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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Urbanization and edge effects interact to drive mutualism breakdown and the rise of unstable pathogenic communities in forest soil

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(36)

Published: Aug. 29, 2023

Temperate forests are threatened by urbanization and fragmentation, with over 20% (118,300 km

Language: Английский

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Urbanized lands degrade surrounding grasslands by deteriorating the interactions between plants and soil microbiome

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 6, 2025

To mitigate overgrazing on grasslands, towns were constructed in some pastoral regions of China to relocate pastoralists. Nevertheless, whether and how the urbanized lands impact surrounding grassland ecosystem remains unclear. We assessed impacts plant soil interactions within grasslands order ensure an eco-sustainable pastoralist relocation. The town with 1 km radius was selected as urbanization sample a nature sample. Plants investigated (NG), areas (T-1 km), 2 (T-2 3 (T-3 km) from center town. In T-1 T-2 km, compared NG, diversity, abundance dominant species, wood saprotroph fungi, water content (SWC), total organic carbon (TOC) decreased, while pathogen pH, phosphatase (TP) increased. Conversely, no such changes observed T-3 km. results Mantel test Partial least squares path model suggest that decrease TOC SWC, along increase pH TP lead decline fungi ultimately resulting reductions diversity species. These indicate can degradation by deteriorating plant-soil interactions.

Language: Английский

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Urbanization leads to asynchronous homogenization of soil microbial communities across biomes

Environmental Science and Ecotechnology, Journal Year: 2025, Volume and Issue: unknown, P. 100547 - 100547

Published: March 1, 2025

Language: Английский

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Mountains are not like poles for symbiotic and saprotrophic soil fungi

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

…the findings highlight the need to move beyond simplistic models that assume uniform responses across taxonomic or functional groups. This study employs a standardized, continent-wide sampling protocol sites spanning from Spain and Greece, in south, Iceland Norway, north, ensuring robust cross-site comparability. By applying various statistical models, including joint species distribution researchers capture both guild-level diversity patterns species-specific elevational latitudinal gradients, with specific effort toward disentangling impacts of climate relative other ecological variables. rigorous approach, combined thorough bioinformatic analyses, meets all important benchmarks for assessing fungal community structure at large spatial scales. All three guilds displayed significant trend operational unit (OTU) richness, but none were elevation latitude (Fig. 1). suggests these two gradients are not direct analogs, despite sharing similar climatic vegetational trends. SAP richness significantly decreased increasing elevation, while REND increased latitude. contrast, ECM nonlinear response, showing positive unimodal relationship elevation. Importantly, guilds, there was no interaction between effects on OTU richness. finding contrasts idea 'mountain passes higher tropics' (Janzen, 1967); is, high elevations low latitudes present more physiological barriers organisms than latitudes. result does not, however, mean an predictor as multiple climate-related variables identified explanatory random forest models. Instead, this indicates additional also strongly impact guild distributions. The range provides strong evidence distributions product 'null' processes. One well-cited explanation pattern bounded domain is mid-domain effect (Colwell et al., 2000), which posits because hard constraints each end (i.e. cannot have any its outside domain), species' ranges will overlap center thereby increase While did find authors convincingly argue absence either based simple geometric space-filling norm. Interestingly, fungi, soil pH emerged elevation-independent driver It well known some evolutionary lineages fungi (e.g. Pezizales) respond favorably (peak observed c. 6), hints importance considering how diverse histories different might differentially their (Petersen, 1985). extent modifying be used management tool optimize maintain interesting possibility uncovered by findings. current working why has globally – temperate forests unique combination host phylogenetic stem density tropical boreal (Kennedy 2012; Tedersoo 2014) partially controlled design. Here, tree held effectively constant latitude, trees per site. However, whether hosts, increases (Nguyen 2016), understory shrubs (Tedersoo 2024), mid-elevations presented. Support nonhost-related factors driving been previously demonstrated Truong al. (2019), who examined communities single (Nothofagus pumilio) Patagonia. Although they found study, showed fungal-associated enzyme activity change That difference attributed shift composition taxa produce proteolytic enzymes elevations. Barbi address shifts Europe, results (2019) suggest documenting changes alone sufficient assess C N cycling environmental gradients. As scientific studies, generate many questions answer. For example, do correspond facultatively saprotrophic lifestyle? given wide substrates targeted, cryptic within litter vs wood saprotrophs latitude? higher-level gradients? notable particular could help inform larger pattern? share dependence plants carbon, morphologically physiologically diverse, evolved > 65 times geological timescale & Smith, 2013), geographical origins, zones (Looney 2016). such, it future studies fully integrate shapes functions distinct lineages. Perhaps most intriguingly, authors' suggested correct. They speculate interval longer history human disturbance low-elevation may erode declines rural–urban (Tatsumi 2023). Testing hypothesis require perhaps surveying intensities intervals logging (Kebli 2012). Regardless questions, step forward demonstrating follow along standardized processing approach strengthens confidence results, global continues reshape ecosystems, like invaluable predicting ecosystem support shifts. gratefully acknowledge financial US National Science Foundation (DEB 2019518 2106069). New Phytologist remains neutral regard jurisdictional claims maps institutional affiliations.

Language: Английский

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Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Ecology, Journal Year: 2025, Volume and Issue: 106(4)

Published: April 1, 2025

Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including responses to conditions at fragment edges, or "edge effects." To understand the communities edge effects, analyzed distributions bacteria, archaea, fungi an experimentally fragmented system open patches embedded within forest matrix. In addition, identified taxa that consistently differed among patch, edge, matrix habitats ("specialists") showed no preference ("nonspecialists"). We hypothesized microbial community turnover would be most pronounced between habitats. also specialist more likely mycorrhizal than nonspecialist because mycorrhizae should different hosts habitats, whereas prokaryotes smaller genomes (indicating reduced metabolic versatility) less able sporulate prokaryotes. Across all replicate sites, patch soils harbored distinct communities. However, sites where contrasts vegetation pH were exhibited larger differences tended from those forest. There similar numbers specialists, but very few taxa. Acidobacteria ectomycorrhizae while Chloroflexi, Ascomycota, Glomeromycota (i.e., arbuscular mycorrhizae) specialists. Contrary our hypotheses, bacteria not spore-formers. found partial support for hypothesis: mycorrhizae, ectomycorrhizae, Overall, results indicate sensitive equally affected, with particular showing strong response edges. context increasing fragmentation worldwide, can help inform efforts maintain structure functioning microbiome.

Language: Английский

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Urbanization alters fungal functional composition in boreal ecosystems by favouring larger‐spore fungi and pathogenic fungi

Functional Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

Abstract Urbanization is a major threat to biodiversity, ultimately influencing ecosystem functions. Fungi, highly taxonomically and functionally diverse group of organisms, underpin many these functions from nutrient cycling symbiotic interactions. Yet, research on how urbanization impacts fungal diversity has primarily focused detecting changes in community structure, rather than understanding the functional implications changes. Here we examined shifts dispersal resource‐use traits due boreal ecosystems. We hypothesized that urban sites may favour large‐spored taxa as they be better suited survive germinate under harsher conditions. Conversely, small‐spored could dominate fragmented habitats, their spores can disperse over longer distances. turnover guilds altered substrates hosts versus natural settings. To test hypotheses, cross‐referenced data five Finnish cities adjacent naturally‐forested areas obtained via metabarcoding with databases spore size guilds. found consistent dominance environments, suggesting greater impact abiotic stress communities habitat fragmentation are believed possess survival structures for germination stressful In terms groups, taxa, such pathogens affecting lichens, plants, animals (including humans), showed an increase abundance This pattern suggests dual effect urbanization, by introducing new susceptible creating conditions existing ones, favouring infections pathogenic fungi. Our study highlights utility combining surveys trait detect environments. results show increases larger beneficial colonise heavily urbanised habitats. The thriving presence genera involved interactions promote prevalence emergence Read free Plain Language Summary this article Journal blog.

Language: Английский

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Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 11, 2025

Abstract Populations facing lethal environmental change can escape extinction through rapid genetic adaptation, a process known as evolutionary rescue. Despite extensive study, rescue is largely unexplored in mutualistic communities, where it likely constrained by the less adaptable partner. Here, we explored empirically likelihood, population dynamics, and mechanisms underpinning an obligate mutualism involving cross-feeding of amino acids between auxotrophic Escherichia coli strains. We found that over 80% populations overcame severe decline when exposed to two distinct types abrupt, stress. Of note, all cases only one strains survived metabolically bypassing auxotrophy. Crucially, consortium exhibited greater sensitivity both stressors than prototrophic control strain, such reversion autonomy was sufficient alleviate stress below levels. This common across other stresses, suggesting may be general feature acid–dependent mutualisms. Our results reveal depend critically on specific physiological details interacting partners, adding rich layers complexity endeavor predicting fate microbial communities intense deterioration.

Language: Английский

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Microbial diversity, dynamics, and metabolic analysis of microorganisms present in wastewater treatment plants in urban areas

Brazilian Journal of Chemical Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

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Urbanization exacerbates climate sensitivity of eastern United States broadleaf trees

Ecological Applications, Journal Year: 2024, Volume and Issue: 34(4)

Published: April 11, 2024

Abstract Tree growth is a key mechanism driving carbon sequestration in forest ecosystems. Environmental conditions are important regulators of tree that can vary considerably between nearby urban and rural forests. For example, trees growing cities often experience hotter drier than their counterparts while also being exposed to higher levels light, pollution, nutrient inputs. However, the extent which these intrinsic differences versus forests influence response climate not well known. In this study, we tested for sensitivity along latitudinal transect eastern United States included Boston, Massachusetts, New York City, York, Baltimore, Maryland. Using dendrochronology analyses cores from 55 white oak ( Quercus alba ), red maple Acer rubrum 41 rubra ) investigated impacts heat stress water on radial individual trees. Across our three‐city found was more closely correlated with cooler Boston Baltimore. Furthermore, significant hindrance latitudes appeared be evenly distributed across latitudes. We trees, but sites City adversely impacted by counterparts, did see urban–rural Trees provide wide range ecosystem services increasing canopy cover typically an component sustainability strategies. light findings urbanization how responds warming climate, suggest municipalities consider interactions when developing tree‐planting palettes estimating capacity contribute broader goals future.

Language: Английский

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