Computational protocol: When Michaelis and Menten met Holling: towards a mechanistic theory of plant nutrient foraging behaviour

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[…] To estimate the range of behavioural foraging traits in plants and parameterize our model, we broadly searched the literature for estimates of Vmax and Km for nitrate and ammonium and translated the reported Vmax and Km into encounter rates and handling times (Table ). In February 2011, we searched the ISI Web of Science for the topic ‘root uptake kinetics’ which returned 870 papers. To make search results more manageable, we filtered the results to the Web of Science Category ‘Plant Sciences’. This produced 509 papers. We then inspected titles and abstracts to reduce the search to only papers that reported parameters for nitrate and/or ammonium. From the remaining 219 papers we read each manuscript to collect parameter estimates. We limited our data collection to papers that estimated parameters based on either fresh or dry weight of roots and that estimated both Vmax and Km using the Michaelis–Menten equation. Despite the fact that all plant papers we reviewed used the two-parameter Michaelis–Menten equation to fit their data, a surprisingly large number of papers only reported Vmax, while failing to report the second parameter, Km. We excluded these papers. Additionally, we limited the data to only plant species with areal shoots so that nutrient capture was achieved exclusively through roots. Fully aquatic plants and algae were therefore excluded, but wetland plants were included. A small number of studies (<10) were not in English, were unavailable after an exhaustive physical and online search or did not report the units of measurement, and these were excluded. When different studies reported estimates of Vmax and Km for the same species, we report these as separate data points [see Supporting Information]. When multiple treatments were employed we used only the control treatment or the equivalent ‘no manipulation’ treatment. These search criteria resulted in a final set of 38 studies, with parameter estimates for nitrate and/or ammonium for 45 distinct plant species, and three species that had been studied more than once [see Supporting Information].Parameter estimates were adjusted uniformly to µmol g−1 min−1 for Vmax and µM for Km. Parameter estimates from fresh weight and dry weight of roots were plotted and interpreted separately. We used linear regressions to compare foraging ability for nitrate and ammonium (R Statistical environment, ). To summarize the taxonomic diversity and patterns in these parameter estimates, we performed a phylogenetic analysis. The hypothesized phylogenetic relationships among species were constructed using the online phylogenetic database and assembly tool, Phylomatic (), with Phylomatic tree version R20120829 as the backbone for our phylogenetic hypotheses. The Phylomatic tree is well resolved up to the level of family, but the tool places all genera as polytomies within family and all species as polytomies within genera (; ). We tested for a phylogenetic signal in the foraging trait data (a and h) by calculating a K statistic using the R library ‘Picante’ (). The K statistic compares the observed phylogenetic signal in the trait with the signal that would be expected under the Brownian motion model of trait evolution. K values >1 imply a strong phylogenetic signal, K values equal to 1 imply the Brownian motion model and K values <1 imply a random or convergent pattern of evolution. Traits were mapped onto the phylogeny for visualization using the ‘plotBranchbyTrait’ tool in the R library ‘phytools’. For several species there were multiple independent estimates of traits. In these cases, we took the average trait value. Traits were ln(x + 1) transformed for normality and to control for differences between fresh and dry weight estimates. There was considerable variation in the methods used among studies to estimate nitrogen foraging parameters [see Supporting Information]. Thus, we envision the phylogenies as a way of summarizing the data with respect to taxonomy, but urge caution in interpreting the phylogenetic signal from these data. […]

Pipeline specifications

Software tools Phylomatic, Picante, Phytools
Application Phylogenetics
Chemicals Quaternary Ammonium Compounds, Nitrogen