Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

Bourhane, Zeina; Lanzén, Anders; Cagnon, Christine; Saïd, Olfa Ben; Mahmoudi, Ebrahim; Coulon, Frédéric; Atai, Emmanuel; Borja, Ángel; Cravo‐Laureau, Cristiana; Duran, Robert

doi:10.1016/j.jhazmat.2021.126789

Cited by 37 publications

(8 citation statements)

References 122 publications

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“…1 The primers include the linkers for barcoding provided by the GenoToul platform. The amplifications were performed in triplicates (Bourhane et al, 2022). Briefly, the amplifications were performed in a total volume of 25 µl, using 12.5 µl of AmpliTaq Gold 360 Master Mix, 0.5 µl of each forward and reverse primers (20 µM), and 5 µl of the DNA extract, as follows: 95 • C for 10 min, 30 cycles of 95 • C for 30 s, 60 • C for 30 s, 72 • C for 40 s, and a final extension step at 72 • C for 10 min.…”

Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

et al. 2023

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Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.

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Section: Dna Extraction Pcr Amplification and Sequencingmentioning

confidence: 99%

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

et al. 2023

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“…Rhodanobacter and Rhodocyclaceae are sensors for the presence of uranium, and Oceanospirillales is a good indicator for oil contamination [ 36 ]. Metagenome-based analysis of microbial diversity and ecology of soil, river, lake, seashore, mangrove, ocean water and sediments could indicate the metabolic architecture of the specific microbiome and could also be a marker for water quality, various pollutants, and chemical contaminations [ 37 , 38 , 39 , 40 , 41 , 42 ] ( Table 1 ). Metagenome of water sediment can also be used for public health risk assessment [ 43 ].…”

Section: Global Trends Of Metagenome Studiesmentioning

confidence: 99%

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

Alzahrani

2021

Microorganisms

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In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

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“…Laccase CueO from E. coli also exhibits an oxidative capacity for PAH compounds in vitro [ 12 , 13 ]. Several reports have shown that selective stress enrichment of microbial communities with higher concentrations of PAHs affects community structure and distribution, and most strains show tolerance to PAHs [ 9 , 14 , 15 ]. However, for such microorganisms, studies of their intrinsic regulatory metabolic mechanisms in resisting PAHs should be explored, but there are still few.…”

Section: Introductionmentioning

confidence: 99%

The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis

Zhu,

Gong,

Wang

et al. 2024

Microorganisms

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Pyrene is a pollutant in the environment and affects the health of living organisms. It is important to understand microbial-mediated pyrene resistance and the related molecular mechanisms due to its toxicity and biodegradability. Due to the unclear response mechanisms of bacteria to PAHs, this study detected the transcriptional changes in Escherichia coli under different pyrene concentrations using transcriptome sequencing technology. Global transcriptome analysis showed that the number of differentially expressed genes (DEGs) in multiple metabolic pathways increased with increasing concentrations of pyrene. In addition, the effects and toxicity of pyrene on Escherichia coli mainly included the up-regulation and inhibition of genes related to carbohydrate metabolism, membrane transport, sulfate reduction, various oxidoreductases, and multidrug efflux pumps. Moreover, we also constructed an association network between significantly differentially expressed sRNAs and key genes and determined the regulatory relationship and key genes of Escherichia coli under pyrene stress. Our study utilized pyrene as an exogenous stress substance to investigate the possible pathways of the bacterial stress response. In addition, this study provides a reference for other related research and serves as a foundation for future research.

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Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

Cited by 37 publications

References 122 publications

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

The Effects and Toxicity of Different Pyrene Concentrations on Escherichia coli Using Transcriptomic Analysis

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