Strategies for tailoring functional microbial synthetic communities

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity soil microorganisms their complex interactions make it challenging to pinpoint the main players life support functions can provide plants, including enhanced tolerance (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity unravel molecular chemical basis interplay specific microbiome functions. While SynComs have been successfully employed dissect or reproduce microbiome-associated phenotypes, assembly reconstitution these often based on generic abundance patterns taxonomic identities co-occurrences but only rarely informed by functional traits. Here, we review recent studies designing reveal common principles discuss multidimensional approaches community design. We propose strategy tailoring design integration high-throughput experimental assays with strains computational genomic analyses capabilities.

Language: Английский

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Insights into the mechanisms driving microbial community succession during pepper fermentation: Roles of microbial interactions and endogenous environmental changes

Food Research International, Journal Year: 2024, Volume and Issue: 179, P. 114033 - 114033

Published: Jan. 21, 2024

Language: Английский

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Bacterial interactions mediated by acetic acid and their impact on flavor profile during acetic acid fermentation stage of Shanxi aged vinegar

Food Bioscience, Journal Year: 2025, Volume and Issue: unknown, P. 105996 - 105996

Published: Jan. 1, 2025

Language: Английский

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Importance of pathobiomes to the success of microbial weed biocontrol agents

Biological Control, Journal Year: 2024, Volume and Issue: 192, P. 105498 - 105498

Published: March 15, 2024

The role of microbial communities in the establishment plant pathogens introduced to new environments as weed biocontrol agents is relatively unexplored. Substantial evidence from crop protection research shows how bulk influence establishment, survival, and success pathogens. Just mismatches between agents, host genotypes, climate can lead failure, we propose that resident microbiomes may be a cause apparent failures. From this perspective, discuss recent progress on plant-associated whose interactions disease development, or "pathobiomes," consider implications for agent evaluation release. Open questions about pathobiomes develop rates provide ample opportunity researchers adapt methods analytical frameworks will enhance programs. We conclude by prioritizing development standard include component release studies. Developing pathobiome-aware selection process improve outcomes.

Language: Английский

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Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 365, P. 121509 - 121509

Published: June 18, 2024

Language: Английский

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Quantitative principles of microbial metabolism shared across scales

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(8), P. 1940 - 1953

Published: Aug. 6, 2024

Language: Английский

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Re-Envisioning the Plant Disease Triangle by Integration of Host Microbiota and a Pivot in Focus to Health Outcomes

Annual Review of Phytopathology, Journal Year: 2024, Volume and Issue: 62(1), P. 31 - 47

Published: April 29, 2024

The disease triangle is a structurally simple but conceptually rich model that used in plant pathology and other fields of study to explain infectious as an outcome the three-way relationship between host, pathogen, their environment. It also serves guide for finding solutions treat, predict, prevent such diseases. With omics-driven, evidence-based realization abundance activity pathogen are impacted by proximity interaction with diverse multitude microorganisms colonizing same evolved into tetrahedron shape, which features added fourth dimension representing host-associated microbiota. Another variant emerged from recently formulated pathobiome paradigm, deviates classical "one pathogen" etiology favor scenario represents conditional complex interactions among its microbiota (including microbes pathogenic potential), result version original where "pathogen" substituted "microbiota." Here, part careful concise review origin, history, usage triangle, I propose next step evolution, replace word "disease" center host-microbiota-environment triad "health." This highlights health desirable (rather than unwanted state) emergent property interactions. Applied discipline pathology, offers expanded range targets approaches diagnosis, prediction, restoration, maintenance outcomes. Its applications not restricted diseases only, underlying framework more inclusive all microbial contributions well-being, including those mycorrhizal fungi nitrogen-fixing bacteria, there never was proper place triangle. may have edge education communication tool convey stress importance healthy plants associated broader public stakeholdership.

Language: Английский

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Ironing out the conflicts: iron supplementation reduces negatives bacterial interactions in the rhizosphere of an Atacama-endemic perennial grass

Environmental Microbiome, Journal Year: 2025, Volume and Issue: 20(1)

Published: March 11, 2025

In plants, root exudates selectively influence the growth of bacteria that colonize rhizosphere. Bacterial communities associated with systems are involved in macro and micronutrients cycling organic matter transformation. particular, iron is an essential micronutrient required for proper functioning iron-containing enzymes processes such as photosynthesis, respiration, biomolecule synthesis, redox homeostasis, cell plants. However, impact changes availability on structure set ecological interactions taking place rhizosphere remains poorly understood. this study, field experiments were conducted to compare effects supplementation (0.1 0.5 mM FeSO4) assembly bacterial community soil bulk a perennial grass present Andes steppe Atacama Desert. The results indicated difference beta diversity between detected before did not persist after supplementation, addition, co-occurrence networks showed significant reduction negative among bacteria, mainly rare taxa (< 0.1% relative abundance). These observations suggest contributes differentiation communities, process linked abundance more abundant species (> abundance) decrease both compartments metal exposure. differential effect competition/cooperation ratio soils microbiome supports hypothesis host limits degree cooperation can be achieved by organ dedicated nutrient absorption.

Language: Английский

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Wetland restoration suppresses microbial carbon metabolism by altering keystone species interactions

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: April 30, 2025

Soil bacteria play a pivotal role in regulating multifaceted functions of terrestrial ecosystems. Unraveling the succession bacterial communities and feedback mechanism on soil organic carbon (SOC) dynamics help embed ecology microbiome into C cycling model. However, how wetland restoration drives community assembly species association to regulate microbial metabolism remains unclear. Here, we investigated diversity, structure co-occurrence network, enzyme activities SOC decomposition restored wetlands for one, three, four years from paddy fields Northeast China. Wetland three increased taxonomic (richness) phylogenetic diversities by 2.39–3.96% 2.13–3.02%, respectively, relative contribution nestedness dissimilarity, indicating richness changed structure. decreased index aerobic Firmicutes 5.04–5.74% due stronger anaerobic condition characterized Fe 2+ /Fe 3+ 0.20 0.64. Besides, network complexity (characterized node number 2.51%, edge 9.62%, positive/negative 6.37%, average degree 5.74% centralization 6.34%). Robustness with increase duration, while vulnerability that stability communities. These results might be because induced decrease Bacilli keystone module, thereby reducing positive within module. Decreased module turn weakened decreasing hydrolase 7.49 5.37 mmol kg −1 h oxidase 627 411 , leading rate 1.39 1.08 g during restoration. Overall, our suggested although after agricultural abandonment it Bacilli-dominated under condition, which decomposition.

Language: Английский

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Polymorphic Plant Architectures: A Pathological Approach to Growing a Building

Published: Feb. 13, 2024

Considering the prospects of Engineered Living Materials (ELMs), a parallel can be drawn between building and tree. How we might grow living follows nearly same processes as how healthy productive forest. Agential systems such plants fungi must respond to navigate in their environment, naturally resulting polymorphic growth architecture defined by local stimuli. A symbiotic relationship two provides ready means shape natural plasticity during plant using pathogenic agents capable inducing morphogenesis. Exotic infection morphologies from pathogens are examined emerging perspective growing building. Transitioning forest pathogen biodesign agent botanical building, host-pathogen symbiosis intrinsically links management both. maybe employed is uniquely transferable across research disciplines

Language: Английский

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