Strengthening marine amphipod DNA barcode libraries for environmental monitoring

Annadurai

et al. 2020

Preprint

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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, Ochrophyta and Rhodophyta). We found 10 species in 3 phyla and 2 genera (Anthophycus and Chnoospora) of Ochrophyta were barcoded for the first time. Uncorrected p-distance calculated using K2P, nucleotide diversity and Tajima’s 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 ecosystem’s health assessment and monitoring.

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

Prasanthi

Annadurai

et al. 2020

Preprint

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

Manikantan

Vijaylaxmi

et al. 2020

Preprint

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Globally, mangrove coverings are disappearing at the rate of 1–2% per annum and 35% have been lost in the last 20 years. Changes in climate and human activities are affecting the mangrove habitats significantly. When the mangroves were transplanted artificially 25 years ago in the Vellar estuary, no mangrove-associated crabs were found. We sampled this mangrove ecosystem and intent to estimate the diversity, species abundance, composition and phylogenetic relationships of barchyuran crabs. We also intend to evaluate the efficacy of DNA barcoding technique in precisely identifying species of brachyuran crab associated with mangroves. Mangrove species such as, Avicennia marina, A. officinalis, Rhizophora apiculata, R. mucronata and R. annamalayana, Acanthus ilicifolius and salt marshes; Suaeda maritima and Prosopis juliflora constituted the artificially created mangrove ecosystem. A total of 2844 crabs were collected, representing 35 species belonging to 20 genera within 8 families. The four species of brachyuran crab, that is, Uca lactae, U. triangularis, Selatium brockii, and Neosarmatium asiaticum contribute >70% of total abundances. The present study recovered an estimated 87.5% of crab species. The maximum association index value (97.7%) was observed between Uca lactea and Uca triangularis. Cluster analysis, grouped the sampled stations according to the type of mangrove species present. It was clear that the type of mangrove species influences brachyuran crabs’ structure and species composition. Clustering analysis also clearly distinguished the mangrove stations and salt-marsh station (control) based on the composition of the brachyuran crab species. In general, the abundances of all collected species of crabs, and particularly Neosarmatium asiaticum, prefers vegetative cover composed of multiple species of mangroves. DNA barcoding analysis shows that 40% of the species collected in this study was barcoded for the first time. In near future, the advent of new high-throughput sequencing technologies will dramatically change bio-monitoring applications and surveys. This will make reference datasets such as ours important. Using the array of diversity and species estimator indices we presented useful data on brachyuran crab diversity associated with artificially created mangrove ecosystem, which will be useful for marine policy makers, coastal ecosystem designers and climate researchers.

Variability in the diet diversity of catfish highlighted through DNA barcoding

Iyyapparajanarasimapallavan

Rahman³

et al. 2020

Preprint

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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 prey items of chordates and macro-invertebrates 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 the 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 chordate 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 in Chordates (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. maculatus’s 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.