The Farm Ecologist: Soil as a composite phenotype of its microbial metagenome (Neal et al. 2020)

So much good stuff that it’s taken me over 2 weeks to get my head around it. The Neal et al. paper was a really dense read, but in a nutshell it 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.

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Soil as expression of the microbial metagenome

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.

If you can wrap your head around the title, you’re already halfway home with this really cool paper.

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 practises (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 the authors:

“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.”

This is consistent with Dr. Christine Jones’ contentions that the liquid carbon pathway is critical to our understanding (and underestimation) of soil carbon sequestration potential:

“Under appropriate conditions, 30–40% of the carbon fixed in green leaves can be transferred to soil and rapidly humified, resulting in rates of soil carbon sequestration in the order of 5–20 tonnes of CO2 per hectare per year. In some instances, high soil carbon sequestration rates have been recorded where there were virtually no ‘biomass inputs’, suggesting that the liquid carbon pathway was the primary mechanism for soil building.”

While some of her claims are controversial, as are the identity and nature of humic substances generally, the critical role of arbuscular mycorrhizae in uptake of carbon-rich root exudates, conversion to soil fungal biomass, i.e. soil carbon sequestration, and water distribution through the soil interface, have been clearly established.

See, for instance:

Cheng, L., Booker, F. L., Tu, C., Burkey, K. O., Zhou, L., Shew, H. D., Rufty, T. W., & Hu, S. (2012). Arbuscular Mycorrhizal Fungi Increase Organic Carbon Decomposition Under Elevated CO2. Science, 337(6098), 1084–1087.

Leake, J., Johnson, D., Donnelly, D., Muckle, G., Boddy, L., & Read, D. (2004). Networks of power and influence: The role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning. Canadian Journal of Botany, 82(8), 1016–1045.

Rygiewicz, P. T., & Andersen, C. P. (1994). Mycorrhizae alter quality and quantity of carbon allocated below ground. Nature, 369(6475), 58.


P.S. Stuck behind a paywall? Don’t be! Any one of these PDFs can be obtained by pasting the DOI [digital object identifier] in front of SciHub’s current working URL (which you can find here, along with a lot of related information and background details about Sci-Hub). I’m currently using

An example: in the Rygiewicz & Andersen (1994) paper above, you’d use: 10.1038/369058a0 in your browser search bar. Copy-paste it and see.

Other options including writing to the authors, or (apparently) #icanhazpdf on Twitter, although I’ve never used it.

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My ‘updates list’ was long this time, as I’ve been working on organizing a set of very climate-oriented papers, so had a lot of new citations to add. Last week I also gave a short guest presentation, titled Integrating Science and Permaculture, in Santa Barbara Community College’s online PDC. That led me to dig up a refreshed list of peer-reviewed studies on permaculture.

All these you can view for free at the most recent update of the Regenerative Agriculture Database on Medium.

I will do my best to keep these updates “in front of” rather than behind a paywall, so please let me know if for any reason you can’t access them.

However, the database construction itself has stalled out due to a funding shortfall. Boo, right? If you’d like to directly contribute to getting it up and running, and fully available to The Farm Ecologist readers, you can donate here through PayPal or to my personal account on Venmo.

All funds go towards the development and hosting of the database, currently deployed on Heroku (free) and hosted by DreamHost ($10.95/mth).

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Finally, a few things to share:

1) Registered dietician Diana Rogers and former biochemist Robb Wolf have published a book, The Sacred Cow, in which they explore the realities and opportunities of raising and eating meat — in particular, cattle. However, they have hit some bumps with publishing and distributing, so could use some direct support if you’re interested in the book.

2) Regenerative rancher, tracker, mother and author Doniga Markegard (of Markegard Family Grass-fed in California’s Bay Area) has two books out — Dawn Again, her personal memoir, and the related story for young teens, Wolf Girl. Both are available through her personal website . I have heard Doniga speak at multiple events and conferences, and while I don’t count myself as a personal friend she is extremely well loved and respected within the regen ag community. Send her some love and order those books, especially for the women and girls in your life.

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And now it’s your turn.

Do you have any specific papers or burning questions you’ve come across that you’d like me to spend time on?

Do you have a favourite author or book that you’d like to share with others, or a project you’re working on?

Hit “Reply” and send ’em over.

Thanks for joining me. Now go feed that soil.


P.S. If you want more input, please do fill out this short survey (shouldn’t take more than 5 minutes) so I get to know more about what you’d like to see and where you’re starting from.

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Evolutionary ecologist who grows a little food on a little plot of land in SoCal. I work at the intersections of food, health, farming, climate and ecology.