Disease-induced changes in plant microbiome assembly and functional adaptation

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Sept. 15, 2021

The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in growth health. Increasing evidence indicates that rhizosphere recruits beneficial microbes to suppress soil-borne pathogens. However, ecological processes govern assembly functions below- aboveground compartments under pathogen invasion are not fully understood. Here, we studied bacterial fungal communities associated with 12 (e.g., soils, roots, stems, fruits) chili pepper (Capsicum annuum L.) using amplicons (16S ITS) metagenomics approaches at main production sites China investigated how Fusarium wilt disease (FWD) affects assembly, co-occurrence patterns, plant-associated microbiomes.The amplicon data analyses revealed FWD affected less on reproductive organs (fruit) than vegetative (root stem), strongest impact upper stem epidermis. Fungal intra-kingdom networks were stable their more sensitive communities. analysis microbial interkingdom network further indicated destabilized induced importance taxa. Although diseased plants susceptible colonization by other pathogenic fungi, can also recruit potential bacteria. Some taxa enriched identified core for microbiomes hub networks. On hand, metagenomic significant enrichment several functional genes involved detoxification, biofilm formation, plant-microbiome signaling pathways (i.e., chemotaxis) plants.Together, demonstrate a could bacteria mitigate changes organ facilitate or its offspring survival. may attract through modulation pathways. These findings significantly advance our understanding interactions provide important harnessing sustainable agriculture. Video abstract.

Language: Английский

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Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: July 5, 2022

Plant response to drought stress involves fungi and bacteria that live on in plants the rhizosphere, yet stability of these myco- micro-biomes remains poorly understood. We investigate resistance resilience an agricultural system using both community composition microbial associations. Here we show tests fundamental hypotheses fungi, as compared bacteria, are (i) more resistant but (ii) less resilient when rewetting relieves stress, found robust support at level composition. Results were complex all-correlations co-occurrence networks. In general, disrupts networks based significant positive correlations among between fungi. Surprisingly, functional guilds rhizosphere leaf strengthened by drought, same was seen for involving arbuscular mycorrhizal rhizosphere. also gradient hypothesis because increased relative frequency correlations.

Language: Английский

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Ecological stability of microbial communities in Lake Donghu regulated by keystone taxa

Ecological Indicators, Journal Year: 2022, Volume and Issue: 136, P. 108695 - 108695

Published: Feb. 21, 2022

Seasonal variations of environmental factors generally result in considerable changes microbiomes, yet we still lack a clear understanding how microbial communities maintain their ecological stability. Here, analyze long-term (nine years) high-throughput sequencing dataset by network analysis to illustrate the stability varies among seasons lake ecosystems. The results showed that networks were distinctly different seasons, and most complex autumn exhibited highest We found strong connecting structures microbes (large modules) significantly (P < 0.05) correlated with water temperature pH, which would negatively affect keystone taxa destabilize communities. more stable removal unstable networks. Moreover, specific due filtering relevant interspecific interactions. These suggested seasonal could influence community via regulation taxa. Thus, be used as indicators reflect findings improve our co-occurrence patterns reveal mechanism aquatic

Language: Английский

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From diversity to complexity: Microbial networks in soils

Soil Biology and Biochemistry, Journal Year: 2022, Volume and Issue: 169, P. 108604 - 108604

Published: March 17, 2022

Network analysis has been used for many years in ecological research to analyze organismal associations, example food webs, plant-plant or plant-animal interactions. Although network is widely applied microbial ecology, only recently it entered the realms of soil shown by a rapid rise studies applying co-occurrence communities. While this application offers great potential deeper insights into structure ecosystems, also brings new challenges related specific characteristics datasets and type questions that can be addressed. In Perspectives Paper we assess ecology due small-scale heterogeneity environment nature datasets. We review different approaches construction are commonly discuss their features limitations. Using test dataset communities from two depths forest soil, demonstrate how experimental designs constructing algorithms affect resulting networks, turn may influence conclusions. will reveal assumptions method, methods preparing dataset, definitions thresholds structure. Finally, particular approached analyzing interpreting properties. Targeting these properties meaningful way allow technique not merely descriptive, but hypothesis-driven research. Analysing networks soils opens window better understanding complexity However, approach unfortunately often draw conclusions which far beyond scientific evidence provide, damaged its reputation analysis. Paper, would like sharpen view real soils, at same time raise awareness regarding limitations ways misused misinterpreted.

Language: Английский

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Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: March 31, 2023

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, crucial for sustaining agricultural growth. Despite its importance, how domestication builds up specific microbiomes metabolic functions, as well the importance of these affected rhizobiomes relevant exudates in maintaining growth, not understood. Here, we firstly investigated bacterial fungal communities wild accessions tetraploid wheat using amplicon sequencing (16S ITS) after 9 years process at main production sites China. We then explored ecological roles exudation shaping microbiome functions integrating metagenomics genomics approaches. Furthermore, established evident linkages between morphology traits keystone taxa based on microbial culture inoculation experiments.Our results suggested that were co-shaped both genotypes status. genomes contributed more variation diversity composition than communities, whereas status exerted much stronger influences communities. In terms interkingdom association networks, destabilized network depleted abundance taxa. Moreover, found shifted from slow growing fungi dominated to fast bacteria dominated, thereby resulting a shift fungi-dominated membership with enrichment carbon fixation genes bacteria-dominated degradation genes. Metagenomics analyses further indicated cultivars possess higher function domesticated cultivars. Notably, cultivar able harness microorganism carrying N transformation (i.e., nitrification, denitrification) P mineralization pathway, inorganic fixation, organic ammonification, solubilization are recruited releasing wheat. More importantly, our metabolite-wide study contrasting functional harnessed different nutrient acquisition strategies jointly determined aboveground phenotypes. observed although wheats distinct domestication-induced recruitment led consistent growth regulation regardless status.Our indicate profoundly assembly provide evidence plants differentiated role root-associated through release sustain belowground multi-nutrient cycles These findings valuable insights into mechanisms underlying plant-microbiome interactions crop improvement sustainable agriculture. Video Abstract.

Language: Английский

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The soil crisis: the need to treat as a global health problem and the pivotal role of microbes in prophylaxis and therapy

Microbial Biotechnology, Journal Year: 2021, Volume and Issue: 14(3), P. 769 - 797

Published: March 10, 2021

Summary Soil provides a multitude of services that are essential to healthily functioning biosphere and continuity the human race, such as feeding growing population sequestration carbon needed counteract global warming. Healthy soil availability is limiting parameter in provision number these services. As result anthropogenic abuses, natural warming‐promoted extreme weather events, Planet Earth currently experiencing an unprecedented crisis deterioration, desertification erosive loss increasingly prejudices it provides. Such pivotal Sustainability Development Goals formulated by United Nations. Immediate coordinated action on scale urgently required slow ultimately reverse healthy soils. Despite ‘dirt‐dust’, non‐vital appearance soil, highly dynamic living entity, whose life overwhelmingly microbial. The microbiota, which constitutes greatest reservoir donor microbial diversity Earth, acts vast bioreactor, mediating myriad chemical reactions turn biogeochemical cycles, recycle wastes, purify water, underpin other Fuelling belowground bioreactor aboveground plant photosynthetic surface captures solar energy, fixes inorganic CO 2 organic carbon, channels fixed energy into soil. In order muster effective response crisis, avoid further restore unhealthy soils, we need new coherent approach, namely deal with soils worldwide patients health care create (i) public system for development policies land use, conservation, restoration, recommendations prophylactic measures, monitoring identification problems (epidemiology), organizing responses, etc., (ii) healthcare charged care: promotion good practices, implementation prophylaxis institution therapies treatment restoration drylands. These systems be national but there also desperate international coordination. To enable effective, evidence‐based strategies will efforts systems, substantial investment wide‐ranging interdisciplinary research disease mandatory. This must lead level understanding soil:biota functionalities underlying key ecosystem enables formulation diagnosis‐prophylaxis‐therapy pathways sustainable protection different types resources climatic zones. conservation‐regenerative‐restorative measures complemented educative‐political‐economic‐legislative framework incentives encouraging knowledge, policy, economic others, laws promote adherence principles restorative management. And: all engaged improving health; everyone has duty ( https://www.bbc.co.uk/ideas/videos/why‐soil‐is‐one‐of‐the‐most‐amazing‐things‐on‐eart/p090cf64 ). Creative application microbes, microbiomes biotechnology central successful operation systems.

Language: Английский

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Organic substitutions improve soil quality and maize yield through increasing soil microbial diversity

Journal of Cleaner Production, Journal Year: 2022, Volume and Issue: 347, P. 131323 - 131323

Published: March 14, 2022

Language: Английский

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High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling

Applied and Environmental Microbiology, Journal Year: 2021, Volume and Issue: 87(21)

Published: Aug. 18, 2021

Revealing the response of soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated effect high salinity on composition and key biogeochemical processes salinized agricultural soils (0.22 19.98 dS m −1 ).

Language: Английский

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Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress

iMeta, Journal Year: 2023, Volume and Issue: 2(1)

Published: Jan. 9, 2023

Abstract Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of responses microbiome to will help in coping with “gray rhino” events environment, thereby contributing an ecologically sustainable future. Considering that microbial ecological networks are tied stability ecosystem functioning abundant rare biospheres different biogeographic patterns important drivers functioning, roles maintaining need be clarified. Here we showed that, increasing salinity induced by freshwater‐to‐seawater transition, diversity reduced significantly taxonomic structure experienced a succession. The complexity were diminished stress. composition microorganisms supporting underwent sharp turnovers during biosphere behaving more robustly than biosphere. Notably, played much role stabilizing under low‐stress environments, but difference between their relative importance narrowed stress, suggesting weakened “Matthew effect” world. With in‐depth insights into ecology our findings highlight adjusting conservation strategies for maintain functions services response rising

Language: Английский

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Decreased soil multifunctionality is associated with altered microbial network properties under precipitation reduction in a semiarid grassland

iMeta, Journal Year: 2023, Volume and Issue: 2(2)

Published: May 1, 2023

Our results reveal different responses of soil multifunctionality to increased and decreased precipitation. By linking microbial network properties functions, we also show that complexity potentially competitive interactions are key drivers multifunctionality.

Language: Английский

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