Unexpectedly dense colonization of soil pore space by microbes

Abstract

Pore surfaces in soil are considered to be sparsely colonised, dispersed only with isolated cells or colonies of bacteria and archaea. Here, we question this ‘empty space’-concept by combining microstructure analysis with molecular biology and provide a data-driven update on habitable surface areas (HSA) in soil. Our unique approach allowed us to provide 1) evidence that microbial densities in soil have been underestimated for decades and 2) two-dimensional simulations of their potential distribution within the soil pore space. Our results demonstrate the need for a new perspective on how densely soil is colonised, with implications for how we think of basic ecological processes such as microbial motility or predation, and how microbial processes, including organic matter dynamics, are ultimately modelled.

Spatial structure affects the establishment and persistence of closed microbial ecosystems

“…The initial cell densities inoculated into our biospheres ranged from 25,000-100,000 cells per square millimeter. These values are within the range observed in temperate forest topsoil aggregates, where the number of neighboring cells (within 20um) reported for cell densities similar to those initially present in our 0.5mm bead treatment were 29, compared to 78 for densities similar to those in our 1.0mm bead treatment (Schmidt et al, 2024). Lower neighbor density translates to less local resources (dead neighbors are a resource), and may have influenced the formation of biofilms, or intraspecific interactions within those that formed (Eigentler et al, 2022).…”