5.3. Inferring function from phylogeny

Although some links exist between the environment and the community composition therein, amplicon sequencing cannot be used to predict microbial function and roles in ecological processes \cite{Fierer_2007,Fierer_2017}. Nevertheless, it can serve as a useful tool to survey microbial communities through detection of a section of a single gene or gene region (Fig. 4). The consequence of targeting a subsection of microbial genomes is that ecological insights that can be extracted from these data remain limited. Function of taxa identified via amplicon sequencing cannot simply be inferred from the phylogeny of these organisms, as complex evolutionary processes (e.g., horizontal gene transfer) play a key role in functional trait distribution across the genomes of microorganisms \citep{Menna_2011}. Function may not necessarily be conserved across phylogenetic levels, and therefore processes cannot be reliably predicted and assigned to taxa using amplicon sequencing targeting phylogenetic markers such as 16S rRNA genes \citep{Nunan_2020,Li2019}. Consequently, we suggest to avoid inferring life strategies of taxa via their classification into a phylum (e.g., equating Proteobacteria with fast-growing r-strategist) and using such assumptions to explain processes in soils for surveys based on general markers such as 16S rRNA genes \citep{Jeewani_2020} and ITS regions \citep{Zhou_2021}.