Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake

Ahmad, Tawseef; Gupta, Gaganjot; Sharma, Anshul; Kaur, Baljinder; El-Sheikh, Mohamed A.; Alyemeni, Mohammed Nasser

doi:10.1371/journal.pone.0248116

Cited by 32 publications

(14 citation statements)

References 74 publications

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“…The LEfSe analysis highlighted the abundance of Pedosphaerales (order) and SH3_11 (genus) in the NHC samples. Pedosphaerales has been isolated from freshwater bodies, such as lakes, in previous studies [ 65 , 66 ]. Moreover, Pedosphaerales has been observed to be the predominant rhizosphere microbiota of many crops [ 67 , 68 ], which indicates the existence of aquatic plant communities in the watershed.…”

Section: Discussionmentioning

confidence: 99%

The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan

et al. 2022

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The Tatun Volcanic Group (TVG), located in northern Taiwan, is characterized by acidic hot springs where the outflow of the hot springs may affect the properties of the associated lotic water bodies. We investigated the bacterial diversity and functional profiles of the Peihuang (PHC), HuangGang (HGC), and Nanhuang Creeks (NHC) located in the TVG basin using 16S rRNA gene sequencing coupled with statistical analyses. Water samples were collected from various streams of the creeks for two months of the year. The NHC showed the highest diversity, richness, and a unique number of phyla, which was followed by the HGC. A reduced number of phyla and a lower diversity was noticed in the PHC. The NHC was found to be abundant in the genera Armatimonas, Prosthecobacter, Pirellula, and Bdellovibrio, whereas the HGC was rich in Thiomonas, Acidiphilium, Prevotella, Acidocella, Acidithiobacillus, and Metallibacterium. The PHC was abundant in Thiomonsa, Legionella, Acidocella, and Sulfuriferula. The samples did not show any strong seasonal variations with the bacterial diversity and abundance; however, the relative abundance of each sampling site varied within the sampling months. The iron transport protein- and the sulfur metabolism-related pathways were predicted to be the key functions in all the creeks, whereas the heavy metal-related functions, such as the cobalt/nickel transport protein and the cobalt–zinc–cadmium efflux system were found to be abundant in the HGC and PHC, respectively. The abundance of Bdellovibrio in the NHC, Diplorickettsia in the HGC, and Legionella in the PHC samples indicated a higher anthropogenic impact over the creek water quality. This study provides the data to understand the distinct bacterial community structure, as well as the functional potentials of the three major watersheds, and helps the knowledge of the impact of the physicochemical properties of the TVG hot springs upon the watersheds.

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Section: Discussionmentioning

confidence: 99%

The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan

et al. 2022

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“…Among the major pathways, amino acid metabolism, carbohydrate metabolism, membrane transport and energy metabolism were signi cant enriched in the polluted microbiomes of river Yamuna regardless of their pollution level. The abundance of Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria predicted using SEED could be correlated with their role in nutrient cycling, carbon metabolism, membrane transport system and stress response regulatory system (Ahmad et al, 2021;Koo et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Impact of Anthropogenic Activity on Community Structure and Function of Microbiomes in Polluted Stretches of River Yamuna at New Delhi, India: Insights From Shotgun Metagenomics

Parida

Behera

Dehury

et al. 2022

Preprint

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The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization has profoundly affected river microflora and their function thus its health. In this study, potential of whole genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like, Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing), and Syntrophobacter fumaroxidans (sulfate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages were also noticed along the downstream of river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e., Nakaseomyces, Aspergillus, Schizosaccharomyces, and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most abundant pollution degrading enzymes in polluted sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

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“…Krona Chart data included the Shannon diversity index of each pup, as well as their relative abundances of various microbial populations. Extrapolated data from QIIME's Krona Chart have previously been used in multidimensional analyses of the estimated relative abundances of microbes in a sample [34][35][36].…”

Section: Bacterial Isolation and Next-generation Sequencingmentioning

confidence: 99%

A Paternal Fish Oil Diet Preconception Modulates the Gut Microbiome and Attenuates Necrotizing Enterocolitis in Neonatal Mice

et al. 2022

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Epidemiology and animal studies suggest that a paternal history of toxicant exposure contributes to the developmental origins of health and disease. Using a mouse model, our laboratory previously reported that a paternal history of in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) increased his offspring’s risk of developing necrotizing enterocolitis (NEC). Additionally, our group and others have found that formula supplementation also increases the risk of NEC in both humans and mice. Our murine studies revealed that intervening with a paternal fish oil diet preconception eliminated the TCDD-associated outcomes that are risk factors for NEC (e.g., intrauterine growth restriction, delayed postnatal growth, and preterm birth). However, the efficacy of a paternal fish oil diet in eliminating the risk of disease development in his offspring was not investigated. Herein, reproductive-age male mice exposed to TCDD in utero were weaned to a standard or fish oil diet for one full cycle of spermatogenesis, then mated to age-matched unexposed females. Their offspring were randomized to a strict maternal milk diet or a supplemental formula diet from postnatal days 7–10. Offspring colon contents and intestines were collected to determine the onset of gut dysbiosis and NEC. We found that a paternal fish oil diet preconception reduced his offspring’s risk of toxicant-driven NEC, which was associated with a decrease in the relative abundance of the Firmicutes phylum, but an increase in the relative abundance of the Negativicutes class.

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Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake

Cited by 32 publications

References 74 publications

The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan

The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan

Impact of Anthropogenic Activity on Community Structure and Function of Microbiomes in Polluted Stretches of River Yamuna at New Delhi, India: Insights From Shotgun Metagenomics

A Paternal Fish Oil Diet Preconception Modulates the Gut Microbiome and Attenuates Necrotizing Enterocolitis in Neonatal Mice

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