Towards exhaustive community ecology via DNA metabarcoding

Molecular Ecology, Год журнала: 2023, Номер 32(23), С. 6320 - 6329

Опубликована: Фев. 10, 2023

Abstract Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability perform inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority published last years used just one or two markers analysed limited number taxonomic groups. Here, we provide overview emerging that can allow all‐taxa biological by combining large specific primers, exploiting power universal primers obtain good information key while limiting overlooked biodiversity. Multiplexes shotgun sequencing capture enrichment may better coverage compared standard metabarcoding, but still require major methodological advances. identify strengths limitations approaches, suggest new development lines might improve broad scale analyses near future. More ecological communities greatly increase value studies, improving understanding consequences ongoing environmental multiple components

Язык: Английский

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Aloe Vera Extract Gel-Biosynthesized Selenium Nanoparticles Enhance Disease Resistance in Lettuce by Modulating the Metabolite Profile and Bacterial Endophytes Composition

ACS Nano, Год журнала: 2023, Номер 17(14), С. 13672 - 13684

Опубликована: Июль 13, 2023

The use of nanotechnology to suppress crop diseases has attracted significant attention in agriculture. present study investigated the antifungal mechanism by which aloe vera extract gel-biosynthesized (AVGE) selenium nanoparticles (Se NPs) suppressed Fusarium-induced wilt disease lettuce (Lactuca sativa). AVGE Se NPs were synthesized utilizing sodium selenite as a source and biocompatible capping reducing agent. Over 21 d, 2.75% total was dissolved into ions, more than 8-fold greater that bare (0.34%). Upon exposure soil applied at 50 mg/kg, fresh shoot biomass significantly increased 61.6 27.8% over infected control NPs, respectively. As compared control, levels citrate, isocitrate, succinate, malate, 2-oxo-glutarate upregulated 0.5–3-fold affected both NPs. In addition, level khelmarin D, type coumarin, 4.40- 0.71-fold controls Additionally, showed upregulation jasmonic acid downregulation abscisic content relative diseased shoots. Moreover, diversity bacterial endophytes with values Shannon index 40.2 9.16% Collectively, these findings highlight potential an effective strategy for nanoenabled sustainable protection.

Язык: Английский

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Comparison of nitrogen removal performance and mechanism from low-polluted wastewater by constructed wetlands with two oxygen supply strategies: Tidal flow and intermittent aeration

Chemosphere, Год журнала: 2022, Номер 313, С. 137364 - 137364

Опубликована: Ноя. 22, 2022

Язык: Английский

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Multi-group biodiversity distributions and drivers of metacommunity organization along a glacial–fluvial–limnic pathway on the Tibetan plateau

Environmental Research, Год журнала: 2023, Номер 220, С. 115236 - 115236

Опубликована: Янв. 5, 2023

Язык: Английский

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Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities

Ecological Applications, Год журнала: 2024, Номер 34(6)

Опубликована: Авг. 8, 2024

Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging on their potential impacts. However, little research has been conducted quantifying actual impacts and assessing causes of species-specific vulnerabilities particular IAS due persistent methodological challenges. The underlying interspecific mechanisms driving therefore remain poorly understood, even though they can substantially improve accuracy risk assessments. Given that interactions ecological are often shaped phenological synchrony, we tested hypothesis temporal mismatches in breeding phenology between native mitigate Focusing American bullfrog (Lithobates catesbeianus), combined an environmental DNA (eDNA) quantitative barcoding metabarcoding survey Belgium with global meta-analysis, integrated citizen-science data phenology. We examined whether presence amphibian was negatively related or abundance bullfrogs this relationship affected mismatches. field study revealed significant negative effect increasing eDNA concentrations richness community structure. These observations were bullfrogs, late spring- summer-breeding being strongly affected, while winter-breeding remained unaffected. This trend confirmed meta-analysis. A observed mismatch impact bullfrogs. Specifically, differing 6 weeks less from more likely be absent than whose differed Taken together, present novel method based combination aqueous quantify biological invaders at level. show strong predictor invasion regardless context. Therefore, advocate for integration alignment IAS's phenologies into frameworks.

Язык: Английский

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Commonly Used Engineered Nanomaterials Improve Soil Health via Suppressing Soil-Borne Fusarium and Positively Altering Soil Microbiome

ACS ES&T Engineering, Год журнала: 2024, Номер 4(4), С. 915 - 927

Опубликована: Янв. 1, 2024

The use of engineered nanomaterials (NMs) as novel antimicrobial agents has garnered significant attention in agriculture. properties 5 mg/kg metal oxide (copper and zinc nanoparticles, CuO ZnO NPs)- carbon (reduced graphene multiwalled nanotubes, rGO MWCNT)-based NMs on two soil-borne fungal pathogens, Fusarium oxysporum f.sp. lactucae (F.o.lact) lycopersici (F.o.lyco), were evaluated over a 21-day incubation period. Both metal- carbon-based reduced the dehydrogenase activity (DHA) Fusarium-infested soil by more than 40% relative to infested controls; efficacy antifungal was NPs > MWCNT. Similar decreases activities urease (UE), sucrase (SC), acid phosphatase (ACP), polyphenol oxidase (PPO) suggest that could effectively inhibit growth time. total available fractions, including extractable fraction, Fe/Mn oxidation state, fraction bound organic matter, increased 5.99–7.29% with metal-based NM compared controls. Shannon index microbial communities soils 12.2–23.5% Similarly, community 10.18–29.86%. Importantly, abundance decreased both NMs. These also beneficial microorganisms soil, such Pseudomonas, which 29.7–96.2% untreated findings demonstrate at appropriate doses subsequent crop damage while simultaneously fostering development soil.

Язык: Английский

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Hydro-morphology and water quality jointly shape the structure and network stability of the plankton community in multi-tributary river basins

Journal of Hydrology, Год журнала: 2024, Номер 643, С. 131945 - 131945

Опубликована: Авг. 31, 2024

Язык: Английский

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Environmental DNA Reveals Multitrophic Insight into the Mechanism of Community Stability Changes in Shallow Eutrophic Lakes

ACS ES&T Water, Год журнала: 2025, Номер unknown

Опубликована: Янв. 16, 2025

Current management of eutrophic lakes primarily targets nutrient reduction and algal bloom control, often overlooking the organismal mechanisms that drive changes in community stability across multitrophic levels. This study employed environmental DNA (eDNA) to examine seasonal dynamics communities typical shallow Dianchi (plateau) Taihu (plain), exploring how eutrophication stress influences composition, networks, stability. We found plateau plain had their respective dominant taxa diversity seasons. The structure networks composed varied significantly seasons, among which Lake exhibited 17.9% higher connectivity 8.2% greater robustness compared Lake. Dominant played a critical role determining through different pathways; 30% variation was attributed bottom-up effects, with algae as core pathway, while 40% mainly explained by top-down fish pathway. These findings underscore lake-specific changes, providing insights into tailored strategies for based on unique ecological processes.

Язык: Английский

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eDNA-based approaches advance ecotoxicology: Insights and best practices from eDNA metabarcoding studies in evaluating stress-induced aquatic (macro-) invertebrate community composition

Ecological Indicators, Год журнала: 2025, Номер 172, С. 113269 - 113269

Опубликована: Фев. 28, 2025

Язык: Английский

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ORDNA: Deep‐learning‐based ordination for raw environmental DNA samples

Methods in Ecology and Evolution, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

Abstract Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring, offering non‐invasive tools to assess ecosystem health. The complexity of eDNA data poses major challenges for conventional ordination methods in understanding assemblage similarities and assessing patterns. Here, we introduce ORDNA (ORDination via Deep Neural Algorithm), a new deep learning method tailored sample ordination. Leveraging artificial neural networks, processes raw sequences from samples directly, bypassing potentially biased cumbersome expert‐based bioinformatic steps. is trained with contrastive self‐supervised approach, the triplet loss, derive two‐dimensional representation based on their read composition. We apply four distinct datasets, demonstrating its robustness superiority over traditional techniques capturing visualizing ecological Our results underline potential advancing analysis, serving as promising tool more accurate efficient assessments.

Язык: Английский

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