- 1Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- 2Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- 3Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
- 4Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- 5Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
- 7Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- 8Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA.
- 9Life & Environmental Sciences Department, University of California Merced, Merced, California, USA.
- 10Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- 11Department of Biology, West Virginia University, Morgantown, WV, USA.
- *A full list of authors appears at the end of the abstract
Growing bacteria, alongside fungi, are the productive core of the soil microbiome. They assimilate soil organic matter and drive biogeochemical transformations. While recent evidence suggests that large parts of the bacterial community are transcriptionally or translationally active, only a subset of bacteria actively divides at any given time. However, the proportion of dividing bacteria and their responses to environmental change remain poorly understood.
Using more than 76,000 taxon-specific growth estimates inferred by 18O-quantitative stable isotope probing from >200 soil samples, we characterized the size and dynamics of the growing fraction of soil bacteria across a range of ecosystems and environmental change treatments (warming, nutrient addition, drought, cooling). We then estimated the percentage of replicating bacterial cells and taxa based on taxon-specific 18O-enrichment, absolute 16S rRNA gene abundances, and predicted gene copy numbers.
Across soils, a significant yet variable proportion of bacterial cells (median: 12%; range: 0.2-65%) were growing, representing about 16% (median; range: 0.9-39%) of the total taxa richness. More than 50% of all taxa were growing exclusively in only 1-2 samples. Environmental change affected the size of the growing community as well as its composition. More than 40% (median; range: 9.7-90%) of the taxa growing at ambient conditions stopped growing when the environment changed, whereas others initiated growth following a shift in conditions.
Our results indicate that the pool of growing bacteria constitutes a significant fraction of the soil microbiome and responds dynamically to changes in the environment through shifts in size and composition with potential implications for soil functioning.
Dennis Metze (1), Bram W. Stone (2), Bruce A. Hungate (3), Joana Séneca (1,4), Rebecca L. Mau (3), Michaela Hayer (3), Alicia M. Purcell (3,5), Jeffrey Propster (3), Brianna K. Finley (6), Xiao Jun A. Liu (7), Benjamin J. Koch (3), Jennifer Pett-Ridge (8,9), Egbert Schwartz (3), Paul Dijkstra(3), César Terrer (10), Steven J. Blazewicz (8), Ember M. Morrissey (11), Kirsten S. Hofmockel (2,12), Jane Marks (3), Andreas Richter (1), Christina Kaiser (1)
How to cite: Metze, D., Stone, B. W., Hungate, B. A., Séneca, J., Mau, R. L., Hayer, M., Purcell, A. M., Propster, J., Liu, X. J. A., Koch, B. J., Pett-Ridge, J., Schwartz, E., Dijkstra, P., Terrer, C., J. Blazewicz, S., Morrissey, E. M., Hofmockel, K. S., Marks, J., Richter, A., and Kaiser, C. and the Team: How many bacteria are growing in soil?, EGU General Assembly 2025, Vienna, Austria, 27 Apr–2 May 2025, EGU25-19125, https://doi.org/10.5194/egusphere-egu25-19125, 2025.
