Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots
Abstract
Abstract For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrientsmore »
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1983999
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- ISME Communications
- Additional Journal Information:
- Journal Name: ISME Communications Journal Volume: 3 Journal Issue: 1; Journal ID: ISSN 2730-6151
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Acharya, Shwetha M., Yee, Mon Oo, Diamond, Spencer, Andeer, Peter F., Baig, Nameera F., Aladesanmi, Omolara T., Northen, Trent R., Banfield, Jillian F., and Chakraborty, Romy. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. United States: N. p., 2023.
Web. doi:10.1038/s43705-023-00265-1.
Acharya, Shwetha M., Yee, Mon Oo, Diamond, Spencer, Andeer, Peter F., Baig, Nameera F., Aladesanmi, Omolara T., Northen, Trent R., Banfield, Jillian F., & Chakraborty, Romy. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. United States. https://doi.org/10.1038/s43705-023-00265-1
Acharya, Shwetha M., Yee, Mon Oo, Diamond, Spencer, Andeer, Peter F., Baig, Nameera F., Aladesanmi, Omolara T., Northen, Trent R., Banfield, Jillian F., and Chakraborty, Romy. Tue .
"Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots". United States. https://doi.org/10.1038/s43705-023-00265-1.
@article{osti_1983999,
title = {Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots},
author = {Acharya, Shwetha M. and Yee, Mon Oo and Diamond, Spencer and Andeer, Peter F. and Baig, Nameera F. and Aladesanmi, Omolara T. and Northen, Trent R. and Banfield, Jillian F. and Chakraborty, Romy},
abstractNote = {Abstract For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.},
doi = {10.1038/s43705-023-00265-1},
journal = {ISME Communications},
number = 1,
volume = 3,
place = {United States},
year = {Tue Jun 06 00:00:00 EDT 2023},
month = {Tue Jun 06 00:00:00 EDT 2023}
}
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