Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012).
Anderson, P. K. et al. Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544 (2004).
Savary, S. et al. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3, 430–439 (2019).
Andrews, J. H. & Harris, R. F. The ecology and biogeography of microorganisms on plant surfaces. Annu. Rev. Phytopathol. 38, 145–180 (2000).
Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant–pathogen interactions. Nat. Rev. Genet. 11, 539–548 (2010).
Mansfield, J. et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol. Plant Pathol. 13, 614–629 (2012).
Poueymiro, M. & Genin, S. Secreted proteins from Ralstonia solanacearum: a hundred tricks to kill a plant. Curr. Opin. Microbiol. 12, 44–52 (2009).
Niehus, R., Picot, A., Oliveira, N. M., Mitri, S. & Foster, K. R. The evolution of siderophore production as a competitive trait. Evolution 71, 1443–1455 (2017).
Bruce, J. B., Cooper, G. A., Chabas, H., West, S. A. & Griffin, A. S. Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens. Evolution 71, 2484–2495 (2017).
Butaite, E., Kramer, J., Wyder, S. & Kummerli, R. Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities. Environ. Microbiol. 20, 3629–3642 (2018).
Smith, E. E., Sims, E. H., Spencer, D. H., Kaul, R. & Olson, M. V. Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa. J. Bacteriol. 187, 2138–2147 (2005).
Butaite, E., Baumgartner, M., Wyder, S. & Kummerli, R. Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nat. Commun. 8, 414 (2017).
Kwak, M. J. et al. Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat. Biotechnol. 36, 1100–1109 (2018).
Berendsen, R. L., Pieterse, C. M. & Bakker, P. A. The rhizosphere microbiome and plant health. Trends Plant Sci. 17, 478–486 (2012).
Compant, S., Samad, A., Faist, H. & Sessitsch, A. J. A review on the plant microbiome: ecology, functions and emerging trends in microbial application. J. Adv. Res. 19, 29–37 (2019).
Wei, Z. et al. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat. Commun. 6, 8413 (2015).
Li, M. et al. Facilitation promotes invasions in plant-associated microbial communities. Ecol. Lett. 22, 149–158 (2019).
Pieterse, C. M. et al. Induced systemic resistance by beneficial microbes. Annu. Rev. Phytopathol. 52, 347–375 (2014).
van der Meij, A., van Wezel, G. P., Hutchings, M. I. & Worsley, S. F. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol. Rev. 41, 392–416 (2017).
Casper, B. B. & Jackson, R. B. Plant competition underground. Annu. Rev. Ecol. Evol. Syst. 28, 545–570 (1997).
Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M. Ecology and evolution of plant microbiomes. Annu. Rev. Microbiol. 73, 69–88 (2019).
Cordero, O. X., Ventouras, L. A., DeLong, E. F. & Polz, M. F. Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc. Natl Acad. Sci. USA 109, 20059–20064 (2012).
Kummerli, R., Schiessl, K. T., Waldvogel, T., McNeill, K. & Ackermann, M. Habitat structure and the evolution of diffusible siderophores in bacteria. Ecol. Lett. 17, 1536–1544 (2014).
Andersen, S. B., Marvig, R. L., Molin, S., Krogh Johansen, H. & Griffin, A. S. Long-term social dynamics drive loss of function in pathogenic bacteria. Proc. Natl Acad. Sci. USA 112, 10756–10761 (2015).
Barber, M. F. & Elde, N. C. Buried treasure: evolutionary perspectives on microbial iron piracy. Trends Genet. 31, 627–636 (2015).
Andrews, S. C., Robinson, A. K. & Rodriguez-Quinones, F. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215–237 (2003).
Colombo, C., Palumbo, G., He, J.-Z., Pinton, R. & Cesco, S. Review on iron availability in soil: interaction of Fe minerals, plants, and microbes. J. Soils Sediments 14, 538–548 (2014).
Miethke, M. & Marahiel, M. A. Siderophore-based iron acquisition and pathogen control. Microbiol. Mol. Biol. Rev. 71, 413–451 (2007).
Hider, R. C. & Kong, X. Chemistry and biology of siderophores. Nat. Prod. Rep. 27, 637–657 (2010).
Lagos, L. et al. Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini-review. J. Soil Sci. Plant Nutr. 15, 504–523 (2015).
Münkemüller, T. et al. How to measure and test phylogenetic signal. Methods Ecol. Evol. 3, 743–756 (2012).
Hibbing, M. E., Fuqua, C., Parsek, M. R. & Peterson, S. B. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8, 15–25 (2010).
Jousset, A., Schmid, B., Scheu, S. & Eisenhauer, N. Genotypic richness and dissimilarity opposingly affect ecosystem functioning. Ecol. Lett. 14, 537–545 (2011).
Kramer, J., Özkaya, Ö. & Kümmerli, R. Bacterial siderophores in community and host interactions. Nat. Rev. Microbiol. 18, 152–163 (2019).
Schofield, R. K. & Taylor, A. W. The measurement of soil pH. Soil Sci. Soc. Am. J. 19, 164–167 (1955).
Loper, J. E. & Henkels, M. D. Availability of iron to Pseudomonas fluorescens in rhizosphere and bulk soil evaluated with an ice nucleation reporter gene. Appl. Environ. Microbiol. 63, 99–105 (1997).
Heuer, H., Krsek, M., Baker, P., Smalla, K. & Wellington, E. M. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63, 3233–3241 (1997).
Tamura, K., Nei, M. & Kumar, S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl Acad. Sci. USA 101, 11030–11035 (2004).
Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Keck, F., Rimet, F., Bouchez, A. & Franc, A. phylosignal: an R package to measure, test, and explore phylogenetic signal. Ecol. Evol. 6, 2774–2780 (2016).
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2018).
Höfte, M., Buysens, S., Koedam, N. & Cornelis, P. Zinc affects siderophore-mediated high affinity iron uptake systems in the rhizosphere Pseudomonas aeruginosa 7NSK2. Biometals 6, 85–91 (1993).
Schwyn, B. & Neilands, J. Universal chemical assay for the detection and determination of siderophores. Anal. Biochem. 160, 47–56 (1987).
Ghysels, B. et al. The Pseudomonas aeruginosa pirA gene encodes a second receptor for ferrienterobactin and synthetic catecholate analogues. FEMS Microbiol. Lett. 246, 167–174 (2005).
Sathe, S., Mathew, A., Agnoli, K., Eberl, L. & Kümmerli, R. Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evol. Lett. 3, 610–622 (2019).
Meyer, J.-M. et al. Use of siderophores to type pseudomonads: the three Pseudomonas aeruginosa pyoverdine systems. Microbiology 143, 35–43 (1997).
Schonfeld, J., Heuer, H., Van Elsas, J. D. & Smalla, K. Specific and sensitive detection of Ralstonia solanacearum in soil on the basis of PCR amplification of fliC fragments. Appl. Environ. Microbiol. 69, 7248–7256 (2003).
Chen, Y. et al. A real-time PCR assay for the quantitative detection of Ralstonia solanacearum in horticultural soil and plant tissues. J. Microbiol. Biotech. 20, 193–201 (2010).
Cardenas, E. et al. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach. Appl. Environ. Microbiol. 76, 6778–6786 (2010).
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Wei, Z. et al. Efficacy of Bacillus-fortified organic fertiliser in controlling bacterial wilt of tomato in the field. Appl. Soil Ecol. 48, 152–159 (2011).
Jeger, M. J. & Viljanen-Rollinson, S. L. H. The use of the area under the disease-progress curve (AUDPC) to assess quantitative disease resistance in crop cultivars. Theor. Appl. Genet. 102, 32–40 (2001).
Source: Ecology - nature.com
