Quantifying biomass, median body size, and biodiversity
With these videos, we identified and characterised protist species in
the communities using the R-package BEMOVI (Altermatt et al., 2015;
Pennekamp et al., 2015; Pennekamp & Schtickzelle, 2013). We first
extracted moving particles’ traits (e.g., speed, shape, size) in the
videos and used such traits to exclude particles that were not protists
to obtain an average abundance of protist individuals per volume. We
used protist biomass as the focal ecosystem function. Specifically, we
measured the total area of protists (as area per volume medium) and used
this “bioarea” as a proxy of biomass (hereafter referred to as
“biomass”)–a fair assumption given that protists have a roundish
shape (see also other work using the same proxy; e.g., Jacquet et al.,
2020; Pennekamp et al., 2018). The area of protists gave us a metric of
body size, from which we calculated the median body size of individuals
in each patch at each time point (the median gives an average metric
robust to different types of distributions). We then used a support
vector machine model to identify protist species
(Cortes et al., 1995; r-package “e1071”: Dimitriadou et al., 2006),
using traits in species monocultures as predictor variables. Finally, we
calculated patch biodiversity using the Shannon Index to account for
relative abundances.