@article {46005,
	title = {Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges},
	journal = {Science of the Total Environment},
	volume = {674},
	year = {2019},
	month = {JUL},
	pages = {288-299},
	type = {Article},
	abstract = {<p>River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firnacutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeoto in G15Y and G15DS, indicating Yamuna River{\textquoteright}s influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem. (C) 2019 Elsevier B.A. All rights reserved.</p>},
	keywords = {Confluence zone, Ganges, Metagenomics, Transient influence, Yamuna},
	issn = {0048-9697},
	doi = {10.1016/j.scitotenv.2019.04.166},
	author = {Samson, Rachel and Shah, Manan and Yadav, Rakeshkumar and Sarode, Priyanka and Rajput, Vinay and Dastager, Syed G. and Dharne, Mahesh S. and Khairnar, Krishna}
}
@article {47763,
	title = {High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India},
	journal = {Science of the Total Environment},
	volume = {807},
	year = {2022},
	month = {FEB },
	pages = {151038},
	type = {Article},
	abstract = {Given a large number of SARS-CoV-2 infected individuals, clinical detection has proved challenging. The wastewater-based epidemiological paradigm would cover the clinically escaped asymptomatic individuals owing to the faecal shedding of the virus. We hypothesised using wastewater as a valuable resource for analysing SARS-CoV-2 mutations circulating in the wastewater of Pune region (Maharashtra; India), one of the most affected during the covid-19 pandemic. We conducted study in open wastewater drains from December 2020- March 2021 to assess the presence of SARS-CoV-2 nucleic acid and further detect mutations using ARTIC protocol of MinION sequencing. The analysis revealed 108 mutations across six samples categorised into 39 types of mutations. We report the occurrence of mutations associated with Delta variant lineage in March-2021 samples, simultaneously also reported as a Variant of Concern (VoC) responsible for the rapid increase in infections. The study also revealed four mutations; S:N801, S:C480R, NSP14:C279F and NSP3:L550del not currently reported from wastewater or clinical data in India but reported worldwide. Further, a novel mutation NSP13:G206F mapping to NSP13 region was observed from wastewater. Notably, S:P1140del mutation was detected in December 2020 samples while it was reported in February 2021 from clinical data, indicating the instrumentality of wastewater data in early detection. This is the first study in India to demonstrate utility of sequencing in wastewater based epidemiology to identify mutations associated with SARS-CoV-2 virus fragments from wastewater as an early warning indicator system. (c) 2021 Elsevier B.V. All rights reserved.},
	keywords = {ARTIC protocol, Epidemiology, Metagenomics, Nanopore sequencing, SARS-CoV-2, wastewater},
	issn = {0048-9697},
	doi = {10.1016/j.scitotenv.2021.151038},
	author = {Dharmadhikari, Tanmay and Rajput, Vinay and Yadav, Rakeshkumar and Boargaonkar, Radhika and Patil, Dhawal and Kale, Saurabh and Kamble, Sanjay P. and Dastager, Syed G. and Dharne, Mahesh S.}
}
@article {49131,
	title = {Investigation of cold-active and mesophilic cellulases: opportunities awaited},
	journal = {Biomass Conversion and Biorefinery},
	volume = {13},
	year = {2023},
	month = {JUL},
	pages = {8829-8852},
	type = {Review},
	abstract = {<p>
	In the recent decade, the global demand and fuel prices have urged a need to track down an alternate resource. Second-generation (2G) biofuel from the lignocellulosic biomass (LCB) is trending as the fundamental alternative resource. Although LCB is the most abundantly available renewable resource, its commercialization into 2G biofuel technology is a major challenge. Efficient LCB hydrolysis requires a proper lignocellulolytic enzyme cocktail. In view to addressing this problem, several researchers are investigating for efficient enzymes to hydrolyze LCB. To date, there are very few commercial enzymes that aid in the breakdown of LCB, and these enzymes are traditionally isolated from culturable microbes. As only 1\% of the microbes can be cultivated in the laboratory, the potentials of the uncultured remain under-explored. In the recent decade, advances in metagenomics using next-generation sequencing (NGS) technologies have revealed the vast diversity of hydrolytic enzymes and multiple domain proteins in the ecosystem. Aiming this, we focus our review on investigating efficient cold-active and mesophilic cellulases from the metagenome. India is an agro-based country with various climatic regions, ranging from warm and humid in the south to mild or moderate and cold or snowy in the Himalayan north; therefore, both cold-active and mesophilic cellulases are needed for LCB to ethanol. Along with downsizing, the conversion cost of LCB to fermentable sugars not only increases the enzymatic conversion but also increases the fermentation efficiency, which ultimately helps to commercialize the second-generation biofuel technology. Metagenomics is an evolving concept, and it has opened new horizons for the discovery of micro-organisms and new enzymes.</p>
},
	keywords = {cellulases, Glycosyl hydrolase, Lignocellulosic biomass, Metagenomics, simultaneous saccharification and fermentation},
	issn = {2190-6815},
	doi = {10.1007/s13399-021-02047-y},
	author = {Chavan, Sambhaji and Shete, Ashvini and Mirza, Yasmin and Dharne, Mahesh S.}
}
