Recent studies and reviews have referred to the limitations of this approach, including compositionality of the data and the problematic nature of
inferring interactions between microorganisms in communities using
sequencing alone (e.g. \cite{Blanchet_2020},
3). Patterns often arise in community data, but interpretation of these
putative interactions remains challenging and limited due to the nature
of the data itself \cite{Blanchet_2020}. Amplicon
sequencing, when used as part of a well-designed experiment, remains an
informative approach for investigating microbial community structure and
potential organismal interactions, as well as for developing new
hypotheses regarding microbial community dynamics (as discussed in more detail below).
Scientists studying microbial communities in soil face unique challenges
at each step of a sequencing experiment. These challenges include the
immense biological diversity of soil organisms that is thought to be higher than any other habitat on earth (citation), temporal variation (e.g. seasonality, root exudation events, REFs), spatial heterogeneity of the soil matrix (citation), and the interpretation of large and complex datasets
in the context of ecosystem dynamics (REFs). After more than a decade of applying amplicon sequencing in soils, we take a look back on the growing understanding of microbial communities and offer a path forward at this turning point in the field. In this perspective,
we aim to describe the unique challenges faced by scientists studying
microbial communities in soil ecosystems, and address common
misconceptions in the analysis and interpretation of amplicon sequencing
data. We provide suggestions for designing sequencing experiments and
analyzing data to gain improved insights into microbial community
structure and dynamics.