Github site https://github.com/Exp-Micro-Ecol-Hub/dmdScheme
User Manual of the dmdScheme
See the vignette “User Manual” at vignette ‘User manual’.
Desription and Definition of the dmdScheme
See the vignette “Description” at vignette ‘Description’.
The R Package
The Definition of the dmdScheme is done in an R package, which gives all the tools to enter the metadata and to export it into xml.
Installation
The package is not yet on CRAN. Therefore it needs to be installed from github. This will install the last verion on github.
For a list of releases see here
## install the devtools package if not installed yet
# install.packages("devtools")
## install the last version of dmdScheme from github incl vignettes
devtools::install_github("Exp-Micro-Ecol-Hub/dmdScheme", build_opts = c("--no-resave-data"))
## install a specific release of dmdScheme from github
devtools::install_github("Exp-Micro-Ecol-Hub/dmdScheme", ref = "v0.8", build_opts = c("--no-resave-data"))for a list of releases see this link on github.
Introduction
See the vignette “Introduction” at vignette ‘Introduction’.
Other Resources
Outdated Presentations
- The dmdScheme - an Introduction by Rainer M Krug.
Appendix
Experimental Microbial Ecology Protocols
In the supplement to their paper to their paper, Altermatt et al. (2015) specify the following sections for a protocoll. The sections are as followed:
1. Materials
1.1 Species used
1.2 Culture medium
1.3 Bacteria
1.4 Apparatus
1.5 Lab practices
1.6 Long term maintenance
1.7 Long term preservation
2. Measurements
2.1 Sampling
2.2 Microscopy
2.3 Image analysis
2.4 Particle counter
2.5 Bacterial density
2.6 Raman microspectroscopy
2.7 Barcoding
2.8 Ge-, prote- and epigenomics
2.9 Respirometry
2.10 Nutrients and decomposition
2.11 Protocol unavailable
2.12 Interactions
3. Manipulations
3.1 Protocol unavailable
3.2 Density
3.3 Disturbance
3.4 Nutrients and viscosity
3.5 Spatial structure
3.6 temperature
3.7 Biotic environmentWe use these sections as a starting point to define a metadata scheme to describe the microcosm experiment.
The sections in the Experimental Microbial Ecology Protocols were supplemented and assessed by reviewing the methods in the papers in the References section below.
References
Altermatt, Florian, Emanuel Fronhofer, Aurélie Garnier, Andrea Giometto, Frederik Hammes, Jan Klecka, Delphine Legrand, et al. 2015. “Big Answers from Small Worlds: A User’s Guide for Protist Microcosms as a Model System in Ecology and Evolution.” Methods in Ecology and Evolution 6 (2): 218–31. https://doi.org/10.1111/2041-210X.12312.
Carrara, Francesco, Andrea Giometto, Mathew Seymour, Andrea Rinaldo, and Florian Altermatt. 2015. “Experimental Evidence for Strong Stabilizing Forces at High Functional Diversity of Microbial Communities.” Ecology in press. https://doi.org/10.1890/14-1324.1.
DeLong, John P. 2012. “Experimental Demonstration of a ‘Rate–Size’ Trade-Off Governing Body Size Optimization.” Evolutionary Ecology Research 14 (3): 343–52. http://www.evolutionary-ecology.com/abstracts/v14/2742.html.
Fox, Jeremy W. 2002. “Testing a Simple Rule for Dominance in Resource Competition.” The American Naturalist 159 (3): 305–19. https://doi.org/10.1086/338543.
Griffiths, Jason I., Owen L. Petchey, Frank Pennekamp, and Dylan Z. Childs. 2018. “Linking Intraspecific Trait Variation to Community Abundance Dynamics Improves Ecological Predictability by Revealing a Growth–Defence Trade-Off.” Functional Ecology 32 (2): 496–508. https://doi.org/10.1111/1365-2435.12997.
Jiang, Lin, and Shivani N. Patel. 2008. “Community Assembly in the Presence of Disturbance: A Microcosm Experiment.” Ecology 89 (7): 1931–40. https://doi.org/10.1890/07-1263.1.
Leary, Daniel J., Jason M. K. Rip, and Owen L. Petchey. 2012. “The Impact of Environmental Variability and Species Composition on the Stability of Experimental Microbial Populations and Communities.” Oikos 121 (3): 327–36. https://doi.org/10.1111/j.1600-0706.2011.19523.x.
McGrady-Steed, J, and PM Harris. 1997. “Biodiversity Regulates Ecosystem Predictability.” Nature 390: 162–65. http://www.nature.com/nature/journal/v390/n6656/abs/390162a0.html.
Pennekamp, Frank, Mikael Pontarp, Andrea Tabi, Florian Altermatt, Roman Alther, Yves Choffat, Emanuel A. Fronhofer, et al. 2018. “Biodiversity Increases and Decreases Ecosystem Stability.” Nature, October. https://doi.org/10.1038/s41586-018-0627-8.
Petchey, Owen L. 2000. “Prey Diversity, Prey Composition, and Predator Population Dynamics in Experimental Microcosms.” Journal of Animal Ecology 69 (5): 874–82. https://doi.org/10.1046/j.1365-2656.2000.00446.x.
Vasseur, David A., and Jeremy W. Fox. 2009. “Phase-Locking and Environmental Fluctuations Generate Synchrony in a Predator–Prey Community.” Nature 460 (7258): 1007–10. https://doi.org/10.1038/nature08208.