaters and adjoining canals. Many workers opined that the distribution of rotifers is cosmopolitan. The significance of rotifers as first food for early larvae was indicated by Fujita. Aquaculture is a fast growing field in fisheries sector and it is gaining more importance as the fish landings and supply are getting irregular. A consistent supply of fish/shellfish can only be achieved through aquaculture. The success of any culture activity depends on the timely production of seeds of finfishes/shellfishes. The availability of wild seed is seasonal and erratic. So, a dependable source of seed of fishes and shellfishes is possible only through large scale production in hatchery. A successful seed production activity depends on the availability of a variety of suitable live feed organisms in sufficient quantities at the proper time for use in the larval stages. As the live feeds promote high growth rates, easy digestion, assimilation and the quality of not contaminating the culture water when compared to other artificial feeds, make the culture of live feed organisms the principal means of providing food for the larvae of finfishes and shellfishes. Rotifers are considered to be an excellent and indispensable food for larvae of many finfishes and crustaceans. It (1960) was the first to culture Brachionus plicatilis for feeding marine fish larvae, and now it is being extensively used as live feed in hatcheries all over the world. They are a group of microscopic organisms coming under the Phylum Rotifera which comprises of about 2000 species. Their slow swimming habits, ability to tolerate a wide range of salinities, parthenogenetic mode of reproduction and ability to get enriched easily, make rotifers an ideal live feed organism. The major factors such as temperature, salinity and food that influence the reproductive potential and thereby the population size of rotifer, Salinity is one of the most important aspect influencing the reproductive rate of rotifers. The feed type and feed concentration play a vital role in influencing the reproductive rate of rotifers. For culture of rotifers, the commonly used micro algae belong to Chlorella, Nannochloropsis, Isochrysis and Tetraselmis. While some studies have suggested that, algal diet has little effect on reproductive rates in 1979 while using the rotifer, Brachionus plicatilis as feed for the larvae of red sea bream, Pagrus major. It is generally accepted that rotifers play a pivotal role in the successful rearing of marine fish larvae.

Salinity Intrusion and Seasonal Water Quality Variations in the Tidal Canals of Cochin

The study conducted on the salinity intrusion and seasonal water quality variations in the tidal canals of cochin. The main objectives are, salinity intrusion profile, water quality variation of the surface water of the canals,hierarchical utility of the water bodies and to understand the non-conservative components in the water body. The parameters monitored werepH,temperature,alkalinity,conductivity,DO(dissolvedoxygen),COD(chemical oxygen demand),BOD(biochemical oxygen demand0,chloride, total hardness, calcium hardness, dissolved phosphate, nitrate, total iron, sulphate, turbidity, total coliform and SUVA at 254nm. The tidal canals of GCDA were found to be creeks extending to the interior, canals inter connecting parts of the estuary or canals with seasonally broken segments. Based on utility the canals could be classified as: canals heavely polluted and very saline,canals polluted by urban waste , canals having fresh water for most part of the year and not much polluted, fresh water bodies heavily polluted. During the rainy months carbon fixation by plankton is nonexistent,and during the dry months Chitrapuzha becomes a sink of phosphate. The study indicated abiotic subrouts for dissolved phosphate and revealed the potential pitfalls in LOICZ modeling exercise on sewage ladentidal canals. It was also found that all canals except for the canals of West cochin and chittoorpuzha have fresh water for some part of the year. The water quality index in the durable fresh water stretches was found to be of below average category.

Further studies on the process of coastal upwelling along the south west coast of India - possible correlations with biological productivity

An attempt is made to study the possible relationship between the process of upwelling and zooplankton biomass in the shelf weters along the south west coast of India between Cape comorin and Ratnagiri based on oceanographic and Zooplankton data collected by the erstwhile FAO/UNDP Pelagic Fishery Project,Cochin between 1973 and 1978. Different factors such as the depth from which the bottom waters are induced upwards during the process of upwelling,the depth to which the bottom waters are drawn, vertical velocity of upwelling and the resultant zooplankton productivity were considered while arriving at the deductions. Except for nutrients and phytoplankton productivity, for which simultaneous data is lacking, all the major factors were taken into consideration before cocluding- xon positive/negative correlation.