Sample size
Although the DNA extraction method may have a strong impact on taxa
recovery in metabarcoding studies (Schiebelhut, Abboud, Gómez Daglio,
Swift & Dawson 2017; Sinha et al. 2017), previous comparisons of
different DNA isolation kits for diatoms have demonstrated compatible
patterns for diversity and community assembly (Vasselon, Domaizon,
Rimet, Kahlert & Bouchez 2017). The present study also shows that
richness and community structure of diatoms are highly correlated
between metabarcoding data of 10 g vs . 0.5 g of sediment samples.
Interestingly, the correlations of relative abundances of matching
diatom genera between metabarcoding and microscopy data sets, resulted
in higher correlation values for the HTS 0.5 data (Fig. S4). However,
other studies comparing metabarcoding results from DNA extracts of
various amounts of substrate have reported contrasting results. For
example, Penton, Gupta, Yu and Tiedje (2016) reported significant
effects of sample size (in terms of input quantity) on the community
structure of fungi and bacteria from soil. Higher diversity estimates
were associated with 10 g of soil DNA extracts compared with 5 g, 1 g
and 0.25 g. Studying meiofaunal communities from marine sediment
samples, Brannock and Halanych (2015) found that different extraction
quantities did not result in significantly different diversity
estimates, however, the OTU community compositions were different.
Exploring various eukaryotes from sediment samples, Nascimento, Lallias,
Bik and Creer (2018) also found significantly different diversity
metrics and community compositions for various sample sizes. They
suggested that larger volumes of sediment are necessary to capture the
representative metazoan communities compared to the non-metazoan
eukaryotes. Therefore, the choice of a quantity of sediment for DNA
extraction may depend on the expected distribution of the target groups
in the substrate, where the detection of more patchily distributed
metazoan communities requires larger quantities of sediment for
analyses. Although it could be hypothesized that sample size may affect
also the recovery of some microbial groups, here we demonstrate that
this was not the case for diatoms from lake sediment samples (when
comparing sample size on 10 g vs . 0.5 g). The benefits of using
only up to 0.5 g of the sample include a more time- and cost-effective
DNA extraction procedure, and the possibility to conduct meaningful
analyses when only a limited amount of sediment is available.