Relic DNA confounds the results of DNA-based study on microeukaryotic succession in aquatic biofilms DOI Creative Commons
Mamun Abdullah Al, Huihuang Chen, Yan Xue

et al.

Ecological Indicators, Journal Year: 2023, Volume and Issue: 158, P. 111350 - 111350

Published: Dec. 6, 2023

High-throughput sequencing has revolutionized the DNA sequence-based study of microbial community and diversity on an unprecedented scale. Relic is widespread in natural aquatic environment; however, extent to which such can bias analysis living microeukaryotic communities unclear. Here, we conducted a 30-day field-control experiment investigating biofilm succession glass slides polyurethane foam units (PFUs) subtropical urban reservoir, using DNA-based approach. The propidium monoazide (PMA) dye was used distinguish relic sequences. Our results showed that biofilms time substratum dependent, correlated with changing environmental conditions, nutrients microalgae. Most importantly, significant influence estimation beta turnover composition, importantly its presence masked successional patterns different taxa. We found strong deterministic processes dominating PFUs biofilms. Depending substrate absence sequences, contrasting assembly mechanisms were observed. In DNA, our 0.53–3.15 % dispersal limitation, 13.16 homogeneous selection overestimated, while 1.06–3.68 homogenizing dispersal, 2.11–10.53 undominated 2.10–10.52 heterogeneous underestimated. This provides insights into value removing when designing studies characterize raise questions about some ecological interpretations molecular ecology have not accounted for effects DNA.

Language: Английский

The performance of different methods in characterizing soil live prokaryotic diversity and abundance is highly variable DOI Creative Commons

Yu-juan Du,

Zelin Wang,

Kaifang Liu

et al.

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Abstract The long‐term persistence of extracellular DNA in soils is well‐documented, yet its impacts on analyzing soil microbial abundance and diversity remain controversial. This primarily arises from our limited comprehension regarding the reliability various methods for studying live microbiotas. In this study, we systematically compared assessed commonly used diversity, including alkaline buffer washing, propidium monoazide (PMA) treatment, DNase pre‐digestion, rRNA‐based analysis, using collected a wide range locations across China. We found that elimination substantially influenced analysis prokaryotic abundance, community profiles, co‐occurrence patterns, but not assembly mechanisms. However, effects varied considerably different methods. pre‐digestion PMA treatment led to significant decreases while washing had negligible effects. As richness, significantly decreased increased it, respectively. Although 67.8% amplicon sequence variants were shared, differences their relative observed While removal simplified network, it also enhanced robustness. According assessment experiments, showed highest efficiency characterizing accuracy. Concerns other include low efficiency, instability, uncertainties result explanation. study suggests characterized by exhibit high variability, recommended communities. These findings provide crucial information optimizing microbiome research methodologies.

Language: Английский

Citations

0
Disinfection of sink drains to reduce a source of three opportunistic pathogens, during Serratia marcescens clusters in a neonatal intensive care unit DOI Creative Commons
Thibault Bourdin,

Marie-Ève Benoit,

Michèle Prévost

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(6), P. e0304378 - e0304378

Published: June 12, 2024

Evaluate the effects of five disinfection methods on bacterial concentrations in hospital sink drains, focusing three opportunistic pathogens (OPs): Serratia marcescens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

Language: Английский

Citations

3
Deciphering the impact of decabromodiphenyl ether (BDE-209) on benthic foraminiferal communities: Insights from Cell-Tracker Green staining and eDNA metabarcoding DOI Creative Commons
Mattia Greco, Eqbal Al-Enezi, Abduljamiu O. Amao

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 466, P. 133652 - 133652

Published: Jan. 29, 2024

Language: Английский

Citations

2
Selective Elucidation of Living Microbial Communities in Fermented Grains of Chinese Baijiu: Development of a Technique Integrating Propidium Monoazide Probe Pretreatment and Amplicon Sequencing DOI Creative Commons
Tao Bo, Jiaojiao Zhang,

Enxiang Zong

et al.

Foods, Journal Year: 2024, Volume and Issue: 13(11), P. 1782 - 1782

Published: June 6, 2024

The fermentation process of Chinese Baijiu’s fermented grains involves the intricate succession and metabolism microbial communities, collectively shaping quality. Understanding composition these living communities within is crucial for comprehending flavor formation mechanisms. However, conducting high-throughput analysis complex system poses significant challenges. Thus, this study addressed challenge by devising a framework using light-flavor Baijiu as model. This combined propidium monoazide (PMA) pretreatment technology with amplicon sequencing techniques. Optimal PMA treatment parameters, including concentration 50 μM incubation in darkness 5 min followed an exposure period min, were identified. Utilizing protocol, viable microorganism biomass ranging from 8.71 × 106 to 1.47 108 copies/μL was successfully detected grain samples. Subsequent revealed distinct community structures between untreated PMA-treated groups, notable differences relative abundance compositions, particularly dominant species such Lactobacillus, Bacillus, Pediococcus, Saccharomycopsis, Issatchenkia Pichia, identified LEfSe analysis. results confirmed efficacy PMA-amplicon analyzing furnished methodological investigating diverse traditional foods. technical holds considerable significance advancing our understanding mechanisms intrinsic

Language: Английский

Citations

1
Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities DOI Creative Commons

Marie C. Thomas,

Gretel Waugh,

Katarina Damjanovic

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 3, 2024

Abstract Background Ecological risk assessments rarely consider the impacts of environmental stress on microbial communities. The incorporation community responses into these evaluations requires establishing sensitivity thresholds based absolute abundance viable taxa. While essential for describing dynamics, sequencing-based analyses are generally limited to assessing relative proportions and fail reveal magnitude or directionality shifts. To address this, we developed validated a workflow combining propidium monoazide (PMA) treatment, 16S rRNA gene amplicon sequencing, quantitative microbiome profiling (QMP) determine taxa in seawater microbiomes. Results Using natural seawater, load estimates from droplet digital PCR (ddPCR) flow cytometry (FC) correlated strongly total intact cell counts, confirming suitability both methods normalising sequencing data. Additionally, demonstrated that PMA at concentrations 2.5–15 µM effectively inhibited amplification DNA membrane-compromised cells, reducing RNA copies by 24–44% untreated samples. Samples with known cells were generated mixing heat-killed enabling data loads estimated via ddPCR FC. This approach facilitated detailed comparisons effects QMP versus (RMP) alpha beta diversity metrics sequence variant (ASV) profiles. Unlike RMP, captured significant shifts composition across samples decreasing cells. Furthermore, RMP failed detect changes ASV-level, while revealed consistent declines. Conclusion PMA-16S workflow, coupled QMP, enhanced accuracy representing dynamics addressing key limitations such as inclusion damaged extracellular misleading identified is particularly suited quantifying direction following exposure, making it directly applicable stress-response modelling supporting integration future regulatory guidelines.

Language: Английский

Citations

1
Relic DNA obscures bacterial diversity and interactions in ballast tank sediment DOI

Zhaozhao Xue,

Haoze He,

Yangchun Han

et al.

Environmental Research, Journal Year: 2024, Volume and Issue: unknown, P. 120715 - 120715

Published: Dec. 1, 2024

Language: Английский

Citations

0
Diatom community assembly and network complexity during different hydrological periods in the Tibetan Plateau floodplain DOI
Xinyuan Liu, Baozhu Pan, Naicheng Wu

et al.

Journal of Cleaner Production, Journal Year: 2024, Volume and Issue: unknown, P. 144022 - 144022

Published: Oct. 1, 2024

Language: Английский

Citations

0
Relic DNA confounds the results of DNA-based study on microeukaryotic succession in aquatic biofilms DOI Creative Commons
Mamun Abdullah Al, Huihuang Chen, Yan Xue

et al.

Ecological Indicators, Journal Year: 2023, Volume and Issue: 158, P. 111350 - 111350

Published: Dec. 6, 2023

High-throughput sequencing has revolutionized the DNA sequence-based study of microbial community and diversity on an unprecedented scale. Relic is widespread in natural aquatic environment; however, extent to which such can bias analysis living microeukaryotic communities unclear. Here, we conducted a 30-day field-control experiment investigating biofilm succession glass slides polyurethane foam units (PFUs) subtropical urban reservoir, using DNA-based approach. The propidium monoazide (PMA) dye was used distinguish relic sequences. Our results showed that biofilms time substratum dependent, correlated with changing environmental conditions, nutrients microalgae. Most importantly, significant influence estimation beta turnover composition, importantly its presence masked successional patterns different taxa. We found strong deterministic processes dominating PFUs biofilms. Depending substrate absence sequences, contrasting assembly mechanisms were observed. In DNA, our 0.53–3.15 % dispersal limitation, 13.16 homogeneous selection overestimated, while 1.06–3.68 homogenizing dispersal, 2.11–10.53 undominated 2.10–10.52 heterogeneous underestimated. This provides insights into value removing when designing studies characterize raise questions about some ecological interpretations molecular ecology have not accounted for effects DNA.

Language: Английский

Citations

0