Differential Response of Bacterial Microdiversity to Simulated Global Change

N. C. Scales, A. B. Chase, S. S. Finks, Ashish Malik, C. Weihe, S. D. Allison, Adam C. Martiny, Jennifer B H Martiny

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Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes termed microdiversity, responds to environmental perturbations and whether such changes are relevant to ecosystem processes. Here, we investigated microdiversity within Curtobacterium, the dominant bacterium found in the leaf litter layer of soil, to simulated drought and nitrogen addition in a field experiment. We first developed and validated Curtobacterium-specific primers of the groEL gene to assess microdiversity within this lineage. We then tracked the response of this microdiversity to simulated global change in two adjacent plant communities, grassland and coastal sage scrub (CSS). Curtobacterium microdiversity responded to drought but not nitrogen addition, indicating variation within the genus of drought tolerance but not nitrogen response. Further, the response of microdiversity to drought depended on the ecosystem, suggesting that litter substrate selects for a distinct composition of microdiversity that is constrained in its response, perhaps related to tradeoffs in resource acquisition traits. Supporting this interpretation, a metagenomic analysis revealed that the composition of Curtobacterium-encoded carbohydrate-active enzymes (CAZymes) varied distinctly across the two ecosystems. Identifying the degree to which relevant traits are phylogenetically conserved may help to predict when the aggregated response of a 16S-defined taxon masks differential responses of finer-scale bacterial diversity to global change.
Original languageEnglish
Article numbere02429-21
Number of pages13
JournalApplied and Environmental Microbiology
Issue number6
Early online date2 Feb 2022
Publication statusPublished - 2 Mar 2022

Bibliographical note

UC Irvine and the LRGCE are located on the ancestral homelands of the Indigenous Kizh and Acjachemen nations.
We thank Alejandra Rodriguez Verdugo, Katrine Whiteson, Kendra Walters, Cynthia Rodriguez, Kristin Barbour, Alberto Barron Sandoval, Joanna Wang, Joia Kai Capocchi, Pauline Uyen Phuong Nguyen, Khanh Thuy Huynh, and Clara Barnosky for their input on analyses and previous drafts and for laboratory help.
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research grants DE-SC0016410 and DE-SC0020382.

Data Availability Statement

The raw amplicon and metagenomic reads can be accessed under the NCBI BioProject accession number PRJNA781975. The BioSample accession numbers are SAMN23310455 for the groEL amplicons and SAMN23390019 for the metagenomic reads.


  • bacteria
  • microdiversity
  • global change


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