If the goal of a study is to assess which organisms may contribute to a given process, amplicon sequencing of functional genes can yield more specific information than broad taxonomic markers. Some examples of these function-specific marker genes include dinitrogen reductase (nifH) and ammonium monoxygenase (amoA) genes to investigate the nitrogen cycle (Aigle et al. 2019 \cite{Angel_2018}; Pjevac et al. 2017, Seneca et al., 2020, \cite{Pester2012} ).
Research applying taxonomic marker genes has revealed insights into shifts in microbial community structure, particularly under conditions of environmental perturbation (ie temperature, nutrient additions, moisture and seasonality; REFs). The use of functional marker genes has also revealed unprecedented insights into the identities of microorganisms invovled in specific environmental processes (REF).
Direct assessments of microbial community structure have been conducted using these methods in habitats ranging from the human gut \cite{Vandeputte_2017,Sinha_2017,Barlow_2020} and aquatic environments \cite{Uyaguari_Diaz_2016,Ding_2020}, to natural and managed soil systems \cite{Thompson_2017}.