Peat-based gnotobiotic plant growth systems forArabidopsismicrobiome research

Paul Schulze-Lefert, James M. Kremer, Reza Sohrabi, Bradley C. Paasch, David Rhodes, Caitlin Thireault, James M. Tiedje, Sheng Yang He

Published: 2021-04-27 DOI: 10.1038/s41596-021-00504-6

gnotobiotic growth systems

Arabidopsis thaliana

microbiome research

peat-based substrates

controlled environments

AI 解读

Supplementary information

Supplementary Information

Supplementary Methods.

Reporting Summary

Supplementary Table 1

Geographic locations of soils used in this study

Supplementary Table 2

OTU information for the example community profiling workflow used to generate the heatmap in Fig. 6

Author Correction: Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq

Generation of heart-forming organoids from human pluripotent stem cells

Design and fabrication of wearable electronic textiles using twisted fiber-based threads

Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo

Chromatin accessibility profiling by ATAC-seq

Deoxyfluorination of phenols for chemoselective18F-labeling of peptides

Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction

Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening

查看全部

Sections

Figures

References

Supplementary information

Round, J. L. & Mazmanian, S. K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313–323 (2009).
Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).
Durán, P. et al. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell 175, 973–983.e14 (2018).
Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017).
Liu, Y.-X., Qin, Y. & Bai, Y. Reductionist synthetic community approaches in root microbiome research. Curr. Opin. Microbiol. 49, 97–102 (2019).
Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528, 364–369 (2015).
Lebeis, S. L. et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349, 860–864 (2015).
Zamioudis, C. et al. Rhizobacterial volatiles and photosynthesis‐related signals coordinate MYB 72 expression in Arabidopsis roots during onset of induced systemic resistance and iron‐deficiency responses. Plant J. 84, 309–322 (2015).
Finkel, O. M. et al. The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol. 17, e3000534 (2019).
Innerebner, G., Knief, C. & Vorholt, J. A. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77, 3202–3210 (2011).
Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl Acad. Sci. USA 110, 6548–6553 (2013).
Spor, A., Koren, O. & Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9, 279–290 (2011).
Adair, K. L. & Douglas, A. E. Making a microbiome: the many determinants of host-associated microbial community composition. Curr. Opin. Microbiol. 35, 23–29 (2017).
Xin, X.-F. et al. Bacteria establish an aqueous living space in plants crucial for virulence. Nature 539, 524–529 (2016).
Andrew, D. R. et al. Abiotic factors shape microbial diversity in Sonoran Desert soils. Appl. Environ. Microbiol. 78, 7527–7537 (2012).
Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl Acad. Sci. USA 103, 626–631 (2006).
Gunning, T. & Cahill, D. M. A soil-free plant growth system to facilitate analysis of plant pathogen interactions in roots. J. Phytopathol. 157, 497–501 (2009).
Jackson, M. B. et al. Ventilation in plant tissue cultures and effects of poor aeration on ethylene and carbon dioxide accumulation, oxygen depletion and explant development. Ann. Bot. 67, (1991).
Kloepper, J. W. & Schroth, M. N. Plant growth–promoting rhizobacteria and plant growth under gnotobiotic conditions. Phytopathology 71, 642–644 (1981).
Henry, A. et al. An axenic plant culture system for optimal growth in long-term studies. J. Environ. Qual. 35, 590–598 (2006).
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).
Adams, C., Jacobson, A. & Bugbee, B. Ceramic aggregate sorption and desorption chemistry: implications for use as a component of soilless media. J. Plant Nutr. 37, 1345–1357 (2014).
Trevors, J. T. Sterilization and inhibition of microbial activity in soil. J. Microbiol. Methods 26, 53–59 (1996).
Shaw, L. J., Beaton, Y., Glover, L. A., Killham, K. & Meharg, A. A. Re-inoculation of autoclaved soil as a non-sterile treatment for xenobiotic sorption and biodegradation studies. Appl. Soil Ecol. 11, 217–226 (1999).
Bank, T. L. et al. Effects of gamma-sterilization on the physico-chemical properties of natural sediments. Chem. Geol. 251, 1–7 (2008).
Berns, A. E. et al. Effect of gamma-sterilization and autoclaving on soil organic matter structure as studied by solid state NMR, UV and fluorescence spectroscopy. Eur. J. Soil Sci. 59, 540–550 (2008).
Wolf, D. C., Dao, T. H., Scott, H. D. & Lavy, T. L. Influence of sterilization methods on selected soil microbiological, physical, and chemical properties. J. Environ. Qual. 18, 39–44 (1989).
Lotrario, J. B. et al. Effects of sterilization methods on the physical characteristics of soil: implications for sorption isotherm analyses. Bull. Environ. Contam. Toxicol. 54, 668–675 (1995).
Seedorf, H. et al. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159, 253–266 (2014).
Lindsey, B. E. III, Rivero, L., Calhoun, C. S., Grotewold, E. & Brkljacic, J. Standardized method for high-throughput sterilization of Arabidopsis seeds. J. Vis. Exp. https://doi.org/10.3791/56587 (2017).
Clough, S. J. & Bent, A. F. Transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).

Peat-based gnotobiotic plant growth systems forArabidopsismicrobiome research

Supplementary information

推荐阅读