Subrata Trivedi

Role of DNA barcoding in marine biodiversity assessment and conservation: An update.

More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.

Fern-synthesized silver nanocrystals: Towards a new class of mosquito oviposition deterrents?

Mosquitoes act as vectors of devastating pathogens and parasites, representing a key threat for millions of humans and animals worldwide. Eco-friendly control tools are urgently required. We proposed a novel method of fern-mediated biosynthesis of silver nanoparticles (AgNP) using Dicranopteris linearis, acting as a reducing and capping agent. AgNP were characterized by UV-vis spectroscopy, Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), zeta potential and particle size analysis. In mosquitocidal assays, the LC50 of D. linearis extract against Aedes aegypti ranged from 165.213 (larva I) to 255.055ppm (pupa). LC50 of D. linearis-synthesized AgNP ranged from 18.905 (larva I) to 29.328ppm (pupa). In the field, the application of D. linearis extract and AgNP (10×LC50) led to 100% larval reduction after 72h. Smoke toxicity experiments conducted against A. aegypti adults showed that D. linearis leaf-, stem- and root-based coils evoked mortality rates comparable to the permethrin-based positive control (58%, 47%, 34%, and 48% respectively). In ovicidal experiments, egg hatchability was reduced by 100% after treatment with 25ppm of AgNP and 300ppm of D. linearis extract. Interestingly, oviposition deterrent assays highlighted that 100ppm of fern extract reduced oviposition rates of more than 65%, while 10ppm of fern-fabricated AgNP reduced oviposition rates of more than 70% in A. aegypti (OAI were -0.52 and -0.55, respectively). Overall, our results highlighted that D. linearis-synthesized AgNP could be useful candidates to develop nano-formulated oviposition deterrents effective against dengue vectors.

Decadal Variation of Nutrient Level in Two Major Estuaries in Indian Sundarbans

The impact of the nutrient level on the water quality in the Hooghly and Matla estuarine complex in Indian Sundarbans was assessed for three decades (1984-2014). Nitrate, phosphate and silicate were used as indicators of nutrient related water quality in the estuarine water. Our first order analysis reflects significant spatio-temporal variations of selected nutrients with relatively higher values in the Hooghly estuary (in the western Indian Sundarbans) compared to the Matla estuary (in the central Indian Sundarbans). Significant variations were observed in dissolved nitrate, phosphate and silicate concentrations between stations and years (p < 0.01). Such pronounced variations may be attributed to the location of highly industrialized and urbanized city of Kolkata, Howrah and Haldia port-cum-industrial complex adjacent to the Hooghly estuary. The sudden rise of selected nutrients during premonsoon, 2009 (irrespective of sampling stations) is directly related to AILA, a super-cyclone that occurred in the lower Gangetic delta during 22nd 25th May, 2009.

The desert wormwood (Artemisia herba-alba) – From Arabian folk medicine to a source of green and effective nanoinsecticides against mosquito vectors

The development of eco-friendly and effective insecticides is crucial for public health worldwide. Herein, we focused on the desert wormwood (Artemisia herba-alba), a plant widely used in Arabian traditional medicine, as a source of green nanoinsecticides against mosquito vectors, as well as growth inhibitors to be employed against microbial pathogens. Ag nanoparticles (AgNPs) fabricated with the A. herba-alba extract were tested on Indian and Saudi Arabian strains of Anopheles, Aedes and Culex mosquitoes. The chemical profile of the A. herba-alba extract was determined by LC-DAD-MS and 1H NMR studies. Then, AgNPs were studied using UV-vis spectroscopy, XRD, FTIR spectroscopy, TEM, and EDX analyses. Artemisia herba-alba-synthesized AgNPs showed high larvicidal toxicity against mosquitoes from both Indian and Saudi Arabian strains. LC50 of AgNPs against Indian strains was 9.76 μg/ml for An. stephensi, 10.70 μg/ml for Ae. aegypti and 11.43 μg/ml for Cx. quinquefasciatus, whereas against Saudi Arabian strains it was 33.58 μg/ml for Ae. aegypti and 38.06 μg/ml for Cx. pipiens. In adulticidal experiments, A. herba-alba extract showed LC50 ranging from 293.02 to 450 μg/ml, while AgNP LC50 ranged from 8.22 to 27.39 μg/ml. Further, low doses of the AgNPs inhibited the growth of selected microbial pathogens. Overall, A. herba-alba can be further considered as a source of phytochemicals, with special reference to saponins, for effective and prompt fabrication of AgNPs with relevant insecticidal and bactericidal activity against species of high public health importance.

DNA Barcoding in Marine Perspectives

Major part of our planet includes the marine habitat which faces severe threat due to overexploitation of its bio resources. Assessment of biodiversity in the massive and diverse marine ecosystem is a challenging task. In this introductory chapter, we give a brief description of the marine habitat and types of marine organisms, followed by the concept of DNA barcoding. We also describe the applications and different initiatives of DNA barcoding in the marine ecosystem. A brief account of DNA barcoding in marine fungi, different groups of animals and plants is also elucidated. This chapter gives a bird’s eye view on the DNA barcoding in the marine perspective.

Seasonal dynamics in the trophic status of water, floral and faunal density along some selected coastal areas of the Red Sea, Tabuk, Saudi Arabia

AbstractEutrophication is posing a threat to the coastal marine ecosystems. The consequence of anthropogenic induced eutrophication of waters has resulted in severe deterioration of surface waters. In this research a preliminary data was collected on eutrophication by environmental monitoring on some selected coastal areas of the Red Sea near Tabuk, Saudi Arabia. Sampling sites were selected from Haql, Sharmaa and Duba (five for each station) and water samples collected in four different seasons (Oct 2013, Jan 2014, April 2014 and July 2014) to study seasonal dynamics of water quality parameters (especially in reference to the trophic status of water). Only one coastal site from each station was found with some eutrophic characteristics. Water samples collected from these eutrophic sites were more alkaline, turbid, with higher nutrient and low dissolved oxygen contents as compared to other sampling sites. Dynamics in relative densities of coastal flora and fauna were also found to be related with coastal water quality. Human settlements, fish markets, boating clubs and tourisms near these coastal areas of the Red Sea were observed as the primary causes of nutrient loading; run-offs during rains carrying nutrients also aggravate the problem. The results of this study may help in estimating the intensity of the problem and as a forecast for time frame to take an action for the conservation of affected coastal marine ecosystems and restoration of degraded coastal areas of the Red Sea.

DNA Barcoding of Primitive Species-Nemertine from Sundarbans Marine Bio-resource

The phylum Nemertea is known as “ribbon worms” or “proboscis worms” or nemertine. Most are very slim, usually, only a few millimetres wide, although a few have relatively short but wide bodies. They are believed to be an ancient order with their origins in the Cambrian period over 500 million years ago. These nemerteans are distributed globally mostly in the temperate tropical region. Nevertheless, this group is mostly neglected and its taxonomy is jumbled with some blurry and incomplete descriptions and thus created perplexity in the identification process. In a case study, the nemertine samples were collected from the Sundarbans delta (one of the largest biodiversity hotspots) and were subjected to DNA Barcoding approach for species level identification. The sequence analysis was done in comparison with the previously characterized species, calculating its genetic distance (Kimura-2-parameter) as well as similarity match with the published sequence. It was found that the samples from the Sundarbans clustered distinctly as a separate clade with respect to other species, which was congruent with the genetic distance. From this study, it was confirmed that the species from this region was novel as compared to other distinguished species, which was nearly impossible with the conventional morphology due to lack of valid diagnostic keys. In this context, DNA taxonomy has proved itself to be a more powerful tool to systematizing taxa in the definite clades, recognition of possible bio-geographic patterns of these species or to uncover possible hidden species.

DNA Barcoding in the Marine Habitat: An Overview

Major part of our planet includes the marine habitat which faces severe threat due to overexploitation of its bio resources. Assessment of biodiversity in the massive and diverse marine ecosystem is a challenging task. In this introductory chapter, we give a brief description of the marine habitat and types of marine organisms, followed by the concept of DNA barcoding. We also describe the applications and different initiatives of DNA barcoding in the marine ecosystem. A brief account of DNA barcoding in marine fungi, different groups of animals and plants is also elucidated. This chapter gives a bird’s eye view on the DNA barcoding in the marine perspective.

DNA Barcoding: Molecular Positioning of Living Fossils (Horseshoe Crab)

Living fossils are the important components of biodiversity. They represent the connection between the extinct and extant species. A living fossil is a living species that appears to be similar to a species otherwise known only from fossils, typically with no close living relatives and the extant species. The study of primitive species gives an idea about the ancestors from which they diverged and bring out many surprising facts which are unknown to the world. In a case study, species belonging to the phylum Arthropoda, Brachiopoda and Molluscs were collected from Sundarbans where Horshshoe Crab was the living fossils (Carcinoscorpius rotundicauda). Lingula sp and some crab species were included as the outgroup. To position this living fossil, DNA barcoding approach was employed as per standard protocol. COI sequencing and subsequently nucleotide analysis of all the species were done and also the molecular clock was constructed to locate their position along with their divergence time in correspondence with the other sequences of the allied taxa viz, Limulus polyphemus, Tachypleus gigas etc. It is found that the Carcinoscorpius rotundicauda are more closely related to its allied taxon Tachypleus gigas as compared to Limulus poluphemus and their divergence period is calculated which is supposed to be the 550 million years ago. Thus, DNA barcoding approach is a useful technique to properly identify species and to construct phylogenetic relationship among the species and subsequent assessment of the species divergence time.

Bioinformatics Tools in Marine DNA Barcoding

Information science has been applied to manage the information generated in molecular biology to produce the field called Bioinformatics. Application of bioinformatics in several ways is an integral part of DNA barcode research. Since the origin of the DNA barcode concept, three major criteria were set up to test the efficiency of barcode regions. These are (i) Universal Primers to amplify the barcode region (ii) Calculation of Barcode gap (intra and interspecies distance) (iii) Species resolution power. For evaluation of these criteria, DNA barcode community is applying bioinformatics tools and algorithms in primer design, distance calculation, phylogenetic analysis, etc. DNA Barcoding produces a huge amount of Cytochrome c oxidase subunit I (COI) sequences information for species identification from animal kingdom of marine biodiversity. Similarly, Consortium of Barcode of Life (CBOL) plant group proposed plastid genes rbcL and matK either singly or in combination as the standard DNA barcode for plants (CBOL Plant Working Group 2009). ITS of the nuclear ribosomal RNA standardized as the universal barcode marker for fungi. Bioinformatics play a major role in storing of DNA barcode information, and it is easy to retrieve from the database. Software-based sequence quality assurance is main starting and check point for the production of barcode sequences. In this chapter, we discussed different tools and methods of bioinformatics and their proper utilization.