Multiple dimensions of bacterial diversity unrelated to functioning, stability and multifunctionality
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Microbiology
- Keywords
- rare biosphere, biodiversity and ecosystem functioning, freshwater, bacterial diversity, biodiversity loss, microcosm, functional redundancy
- Copyright
- © 2016 Roger et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Multiple dimensions of bacterial diversity unrelated to functioning, stability and multifunctionality. PeerJ PrePrints 4:e1688v1 https://doi.org/10.7287/peerj.preprints.1688v1
Abstract
Bacteria are essential for many ecosystem services but our understanding of factors controlling their functioning is incomplete. While biodiversity has been identified as an important driver of ecosystem processes in macrobiotic communities, we know much less about bacterial communities. Due to the high diversity of bacterial communities, high functional redundancy is commonly proposed as an explanation for a lack of clear effects of diversity. The generality of this claim has, however, been questioned. We present the results of an outdoor dilution-to-extinction experiment with four lake bacterial communities. We found no general effects of bacterial diversity in terms of effective number of species, phylogenetic diversity or functional diversity on (i) bacterial abundance, (ii) temporal stability of abundance, (iii) nitrogen concentration, or (iv) multifunctionality. A literature review of 21 peer-reviewed studies that used dilution-to-extinction to manipulate bacterial diversity corroborated our findings: only about 25% found positive relationships. Combined, these results suggest that bacterial communities are able to uphold multifunctional ecosystems even at extensive reductions in diversity.
Author Comment
This is a preprint submission to PeerJ Preprints. The full code used for the analysis presented in this preprint, including all the raw data except the sequencing data is provided in Appendix 2, which can be accessed at https://github.com/FabianRoger/Roger_et_al_Supplementary.
Supplemental Information
Appendix 3 - Detailed methods for the literature review
Figure S1. Photography showing the experimental setup
Photography showing the experimental setup. The 2 L glass bottles with the bacterial communities are randomly distributed among the two water basins and floating within the closed PVC cylinders. Each basin contains about 1000 L of water, mimicking temperature conditions in a shallow lake.
Table S1: Summery of studies included in the literature review
Figure S2. The temperature in the water basins over the course of the experiment in degree Celsius
The temperature in the water basins over the course of the experiment in degree Celsius. The temperature was logged continuously with a HOBO® temperature logger, submerged in a glass bottle that is identical to the experimental units. The dashed line at the beginning of the graph shows the period before the bottles were transferred to the water bathes. The vertical grey dashed lines demark the sampling dates. The three experimental periods are color coded: blue is the regrowth phase before the first sampling, red is the period between the first and the second sampling and red is the period after the second sampling to the end of the experiment. The horizontal straight lines show the respective average temperatures.
Figure S3. Sensitivity of the calculated diversity to rarefaction level
Figure_S_1.pdf Sensitivity of the calculated diversity to rarefaction level. The graph shows pairwise correlations between the effective number of species calculated on the unrarefied dataset and at 4 rarefaction levels (10 000, 7000, 4000 and 1000 reads). The lower triangle shows the pairwise scatterplots, the upper panels give the corresponding r-squares.
Figure_S_1.pdf Figure S4. Bacterial cell abundance (cells*ml-1) over the course of the experiment for all lakes and dilutions
Bacterial cell abundance (cells*ml-1) over the course of the experiment for all lakes and dilutions. Each panel corresponds to a dilution treatment labeled as in main Figure 1. The grey dashed vertical lines demark the sampling dates.
Figure_S_1.pdf Figure S5. Pairwise correlations of the three diversity metrics, by lake
Figure_S_1.pdf Pairwise correlations of the three diversity metrics, by lake. The lower triangle shows the pairwise scatterplots, the upper triangle shows the Pearson correlation coefficients by lake. The diversity values are the averages over the three sampling dates.
Figure_S_1.pdf Figure S6. Cell abundance, stability of cell abundance, DIN concentration and multifunctionality as functions of the three dimensions of diversity
Figure_S_1.pdf Cell abundance, stability of cell abundance, DIN concentration and multifunctionality as functions of the three dimensions of diversity. Diversity is averaged over the three sampling dates. Spearman rank correlation coefficients and p-value are given in each panel. effN = effective number of species, PD = phylogenetic diversity, FuncDiv = functional diversity.