Abstract

Microbial community analysis via amplicon sequencing has become a standard parameter in soil research. The complexity of soil and the organisms therein, however, necessitate careful treatment of mainly descriptive sequencing data to prevent mis- or over-interpretation of the data. In this perspective, we aim at highlighting the challenges of using marker-gene based surveys in soil but also discuss the potentials for soil ecological reserach.
Turning point of the field. Soil science is getting swampted with articles but journals are not really prepared for that (e.g. editorial boards, guidelines).

1. Introduction

Soil is one of the most biologically diverse and heterogeneous ecosystems, presenting unique challenges to scientists in the fields of soil and microbial ecology \cite{Bickel2020}. The critical role of microorganisms as drivers of biogeochemical processes is well-documented, and a major goal of soil ecology remains to decipher the link between the diversity of soil microbial communities, and their function in the environment \cite{Hinsinger_2009,Manzoni_2012}. Historically, studies of microbial community analysis revealed a rather narrow perspective of diversity by targeting mainly cultivable bacteria, taxa of high abundance or microorganisms grouped according to morphological or physiological properties  \cite{Staley1985,Steen_2019,Frosteg_rd_2011}. The introduction of next-generation sequencing  technologies such as amplicon sequencing has revolutionized our understanding of microbial diversity by enabling investigation of community composition with much greater taxonomic resolution than before.
Amplicon sequencing (also termed metabarcoding) is based on PCR-amplification of variable regions of DNA within a conserved marker gene \cite{Go_biewski_2019}. The accessibility of established assays, affordable costs, as well as the availability of free analysis software packages have facilitated the broad use of amplicon sequencing for characterization of the microbiological diversity in environmental reserearch \cite{Caporaso_2012}. In the field of soil science, its application has accelerated in the last decade as evident by the growing number of studies published in specialized journals (Figure 1). The majority of these manuscripts report the analysis of soil community composition and diversity based on taxonomic marker genes such as 16S rRNA and ITS (Nilsson et al. 2019, other REFs). In addition, functional genes can be targeted to obtain information on the organism that may contribute to a specific environmental process \cite{Angel_2018,S_neca_2020,Aigle_2020}.
The meaningful descriptive work in the field of soil ecology has enabled researchers to successfully  investigate the composition and dynamics of microbial communities. Our understanding of soil microbial diversity has increased dramatically and the activity of microbial communities has now been widely accepted in soil research where research questions were historically often tackled from the perspective of individual disciplines such as chemistry, physics, and biology \cite{Baveye_2018}. As evident by the the high number of studies being published lately, it is safe to say that microbial community analysis via marker-gene sequencing is becoming a standard tool in soil research. This marks a critical turning point in the field which makes it necessary to discuss potentials, challenges, and pitfalls of the technique applied by soil scientists.