Biology subjects

PrasannaKumar, C.

Publications and source records attributed to PrasannaKumar, C..

5 recordsLinked to original sources

bioRxiv2020

Variability in the diet diversity of catfish highlighted through DNA barcoding

Identification and quantification of fish diet diversity was the first step in understanding the food web dynamics and ecosystem energetics, where the contribution of DNA barcoding technique has been important. We used DNA barcoding to identify the stomach contents of a euryhaline, benthophagous catfish Ariius maculatus. From 40 catfish stomach items sampled in two different seasons, we barcoded 67 piscine and macro-invertebrates prey items, identified as belonging to 13 species in 4 major phyla (viz., Chordate, Arthropod, Annelida and Mollusca). It is important to note that the mollusc taxa (Meritrix meritrix and Perna viridis) and a species of fish (Stolephorus indicus) could not be found among the gut contents of A. maculatus sampled during the pre- and post-monsoon season, respectively. Among the piscine diets of A. maculatus, Eubleekeria splendens (23.5%) and Stolephorus indicus (23.5%) were the major prey taxa during pre-monsoon season. The hermit crabs forms the major constituents of both pre- and post-monsoon seasons, among invertebrate taxa. Polychaete, Capitella capitata (25.92%) was abundantly consumed invertebrates next to hermit crabs. We noticed that in pre-monsoon A. maculatus was more piscivorous than post-monsoon. As revealed through Kimura-2 parametric pair{-}wise distance analysis, the diet diversity was relatively higher in post-monsoon. The accumulation curve estimated 57 haplotypes within 14 barcoded species (including the host A. maculatus). Majority of haplotypes were found among fishes (47.36%) followed by Arthropods (28.07%), Annelids (14.03%) and Mollusca (10.52%), respectively. This study also highlights that there is a growing concern about A. maculatuss aggressive predation on commercially important stocks of fish and invertebrates. We will continue to expand the coverage of species barcoded in the reference database, which will become more significant as meta- and environmental DNA barcoding techniques become cheaper and prevalent.

zoology↗

bioRxiv2020

Diversity, phylogeny, and DNA barcoding of brachyuran crabs in artificially created mangrove environments

Globally, at the rate of 1-2 percent per annum, mangrove coverings are disappearing and 35 percent have been lost in the last 20 years due to changes in climate and human activities. No mangrove-associated crabs were found when the mangroves were artificially transplanted 25 years ago in the Vellar estuary. This mangrove ecosystem was sampled for brachyuran biodiversity estimation, species abundance, composition and evaluation of the effectiveness of DNA barcoding in brachyuran crabs species identification. A total of 2844 crabs were collected, representing 35 species within 8 families belonging to 20 genera. Four brachyuran crab species, that is, Uca lactae, U. Triangularis, Selatium brockii, and Neosarmatium asiaticum account for >70% of the total abundance. An approximate 87.5% of crab species estimated to occur by various species estimator were recovered in the present study. Between Uca lactea and U. triangularis, the maximum association index value was observed (97.7%). Cluster analysis grouped the sampled stations according to the types of mangrove species, clearly influencing the structure and composition of the brachyuran crabs. In general, vegetative cover composed of multiple species of mangroves is preferred for the abundance of all collected crabs species, and particularly Neosarmatium asiaticum. Analysis of DNA barcoding indicates that 40% of the brachyuran species gathered in this sample were first barcoded. The advent of new high-throughput sequencing technologies will change biomonitoring applications and surveys drastically in the near future, making reference datasets like ours relevant.

zoology↗

bioRxiv2020

Identifying seaweeds species of Chlorophyta, Ochrophyta and Rhodophyta using DNA barcodes

Strengthening the DNA barcode database is important for a species level identification, which was lacking for seaweeds. We made an effort to collect and barcode seaweeds occurring along Southeast coast of India. We barcoded 31 seaweeds species belonging to 21 genera, 14 family, 12 order of 3 phyla (viz., Chlorophyta, Phaeophyta and Rhodophyta). We found 10 species in 3 phyla and 2 genera (Anthophycus and Chnoospora) of Phaeophyta were barcoded for the first time. Uncorrected p-distance calculated using K2P, nucleotide diversity and Tajimas test statistics reveals highest values among the species of Chlorophyta. Over all K2P distance was 0.36. The present study revealed the potentiality of rbcL gene sequences in identification of all 3 phyla of seaweeds. We also found that the present barcode reference libraries (GenBank and BOLD) were insufficient in seaweeds identification and more efforts were needed for strengthening local seaweed barcode library to benefit rapids developing field such as environmental DNA barcoding. We also show that the constructed barcode library could aid various industrial experts involved in seaweed bio-resource exploration and taxonomy/non-taxonomic researches involved in climate, agriculture and epigenetics research in precise seaweed identification. Since the rise of modern high-throughput sequencing technologies is significantly altering bio-monitoring applications and surveys, reference datasets such as ours will become essential in ecosystems health assessment and monitoring.

plant biology↗

bioRxiv2020

DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species

For the yeast population and diversity, marine habitats are the least explored niches and the lack of validated database is considered to be a drawback for yeast research. The aim of the present study is to create a comprehensive DNA barcode library for marine derived yeast species isolated from organic burial hotspots such as coastal sediment in mangrove and continental shelf ecosystems. As we enriched, isolated and ITS gene sequenced 1017 marine derived yeast isolates belonging to 157 marine species in 55 genera, 28 families, 14 orders, 8 classes of 2 Phyla (viz., Ascomycota and Basidiomycota) of which 13 yeast species were first time barcoded. We witnessed yeast species of both terrestrial and marine endemic origin in the barcode datasets. Due to the large volume of sequencing trace files, the variable length of extracted sequences, and the lack of reference sequences in public databases, difficulties were faced in taxonomic sequence validation. The length of the majority of the sequences (99.42%) were more than or equal to 600 base pairs. BLAST analysis revealed that 13 yeast species were barcoded for the first time. The genus, Candida was the speciose genera isolated in this study. K2P intra-species distance analysis performed for selective groups yielded an average of 0.33%, well below the previously proposed yeast barcode gap. ITS gene NJ-tree based identification conducted for selective species in Ascomycota and Basidomycota, precisely clustered the same species into one group, indicating the efficacy of ITS gene in yeast species delineation. Besides isolating some of the common marine yeast species such as Candida oceani, Bandonia marina and Yarrowia lipolytica, we found approximately 60% of the yeast species isolates were previously unrecorded from the marine environment (example; Cystobasidiopsis lactophilus, Slooffia cresolica, Udeniozyma ferulica, Colacogloea falcatus and Pichia guilliermondii), of which 16.5% were recognised as potential human pathogens (example; Candida orthopsilosis, C. rugosa, Debaryomyces fabryi and Yamadazyma triangularis). Apart from releasing the barcode data in GenBank, provisions were made to access the entire dataset along with meta-data in the Barcode of life database (http://dx.doi.org/10.5883/DS-MYIC). This research constitutes the largest dataset to date for collecting marine yeast isolates and their barcodes. As meta- and environmental barcoding analysis were expanding its scope including environmental assessment and monitoring, the datasets such as ours will be more useful.

microbiology↗

bioRxiv2020

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

Environmental DNA barcoding technology is gaining innovative applications. The effectiveness of current DNA barcode reference libraries in identifying amphipod barcodes and/or strengthening the existing library was tested. From 2500 amphipod individuals we barcoded 22 amphipod species belonging to 17 genera, 13 families among which 13 species were first time barcoded. More than 80 percent of the species were new distributional records. The minimum and maximum inter-specific pair-wise distance values was respectively 0.16 and 5.51 percent. Defining family specific species threshold values would be imperative, rather than expecting a universal barcode gap for amphipod species. The overall mean pair-wise distance, nucleotide diversity and Tajimas statistics were 3.59 percent, 0.27 and 2.62, respectively. There is a strong need to increase the number of amphipod species barcodes in the reference database. For better facilitation of environmental monitoring, the datasets could be exclusively accessed at BOLD through http://dx.doi.org/10.5883/DS-MAOI.

zoology↗