Soil‑microbe systems are self‑organising states

by Susan Cousineau

(Instagram @susan.cousineau)

Neal, A. L., Bacq-Labreuil, A., Zhang, X., Clark, I. M., Coleman, K., Mooney, S. J., Ritz, K., & Crawford, J. W. (2020). Soil as an extended composite phenotype of the microbial metagenome. Scientific Reports, 10(1), 10649. https://doi.org/10.1038/s41598-020-67631-0

 

This paper was a really dense read, but in a nutshell establishes soil as a self-organizing system derived from the interplay of microbial genetics (not just the whole organisms) and soil characteristics, rather than a reducible, mechanical system of many parts. While that may at first glance seem kind of self-evident, here's the peer-reviewed science to back it up.

 

The authors determined that the soil isn't just influenced by microbes; and microbial populations aren't just influenced by soil type, structure, soil organic matter, and so on.

Instead, soil is literally an emergent expression of the genetic composition of microbial populations that inhabit it. That means that distinctive sets of alleles (versions of individual genes) are associated with, and in turn determine through positive feedbacks, different states of soil physical structure, specifically porosity, which is driven by organic carbon flux.  

• Soil management practices (comparing fallow, conventional wheat cropping, and grassland conversion) result in emergence of distinct associations between physical structure and biological functions
• These associations in turn determine the flux, resilience and efficiency of nutrient delivery to plants (including water).
• Nutrients (e.g. fertilization) and physical interventions (e.g. tillage) influence physical structure, which determines the air–water balance (e.g. anoxia) in soil and transport rates.

So far, this all seems pretty familiar, right?

What the authors determined, though, through a combination of soil X-rays and CT scans (to visualize the size and connectivity of soil pores), chemical analyses, and metagenomics of the soil microbiome, is unique in that it shows distinct assemblages of genes, not just organisms, associated with different types of management. And that these assemblages don't just vary from one type of management to the next -- they are altogether distinct from one another.

They were able to show that. . .

• The quality of organic carbon inputs (e.g. plant-derived carbon), the prevalence of anaerobic microsites, and delivery of nutrients to microorganisms attached to soil surfaces -- all of which are in large part determined by soil porosity (structure), which is in turn driven by carbon content -- result in selective pressures upon the soil microbiome at the level of individual genes rather than entire organisms.
• As a result, distinctive gene assemblages characterise each soil state, with increased gene abundances for cell motility and external enzymatic activity in depleted soils (fallow and arable), with low soil porosity; and increased abundances for bacterial-bacterial and bacterial-Eukaryotic interactions in grassland soil, with higher soil porosity.
• The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant‑derived organic carbon.

To quote:
"We provide new evidence supporting the theory that soil‑microbe systems are self‑organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content, as the critical factor in soil systems."

 

I've attached the PDF, with my highlights. If you want a clean copy, and are behind a paywall, you can drop the DOI into Sci-Hub (currently www.sci-hub.tw works) and get the PDF.