5. Persistent challenges in linking sequences to ecology
Inferring function from taxonomic affiliation/phylogeny
As amplicon sequencing is the detection of a section of a single gene,
the taxonomic resolution and ecological insights that can be extracted
remain limited. It is critical to consider that taxonomic
classifications can be influenced by the reference database selected,
many of which remain incomplete due to bias in the types of organisms
for which we have reference sequences
(51). Often it
occurs that ASVs within a given study are similar to a given taxon at
the phylum level taxonomic rank but cannot be described at the lower
taxonomic levels.
Function cannot not simply be inferred from phylogeny. For example, assignment of taxa into r-strategists via their taxonomic affiliation with a phylum that is generally assumed to represent fast-growing organisms among soil microbiologists (e.g. Proteobacteria), and using these assumptions to explain processes in soil samples, should be avoided (Jeewani et al. 2020). In such cases, we recommend to follow up by either FISH-counting of the identified species, to include functional gene-targeted sequencing, or SIP experiments to learn more about the species or community that is hypothesized to perform an ecosystem process.