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5. Unraveling the potential of microbial communities for lake bioremediation via the metagenomics tool: a review

Author

Sampurna Nandy and Atya Kapley

Subjects
bioinformatics, lake rejuvenation, next-generation sequencing, shotgun metagenomics, Environmental technology. Sanitary engineering, TD1-1066, Environmental sciences, GE1-350
Abstract

Characterization of ubiquitous microorganisms has encountered many challenges, such as determining unknown microorganisms, their interactions, and unresolved functions in natural environments. Evolution in metagenomics and tools, however, has revolutionized assessment methodologies. Metagenomics has enabled unearthing the secret microbial treasure in a culture-independent manner and has proven more successful than conventional methodologies. It has provided an unparalleled platform for functional and taxonomic characterization of microbiota dwellings in altered lakes. Of late, many research articles have used metagenomics to understand microorganisms’ role in environmental clean-up. Consequently, these studies have been consolidated in the form of review articles. However, most of them are related to microbial characterization, procedure of metagenomics, and wastewater treatment, whereas only a few were directly related to lake bioremediation. Therefore, this review highlights the applications of metagenomics for unraveling microbial potential for lake rejuvenation. A paradigm shift from conventional to recent breakthroughs in metagenomics is also emphasized. The review also discusses merits, demerits of previous molecular techniques, and potential of metagenomics for understanding the microbial world in contaminated environments. Furthermore, the review discusses recent metagenomic studies for lake rejuvenation. Finally, future research directions are proposed for designing possible strategies for lake rejuvenation. HIGHLIGHTS Metagenomics is evaluated as a novel tool for studying microbial communities’ taxonomic and functional capabilities.; The paradigm shift from conventional to recent metagenomics advancements is reviewed.; Potential of metagenomics for designing an accelerated remediation process for lakes is emphasized.;

Published
2024
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10. Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences

Author

Kapley A, Raje DV, and Purohit HJ

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus. Results Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment. Conclusions The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples.

Published
2003
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38. List of contributors

Author

Aladekoyi, Oluwatosin Joseph, primary, Amoozegar, Mohammad Ali, additional, Andraskar, Jayanta, additional, Bernal, Anahí Romina, additional, Bharagava, Ram Naresh, additional, Bisaria, Kavya, additional, Chandra, Ram, additional, Das, Jayashankar, additional, Das, Plaban, additional, Dastgheib, Seyed Mohammad Mehdi, additional, Dave, Sushma, additional, de Figueroa, Lucia Inés Castellanos, additional, Dhanya, M.S., additional, Díez, Sergi, additional, Enerijiofi, Kingsley Erhons, additional, Falade, Ayodeji Osmund, additional, Fernández, Pablo Marcelo, additional, Goutam, Surya Pratap, additional, Gupta, Pankaj Kumar, additional, Haq, Izharul, additional, Himanshu, Sushil Kumar, additional, Jha, Pamela, additional, Jin, Ruofei, additional, Jobby, Renitta, additional, Kalamdhad, Ajay S, additional, Kapley, Atya, additional, Kishor, Roop, additional, Kumar, Adarsh, additional, Kumar, Ajay, additional, Kumar, Manish, additional, Kumar, Naveen, additional, Kumar, Vineet, additional, Lanjewar, Krutika, additional, Liu, Guangfei, additional, Marrugo-Madrid, Siday, additional, Marrugo-Negrete, Jose Luis, additional, Mehrotra, Tithi, additional, Mishra, Ambuj, additional, Montes, German Enamorado, additional, Najam, Tayyaba, additional, Nandy, Sampurna, additional, Pareek, Nidhi, additional, Pico, Mario Viña, additional, Prakash, Jai, additional, Rahman, Mohammed M., additional, Saxena, Gaurav, additional, Sen, Rajdip, additional, Shah, Syed Shoaib Ahmad, additional, Shavandi, Mahmoud, additional, Shen, Lingyu, additional, Singh, Anshu, additional, Singh, Rachana, additional, Singh, Surabhi, additional, Sinha, Surbhi, additional, Somee, Maryam Rezaei, additional, Turull, Marta, additional, Tyagi, Bhawna, additional, Unuofin, John Onolame, additional, Ventosa, Antonio, additional, Viñarta, Silvana Carolina, additional, Vivekanand, V., additional, Wang, Jing, additional, Yadav, Basant, additional, Yu, Huali, additional, Zainith, Surabhi, additional, Zamani, Nina, additional, Zhang, Yuanyuan, additional, Zhou, Jiti, additional, and Zolfaghar, Mahdis, additional

Published
2021
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40. Antibiotic resistance in wastewater: Indian scenario

Author

Kapley, Atya, primary, Sheeraz, Mohammed Shahique, additional, Kukade, Sushrut, additional, Ansari, Aamir, additional, Qureshi, Asifa, additional, Bajaj, Abhay, additional, Khan, Noor Afshan, additional, Tandon, Shalini, additional, Jain, Rachana, additional, Dudhwadkar, Swapnil, additional, Sharma, Shubhi, additional, and Siva, Archana Bharadwaj, additional

Published
2023
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45. List of contributors

Author

Adassooriya, Nadeesh M., primary, Ajayi, Ayodeji Samuel, additional, Akinnola, Olayemi Oluseun, additional, Benson, N.U., additional, Borah, Preetismita, additional, Bux, Faizal, additional, Devi, Pooja, additional, Dhodpakar, Rita, additional, Dubey, Shikha, additional, Dutta, Snigdha, additional, Effiok, W.W., additional, Enueme, Isioma Nneamaka, additional, Egwari, L.O., additional, Gusain, Deepak, additional, Hariganesh, S., additional, Hong, Yu, additional, Islam, Nazim Forid, additional, Kapley, Atya, additional, Kar, Sonika, additional, Kaur, Tarandeep, additional, Kumar, Manish, additional, Kwarciak-Kozłowska, Anna, additional, Liu, Xiaoya, additional, Maruthamani, D., additional, Mishra, Brijesh K., additional, Ogunleye, Bimpe Omowunmi, additional, Poleneni, Sandhya Rao, additional, Prasad, Majeti Narasimha Vara, additional, Priya, Tanwi, additional, Radhapyari, Keisham, additional, Rangabhashiyam, S., additional, Rienzie, Ryan, additional, Sarma, Hemen, additional, Sendanayake, L.R., additional, Senthilkumaran, Balasubramanian, additional, Sharma, Yogesh Chandra, additional, Srivastav, Arun Lal, additional, Thokchom, Binota, additional, Ugboko, H.U., additional, Vadivel, S., additional, and Yadav, Shailendra, additional

Published
2020
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