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Tomato microbiome under long‐term organic and conventional farming

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis

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High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea

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Actinotalea suaedae sp. nov., isolated from the halophyte Suaeda physophora in Xinjiang, Northwest China

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Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina

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Plant-assisted selection: a promising alternative for in vivo identification of wheat (Triticum turgidum L. subsp. Durum) growth promoting bacteria

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Fertilization effects on microbial community composition and aggregate formation in saline‐alkaline soil

inferredcites →https://doi.org/10.1016/b978-0-12-819715-8.00007-0openalex-snapshot

Sugarcane microbiome: role in sustainable production

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Two types nitrogen source supply adjusted interaction patterns of bacterial community to affect humifaction process of rice straw composting

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The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

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Nitrogen footprint and nitrogen use efficiency of greenhouse tomato production in North China

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Responses of soil fertility and microbiomes of atrazine contaminated soil to remediation by hydrochar and persulfate

inferredcites →https://doi.org/10.1016/j.mib.2019.10.010openalex-snapshot

Reductionist synthetic community approaches in root microbiome research

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Comparing the yields of organic and conventional agriculture

inferredcites →https://doi.org/10.1038/nrmicro.2017.87openalex-snapshot

Embracing the unknown: disentangling the complexities of the soil microbiome

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Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

inferredcites →https://doi.org/10.1038/s41396-020-0648-9openalex-snapshot

Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean

inferredcites →https://doi.org/10.1038/s41477-018-0139-4openalex-snapshot

Core microbiomes for sustainable agroecosystems

inferredcites →https://doi.org/10.1038/s41522-021-00204-9openalex-snapshot

Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum

inferredcites →https://doi.org/10.1038/s41564-020-0719-8openalex-snapshot

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes

inferredcites →https://doi.org/10.1038/s41586-020-2185-0openalex-snapshot

A plant genetic network for preventing dysbiosis in the phyllosphere

inferredcites →https://doi.org/10.1038/s41587-019-0104-4openalex-snapshot

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

inferredcites →https://doi.org/10.1038/s41598-017-01269-3openalex-snapshot

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle

inferredcites →https://doi.org/10.1038/s41598-022-09818-1openalex-snapshot

Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management

inferredcites →https://doi.org/10.1073/pnas.1302837110openalex-snapshot

Diversity and heritability of the maize rhizosphere microbiome under field conditions

inferredcites →https://doi.org/10.1080/1065657x.2016.1238786openalex-snapshot

Effects of Long-Term Use of Compost on N2O and CO2Fluxes in Greenhouse Vegetable Systems

inferredcites →https://doi.org/10.1093/femsec/fiaa052openalex-snapshot

Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling

inferredcites →https://doi.org/10.1093/femsec/fiab018openalex-snapshot

Tillage shapes the soil and rhizosphere microbiome of barley—but not its susceptibility towards Blumeria graminis f. sp. hordei

inferredcites →https://doi.org/10.1094/pbiomes-05-17-0023-ropenalex-snapshot

The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

inferredcites →https://doi.org/10.1094/phyto-12-11-0349openalex-snapshot

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

inferredcites →https://doi.org/10.1101/081257openalex-snapshot

UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

inferredcites →https://doi.org/10.1111/1574-6968.12377openalex-snapshot

The communities of tomato (Solanum lycopersicumL.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing

inferredcites →https://doi.org/10.1111/1751-7915.13640openalex-snapshot

Synthetic community with six Pseudomonas strains screened from garlic rhizosphere microbiome promotes plant growth

inferredcites →https://doi.org/10.1111/j.1365-2664.2005.01005.xopenalex-snapshot

The effects of organic agriculture on biodiversity and abundance: a meta‐analysis

inferredcites →https://doi.org/10.1111/j.1462-2920.2006.01028.xopenalex-snapshot

Structure and activity of bacterial community inhabiting rice roots and the rhizosphere

inferredcites →https://doi.org/10.1111/j.1574-6968.2007.00918.xopenalex-snapshot

Bacterial endophytes: recent developments and applications

inferredcites →https://doi.org/10.1111/j.1654-1103.2003.tb02228.xopenalex-snapshot

VEGAN, a package of R functions for community ecology

inferredcites →https://doi.org/10.1111/j.2041-210x.2010.00078.xopenalex-snapshot

Testing the significance of canonical axes in redundancy analysis

inferredcites →https://doi.org/10.1111/nph.16890openalex-snapshot

Host selection shapes crop microbiome assembly and network complexity

inferredcites →https://doi.org/10.1126/science.aaw9285openalex-snapshot

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

inferredcites →https://doi.org/10.1128/mbio.02527-14openalex-snapshot

The Soil Microbiome Influences Grapevine-Associated Microbiota

inferredcites →https://doi.org/10.1139/cjm-2020-0002openalex-snapshot

Corn microbial diversity and its relationship to yield

inferredcites →https://doi.org/10.1146/annurev-arplant-050312-120106openalex-snapshot

Structure and Functions of the Bacterial Microbiota of Plants

inferredcites →https://doi.org/10.1186/1471-2180-12-1openalex-snapshot

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

inferredcites →https://doi.org/10.1371/journal.pone.0223847openalex-snapshot

Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants

inferredcites →https://doi.org/10.15302/j-fase-2020346openalex-snapshot

Rhizosphere immunity: targeting the underground for sustainable plant health management

inferredcites →https://doi.org/10.1609/icwsm.v3i1.13937openalex-snapshot

Gephi: An Open Source Software for Exploring and Manipulating Networks

inferredcites →https://doi.org/10.3389/fmicb.2018.02977openalex-snapshot

Xylem Sap Proteomics Reveals Distinct Differences Between R Gene- and Endophyte-Mediated Resistance Against Fusarium Wilt Disease in Tomato

inferredcites →https://doi.org/10.3389/fmicb.2019.00342openalex-snapshot

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici)

inferredcites →https://doi.org/10.3389/fmicb.2019.01927openalex-snapshot

Bacterial Profiling and Dynamic Succession Analysis of Phlebopus portentosus Casing Soil Using MiSeq Sequencing

inferredcites →https://doi.org/10.3389/fmicb.2021.798476openalex-snapshot

Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

inferredcites →https://doi.org/10.3389/fpls.2015.00490openalex-snapshot

Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices

inferredcites →https://doi.org/10.3389/fpls.2019.00945openalex-snapshot

Pochonia chlamydosporia Induces Plant-Dependent Systemic Resistance to Meloidogyne incognita

inferredcites →https://doi.org/10.3389/fpls.2019.00979openalex-snapshot

Endophyte-Mediated Resistance in Tomato to Fusarium oxysporum Is Independent of ET, JA, and SA

inferredcites →https://doi.org/10.3390/microorganisms8020170openalex-snapshot

Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota

inferredcites →https://doi.org/10.3390/microorganisms8111708openalex-snapshot

Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

inferredcites →https://doi.org/10.3791/57932openalex-snapshot

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4685843openalex-extracted

Rhizosphere Microbial Composition Patterns and Factors Driving Community Construction in the Wild Endangered Plant Lilium Tsingtauenserhizosphere Microbial Composition Patterns and Factors Driving Community Construction in the Wild Endangered Plant Lilium Tsingtauense

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The active effect of Rhizophagus irregularis inoculants on maize endophytic bacteria community

inferred← citeshttps://doi.org/10.1002/imt2.133openalex-snapshot

Rhizosphere interface microbiome reassembly by arbuscular mycorrhizal fungi weakens cadmium migration dynamics

inferred← citeshttps://doi.org/10.1002/imt2.135openalex-snapshot

Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

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Host selection tendency of key microbiota in arid desert lichen crusts

inferred← citeshttps://doi.org/10.1002/ppp3.70134openalex-snapshot

Novel applications of the tomato microbiome: Roles and considerations for agriculture, human health, and society

inferred← citeshttps://doi.org/10.1007/s00253-023-12641-xopenalex-snapshot

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis

inferred← citeshttps://doi.org/10.1007/s11104-025-08092-0openalex-snapshot

Organic farming promotes general disease suppression and modulates functional potential of rhizosphere microbiome in mustard

inferred← citeshttps://doi.org/10.1016/j.apsoil.2026.107190openalex-snapshot

Rhizosphere prokaryotic microbiota of aquaponic systems (Oreochromis niloticus-Solanum lycopersicum L.) comprises bacterial and archaeal lineages involved in nitrogen metabolism

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Seasonal dynamics of cross-trophic interactions and bottom-up effects: Implications for biodiversity conservation in dam-regulated Rivers

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Integration of intercropping with reduced N fertilization enhances soil micro-food web complexity and stability: Insights from soil biodiversity and multitrophic associations

inferred← citeshttps://doi.org/10.1016/j.jhazmat.2024.133788openalex-snapshot

Deciphering soil resistance and virulence gene risks in conventional and organic farming systems

inferred← citeshttps://doi.org/10.1016/j.lssr.2026.01.010openalex-snapshot

The microbial communities of a tomato crop grown in Veggie under different lighting regimes on the International Space Station

inferred← citeshttps://doi.org/10.1093/hr/uhaf092openalex-snapshot

Metabolite-mediated responses of phyllosphere microbiota to powdery mildew infection in resistant and susceptible black currant cultivars

inferred← citeshttps://doi.org/10.1093/jambio/lxaf273openalex-snapshot

Phyllosphere microbiome shifts reveal Gluconobacter japonicus T12B as a biocontrol agent against Xanthomonas in tomato through genomic and functional characterization

inferred← citeshttps://doi.org/10.1128/spectrum.00966-24openalex-snapshot

Altitudinal variation in rhizosphere microbial communities of the endangered plant Lilium tsingtauense and the environmental factors driving this variation

inferred← citeshttps://doi.org/10.1186/s12870-025-07068-7openalex-snapshot

Rare taxa as the major drivers of the secondary metabolite accumulation in Rheum tanguticum

inferred← citeshttps://doi.org/10.1186/s40168-025-02281-wopenalex-snapshot

Synthetic microbial community in pristine environment promotes the growth of the endangered plant Lilium tsingtauense

inferred← citeshttps://doi.org/10.1590/1413-7054202347006223openalex-snapshot

Soil enzyme activities and microbial community modulation after addition of poultry litter amendment enriched with Bacillus spp.

inferred← citeshttps://doi.org/10.17584/rcch.2023v17i1.15702openalex-snapshot

Bacterial microbiome and physicochemical properties of irrigation water and soil in Chonto type tomato from Boyaca, Colombia

inferred← citeshttps://doi.org/10.3389/fagro.2026.1755662openalex-snapshot

Natural farming as a sustainable agricultural approach enhances soil health and microbial diversity in wheat cultivation: a metagenomic perspective

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1453699openalex-snapshot

Exploring the impact of plant genotype and fungicide treatment on endophytic communities in tomato stems

inferred← citeshttps://doi.org/10.3389/fmicb.2026.1886660openalex-snapshot

Saline-alkali gradients reshape soil microbial network complexity and niche breadth

inferred← citeshttps://doi.org/10.3390/agronomy14071456openalex-snapshot

A Reasonable Rotation Fallow Mode Enhances the Complexity of the Soil Bacterial Network and Enriches Nitrogen-Cycling-Related Taxa

inferred← citeshttps://doi.org/10.3390/children11070770openalex-snapshot

The Association of Neonatal Gut Microbiota Community State Types with Birth Weight

inferred← citeshttps://doi.org/10.3390/microorganisms11071633openalex-snapshot

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

inferred← citeshttps://doi.org/10.3390/w15132328openalex-snapshot

Synergistic Removal of β-Hexachlorocyclohexane from Water via Microorganism–Plant Technology and Analysis of Bacterial Community Characteristics

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