This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.

Eclipta alba (L.) is a valuable medicinal plant. However, its medicinal efficacy can be affected by geminivirus infection. Therefore, identification of healthy specimen is essential before to use as medicine. The present study provided the taxonomic characterization of geminivirus infected and healthy E. alba plant by studying apparent morphology and microscopic features through light and scanning electron microscopy. Before taxonomic characterization infected and healthy specimens were separated through molecular detection of geminivirus. Results of morphological studies reported that geminivirus infected E. alba plant showed systematic symptoms of infection like stunted growth, distortion and chlorosis of leaves, decrease in size of root, shoot and fruit, and so forth in comparison to healthy specimen. Anatomical findings reported that in both plants anomocytic and anisocytic types of stomata with multicellular warty trichomes were present. However, variations were observed in quantitative measures such as size of trichomes, epidermal, subsidiary and guard cells. Palynological observations identifies that both plants possessed tricolporate type of pollen but variation was mainly observed in size and shape of pollen, thickness of exine and intine, P/E ratio, pore size, interspecific difference, size of colpi, and pollen ornamentation. Overall this study concluded that both healthy and infected E. alba do not reported much variations in qualitative taxonomic features, but can be differentiated in terms of quantitative taxonomic evidences. Future studies are recommended for pharmacological analysis of both healthy and virus infected plants. RESEARCH HIGHLIGHTS: Eclipta alba has incredible therapeutic worth, but due to geminivirus infection the plant is affecting badly. Hence, the present studies give a comprehensive taxonomic report on the geminivirus infected and healthy plant species.

The biodegradation of biorecalcitrant opioid drug tramadol (TRAM) was studied in a model biodegradation experiment performed with an enriched activated sludge culture pre-adapted to high concentration of TRAM (20 mg/L). TRAM and its transformation products (TPs) were determined by applying ultrahigh-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF-MS), the sludge culture was characterized using a 16S rRNA gene amplicon sequencing, whereas ecotoxicological evaluation was performed based on determination of toxicity to freshwater algae. Tramadol removal was much faster (t1/2 = 1.3 days) and more efficient in glucose-containing mineral medium (cometabolic conditions) than in a medium without glucose. The elimination of the parent compound resulted in the formation of five TPs, two of which (TP 249 and TP 235) were identified as N-desmethyltramadol (N-DM TRAM) and N,N-didesmethyltramadol (N,N-diDM TRAM). The remaining 3 TPs (TP 277a-c) were isomeric compounds with an elemental composition of protonated molecules C16H24NO3 and a putative structure which involved oxidative modification of the dimethylamino group. Pronounced changes in the taxonomic composition of the activated sludge were observed during the enrichment, especially regarding an enhanced percentage of 8 genera (Bacillus, Mycobacterium, Enterobacter, Methylobacillus, Pedobacter, Xanthobacter, Leadbetterella and Kaistia), which might be related to the observed transformations. The removal of TRAM resulted in proportional reduction of algal toxicity, implying a positive result of the accomplished transformation processes.

A novel marine bacterium, designated strain GH1-24T, was isolated from a tidal mudflat sample collected at Gangwha Island, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequence comparison exhibited that the novel isolate was most closely related to Sneathiella and formed a tight cluster with Sneathiella glossodoripedis JCM 23214T with 98.1 % sequence similarity. The 16S rRNA gene sequence similarities to other Sneathiella species were low: Sneathiella chinensis LMG 23452T (96.1 %) and Sneathiellachungangensis CAU 1294T (95.8 %). Cells of the organism were Gram-reaction-negative, strictly aerobic, catalase- and oxidase-positive, motile rods and showed growth at 0.5-6 % NaCl, 20-42 °C and pH 6.0-8.0. The G+C content of the DNA was 54.9 mol%. The major isoprenoid quinone was Q-10. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C19 : 0cyclo ω8c. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The results of phenotypic and phylogenetic analyses and DNA-DNA relatedness studies suggest that the isolate can be a member of a novel species of the genus Sneathiella, for which the name Sneathiellalimimaris sp. nov. is proposed. The type strain is GH1-24T (=KCTC 52846T=NBRC 113276T).