DNA barcoding, an effective tool for species identification: a review.

DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.

Soil ciliates of the Indian Delhi Region: Their community characteristics with emphasis on their ecological implications as sensitive bio-indicators for soil quality.

The present investigation aims to study the diversity of ciliates from different habitats in and around Delhi, India, and the correlation of this diversity with soil quality {agricultural lands (site 1 and 2), dump yards (site 3 and 4), sewage treatment plant (site 5), residential land (site 6), landfill (site 7) and barren land (site 8)}. Various physicochemical parameters of the different soil samples were studied and analysed for soil texture, interstitial water, pH, conductivity, total organic carbon, total organic matter, total nitrogen and phosphorous content, using standard protocols. Seventeen ciliate taxa belonging to four classes, seven orders, ten families, and 17 genera were recorded, with the maximum number of species (eleven) belonging to the class Spirotrichea. Ciliate diversity was highest at sites 5 and 6 and lowest at sites 1 and 2. Spathidium sp. was the dominant species in the conditioned land (site 8), while the ciliate Colpoda sp. was present in all the sites examined, showing the highest population density in the sewage treatment plant site (site 5). Statistical analysis showed that ciliate diversity was positively correlated to physicochemical parameters such as interstitial water, total organic matter and organic carbon, total nitrogen and total phosphorous content. Analyses of spirotrichs/colpodids (S/C) ratio and diversity indices implied that the habitat conditions of sites 1, 2, 3 and 8 are relatively unfavourable for soil ciliates to flourish; while sites 4, 5, 6 and 7 provided more favourable conditions. The ubiquity of ciliate distribution suggests their important role in the soil food webs and nutrient cycling, and their community structure and specific characteristics appear to be of major importance for soil formation. A full understanding of soil ciliate diversity and physicochemical parameters helps to inform best practice for improving soil quality as well as conservation practices for sustainable development and management of farms and cultivated lands. In conclusion, ciliate diversity serves as an important and sensitive bio-indicator for soil quality.

Techniques and tools for species identification in ciliates: a review.

Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a 'total evidence' approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.

Morphology and morphogenesis of a new oxytrichid ciliate, Notohymena limus n. sp. (Ciliophora, Oxytrichidae) from Delhi, India.

The morphology and morphogenesis of a new oxytrichid ciliate, Notohymena limus n. sp. were studied in vivo and after protargol impregnation. The new ciliate was isolated from the sewage sludge at Delhi Jal Board Sewage Treatment Plant located at Rithala, Delhi, India, using the non-flooded Petri dish method. N. limus n. sp. is characterized as follows: flexible dorsoventrally flattened ellipsoidal body; Notohymena-pattern undulating membranes; adoral zone of membranelles (AZM) occupied about 39% of the body length, and consists of around 26 membranelles; large and deep buccal cavity; colorless subpellicular granules present in groups and arranged around the bases of dorsal bristles; 4 macronuclear nodules; 2 micronuclei; 18 fronto-ventral-transverse (FVT) cirri in typical Oxytricha-pattern; 6 dorsal rows of bristles; 3 caudal cirri; about 16 right and 15 left marginal cirri; N. limus n. sp. is a new species on the basis of the combination of morphological, morphometric and morphogenetic characteristic features.