Recent studies apply functional predictions using packages such as PICRUSt2 \citep{Douglas_2020} or Tax4Fun \citep{A_hauer_2015}, which suggest that metagenomes (and therefore functional potential of organisms) can be extrapolated from the sequenced amplicon using phylogenetic markers. In the case of fungi, FUNGuild or FungalTraits have been developed, which parses OTUs/ASVs into functional guilds based on similarity to existing reference sequences \citep{Nguyen_2016,P_lme_2020}. The main limitation of these approaches lies in the fact that they are dependent on a single gene, and the completeness of reference sequence databases, many of which remain incomplete due to bias in the types of organisms
for which we have references (section 3, \citep{Choi_2016}). However, these prediction-based software packages can be used to generate valuable hypotheses for further investigation or an additional line of evidence to support a finding. In such cases, we recommend to follow up by either FISH-counting of the identified species, functional gene-targeted sequencing, or SIP experiments to learn more about the species or community that is hypothesized to be responsible/involved in an ecosystem process (further discussed in section 7).