Some of these approaches remain limited at present due to the sheer biological diversity of soil ecosystems. However, with an expanding view of the diversity of microorganisms and growing number of published reference genomes, more accurate quantitative approaches are within reach. In combining sequencing with quantitative measurements, one can obtain absolute abundances of organisms in a given sample, making investigations of complex microbial communities more robust.
Investigating microbial community composition in soils presents unique challenges in comparison to similar studies in well-mixed environments, as for example limnic or marine ecosystems. Microbial life in soil is largely incluenced by physico-chemical heterogeneities even over very short distances where particle sizes of minerals and their distribution, pore sizes and pathways, organic matter types and distribution, and water saturation vary in space rendering soil a highly complex environment for microorganisms  \cite{Young_2004,Vos_2013} (4–6)⁠. Compared to well-mixed systems, microbial growth and activity in soil is strongly limited by the complex network of pores and diffusion in the aqueous phase and gas transport (\cite{Bickel2020a}, 9)⁠. The soil microarchitecture should therefore be considered a major parameter that governs the potential for microorganisms to interact with each other.
Yet most studies investigating the diversity, composition, and networks of soil microbiomes disregard this heterogeneous structure and its inherent consequences for microbial interaction. In practice, researchers commonly use samples of 250 - 500 mg of fresh soil and extract nucleic acids that will eventually be subjected to high-throughput sequencing. Owing to the disruption of microbial cells for the extraction of nucleic acids via bulk homogenization approaches such as bead beating, the physical structure and the spatial arrangements of cells in a soil sample are obscured. Such extractions integrate millions of microbial cells (10)⁠ and thousands of microbial species (11)⁠ into a single pool of nucleic acids that does not contain information on the spatial distribution of microbial cells anymore. This practice does not pose a problem as long as no conclusions are drawn on the interaction of microbial taxa or individual cells within a soil sample. DNA extractions from soil samples represent a macroscopic measurement of the “whole” microbial community that as such cannot reveal the potential for interaction of its individual members. Therefore, and for reasons of compositionality (section XYZ), we advise researchers to be very careful before inferring information on microbial interactions from sequencing data based solely on bulk sample analysis.