Environmental DNA metabarcoding from flowers reveals arthropod pollinators, plant pests, parasites, and potential predator–prey interactions while revealing more arthropod diversity than camera traps

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(3), P. 551 - 569

Published: March 29, 2023

Abstract Arthropods can strongly impact ecosystems through pollination, herbivory, predation, and parasitism. As such, characterizing arthropod biodiversity is vital to understanding ecosystem health, functions, services. Emerging environmental DNA (eDNA) methods targeting trace eDNA left behind on flowers have the potential track interactions. The goal of this study was determine extent which metabarcoding identify plant‐arthropod arthropod‐arthropod interactions assess compared conventional sampling. We deployed camera traps document activity specific flowers, sampled from those same then performed a analysis that targets partial fragment cytochrome c oxidase subunit I gene (COI) all present. found our detected small pollinators, plant pests, parasites, shed light predator–prey while detecting 55 species just 21 trapping. trapping survey, however, larger, more conspicuous nectarivores successfully. also explored ecology residual eDNA, finding rainfall had significant negative effect ability detect eDNA. Preliminary evidence indicates flower may amount be detected. provide clues highlights insights gained future studies. show valuable tool for not only pollinator communities but revealing among plants, predators. Future research should focus how improve detection large pollinators/nectivores studying further explore method's utility.

Language: Английский

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Loss of Airway Phylogenetic Diversity Is Associated with Clinical and Pathobiological Markers of Disease Development in COPD

American Journal of Respiratory and Critical Care Medicine, Journal Year: 2024, Volume and Issue: 210(2), P. 186 - 200

Published: Jan. 23, 2024

The airway microbiome has the potential to shape chronic obstructive pulmonary disease (COPD) pathogenesis, but its relationship outcomes in milder is unestablished.

Language: Английский

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Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(8)

Published: June 25, 2024

ABSTRACT Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles biogeochemical cycles ecosystem functions. Despite extensive research on soil pH as a predictor of microbial community composition, limitation these studies lies determining whether bacterial and/or fungal communities directly or indirectly influenced by pH. We conducted controlled laboratory experiment to investigate effects amendment (+/- 1–2 units) with six levels two contrasting Chinese agricultural soils (pH 8.43 Dezhou, located North China Plain, Shandong vs 6.17 Wuxi, Taihu Lake region, Jiangsu, east China). Results showed that diversity composition were related pH, but much lower than soils. The more closely associated Wuxi compared Dezhou alpha peaked near situ both soils, displaying quadratic fitting pattern. Redundancy analysis variation partition indicated affected imposing physiological constraint bacteria altering characteristics (e.g., nutrient availability). study also examined complete curves taxa relative abundances at phylum family response relationships conforming pattern, indicating is reliable predictor. Furthermore, transformation nitrogen functional genes involved cycle, methane production consumption. Overall, results from this would enhance our comprehension how farmlands will respond changes, contribute effective management conservation strategies. IMPORTANCE This delves into impact communities, investigating influences communities. subjected unit amendment. indicate was shaped through constraints limitations. found responded Additionally, significantly influence predicted abundance cycle well consumption processes. These insights can develop

Language: Английский

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Achieving Long-Term Stability of Partial Nitrification and Autotrophic Denitrification in an MABR via Sulfide Dosing

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(28), P. 12532 - 12541

Published: June 28, 2024

While partial nitrification (PN) has the potential to reduce energy for aeration, it proven be unstable when treating low-strength wastewater. This study introduces an innovative combined strategy incorporating a low rate of oxygen supply, pH control, and sulfide addition selectively inhibit nitrite-oxidizing bacteria (NOB). led stable PN in laboratory-scale membrane aerated biofilm reactor (MABR). Over period 260 days, nitrite accumulation ratio exceeded 60% synthetic sewage containing 50 mg NH

Language: Английский

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Microbiota modulation by dietary oat beta-glucan prevents steatotic liver disease progression

JHEP Reports, Journal Year: 2024, Volume and Issue: 6(3), P. 100987 - 100987

Published: Jan. 3, 2024

Changes in gut microbiota metabolic dysfunction-associated steatotic liver disease (MASLD) are important drivers of progression towards fibrosis. Therefore, reversing microbial alterations could ameliorate MASLD progression. Oat beta-glucan, a non-digestible polysaccharide, has shown promising therapeutic effects on hyperlipidemia associated with MASLD, but its impact and most importantly MASLD-related fibrosis remains unknown.

Language: Английский

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GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis

mSystems, Journal Year: 2024, Volume and Issue: 9(2)

Published: Jan. 8, 2024

Taxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, Greengenes2, Genome Taxonomy Database, or Ribosomal Database Project. To overcome these issues, we created Greengenes-SILVA-RDP database (GSR-DB), accurate comprehensive taxonomic annotations 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent reliable annotations. Our evaluation analyses showed that GSR-DB outperforms providing species-level resolution, especially based on mock-community analysis, making it game-changer for microbiome studies. Moreover, is designed to be accessible researchers with limited computational resources, powerful tool scientists across the board. Available full-length sequences commonly used hypervariable regions, including V4, V1–V3, V3–V4, V3–V5, go-to robust microbial analysis.

Language: Английский

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Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 22, 2024

Global wildfire activity has increased since the 1970s and is projected to intensify throughout 21st century. Wildfires change composition biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms SOM often increase postfire, response more biodegradable remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach identify sources characterize metabolome immediately postfire. Using amplicon (16S/ITS) sequencing gas chromatography–mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, Protobacteria) specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating soils contain variety substrates support Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed was lower molecular weight featured 20 43% nitrogen-containing than unburned soil. We also measured higher water extractable carbon concentrations CO2 efflux soils. The observed enrichment heterotrophs demonstrates resilience these burning, providing important implications for postfire plant recolonization ecosystem recovery.

Language: Английский

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Effects of Fishmeal Substitution with Mealworm Meals (Tenebrio molitor and Alphitobius diaperinus) on the Growth, Physiobiochemical Response, Digesta Microbiome, and Immune Genes Expression of Atlantic Salmon (Salmo salar)

Aquaculture Nutrition, Journal Year: 2024, Volume and Issue: 2024(1)

Published: Jan. 1, 2024

A 12‐week growth trial was conducted to assess the effects of mealworm meals, as a substitution for fishmeal, on growth, physiobiochemical responses, digesta microbiome, and immune‐related genes expression Atlantic salmon ( Salmo salar ). Twenty parr (38.5 ± 0.1 g, initial weight) were stocked into each 16 tanks in recirculating aquaculture system. fishmeal‐based diet (100% FM) used control treatment compared with three test diets where: (1) fishmeal partially (50%) replaced defatted meal, Tenebrio molitor (50% DMM), (2) fully meal (3) whole lesser Alphitobius diaperinus WMM). All substitutions done crude protein basis. Each four experimental evaluated quadruplicate part randomized design. The results indicated that showed high survival (greater or equal 98.8%), no significant difference final feed efficiency, feces stability condition indices. Hepatosomatic index lower fish fed 100% DMM 50% WMM when FM). Whole‐body proximate amino acid compositions not statistically different between treatments, while essential fatty acids, including linolenic, eicosapentaenoic acid, homo‐a‐linolenic, DMM. Plasma parameters (total protein, alanine aminotransferase, alkaline phosphatase, total iron‐binding capacity), hepatic peroxide, antioxidant enzymes significantly affected by dietary substitutions, whereas plasma immunoglobulin M higher levels inclusion meals impacted overall microbiome composition but richness evenness microbiomes control. most common genus all treatments Pseudomonas , which has been previously shown have both commensal pathogenic members. relative expressions (IGF‐I) synthesis (TIPRL) (IgM, IgD, IgT) upregulated diet. Overall, this study suggests tested could be suitable alternatives salmon.

Language: Английский

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Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3

Gut Microbes, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 2, 2024

Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and typically used the treatment of various inflammatory conditions, including infectious diseases. However, its effect on intestinal mucosa, microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily with hyperbaric affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible Clostridioides difficile infection (CDI), an enteric pathogen highly associated colitis. These observations closely linked decline in level microbiota-derived short-chain fatty acids (SCFAs). Butyrate, SCFA produced primarily by anaerobic microbial species, mitigated HBO-induced susceptibility CDI increased epithelial barrier integrity group 3 innate lymphoid cell (ILC3) responses. Mice displaying tissue-specific deletion HIF-1 RORγt-positive cells exhibited no protective butyrate during CDI. In contrast, reinforcement signaling through conditional VHL disease outcome, even after HBO therapy. Taken together, conclude induces dysbiosis impairs production SCFAs affecting HIF-1α-IL-22 axis ILC3 response subsequent C. infection.

Language: Английский

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Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

EFSA Supporting Publications, Journal Year: 2024, Volume and Issue: 21(2)

Published: Feb. 1, 2024

Scientific interest in the use of environmental microbiomes for risk assessment is rapidly growing, as exemplified by various EFSA opinions. In absence official regulatory guidelines on how to integrate assessment, aims this report are therefore determine whether microbiome studies can be used such purposes, and propose a roadmap integration assessments under EFSA's remit. The identifies current gaps (in terms knowledge from technical point view) barriers that might delay implementation methods, offers recommendations standardised (multi-)omics techniques purposes. Our main findings identified five priorities: (i) defining core (what it encompasses what made of, including identification bioindicators) assess impact any type disturbance; (ii) standardising methodologies protocols, sampling interpretation, guarantee comparability analyses; (iii) developing tools facilitate interpretation; (iv) collecting microbiome-based data shared, curated maintained databases; (v) setting up European Network Microbiome Laboratories reach an agreement standardise studies, interactions between researchers access or samples, actively include multiple stakeholders discussions involving assessment. There both short- longer-term priorities, all which highlight need mobilise concurrently different agencies institutions, well research. also points out capacity building training, acceptance emerging technology, communication issues. These will hopefully contribute elaboration widely accepted framework dealing with.

Language: Английский

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