Patterns in soil microbial diversity across Europe

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июнь 8, 2023

Factors driving microbial community composition and diversity are well established but the relationship with functioning is poorly understood, especially at large scales. We analysed biodiversity metrics distribution of potential functional groups along a gradient increasing land-use perturbation, detecting over 79,000 bacterial 25,000 fungal OTUs in 715 sites across 24 European countries. found lowest less-disturbed environments (woodlands) compared to grasslands highly-disturbed (croplands). Highly-disturbed contain significantly more chemoheterotrophs, harbour higher proportion plant pathogens saprotrophs, have less beneficial symbionts woodlands extensively-managed grasslands. Spatial patterns communities predicted functions best explained when interactions among major determinants (vegetation cover, climate, soil properties) considered. propose guidelines for environmental policy actions argue that taxonomical should be considered simultaneously monitoring purposes.

Язык: Английский

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Microbes to support plant health: understanding bioinoculant success in complex conditions

Current Opinion in Microbiology, Год журнала: 2023, Номер 73, С. 102286 - 102286

Опубликована: Март 4, 2023

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for performance health. When applied in agriculture improve crop yield performance, these commonly referred as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically the field, hampering applicability. Invasion of rhizosphere microbiome a critical determinant success. complex phenomenon that shaped interactions local, resident host plant. Here, we explore all dimensions cross-cutting ecological theory molecular biology microbial invasion rhizosphere. We refer famous Chinese philosopher strategist Sun Tzu, who believed solutions problems require deep understanding themselves, review major biotic factors determining effectiveness.

Язык: Английский

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Targeted genome-modification tools and their advanced applications in crop breeding

Nature Reviews Genetics, Год журнала: 2024, Номер 25(9), С. 603 - 622

Опубликована: Апрель 24, 2024

Язык: Английский

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Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

Nature Biotechnology, Год журнала: 2023, Номер 42(9), С. 1384 - 1393

Опубликована: Ноя. 20, 2023

The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks spatial patterns. Existing technology does not allow simultaneous investigation between a multitude its colonizing microorganisms, which limits our understanding host-microorganism within plant or animal tissue. Here we present metatranscriptomics (SmT), sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for transcriptome- microbiome-wide characterization tissues 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as model system, find tissue-scale bacterial fungal hotspots. By network analysis, study inter- intrakingdom well response to microbial provides an answering fundamental questions on host-microbiome interplay.

Язык: Английский

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Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 2, 2024

In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as phyllosphere microbiota. However, underlying mechanisms of host-driven assembly these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment rice microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals strong between genotype members four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales Xanthomonadales. Some associations are to distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified main driver enrichment bacteria belonging Pseudomonadales. 4-HCA can be synthesized by plant's OsPAL02 from phenylpropanoid biosynthesis pathway. knockout mutant results in reduced Pseudomonadales abundance, dysbiosis microbiota consequently higher susceptibility plants disease. Our provides direct link metabolite homeostasis opening possibilities new breeding strategies.

Язык: Английский

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Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 11, 2024

Despite the plant health-promoting effects of microbiota, these assemblages also comprise potentially detrimental microbes. How immunity controls its microbiota to promote health under conditions remains largely unknown. We find that commensal bacteria isolated from healthy Arabidopsis plants trigger diverse patterns reactive oxygen species (ROS) production dependent on immune receptors and completely NADPH oxidase RBOHD selectively inhibited specific commensals, notably Xanthomonas L148. Through random mutagenesis, we L148 gspE, encoding a type II secretion system (T2SS) component, is required for damaging rbohD mutant plants. In planta bacterial transcriptomics reveals suppresses most T2SS gene expression including gspE. colonization protected against pathogen, when gspE was by ROS or mutation. Thus, negative feedback loop between tames leaf turns it into microbe beneficial host.

Язык: Английский

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Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome

Environmental Science & Technology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 11, 2025

Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence prevalence heterocyclic compounds soil pose significant risks to health. However, understanding links between microbial responses remains challenging due complexity communities their various chemical structures. This study developed a machine-learning approach that integrates properties structures with diversity bacteria functions predict impact on community improve design eco-friendly compounds. We screened key compounds─particularly those topological polar surface areas (<74.2 Å2 or 111.3–154.1 Å2), carboxyl groups, dissociation constant, which maintained high bacterial functions, revealing threshold effects where specific structural parameters dictated responses. These stabilize increase beneficial carbon nitrogen cycle functions. By applying these parameters, we quantitatively assessed eco-friendliness scores 811 compounds, providing robust foundation for guiding future applications. Our disentangles critical structure-related influence establishes computational framework designing ecological benefits from an perspective.

Язык: Английский

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Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 2, 2023

Plant-associated microbiomes contribute to important ecosystem functions such as host resistance biotic and abiotic stresses. The factors that determine community outcomes are inherently difficult identify under complex environmental conditions. In this study, we present an experimental analytical approach explore microbiota properties relevant for a microbiota-conferred phenotype, here plant protection, in reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification regression analyses well empirical validation test potential explanatory structure composition, including evenness, total commensal colonization, phylogenetic diversity, strain identity. find identity be the most predictor pathogen reduction, with machine learning algorithms improving performances compared random classifications (94-100% versus 32% recall) non-modelled predictions (0.79-1.06 1.5 RMSE). Further confirms three main drivers reduction two additional confer protection combination. Beyond specific application presented our provide framework can adapted help features function other biological systems.

Язык: Английский

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Cooperative virulence via the collective action of secreted pathogen effectors

Nature Microbiology, Год журнала: 2023, Номер 8(4), С. 640 - 650

Опубликована: Фев. 13, 2023

Язык: Английский

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Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags

Nature Microbiology, Год журнала: 2024, Номер 9(4), С. 1103 - 1116

Опубликована: Март 19, 2024

Abstract Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags showed they differentiated high precision. WISH-tags were introduced into model non-model bacterial members mouse plant microbiota. Intrastrain priority effects tested using one species barcoded bacteria in murine gut Arabidopsis phyllosphere, both without microbiota context. observed colonization resistance against late-arriving strains Salmonella Typhimurium gut, whereas phyllosphere accommodated Sphingomonas latecomers manner proportional to their presence at late inoculation timepoint. This demonstrates are resource deciphering microbiome assembly across biological systems.

Язык: Английский

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