Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: March 4, 2025

As the first line of defense against external pathogens, skin and its resident microbiota are responsible for protection eubiosis. Innovations in DNA sequencing have significantly increased our knowledge microbiome. However, current characterizations do not discriminate between from live cells remnant dead organisms (relic DNA), resulting a combined readout all microorganisms that were currently present on rather than actual living population Additionally, most methods lack capability absolute quantification microbial load skin, complicating extrapolation clinically relevant information. Here, we integrated relic-DNA depletion with shotgun metagenomics bacterial determination to quantify cell abundances across different sites. Though discovered up 90% be relic DNA, saw no significant effect this relative taxa determined by sequencing. Relic-DNA prior strengthened underlying patterns microbiomes volunteers reduced intraindividual similarity. We abundance fraction alive several common body sites found taxa-specific differential bacteria regions estimates generated total (live + dead) Our results reveal bias has low biomass samples like skin. The similarity following highlights introduced traditional (total DNA) diversity comparisons samples. divergent levels viability measured sites, along inconsistencies vs sequencing, suggest an important hypothesis certain being susceptible pathogen infection. Overall, study demonstrates characterization microbiome overcomes provide baseline will further improve mechanistic studies infection, disease progression, design therapies Video Abstract.

Language: Английский

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Effects of nitrogen-driven eutrophication on the horizontal transfer of extracellular antibiotic resistance genes in water-sediment environments

Environmental Research, Journal Year: 2025, Volume and Issue: 274, P. 121317 - 121317

Published: March 6, 2025

Language: Английский

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

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

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Assessing the Relative Concentration Efficiency and Spatial–Temporal Distribution of Plasmid pBI143 in Raw Wastewater

Environmental Science & Technology Letters, Journal Year: 2024, Volume and Issue: 11(8), P. 812 - 817

Published: July 2, 2024

Language: Английский

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Using cyanobacteria and other phytoplankton to assess trophic conditions: A qPCR-based, multi-year study in twelve large rivers across the United States

Water Research, Journal Year: 2023, Volume and Issue: 235, P. 119679 - 119679

Published: Jan. 30, 2023

Language: Английский

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Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(17), P. 4940 - 4952

Published: July 15, 2023

Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet effects of relic DNA on community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial microeukaryotic compositions were characterized using propidium monoazide (PMA) treatment coupled with high-throughput sequencing a river-reservoir ecosystem. Beta diversity analysis showed significant difference composition between both PMA untreated treated bacteria microeukaryotes; however, differentiating effect was much stronger for microeukaryotes. Relic only resulted underestimation relative abundances Bacteroidota Nitrospirota, while other taxa exhibited no changes. As some phytoplankton (e.g. Chlorophyta, Dinoflagellata Ochrophyta) fungi greater after removal, whereas Cercozoa Ciliophora opposite trend. Moreover, removal weakened size complexity cross-trophic networks significantly changed relationships environmental factors composition. However, there rates temporal turnover samples either or Overall, our results imply that presence waters can give misleading information composition, co-occurrence their conditions. More abundance, decay rate functioning nonviable freshwater ecosystems are highly recommended future.

Language: Английский

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Environmental DNA enhances comprehension of the spatial and temporal dynamics of fish diversity in a coastal lagoon

Estuarine Coastal and Shelf Science, Journal Year: 2024, Volume and Issue: 304, P. 108824 - 108824

Published: June 3, 2024

Transitional environments have great ecological value and high productivity, many species can benefit from their sheltered conditions food resources. In this study, we performed for the first time a fish-targeted eDNA metabarcoding of 12S rRNA gene at 16 sites broadly covering different water bodies Marano Grado Lagoon (northern Adriatic Sea) in two seasons. The was collected same as beach seine net, allowing direct comparison approaches. With detected 34 species, all functional guilds occurring lagoon. Species regional interest, that uses area nursery feeding ground, diadromous highlighting connectivity between freshwater marine habitats, were found. While some constantly present (e.g. Atherina boyeri, Sparus aurata), others (Squalius cephalus, Platichthys flesus) influenced by salinity (higher lower Marano), which confirmed main driver environment. with traditional methods, identified 18 (11 both approaches), showed is very sensitive detecting most biodiversity lagoon limited sampling effort. Few relevant (Chelon saliens, Knipowitschia panizzae) lacked reference sequences, need to be implemented databases. Our study represents significant advance understanding fish dynamics contributes improvement management strategies these ecologically habitats.

Language: Английский

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Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity

Science Advances, Journal Year: 2023, Volume and Issue: 9(51)

Published: Dec. 22, 2023

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging 0.982 0.409 (seawater brine). Average decreased exponentially aw, nuanced trends evident at the single-cell level: The proportion of active remained high (>50%) even after NaCl saturation, and subsets spiked as aw decreased. Intracommunity heterogeneity increased seawater transitioned brine, suggesting phenotypic physiological stress. No was detected 0.409-aw brine (an MgCl2-dominated site) despite presence cell-like structures. Extrapolating our data, predict an limit for detectable 0.540, which is beyond currently accepted life based on cell division. This work demonstrates utility single-cell, metabolism-based techniques detecting expands potential habitable space Earth beyond.

Language: Английский

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The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 945, P. 173846 - 173846

Published: June 12, 2024

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting dynamic interaction with local climate depth. We employed an innovative DNA separation method to characterize microbial assemblages low-biomass environments such as deserts distinguish between intracellular (iDNA) extracellular (eDNA) soils. This approach, combined analyses of physicochemical properties co-occurrence networks, investigated across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, humid) along the Chilean Coastal Cordillera. The yielded distinctive unimodal pattern iDNA pool alpha diversity, increasing from arid semi-arid climates decreasing humid environments, highlighting rapid feedback community moisture. In region, harsh surface conditions restrict growth, leading peak abundance diversity occurring slightly deeper layers than other sites. Our findings confirmed association specialist bacteria ecosystem-functional traits. observed transitions Halomonas Delftia, resistant extreme Class AD3 genus Bradyrhizobium, associated plants organic matter environments. distance-based redundancy analysis (dbRDA) revealed that pH moisture were key parameters influenced variation. eDNA correlated better environment community, whereas was more sensitive changes parameters. depth found influence significantly but not which might be related depth-related metabolic activity. investigation into uncovered deterministic assembly distinct modules unique taxa, thereby showing connections environmental factors. study additionally effects on living dead communities, emphasizing need pools.

Language: Английский

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Investigation of the water environmental DNA/RNA profile for non‐invasive biomonitoring of the fish pathogen Aeromonas salmonicida subsp. salmonicida and detection of immune responses in rainbow trout (Oncorhynchus mykiss)

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(4)

Published: July 1, 2024

Abstract Aquaculture industries face challenges in fish production, primarily due to disease occurrence. Clinical manifestations of these diseases often indicate a considerable advancement the pathological process. Infected experience morbidity, leading compromised welfare and substantial economic losses for production facilities. Therefore, prophylaxis early detection pathogens could allow facility managers intervene or treat before clinical signs occur. For first time, environmental DNA/RNA (collectively eNA) was used detect salmonid pathogen Aeromonas salmonicida subsp. water hosting rainbow trout ( Oncorhynchus mykiss ). This took place under controlled experimental conditions, occurrence outcome mortality. The concentration bacteria determined by using standard curve. To determine window possible intervention, bacterial measured from an stage throughout when became moribund. Furthermore, acute phase protein, serum amyloid A produced trout, detected found be up‐regulated 4 days post challenge. It thereby shown that it is strong immune responses non‐invasive manner. eNA can as tool infection becomes severe. will facilitate interventions limit increase fish, which becoming requirement more sustainable ethical animal production.

Language: Английский

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