Differences in community structure
If the study interest is in community structure and not in richness
estimates then preservation choices become even less important. In fact,
the similarity of communities obtained through the different
preservation conditions is surprisingly high (see Procrustes correlation
coefficients; Fig. 4); the amount of variation explained by preservation
conditions was much lower than the observed differences among habitats
(see redundancy analysis), and multivariate analyses consistently
allowed to detect community differences among habitats (Fig. 3). In
other words, metabarcoding is able to identify the ecological
differences among sites, independently of the preservation approach.
Even though metabarcoding analyses are sensitive to methodological
choices, estimates of relationships between diversity and the
environment are often robust (Calderón‐Sanou et al., 2020; Ji et al.,
2013), and this is a very good news if we want to apply these approaches
to broad-scale monitoring programs, aiming at assessing the effects of
environmental changes.
Bacteria were the only taxon for which we detected significant
differences between the “control” and the preservation conditions,
with ≈3% of variability explained by differences between the
“control” and the desiccation treatments. The observed differences
most likely refer to some taxa that are affected by the dry conditions
and could lead to a overrepresentation of some taxa that are more
resistant under these conditions. Differences between the desiccation
treatments and the control were small, and only one out of 660 MOTUs
showed a significant variation in abundance with the control. This MOTU
(belonging to the Bacteroidetes phylum of bacteria, see Supporting
Information) was generally abundant in the control and preservation
conditions 2 and 3 (average frequency of reads around 10%) while it
drastically decreased under preservation conditions 4 and 5 (Fig. S1).
Nevertheless, the significant differences observed for some taxa and
preservation conditions stress the importance of selecting the
preservation method before starting a monitoring program and using it
consistently through the whole monitoring, to avoid confusion between
the effects of methods and of environmental changes.