Associations with rhizosphere bacteria can confer an adaptive advantage to plants

Haney, Cara H.; Samuel, Buck S.; Bush, Jenifer; Ausubel, Frederick M.

doi:10.1038/nplants.2015.51

Cited by 373 publications

(306 citation statements)

References 47 publications

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“…Relative proportions of many of these genera were often comparable between the apples and nonapples (Dataset S1D), although there was no single phylotype that was found in all samples (Dataset S1E). Although likely an underestimate of the total diversity in these samples (Experimental Procedures), ∼2,400 observed OTUs represent four-to fivefold fewer than that observed in bulk soil samples and comparable to the levels that are observed in specialized niches like the rhizosphere (18,19). The specificity of the bacterial genera observed is supported by previous studies of analyses of fruit surfaces (20) (especially the apple phyllosphere) (21) and also microbiome studies of other fruit-associated animals like Drosophila (22,23).…”

Section: Resultssupporting

confidence: 66%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.Caenorhabditis elegans | host-microbe interactions | ecology B iological organisms constantly live in contact with other organisms in a complex web of ecological interactions, which include prey-predator, host-parasite, competitive, or positive symbiotic relationships. Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1-3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one. The many aspects of organismal biology that were shaped by evolution in natural environments are thus undetectable in the artificial laboratory environment and can only be revealed in the presence of other interacting species. Examples include feeding behavior, metabolism of diverse natural food sources, interactions with natural pathogens that have shaped the organism's immune system, behavioral traits, and regulation of development and reproduction. At the genomic level, many individual genes may not be required in a standard laboratory environment but their role may be revealed by using more diverse and relevant environments (4, 5).The nematode Caenorhabditis elegans is a typical example of a model organism that has been disconnected from its natural ecology: although the species has been studied intensively in the laboratory for half a century, its habitat and natural ecology-what it naturally feeds on, its natural predators and pathogens,

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Section: Resultssupporting

confidence: 66%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

321

479

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“…Several studies have demonstrated the beneficial effects exerted by PGP bacteria on the laboratory scale (Bhardwaj et al 2014;Gontia-Mishra et al 2014;Daffonchio et al 2015;Haney et al 2015), but relatively less data are available under on the field scale (Bashan et al 2014 and references therein;Nelissen et al 2014). Translating laboratory results to field trials is important for the future development of crop productivity (Tuberosa 2012;Bashan et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Root-associated bacteria promote grapevine growth: from the laboratory to the field

et al. 2016

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Background and Aims Laboratory and greenhouse experiments have shown that root-associated bacteria have beneficial effects on grapevine growth; however, these effects have not been tested in the field. Here, we aimed to demonstrate whether bacteria of different geographical origins derived from different crop plants can colonize grapevine to gain a beneficial outcome for the plant leading to promote growth at the field scale. Methods To link the ecological functions of bacteria to the promotion of plant growth, we sorted fifteen bacterial strains from a larger isolate collection to study in vitro Plant Growth Promoting (PGP) traits. We analysed the ability of these strains to colonise the root tissues of grapevine and Arabidopsis using greenfluorescent-protein-labelled strain derivatives and a cultivation independent approach. We assessed the ability of two subsets randomly chosen from the 15 selected strains to promote grapevine growth in two field-scale experiments in north and central Italy over two years. Parameters of plant vigour were measured during the vegetative season in de novo grafted vine cuttings and adult productive plants inoculated with the bacterial strains. Results Beneficial bacteria rapidly and intimately colonized the rhizoplane and the root system of grapevine. In the field, plants inoculated with bacteria isolated from grapevine roots out-performed untreated plants. In both the tested vineyards, bacteria-promotion effects largely rely in the formation of an extended epigeal system endowed of longer shoots with larger diameters and more nodes than non-inoculated plants.Conclusions PGP bacteria isolated in the laboratory can be successfully used to promote growth of grapevines in the field. The resulting larger canopy potentially increased the photosynthetic surface of the grapevine, promoting growth.

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“…Microbial strains with candidate functions can be combined into simple synthetic microbiomes (containing few to several dozen species) as clinical tools to promote host health or as streamlined models of microbiomes in nature [27,89]. Advantages: Synthetic microbiomes allow increased control over microbiome composition, potentially testing antagonistic versus synergistic effects among strains on host performance [90], uncovering host loci that mediate microbiome taxonomic makeup [91], or to reverse effects of dysbiosis, for instance in cases of Clostridium infections in humans [26].…”

Section: Synthetic Microbiomesmentioning

confidence: 99%