Abstract
Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.
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Data availability
Sequence data and sample metadata have been previously deposited in NCBI Sequence Read Archive under the project number PRJNA521534. Any additional metadata and intermediate data products are available at https://github.com/bramstone/density-dependence-qSIP.
Code availability
All analytical and statistical code has been made available at https://github.com/bramstone/density-dependence-qSIP.
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Acknowledgements
We thank the editorial team and two anonymous reviewers for their suggestions and improvements.
Funding
BWS is grateful for support from the Linus Pauling Postdoctoral Distinguished Fellowship program through Pacific Northwest National Laboratory. This research was supported by grants from the United States Department of Energy’s Biological Systems Science Division Program in Genomic Science (Nos. DE-SC0016207 and DE-SCSC0020172, and the Lawrence Livermore National Laboratory ‘Microbes Persist' Soil Microbiome Scientific Focus Area (SCW1632) and by the National Science Foundation (No. DEB-1645596). Research conducted at Lawrence Livermore National Laboratory was supported by the Department of Energy Office of Science, via awards SCW1679 and SCW1590, conducted under the auspices of Department of Energy Contract DE-AC52- 07NA27344. Research conducted at Pacific Northwest National Laboratory was supported by the Department of Energy Office of Science, via awards FWP 68907 and FWP 74475, conducted under the auspices of Department of Energy Contract DE-AC05-76RL01830.
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PD, MH, KSH, XJL, RLM, JPR, ES, and BAH designed the experiment and interpreted the findings. XJL, MH, and RLM collected and processed the samples. MH and RLM performed the laboratory work and generated the data. BWS analyzed the data and wrote first draft of manuscript. SJB and BJK interpreted the findings and contributed to the figure design and captions. All the authors contributed meaningfully to revisions.
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Stone, B.W., Blazewicz, S.J., Koch, B.J. et al. Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community. Oecologia 201, 771–782 (2023). https://doi.org/10.1007/s00442-023-05322-z
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DOI: https://doi.org/10.1007/s00442-023-05322-z