DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh

Biological Detoxification of Aflatoxin B1 by Enterococcus faecium HB2-2

Aflatoxin B1 (AFB1) contamination in food and feed is a global health and economic threat, necessitating the immediate development of effective strategies to mitigate its negative effects. This study focuses on the isolation and characterization of Enterococcus faecium HB2-2 (E. faecium HB2-2) as a potent AFB1-degrading microorganism, using morphological observation, biochemical profiling, and 16S rRNA sequence analysis. An incubation of E. faecium HB2-2 at 32 °C for 96 h in a pH 10 nutrient broth (NB) medium resulted in a remarkable degradation rate of 90.0% for AFB1. Furthermore, E. faecium HB2-2 demonstrated 82.9% AFB1 degradation rate in the peanut meal, reducing AFB1 levels from 105.1 to 17.9 μg/kg. The AFB1 degradation ability of E. faecium HB2-2 was found to be dependent on the fermentation supernatant. The products of AFB1 degradation by E. faecium HB2-2 were analyzed by liquid chromatography-mass spectrometry (LC-MS), and a possible degradation mechanism was proposed based on the identified degradation products. Additionally, cytotoxicity assays revealed a significant reduction in the toxicity of the degradation products compared to the parent AFB1. These findings highlight the potential of E. faecium HB2-2 as a safe and effective method for mitigating AFB1 contamination in food and feed.

Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L

Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.

A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Unveiling the molecular identity of the diminutive cyprinid, Horadandia brittani (Teleostei: Cyprinidae), a species endemic to Southern India

BACKGROUND

Horadandia brittani is a small cyprinid fish species initially discovered in the coastal floodplains of southern India. For almost 50 years, the genus Horadandia was monotypic with a single species confined to Sri Lanka. In 1992, a new species H. brittani was described from south-western India. Despite being described as a separate species, H. brittani was later considered a synonym of H. atukorali, but in 2013, researchers recognized it as a distinct species based on morphological differences. Despite this clarification, there was still a need to validate the identity of H. brittani and determine its evolutionary relationship with its closely related species using DNA sequences.

METHODS

To address the uncertainties surrounding the identity of H. brittani, the present study utilized molecular techniques to generate DNA sequences. Sample collection involved obtaining specimens of H. brittani from their natural habitats. Subsequently, DNA was extracted from the collected samples, and the mitochondrial cytochrome C oxidase (COI) gene was amplified using appropriate methods.

RESULTS

The analysis of DNA sequences obtained from the COI gene revealed significant genetic distinctions between H. brittani and H. atukorali. The genetic distance values between these two species ranged from 3.21 to 3.63%, clearly indicating that these two species are genetically separate entities. The study successfully established the phylogenetic relationships between H. brittani and H. atukorali based on the COI gene sequences, further confirming the validity of H. brittani as a distinct and separate species.

CONCLUSION

The findings of this study conclusively demonstrate that H. brittani is a valid and separate species, distinct from H. atukorali. The genetic analysis based on mitochondrial COI gene sequences provided strong evidence for the differentiation between these two species. The molecular data generated in this research can be used to identify H. brittani quickly and accurately in the future.

Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding

Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India)

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

DNA barcoding and phylogenetic relationship of two fish species of genus Garra (Family: Cyprinidae) from Aravalli region of Southern Rajasthan based on mtDNA COI sequences

The genus Garra (stone sucker), Family Cyprinidae, consists of a group of species that are remarkably similar in morphology. These species are often difficult to distinguish based on external morphological approach. To resolve the existing uncertainty about the relationships and groups of these fishes, an attempt has been made to study the phylogenetic relationships of Garra gotyla and Garra mullya using mtDNA COI gene sequences from Aravalli region of Southern Rajasthan. The sequences were submitted to NCBI GenBank to establish and validate the taxonomical identification of the samples. A total of 5 COI sequences were generated. The overall GC content of Garra gotyla and Garra mullya were 44.13 and 43.00% respectively. The genetic distance within groups was 0.001 and 0.01 for G. gotyla and G. mullya respectively. The Neighbour-joining tree of two fish species using COI gene data revealed two distinct groups with 0.157 divergence. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.