Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints

Environmental Toxicology and Chemistry, Journal Year: 2024, Volume and Issue: 43(5), P. 1012 - 1029

Published: Feb. 28, 2024

Abstract The use of novel high-throughput sequencing (HTS) technologies to examine the responses natural multidomain microbial communities scrubber effluent discharges marine environment is still limited. Thus, we applied metabarcoding targeting planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, protozooplankton) in mesocosm experiments with from a polluted an unpolluted site. Furthermore, metagenomic analysis revealed changes taxonomic functional dominance after additions. results indicated clear shift such additions, which favored bacterial taxa known oil polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness eukaryotes employing variable trophic strategies, suggesting that environmentally relevant can influence community structure. Clusters Orthologous Genes associated pathways PAHs monocyclic hydrocarbon degradation increased numbers at treatments additions acutely. genes are express enzymes acting various substrates including PAHs. indications, combination abrupt decrease most abundant below limit detection—much faster than their half-lives—could point toward bacterioplankton-initiated rapid ultimate toxic contaminants effluent. implementation HTS could be valuable tool develop multilevel biodiversity indicators impacts on environment, lead improved impact assessment. Environ Toxicol Chem 2024;43:1012–1029. © 2024 Authors. Environmental Toxicology Chemistry published by Wiley Periodicals LLC behalf SETAC.

Language: Английский

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New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 927, P. 171851 - 171851

Published: March 20, 2024

Untargeted metabolomics is a non-a priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if metabolite annotation remains lacunar due database gaps, global metabolomic fingerprint allows for trend analyses dose-response curves hundreds cellular metabolites. Analysis dose/time-response curve trends (biphasic or monotonic) untargeted features would thus allow use all chemical signals obtained in order determine stress levels (defense damage) organisms. To develop this approach context time-dependent microbial community changes, mature river biofilms were exposed 1 month four cobalt (Co) concentrations (from background concentration × 10−6 M) an open system artificial streams. The meta-metabolomic response was compared against multitude biological parameters (including bioaccumulation, biomass, chlorophyll content, composition structure prokaryotic eukaryotic communities) monitored at set exposure times h 28 days). Cobalt extremely rapid responses meta-metabolome, with time range inducing defense (TRIDeR) around 10 s, damage (TRIDaR) several hours. whose had been altered Co bioaccumulation (reduced contents changes diversity communities), (CRIDeR) similar initiation thresholds (1.41 ± 0.77 10−10 M Co2+ added medium) up meta-metabolome level every point. In contrast, (CRIDaR) increased biofilms. present study demonstrates biofilm are rapidly sustainably impacted, even within tolerant resistant communities.

Language: Английский

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Microbial Ecotoxicology—40 Years on

Life, Journal Year: 2025, Volume and Issue: 15(4), P. 514 - 514

Published: March 21, 2025

Although ecotoxicology was emerging as a field through the 1970s, incorporation of microbial indicators into framework has been slower to evolve. The exploration microbes sensitive toxicity tests began in late 70s and early 80s (with emergence Microtox® other simple tests). However, applications have limited, beyond water wastewater screening. This opinion piece reflects my own perspective on field—from excitement 1990s for its possibilities, sense frustration at slow pace new development field—despite surge “omics” options. While microbiology still fails lead ecotoxicology, potential remains.

Language: Английский

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Exploring microbial diversity in relation to hydrological signatures and anthropic pressures in the Beauce Aquifer, France

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 977, P. 179402 - 179402

Published: April 15, 2025

Groundwater is one of the largest reservoirs liquid fresh water on earth. Aquifers are complex environments where quality can be affected by geological origins, geochemistry and biological activity. These under pressure due to climate change pollution. Strongly involved in biogeochemistry groundwater ecosystems, microorganisms also contribute reducing pollution potentially used as indicators quality. However, diversity role remains largely unknown. The present work aimed characterize bacterial 60 wells over 8000 km2 Beauce Aquifer, France, determine baseline expected relation hydro geochemical signatures identify variations that could anthropogenic pressures. We analysed amplicon sequence variants (ASVs) 16S rRNA gene well abundance functional genes associated arsenic nitrate (aioA, arsB, narG), organic carbon contents composition. Bacterial co-occurrences were found according hydrogeochemical identified aquifer. A lower was measured confined aquifers, low oxygen conditions occurred with high levels dissolved iron manganese. This indicate a higher vulnerability face pressure. Finally, composition linked each signature several differed from this identified.

Language: Английский

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Metatranscriptomic profiles reveal the biotransformation potential of azithromycin in river periphyton

Water Research, Journal Year: 2024, Volume and Issue: 251, P. 121140 - 121140

Published: Jan. 21, 2024

Language: Английский

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Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(4)

Published: March 12, 2024

Abstract Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform functions necessary for agricultural production, it is thus important evaluate performance these through lens organisms, especially microbes. They provide numerous services plants, including growth promotion, nutrient supply, tolerance environmental stresses protection against pathogens. An overwhelming majority studies confirm are beneficial microorganisms. However, three practices were identified as posing potential ecotoxicological risks: recycling organic waste products, plastic mulching, pest disease management biopesticides. The first two because they can be source contaminants; third impacts non-target Consequently, developing strategies allow safe increasingly growing matter stocks produced cities factories, assessment impact biopesticides microorganisms, represent challenges will face future.

Language: Английский

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Microbial communities and their role in enhancing hemp fiber quality through field retting

Applied Microbiology and Biotechnology, Journal Year: 2024, Volume and Issue: 108(1)

Published: Nov. 5, 2024

Abstract The current development of industrial hemp “ Cannabis Sativa L.” fibers for technical textiles and applications requires high-quality with homogeneous properties. However, several factors have been reported to influence the fibers’ intrinsic properties, including a post-harvest process known as retting. This plays crucial role in facilitating mechanical extraction from stems. Retting involves degradation amorphous components surrounding fiber bundles enabling their decohesion Microorganisms play central mediating this bioprocess. During retting, they colonize stems’ surface. Therefore, biochemical plant cell wall, acting natural binding between fibers, undergo breakdown through production microbial enzymes. Although its critical role, farmers often rely on empirical retting practices, considering various biotic abiotic factors, resulting heterogenous These limit due inconsistent Thus, purpose review is enhance our comprehension how influences dynamics communities and, consequently, evolution properties stems throughout process. Better understanding effective management, leading high-value fibers. Key points • enables wall components, controlling Microbial enzymatic activity successful bundles. Understanding mechanisms essential consistent .

Language: Английский

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

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

Published: Dec. 3, 2024

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

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Editorial: thematic issue on microbial ecotoxicology

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(8)

Published: July 12, 2024

Ima gine you ar e a micr obe and are exposed to chemical contamination.Will be at risk?How will react, by which means?Just die?Expr ess some form of ada ptation using specific r esistance mec hanisms?Reduce toxicity c hemicals degr ading them, or negative tactic mov ement?Toler ate their pr esence thanks emergent properties your surrounding microbial comm unity?Expr other esilience wait for better times, return functional state after more less long period, depending on the intensity contamination?Alongside these questions that ecotoxicologists eager answer, question "Why do we need eserv monitor integrity environmental microbes communities they form?"has been core emerging multidisciplinary field obial ecotoxicology.Ov er last decade, have organized through international EcotoxicoMic network ( https://ecotoxicomic.or g ), whic h now counts 282 members from 46 countries.With three conferences in 2017 (Ly on, F rance), 2020 (online due COVID pandemic), 2022 (Montpellier, netw ork has addressed interactions , effects risks exposure systems generated new researc perspectiv es.A forthcoming fourth Ecotoxi-coMic conference take place Gothenburg (Sweden) 12-14 November 2024 https:// ecotoxicomic.org/ecotoxicomic-2024 ).Micr oor ganisms hav become ppr eciated as k ystone contributors numerous ecosystemic processes (Cavicchioli et al. 2019 including but not limited (i) cycling carbon, nitrogen, phosphorus, iron, sulfur; (ii) biological control pathogens; (iii) attenuation pollution; (iv) production consumption greenhouse gases; (v) contribution soil structure; (vi) biomass nutrients higher trophic levels.Micr unities also constitute ric hest genetic pool, can harnessed biotechnology.All this very much speaks favor fundamental role ecotoxicology play ecosystem ation functioning today.Indeed, high diversity, plasticity, adaptability, esponses obes hemical pollution ovides unique opportunity discover quantify associated crucial functions, explore responses world, impact contaminant eco-dynamics, ecosystems human health (Fig. 1 ).Thanks experimental oac hes tec hnologies av ailable today, curr ent esearc anges fr om labor atory studies detailed hanisms gene expression linked contaminants toxic model ganisms, integr ativ complex envir onmental scales.Given complexity investigated interactions, incr easingl y in-depth explor re- Recei v

Language: Английский

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New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 16, 2023

Abstract Untargeted metabolomics is a non- priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if metabolite annotation remains lacunar due database gaps, global metabolomic fingerprint allows for trend analyses dose-response curves hundreds cellular metabolites. The combination untargeted features benchmark-dose (BMD) calculations then makes it possible determine concentration range inducing defense responses (CRIDeR) damage (CRIDaR). To develop this approach in context time-dependent microbial community changes, mature river biofilms were exposed 1 month four cobalt (Co) concentrations (background concentration, x 10 -7 , 5 - 6 M) an open system artificial streams. meta-metabolomic response was compared against multitude biological parameters (including bioaccumulation, biomass, chlorophyll content, composition structure prokaryotic eukaryotic communities) monitored at set exposure times (from hour 28 days). Cobalt extremely rapid meta-metabolome, with time (TRIDeR) around ten seconds, (TRIDaR) several hours. whose had been altered Co bioaccumulation (reduced contents changes diversity communities), CRIDeRs similar initiation thresholds (1.41 ± 0.77 -10 M 2+ added medium) up meta-metabolome level every point. In contrast, CRIDaR increased biofilms. present study demonstrates biofilm are rapidly sustainably impacted, even within tolerant resistant communities. Graphical abstract Highlights Prokaryotic structures impacted after h Biofilm 36 s faster than communities Short- have CRIDeR Long-term higher

Language: Английский

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