DNA Metabarcoding from Microbial Communities Recovered from Stream and Its Potential for Bioremediation Processes

Ottoni, Júlia Ronzella; Grignet, Rosane dos Santos; Barros, Maria Gabriela Azevedo; Bernal, Suzan Prado Fernandes; Panatta, Andressa Alves Silva; Lacerda-Júnior, Gileno Vieira; Centurion, Victor Borin; Delforno, Tiago Palladino; Gonçalves, Caroline da Costa Silva; Passarini, Michel Rodrigo Zambrano

doi:10.1007/s00284-021-02752-x

Cited by 5 publications

(6 citation statements)

References 40 publications

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“…Moreover, Proteobacteria can transform and reduce heavy metals through the detoxification, precipitation, and adsorption mechanisms (Liang et al, 2022). Proteobacteria are considered the most metabolically versatile bacteria (Ottoni et al, 2022), and Proteobacteria are able to proceed different types of metabolic pathways, indicating that Proteobacteria can be distributed and reproduce in different ecosystems (Li et al, 2021; Ottoni et al, 2022). Thus, Proteobacteria are highly abundant at different sampling sites in this study.…”

Section: Resultsmentioning

confidence: 99%

“…They are also involved in different metabolic reactions (Chen et al, 2019). Researchers indicate that Proteobacteria were the ample phylum in sediments from several Taiwan rivers (Hung et al, 2021(Hung et al, , 2022Nagarajan et al, 2022;Ottoni et al, 2022). They could reproduce in heavy-metal-polluted environments and become governing bacteria (Hung et al, 2022;Nagarajan et al, 2022).…”

Section: Sediment Bacterial Diversity Analysismentioning

confidence: 99%

“…Results from other studies suggest that the heavy metals can cause significant pressures on microorganisms, render the change of microbial diversity, resist gene delivery in sediment environments, and inhibit the sensitive species (Gupta et al, 2022; Li et al, 2021; Nyoyoko, 2022). Illumina sequencing has been used to V3–V4 hypervariable regions of the 16S rRNA gene for the investigation of bacterial species in sediment samples (Gupta et al, 2022; Luo et al, 2020; Ottoni et al, 2022). In this study, the effects of heavy metals on bacterial diversity and dominant bacterial species in sediments were evaluated using metagenomics.…”

Section: Introductionmentioning

confidence: 99%

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Toxicity evaluation of a heavy‐metal‐polluted river: Pollution identification and bacterial community assessment

Verpoort

et al. 2023

Water Environment Research

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The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavymetal-contaminated sediments in the Salt River were investigated. The geo-accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2-32.0) is higher than in the downstream (14.0-19.7) and upstream (9.2-17.1). It could be because of the continuous inputs of heavymetal-contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non-point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities.Metal-tolerant bacterial phyla (Proteobacteria: 24.4%-46.4%, Bacteroidetes:1.3%-14.8%, and Actinobacteria: 2.3%-11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%-37.6% and Chloroflexi: 5.8%-7.2%) with relatively high abundance were detected. Metal-tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy-metal-polluted ecosystem caused the variations in bacterial communities.

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Section: Resultsmentioning

confidence: 99%

Section: Sediment Bacterial Diversity Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Toxicity evaluation of a heavy‐metal‐polluted river: Pollution identification and bacterial community assessment

Verpoort

et al. 2023

Water Environment Research

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“…Sequence reads were analysed using QIIME 2 (https://qiime2.org) [7]. Taxonomy was assigned to amplicon sequence variants (ASVs) against the SILVA132 99% OTUs reference sequences (SILVA) [8][9][10]. The functional potential was predicted using FAPROTAX.…”

Section: Microbial Diversity and Metabolic Capabilitiesmentioning

confidence: 99%

Management and Stimulation of High Metabolic Rates of Biomes to Effectively Remediate Mine Drainage

Potgieter

Cason

DeFlaun

et al. 2022

J. Hum. Earth Future

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Drainages from mining operations frequently contain elevated levels of contaminants of concern (CoC). Indigenous adapted bacterial communities are characterized and the ability to reduce many CoC is showcased in different treatment implementations. Each contaminated site consists of a distinct prokaryotic community that in turn requires a specific C:N:P balanced environment to contribute to site remediation. This balanced bioremedial strategy is managed both for in situor fix-filmed bioreactors, using electron donor selection and ratios, redox potential, and hydraulic retention times. These communities can effectively treat elevated levels of hexavalent chromium (10 mg/L), nitrate (110 mg/L), and sulfate (1 250 mg/L) in a one-pot balanced system. Doi: 10.28991/HEF-2022-03-02-06 Full Text: PDF

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“…In addition, plant and animal parasites can negatively impact agricultural production and human health. Precisely because of their diversity and roles in ecosystems, nematodes are well recognized as biological indicators of environmental change in terrestrial, marine, and freshwater ecosystems, including pollution, environmental disturbances, and climate warming ( Hodda et al, 2009 ; Neher, 2010 ; Porazinska et al, 2021 ; Ottoni et al, 2022 ).…”

mentioning

confidence: 99%

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Gattoni

Gendron

Sandoval-Ruiz

et al. 2023

Journal of Nematology

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Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.

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DNA Metabarcoding from Microbial Communities Recovered from Stream and Its Potential for Bioremediation Processes

Cited by 5 publications

References 40 publications

Toxicity evaluation of a heavy‐metal‐polluted river: Pollution identification and bacterial community assessment

Toxicity evaluation of a heavy‐metal‐polluted river: Pollution identification and bacterial community assessment

Management and Stimulation of High Metabolic Rates of Biomes to Effectively Remediate Mine Drainage

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

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