Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture

New Phytologist, Journal Year: 2024, Volume and Issue: 242(6), P. 2401 - 2410

Published: March 17, 2024

Summary The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the frequently fluctuates with soil environment, recent studies have demonstrated that a small proportion of is consistently assembled specific genotype regardless condition, which determined by host genetics. Based on these breakthroughs, involved exploiting plant‐beneficial function microbiome, we propose to divide into environment‐dominated genetic‐dominated components based their different assembly mechanisms. Subsequently, two strategies explore agricultural production are suggested, is, precise management agronomic practices, elucidation genetic basis breeding microbiome‐assisted crop varieties. We finally present major challenges need be overcome implement modulating microbiome.

Language: Английский

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Shared governance in the plant holobiont and implications for one health

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(3)

Published: Feb. 13, 2024

Abstract The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner a century ago. Both concepts are strongly supported results from new field microbiome research. Here, we present ecological and genetic features that underpin principles shared governance between hosts microbes summarize relevance in context global change. Moreover, uncover knowledge gaps arise when integrating broader perspective holobiome as well one planetary health concepts. Action needed to consider interacting at scale, prediction control function improve human environmental outcomes.

Language: Английский

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Ralstonia solanacearum differentially modulates soil physicochemical properties and rhizospheric bacteriome of resistant and susceptible tobacco cultivars

Microbiological Research, Journal Year: 2024, Volume and Issue: 281, P. 127604 - 127604

Published: Jan. 10, 2024

Language: Английский

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iMetaOmics: Advancing human and environmental health through integrated meta‐omics

iMetaOmics., Journal Year: 2024, Volume and Issue: 1(1)

Published: Aug. 8, 2024

iMetaOmics is a quarterly international journal with the priority of publishing research work within scope One Health, featured well-designed omics. The also welcomes systematic integration extensive public datasets, new and meaningful perspectives, re-analysis high-impact data yielding different/valuable conclusions. microbiome plays critical roles in human [1], animal [2], plant nutrition health [3], food [4], environment [5], as well other aspects society (Figure 1). Metaomics, including metabarcoding, metagenomics, metatranscriptomics, metaproteomics, metabolomics, provide unique powerful tools to better understand taxonomy functions microbiome, biology, [6]. Aiming fill gap lacking top journals field Asia, iMeta Science Society its thousands Chinese scientist members found young but journal—iMeta (ISSN: 2770-5986; eISSN: 2770-596X). It has published more than 200 high-quality papers since 2022, original articles, reproducible methods protocols, systemic reviews peers updated novel findings, easy-to-use analytic tools, knowledge [7]. These publications include are not limited gut pertaining diseases [8], microbiota animals (e.g., chicken [9], pig [10], panda [11]), pan-cancer [12] pan-genome [13], soil associated diversity defense [14, 15], popular for metaomics analyses [16-18]. With great efforts contributions our stakeholders, like publisher, editorial board members, authors, reviewers, received first impact factor 23.7 2024, gradually accumulating broad diverse audiences readership, especially attracting explosive growth submissions recent days. To cope significantly increased submissions, we have from bimonthly journal. However, publication space maintaining high standard iMeta, still reject 90% although many them did an excellent work. Due success officially launching sister (eISSN: 2996-9514, ISSN: 2996-9506), further publish articles [19-23], [24-28], state-of-the-art methodologies [29, 30] satisfy increasing submission demand iMeta. Taking advantage same team, rejected manuscripts valuable/meaningful findings will be transferred iMetaOmics, together detailed comments reviewers. In this context, following review process shortened promote rapid publishing. Before official launch, 12 already been upon approval by authors issue. Currently, featuring reanalysis expected that establish reputation soon, attract wide range interest readers, contribute progress Human Environmental Health studies. Authors' own priority, while utilization analysis robust experimental validation can considered. Multiple evidence required support conclusion. New strategies advantage, indispensable. All used without reasonable concerns should publicly/temporally accessible reviewers editors. A video tutorial, software download, installation, operation, result displaying, highly recommended bioinformatic tools. Additionally, necessary ethics numbers, clear layouts, figures, significant expected. Chun-Lin Shi: Writing—original draft; writing—review editing. Tong Chen: Writing—review Canhui Lan: Ren-You Gan: Jun Yu: Fangqing Zhao: Yong-Xin Liu: editing; conceptualization. Zhao Yu hold position Editor-in-Chief iMetaOmics. Liu, Chen, Lan, Shi Gan Executive Editors

Language: Английский

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Endophytic bacterial communities in wild rice (Oryza officinalis) and their plant growth-promoting effects on perennial rice

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 14, 2023

Endophytic bacterial microbiomes of plants contribute to the physiological health host and its adaptive evolution stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis unique perennial wild species in China with rich genetic resources. However, communities this their plant growth-promoting (PGP) traits remain largely unknown. In study, root, stem, leaf tissues O. were characterized using 16S rRNA gene Illumina sequencing. Culturable endophytes also isolated from PGP traits. The microbiome analysis showed more complex structure powerful function community roots compared those other tissue compartments. Each compartment had specific biomarkers, including Desulfomonile Ruminiclostridium roots; Lactobacillus, Acinetobacter, Cutibacterium Dechloromonas stems; Stenotrophomonas, Chryseobacterium, Achromobacter Methylobacterium leaves. A total 96 strains phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, siderophore or indole-3-acetic acid (IAA) production officinalis. Among them, 11 identified as Enterobacter mori, E. ludwigii, cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae Kosakonia oryzae selected inoculation based on IAA These promising effects seedlings. They promoted form strong root system, stimulate biomass accumulation, increase chlorophyll content uptake, could fulfil ecologically cultivation model rice. results provide insights into endosphere application There prospect mining beneficial species, rewild cultivated varieties promote growth.

Language: Английский

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Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

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

Published: Sept. 30, 2023

Abstract Background Microbiome recruitment is influenced by plant host, but how host impacts the assembly, functions, and interactions of perennial root microbiomes poorly understood. Here we examined prokaryotic fungal communities between rhizosphere soils endophytic compartment in two native Miscanthus species ( sinensis floridulus ) Taiwan further explored roles on root-associated microbiomes. Results Our results suggest that genetic variation, edaphic factors, site had effects soil microbial community compositions both , with a greater effect variation observed for communities. Host also exerted stronger core than non-core each microhabitat species. From to endophytes, co-occurrence network stability increased, decreased. Furthermore, found were more strongly driven deterministic processes rather stochastic processes. Root-enriched OTUs belong Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, [Saprospirae] species, while taxa enriched are widely distributed among different phyla. Conclusions We provide empirical evidence plays important microbiome . The this study have implications future bioenergy crop management providing baseline data inform translational research harness sustainably increase agriculture productivity.

Language: Английский

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Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes

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

Published: Jan. 1, 2024

Antibiotic resistance in plant-associated microbiomes poses significant risks for agricultural ecosystems and human health. Although accumulating evidence suggests a role plant genotypes shaping their microbiome, almost nothing is known about how the changes of genetic information affect co-evolved microbiome carrying antibiotic genes (ARGs). Here, we selected 16 wheat cultivars experimentally explored impact host variation on phyllosphere ARGs, metabolites. Our results demonstrated that significantly influenced resistomes. Wheat exhibiting high ARGs were linked to elevated Pseudomonas populations, along with increased abundances aeruginosa biofilm formation genes. Further analysis 350 spp. genomes from diverse habitats at global scale revealed nearly all strains possess multiple virulence factor (VFGs), mobile elements (MGEs) genomes, albeit lower nucleotide diversity compared other species. These findings suggested proliferation contributed resistance. We further observed direct links between upregulated leaf metabolite DIMBOA-Glc, spp., enrichment which corroborated by microcosm experiments demonstrating DIMBOA-Glc enhanced relative abundance Overall, alterations metabolites resulting throughout evolution may drive development highly specialized microbial communities capable enriching ARGs. This study enhances our understanding plants actively shape clarifies

Language: Английский

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Balancing Nature and Nurture: The Role of Biocontrol Agents in Shaping Plant Microbiomes for Sustainable Agriculture

Microorganisms, Journal Year: 2025, Volume and Issue: 13(2), P. 323 - 323

Published: Feb. 2, 2025

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent characteristics and environmental factors shape plant-associated microbiota. These determine which thrive they interact plants; certain conditions favor beneficial bacteria, others support pathogens. In this mini-review, we focus on an additional factor influencing microbiomes their surrounding environments: use of biocontrol agents. The increasing application microbial inoculants metabolites as strategies agriculture has created a critical knowledge gap about effects introducing non-native species into natural ecosystems. inoculation plants environments exogenous microorganisms potential alter community diversity composition, presenting opportunities challenges for sustainable agricultural practices.

Language: Английский

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Harnessing Aspergillus and host M genes for sustainable phyllosphere microbiome engineering

Crop Health, Journal Year: 2025, Volume and Issue: 3(1)

Published: March 4, 2025

Language: Английский

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Contrasting roles of abundant and rare root-associated fungi in wheat: Community assembly, heritability and agronomic impacts

Applied Soil Ecology, Journal Year: 2025, Volume and Issue: 209, P. 106032 - 106032

Published: March 15, 2025

Language: Английский

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