microSTRESSdb: a curated database for prioritizing bacteria alleviating plant abiotic stress
Microbiological Research, pp. 128762
Abstract
Plant-associated bacteria can enhance plant tolerance to abiotic stresses such as drought, salinity, nutrient limitation and heavy metal contamination. Although bacterial genes involved in plant abiotic-stress alleviation have been experimentally characterised in individual studies, the corresponding sequences and evidence remain dispersed across publications and general-purpose repositories, limiting their systematic reuse for the annotation of new microbial datasets. Here, we present microSTRESSdb, a curated database of genes experimentally tested for their roles in plant abiotic stress alleviation. Version 1.0 of this database contains 72 protein sequences spanning four abiotic stress categories, with metadata on gene product, source organism and accompanying literature. To detect homologues of these stress-associated genes in bacterial genomes and plasmids, we also provide the pipeline and web interface microSTRESS. This pipeline performs BLAST-based screening of input proteomes, integrates hit-level metadata, evaluates pathway completeness and generates interactive HTML reports summarising stress-category coverage, gene functions and a Stress Potential Index (SPI). As use cases, we applied microSTRESS to 3,028 genomes across Pseudomonas and Bacillus and showed that the genomes of the soil- and plant-associated strains contained homologues of several stress-associated genes. Next, we evaluated whether microSTRESS could transfer existing gene-level evidence to the prioritisation of previously uncharacterised bacteria. In an Arabidopsis thaliana drought bioassay with 29 rhizosphere strains, higher drought-specific SPI values were associated with improved maintenance of plant biomass under water limitation, with this association being significant for Flavobacterium but not reaching significance for Pseudomonas . Together, microSTRESSdb and microSTRESS convert experimentally supported gene–phenotype evidence into a standardized and reusable framework for stress-oriented annotation, comparative analysis and genome-guided prioritization of candidate bacteria.
Authors 7
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Leiden University · Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Netherlands Institute of Ecology · University of Applied Sciences Leiden
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherland
Institute of Biology, Leiden University, Leiden, The Netherland
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Leiden University · Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Netherlands Institute of Ecology · University of Applied Sciences Leiden
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherland
Institute of Biology, Leiden University, Leiden, The Netherland
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Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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Leiden University · Netherlands Institute of Ecology · University of Applied Sciences Leiden
Affiliation as printed
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherland
Institute of Biology, Leiden University, Leiden, The Netherland
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Leiden University · Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · University of Applied Sciences Leiden
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
Institute of Biology, Leiden University, Leiden, The Netherland
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Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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Leiden University · Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Netherlands Institute of Ecology · University of Applied Sciences Leiden
Affiliation as printed
Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherland
Institute of Biology, Leiden University, Leiden, The Netherland