Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia

Alotaibi, Modhi O.; Mohammed, Afrah E.; Eltom, Kamal H.

doi:10.1016/j.sjbs.2022.03.001

Cited by 7 publications

(3 citation statements)

References 41 publications

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“…Pseudomonadota, commonly known as coliforms, is well-adapted to high-nutrient environments where it may proliferate quickly (Krishna et al, 2020;Senevirathna et al 2022). Similar research has been performed by (Alotaibi et al 2022). (Nunez Salazar et al, 2020) that Proteobacteria was found to be the most abundant phylum in all of their research , with the maximum abundance in the area where human intervention was discovered, according to a recent metagenomic study.…”

Section: Resultssupporting

confidence: 72%

Seasonal Fluctuation of Water Quality and Ecogenomic Phylogeny of Novel Potentional Microbial Pollution Indicators of Veshaw River-Western Himalaya

Rather

Ara

Padder

et al. 2022

Preprint

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Almost a billion people, especially in developing countries, need safe water. Several studies in India show that most drinking water sources have high coliform counts. Standard quality control is needed. This study was conducted in rural parts of South Kashmir in the Western Himalaya from February to January, 2020–2022. Water samples were taken from the river from upstream to downstream using standard water sampling techniques. The purpose of this study was to investigate the detection and molecular identification of coliforms in drinking water and the chemical water quality associated with coliform-contaminated drinking water, which summarises river water pollution. The results showed significant variation in water quality measures, indicating increased pollution levels downstream. In all seasons, the highest coliform count was recorded at Sangam (downstream) of the river. In the summer season at Sangam it was recorded (72.2600 cfu 106/l) and no coliform count was found at Kongwaton (upper stream) during the winter season near the source of the Veshaw river. In all seasons, the highest values of water quality parameters (pH 6.847, EC 71.620 dS/m, BOD 1.120 mg/l, and COD 24.637 mg/l) were recorded at Sangam (downstream) of the river during the summer season. In the winter season at Kongwaton, the lowest values of water quality parameters were pH 8.947, EC 253.680 dS/m, BOD 4.963 mg/l, and COD 51.440 mg/l. The existence of coliforms in water indicates current faecal contamination and determines the presence of disease-causing pathogens. The goal of this work is to examine the level of total coliform contamination, coliform species identification, and chemical water quality properties of drinking water and its associated factors, which implies the pollution level in the river. Total DNA was collected and sequenced for 16S rDNA and metagenomics. Universal primers were used to amplify the bacterial 16S rRNA. Using BLAST, the amplified 16S rRNA gene sequence was matched to the NCBI database. A metagenomic study found 27 species that had different relative abundances. These species include E. coli, Escherichia fergusonii, Escherichia albertii, Klebsiella grimontii, and Shigella dysenteriae. This study is thought to be the first to discriminate against E. fergusonii, Escherichia albertii, Klebsiella grimontii, and Shigella dysenteriae from E. coli and to report on E. fergusonii and E. albertii, Klebsiella grimontii, and Shigella dysenteriae in the river Veshaw water sources in Kulgam, Western Himalaya.

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Section: Resultssupporting

confidence: 72%

Seasonal Fluctuation of Water Quality and Ecogenomic Phylogeny of Novel Potentional Microbial Pollution Indicators of Veshaw River-Western Himalaya

Rather

Ara

Padder

et al. 2022

Preprint

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“…In most of the metagenomic studies from lake water systems in India revealed the dominance of Proteobacteria, Bacteroidetes, Chloroflexi Firmicutes, Actinobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes (Ahmad et al 2021 ; Ghosh et al 2021 ; Rathur et al 2017; Raina et al 2019 ; Chakraborty et al 2020a ; b; 2021 ). Similar results were reported from different countries lake ecosystems such as Wadi Namar Lake from Riyadh, Saudi Arabia (Alotaibi et al 2022 ), Keenjhar, Rawal and Saif-ul-Muluk lakes in Pakistan (Saleem et al 2019 ), and Lake Meyghan, Iran (Naghoni et al 2017 ).…”

Section: Lake Ecosystemsupporting

confidence: 79%

Bacterial diversity in the aquatic system in India based on metagenome analysis—a critical review

Jasna

Nathan

Parvathi

et al. 2023

Environ Sci Pollut Res

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Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.

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“…Our study found that unclassi ed bacteria, i.e.,Proteobacteria, Bacteroidota, and Actinobacteriota, were the dominant species in all three lakes studied: Aidyn, Brusyanoe, and Rybny Sakryl lakes. These bacterial species are common in majority of the lakes [25,26,27,28,29,30,31,32].…”

Section: Discussionmentioning

confidence: 99%

Assessment of the Microbiome Diversity in Lakes of the West Kazakhstan Region

Khabibullovich

Galikhanovich

2023

Preprint

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Background Metagenomic analysis was used in this investigation to present the results of the microbiome studies on Aidyn, Brusyanoe, and Rybny Sakryl lakes in the West Kazakhstan region. The technological basis of the research was high-performance Illumina next-generation sequencingResults The sequencing of 36 amplicon libraries yielded at least 20,000 sequences per library, which were subjected to primary taxonomic analysis; 4000 taxons were identified to belong to approximately 400 genera. Results showed that unclassified bacteria, Proteobacteria, Bacteroidota, and Actinobacteriota were dominant. According to the Shannon metric, the samples from Brusyanoe lake had the richest and the most even communities. Subsequently, samples from the Aidyn and Rybny Sakryl lakes, which also had the most even communities according to the Simpson metric. The study also revealed that the taxonomic structure of microbiomes from different lakes had several common features. All samples were characterized by the presence of the following groups of bacteria: Verrucomicrobiae, Gammaproteobacteria and Alphaproteobacteria, Cyanobacteria, Bacteroidia, Actinobacteria, and Acidimicrobiia. Furthermore, comparative analysis of the taxonomic structure of communities showed differences in their structure at the class level as well. Beta-diversity indicated that the taxonomic composition of the communities varied and depended on the sampling location. Weighted Uni Fracmetric, which reflects the similarity in the qualitative composition of the communities, suggested an even taxonomic composition only for the Rybny Sakryllake microbiome. Microbiome samples from Aidyn and Brusyanoe lakes were characterized by the presence of Candidatusaquilinia (2.6–7.5%) and a relatively high content of Algoriphagus (2–8%). Common features between the Aidyn and Rybny Sakryl lake samples included a relatively abundant Methylophilaceae (1.3–3.8%).Conclusion The conducted studies revealed differences in microbiome composition in Aydi, Brusyanoe and Rybny Sakryl lakes.Data analyses revealed that the results of the metagenomic study of the microbiome of inland water bodies can be used as markers to elucidate the ecological state of the lakes examined in the present study. Furthermore, microbial communities adapted to water with significantly high salt contents are predominantly found in the Aidyn lake. However, microbial communities existing in freshwaters with low salt content are typically foundin the Rybny Sakryl and Brusyanoe lakes.

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Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia

Cited by 7 publications

References 41 publications

Seasonal Fluctuation of Water Quality and Ecogenomic Phylogeny of Novel Potentional Microbial Pollution Indicators of Veshaw River-Western Himalaya

Seasonal Fluctuation of Water Quality and Ecogenomic Phylogeny of Novel Potentional Microbial Pollution Indicators of Veshaw River-Western Himalaya

Bacterial diversity in the aquatic system in India based on metagenome analysis—a critical review

Assessment of the Microbiome Diversity in Lakes of the West Kazakhstan Region

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