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Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions

  • 1.

    Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663. https://doi.org/10.1111/1574-6976.12028 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 2.

    Bhattarai, A., Bhattarai, B. & Pandey, S. Variation of soil microbial population in different soil horizons. J. Microbiol. Exp. 2, 00044. https://doi.org/10.15406/jmen.2015.02.00044 (2015).

    Article 

    Google Scholar 

  • 3.

    Liu, F. et al. Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly. BMC Microbiol. 19, 201. https://doi.org/10.1186/s12866-019-1572-x (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 4.

    Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. U.S.A. 112, E911-920. https://doi.org/10.1073/pnas.1414592112 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 5.

    Vives-Peris, V., de Ollas, C., Gomez-Cadenas, A. & Perez-Clemente, R. M. Root exudates: From plant to rhizosphere and beyond. Plant Cell Rep. 39, 3–17. https://doi.org/10.1007/s00299-019-02447-5 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 6.

    Qu, Q. et al. Rhizosphere microbiome assembly and its impact on plant growth. J. Agric. Food Chem. 68, 5024–5038. https://doi.org/10.1021/acs.jafc.0c00073 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 7.

    Schmidt, J. E., Kent, A. D., Brisson, V. L. & Gaudin, A. C. M. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome 7, 146. https://doi.org/10.1186/s40168-019-0756-9 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 8.

    Cordero, J., de Freitas, J. R. & Germida, J. J. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can. J. Microbiol. 66, 71–85. https://doi.org/10.1139/cjm-2019-0330 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 9.

    Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403. https://doi.org/10.1016/j.chom.2015.01.011 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 10.

    Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90. https://doi.org/10.1038/nature11237 (2012).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Leoni, C. et al. Plant Health and Rhizosphere microbiome: Effects of the bionematicide Aphanocladium album in tomato plants infested by Meloidogyne javanica. Microorganisms https://doi.org/10.3390/microorganisms8121922 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 12.

    Vitulo, N. et al. Bark and grape microbiome of vitis vinifera: Influence of geographic patterns and agronomic management on bacterial diversity. Front. Microbiol. 9, 3203. https://doi.org/10.3389/fmicb.2018.03203 (2018).

    Article 
    PubMed 

    Google Scholar 

  • 13.

    Hu, J. et al. Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development. Environ. Microbiol. 22, 5005–5018. https://doi.org/10.1111/1462-2920.15097 (2020).

    Article 
    PubMed 

    Google Scholar 

  • 14.

    Qiao, Q. et al. The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage. Sci. Rep. 7, 3940. https://doi.org/10.1038/s41598-017-04213-7 (2017).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Baudoin, E., Benizri, E. & Guckert, A. Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting. Appl. Soil. Ecol. 19, 135–145. https://doi.org/10.1016/S0929-1393(01)00185-8 (2002).

    Article 

    Google Scholar 

  • 16.

    DeAngelis, K. M. et al. Selective progressive response of soil microbial community to wild oat roots. ISME J. 3, 168–178. https://doi.org/10.1038/ismej.2008.103 (2009).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 17.

    Ding, L. J. et al. Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiz040 (2019).

    Article 
    PubMed 

    Google Scholar 

  • 18.

    Fan, K. et al. Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields. Soil Biol. Biochem. 113, 275–284. https://doi.org/10.1016/j.soilbio.2017.06.020 (2017).

    CAS 
    Article 

    Google Scholar 

  • 19.

    Jaiswal, S. K., Mohammed, M. & Dakora, F. D. Microbial community structure in the rhizosphere of the orphan legume Kersting’s groundnut [Macrotyloma geocarpum (Harms) Marechal & Baudet]. Mol. Biol. Rep. 46, 4471–4481. https://doi.org/10.1007/s11033-019-04902-8 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 20.

    Kuramae, E. E. et al. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol. Ecol. 79, 12–24. https://doi.org/10.1111/j.1574-6941.2011.01192.x (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 21.

    Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120. https://doi.org/10.1128/AEM.00335-09 (2009).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 22.

    Mendes, L. W., Kuramae, E. E., Navarrete, A. A., van Veen, J. A. & Tsai, S. M. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 8, 1577–1587. https://doi.org/10.1038/ismej.2014.17 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 23.

    Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. U.S.A. 110, 6548–6553. https://doi.org/10.1073/pnas.1302837110 (2013).

    ADS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Perez-Jaramillo, J. E. et al. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome 7, 114. https://doi.org/10.1186/s40168-019-0727-1 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 25.

    Sugiyama, A., Ueda, Y., Zushi, T., Takase, H. & Yazaki, K. Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS ONE 9, e100709. https://doi.org/10.1371/journal.pone.0100709 (2014).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 26.

    Xu, J. et al. The structure and function of the global citrus rhizosphere microbiome. Nat. Commun. 9, 4894. https://doi.org/10.1038/s41467-018-07343-2 (2018).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Haldar, S. & Sengupta, S. Impact of plant development on the rhizobacterial population of Arachis hypogaea: A multifactorial analysis. J. Basic Microbiol. 55, 922–928. https://doi.org/10.1002/jobm.201400683 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 28.

    Dai, L. et al. Effect of drought stress and developmental stages on microbial community structure and diversity in peanut rhizosphere soil. Int. J. Mol. Sci. https://doi.org/10.3390/ijms20092265 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 29.

    Desmae, H. et al. Genetics, genomics and breeding of groundnut (Arachis hypogaea L.). Plant Breed 138, 425–444. https://doi.org/10.1111/pbr.12645 (2019).

    Article 
    PubMed 

    Google Scholar 

  • 30.

    Pandey, M. K. et al. Translational genomics for achieving higher genetic gains in groundnut. Theor. Appl. Genet. 133, 1679–1702. https://doi.org/10.1007/s00122-020-03592-2 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 31.

    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583. https://doi.org/10.1038/nmeth.3869 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 32.

    Parks, D. H. et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat. Biotechnol. 38, 1079–1086. https://doi.org/10.1038/s41587-020-0501-8 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 33.

    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004. https://doi.org/10.1038/nbt.4229 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 34.

    Lalucat, J., Mulet, M., Gomila, M. & Garcia-Valdes, E. Genomics in bacterial taxonomy: impact on the genus pseudomonas. Genes https://doi.org/10.3390/genes11020139 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Correa-Galeote, D., Bedmar, E. J., Fernandez-Gonzalez, A. J., Fernandez-Lopez, M. & Arone, G. J. Bacterial communities in the rhizosphere of Amilaceous Maize (Zea mays L.) as assessed by pyrosequencing. Front. Plant Sci. 7, 1016. https://doi.org/10.3389/fpls.2016.01016 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Xu, Y. et al. Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.). Int. Microbiol. 23, 453–465. https://doi.org/10.1007/s10123-020-00118-0 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 37.

    Hamonts, K. et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. 20, 124–140. https://doi.org/10.1111/1462-2920.14031 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 38.

    Ansari, F. A. & Ahmad, I. Isolation, functional characterization and efficacy of biofilm-forming rhizobacteria under abiotic stress conditions. Antonie Van Leeuwenhoek 112, 1827–1839. https://doi.org/10.1007/s10482-019-01306-3 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 39.

    Singh, T. B. et al. Identification, characterization and evaluation of multifaceted traits of plant growth promoting rhizobacteria from soil for sustainable approach to agriculture. Curr. Microbiol. 77, 3633–3642. https://doi.org/10.1007/s00284-020-02165-2 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 40.

    Govindasamy, V. et al. Multi-trait PGP rhizobacterial endophytes alleviate drought stress in a senescent genotype of sorghum [Sorghum bicolor (L.) Moench]. 3 Biotech 10, 13. https://doi.org/10.1007/s13205-019-2001-4 (2020).

    Article 
    PubMed 

    Google Scholar 

  • 41.

    Abedinzadeh, M., Etesami, H. & Alikhani, H. A. Characterization of rhizosphere and endophytic bacteria from roots of maize (Zea mays L.) plant irrigated with wastewater with biotechnological potential in agriculture. Biotechnol. Rep. 21, e00305. https://doi.org/10.1016/j.btre.2019.e00305 (2019).

    Article 

    Google Scholar 

  • 42.

    Hashem, A., Tabassum, B. & Allah, F. A. Bacillus subtilis: A plant-growth promoting rhizobacterium that also impacts biotic stress. Saudi J. Biol. Sci. 26, 1291–1297. https://doi.org/10.1016/j.sjbs.2019.05.004 (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 43.

    Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542. https://doi.org/10.1038/s41564-017-0012-7 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 44.

    Gomez-Lama Cabanas, C. et al. Indigenous Pseudomonas spp. strains from the olive (Olea europaea L.) rhizosphere as effective biocontrol agents against Verticillium dahliae: From the host roots to the bacterial genomes. Front. Microbiol. 9, 277. https://doi.org/10.3389/fmicb.2018.00277 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Ansari, F. A. & Ahmad, I. Fluorescent pseudomonas-FAP2 and Bacillus licheniformis interact positively in biofilm mode enhancing plant growth and photosynthetic attributes. Sci. Rep. 9, 4547. https://doi.org/10.1038/s41598-019-40864-4 (2019).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Pandey, K. K., Mayilraj, S. & Chakrabarti, T. Pseudomonas indica sp. nov., a novel butane-utilizing species. Int. J. Syst. Evol. Microbiol. 52, 1559–1567. https://doi.org/10.1099/00207713-52-5-1559 (2002).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 47.

    Shade, A., Jacques, M. A. & Barret, M. Ecological patterns of seed microbiome diversity, transmission, and assembly. Curr. Opin. Microbiol. 37, 15–22. https://doi.org/10.1016/j.mib.2017.03.010 (2017).

    Article 
    PubMed 

    Google Scholar 

  • 48.

    Adam, E., Bernhart, M., Müller, H., Winkler, J. & Berg, G. The Cucurbita pepo seed microbiome: Genotype-specific composition and implications for breeding. Plant Soil 422, 35–49. https://doi.org/10.1007/s11104-016-3113-9 (2018).

    CAS 
    Article 

    Google Scholar 

  • 49.

    Truyens, S., Weyens, N., Cuypers, A. & Vangronsveld, J. Bacterial seed endophytes: Genera, vertical transmission and interaction with plants. Environ. Microbiol. Rep. 7, 40–50. https://doi.org/10.1111/1758-2229.12181 (2015).

    Article 

    Google Scholar 

  • 50.

    Kong, H. G., Song, G. C. & Ryu, C.-M. Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory. Environ. Microbiol. Rep. 11, 479–486. https://doi.org/10.1111/1758-2229.12760 (2019).

    Article 
    PubMed 

    Google Scholar 

  • 51.

    Frindte, K., Pape, R., Werner, K., Loffler, J. & Knief, C. Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients. ISME J. 13, 2031–2043. https://doi.org/10.1038/s41396-019-0409-9 (2019).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Cook, R. J. et al. Molecular mechanisms of defense by rhizobacteria against root disease. Proc. Natl. Acad. Sci. U.S.A. 92, 4197–4201. https://doi.org/10.1073/pnas.92.10.4197 (1995).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Chaparro, J. M., Badri, D. V. & Vivanco, J. M. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 8, 790–803. https://doi.org/10.1038/ismej.2013.196 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 54.

    Sharma, S. B., Sayyed, R. Z., Trivedi, M. H. & Gobi, T. A. Phosphate solubilizing microbes: Sustainable approach for managing phosphorus deficiency in agricultural soils. Springerplus 2, 587. https://doi.org/10.1186/2193-1801-2-587 (2013).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 55.

    Kumar, A., Prakash, A. & Johri, B. N. In Bacteria in Agrobiology: Crop Ecosystems (ed. Maheshwari, D. K.) 37–59 (Springer, 2011).

    Chapter 

    Google Scholar 

  • 56.

    Sachdev, D., Nema, P., Dhakephalkar, P., Zinjarde, S. & Chopade, B. Assessment of 16S rRNA gene-based phylogenetic diversity and promising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat. Microbiol. Res. 165, 627–638. https://doi.org/10.1016/j.micres.2009.12.002 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 57.

    Lareen, A., Burton, F. & Schafer, P. Plant root-microbe communication in shaping root microbiomes. Plant Mol. Biol. 90, 575–587. https://doi.org/10.1007/s11103-015-0417-8 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1. https://doi.org/10.1093/nar/gks808 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 59.

    Callahan, B. J., Sankaran, K., Fukuyama, J. A., McMurdie, P. J. & Holmes, S. P. Bioconductor workflow for microbiome data analysis: From raw reads to community analyses. F1000Res 5, 1492. https://doi.org/10.12688/f1000research.8986.2 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 60.

    R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (2019).

  • 61.

    Alishum, A. DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea. doi: 10.5281/zenodo.2541239 (2019).

  • 62.

    Callahan, B. Silva taxonomic training data formatted for DADA2 (Silva version 132). doi: 10.5281/zenodo.1172783 (2018).

  • 63.

    Callahan, B. RDP taxonomic training data formatted for DADA2 (RDP trainset 16/release 11.5). doi: 10.5281/zenodo.801828 (2017).

  • 64.

    McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217. https://doi.org/10.1371/journal.pone.0061217 (2013).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 65.

    Kassambara, A. ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.2.5. https://CRAN.R-project.org/package=ggpubr (2020).

  • 66.

    Lahti, L. & Shetty, S. Tools for microbiome analysis in R Version 2.1.26. http://microbiome.github.com/microbiome (2017).

  • 67.

    Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–6. https://CRAN.R-project.org/package=vegan (2019).

  • 68.

    Martinez Arbizu, P. pairwiseAdonis: Pairwise Multilevel Comparison using Adonis. R package version 0.0.1. (2017).

  • 69.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550. https://doi.org/10.1186/s13059-014-0550-8 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).

    Book 

    Google Scholar 

  • 71.

    Martin, C. ggConvexHull: Add a convex hull geom to ggplot2. R package version 0.1.0. http://github.com/cmartin/ggConvexHull (2017).

  • 72.

    Campitelli, E. ggnewscale: Multiple Fill and Colour Scales in ‘ggplot2’. R package version 0.4.1. https://CRAN.R-project.org/package=ggnewscale (2020).

  • 73.

    Slowikowski, K. ggrepel: Automatically Position Non-Overlapping Text Labels with ‘ggplot2’. R package version 0.8.2. https://CRAN.R-project.org/package=ggrepel (2020).

  • 74.

    Dowle, M. & Srinivasan, A. data.table: Extension of `data.frame`. R package version 1.12.8. https://CRAN.R-project.org/package=data.table (2019).

  • 75.

    Ammar, R. randomcoloR: Generate Attractive Random Colors. R package version 1.1.0.1. https://CRAN.R-project.org/package=randomcoloR (2019).

  • 76.

    Wickham, H. & Henry, L. tidyr: Tidy Messy Data. R package version 1.0.0. https://CRAN.R-project.org/package=tidyr (2019).

  • 77.

    Wichmann, H. & Seidel, D. scales: Scale Functions for Visualization. R package version 1.1.0. https://CRAN.R-project.org/package=scales (2019).

  • 78.

    Neuwirth, E. RColorBrewer: ColorBrewer Palettes. R package version 1.1–2. https://CRAN.R-project.org/package=RColorBrewer (2014).


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