It’s the Soil Biology, Stupid!

“In soil/natural ecosystems, microorganisms including bacteria and fungi exist in a very large number and play a very crucial role in maintaining major biogeochemical cycles, plant nutrition, plant health, soil fertility, soil structure, and degrading organic pollutants and remediation of toxic metals. Therefore, microorganisms are key players in important ecological processes, such as carbon, nitrogen, phosphorous, and sulfur biogeochemical cycle, and directly influence all lives on Earth. It is noted that 1 gm of soil/sediment may contain l0 to the 9th bacterial cells…It constitutes 60% of the total biomass of the Earth, and it represents two to three orders greater biomass than the total plant and animal cells. Therefore, a large number of microorganisms and their genetic diversity are unexplored, and that is directly involved in maintaining major nutrient cycles, global climate change, and the greenhouse effect. So understanding this unexplored genetic diversity is a high-priority issue in microbial ecology.”

The above paragraph is from a paper on Molecular Genomic Techniques (Paul et al 2018) minus the references. Huge and ongoing improvement of molecular techniques, sequencing technology, and bioinformatics have revolutionized the field of soil microbial ecology. By learning more about what soil microbes do individually as well as collectively (in quorems), soil scientists are better understanding the huge role soil microbes play especially in nutrient cycling, carbon/nitrogen/phosphorus utilization, carbon sequestration, methane mitigation, soil fertility, and plant nutrient density.

Though apparently some researchers, especially in the UK, haven’t received the memo. For example , Rothamsted, in their report (Poulton, P et al, 2018). looked at soil types and other parameters in the plots they’ve monitored, but didn’t once mention a word in regards to soil biology. FCRN’s Grazed and Confused report (Garnett et al. 2017) does the same. This FCRN’s meta-analysis doesn’t seem to recognize the role that soil microbes play in carbon sequestration or respiration let alone nitrogen nitrification and denitrifcation. Again the words soil microbes or soil biology are never noted in this 129 page FCRN report.

johnson clip
Just above is a clip from a graphic from one of Dr. David Johnson’s recent presentations. This clip, and the whole chart attached  at the bottom before the references below, details the different types of bacteria and fungi present in the soils for some of Johnson’s current research. On the far right side, what some of these bacteria and fungi do are listed. As Johnson explained in email correspondences, Roche/454 FLX Pyrosequencer and Illumina HiSeq technology are very new (post 2011). This technology has made the sequencing of DNA and identification of microbes faster and more reliable.

Current research has shown microbes help build soil organic matter [SOM] through decomposition and the carbon pathway (Liang et al 2017), that is root exudates . Roots exude carbon that feed microbes, and soil organic matter is, in part, formed by microbes eating one another, pooping and dying, that is microbial waste and necromass. Thus carbon capture and utilization is driven by soil microbes (Kallenbach et al 2016). The more plant diversity above ground, the more microbial diversity below ground (Eisenhauer et al. 2017) because different plants exude different exudates to feed different microbes (Zhalninal et al. 2018).  Johnson’s recent and ongoing research has shown that higher fungi to bacteria ratios lead to more carbon capture and less carbon respiration (Johnson et al 2015, Johnson 2017). Another paper (Li et al. 2017) notes, “The understanding of SOM formation and C sequestration continues to evolve….C sequestration is mediated by soil microbes as they are involved in the majority of processes in C storage and decomposition…”

Additionally another meta-analysis (Derner et al. 2017),  that reviewed papers not accounting for soil biology, concluded the following:

“…Newly emergent fields of soil microbiology should provide additional insight into microbial function and processes that affect C sequestration under normal and widely fluctuating precipitation patterns found in arid and semi-arid environments. There is a need to move from the basic approach of soils and soil ecology to a more fundamental and functional understanding of the processes and mechanisms that affect SOC dynamics and how they are influenced by land management, environment and their interaction. For example, management strategies may offer opportunity to enhance soil fungal activity and C storage…”

So what can we conclude from the long‐term experiments (Poulton et al, 2018) at Rothamsted Research Institute in their research plots? If you plough and plant monocrops in various soil types over long periods of time, and don’t do anything to improve the diversity of the soil microbiology, except apply manure, you will not capture enough carbon to meet the 4 per 1000 Paris accord goal for carbon sequestration. What you can’t deduced from any of this research is whether or not using methods to improve soil microbiology (like using diverse plant covers, not tilling, reducing chemical inputs and integrating properly managed livestock) will enhance carbon capture and sequestration.

improve carbon

Above is a slide from a presentation by James Sinton, CEO of the Fair Carbon Exchange, at the 2017 Living Soils Symposium in Montreal. In this presentation, Carbon Sequestration in Soils, he discusses how soil microbes, particularly mycorrhizzal fungi keep carbon in the soil. And toward the end of the presentation around the twenty five minute mark, he discusses how to maximize soil carbon sequestration as noted in this  slide above. Carbon sequestration also improves water retention, the capacity for soils to contain more nitrogen, soil fertility, and thus plant nutrient density. So carbon sequestration is a lot more than just a means to draw down carbon from the atmosphere to mitigate climate change.

Now the problem with meta-analysis of older soil science documenting carbon sequestration rates, as was done by FCRN (Garnett et al. 2017), is that a lot of this old data didn’t account for any of the parameters that Stinton described in his slide and, in general, any of the newer soil science quickly noted above showing that carbon sequestration, as well as other cycles, are driven by microbes. Again, FCRN didn’t mention soil microbiology.including these three critical words: arbscular mycorrhizal fungi [AMF].  FCRN also didn’t seem to even understand that as long as there is photosynthesis from diverse covers, soils continue to make more soil via decomposition and microbial waste plus necromass, so “saturated” soil keeps forming more soil that can capture more carbon.

So when looking at degraded systems, what the microbial status is of those soil ecosystems needs to be known, and then improved to increase carbon capture. If there was no such microbial analysis of the soil when older research was done, there’s really no way to assess whether or not carbon sequestration rates actually reflect the potential of the soil noted in that older research to capture carbon. So getting  an average of carbon sequestration rates from older papers and then proclaiming that this average amount is all that soil can capture is something of a foolhardy and pedantic exercise. Instead using that old research as  a starting point,  researchers need to get back out into the field and see what exactly happens, for example,  when the soil biology has been restored and made fungi dominant.  This is what Dr. David Johnson is doing at New Mexico State University. Re-parsing old data is largely irrelevant.  Determining what land management systems for both crops and livestock that most enhance soil microbial activity especially AMF is what’s truly needed and essential.

When there’s quickly evolving methodologies leading to a lot of new discoveries,  papers from five to ten years ago have to be put in a different, maybe no longer as salient, context. Plus many of the old school scientists are still not accounting for what’s essentially been a paradigm shift in thinking. So people like FCRN’s Tara Garnett are sort of like the Marie Antoinettes of the soil revolution. They’re on the wrong side of history.

Sadly FCRN’s report was equally amiss (and reductive) on a lot of the climatic methane science as well,  particularly in understanding the roll of both biosphere and troposphere sinks in oxidizing methane from numerous sources via both methanotrophic bacteria and hydroxyl free radicals. Part of the reason atmospheric  levels of methane are again rising post 2007 is due to these methane sinks no longer being as effective. There’s less methanotrophic activity with the application of synthetic nitrogen as well as due to bare fallows, tillage and other more traditional farming practices (Tiwari et al. 2015). There may also be  fewer hydroxyl free radicals  (Rigby et al. 2017) in part due to increases in carbon monoxide and methane from more frequent and intense  forest fires (Worden et al 2017) and increased natural gas extraction (Hristov, A et al. 2017).  Hydroxyl free radicals combine with carbon monoxide to form carbon dioxide as well as oxidized methane to produce water and carbon dioxide that becomes part of the carbon cycle (Prinn, 2014) . Though Garnett seems to just like blaming  cows for all our environmental problems. Unfortunately nothing is as simple as that.  Ironically, Garnett and FCRN also seem to want to find new ways (e.g. lab and plant based meats) to use deleterious industrial agriculture practices  rather than dealing with any  real solutions that will regenerate land, soil health, soil ecosystems and soil fertility as well as mitigate climate change.

Regardless, a more detailed look at the climatic science of methane is a subject for another article.

David Johnson reduced poster chart with the types of bacteria in the soil


Paul, D et al. 2018. Molecular Genomic Techniques for Identification of Soil Microbial Community Structure and Dynamics

Poulton, P et al, 2018. Major limitations to achieving “4 per 1000” increases in soil organic carbon stock in temperate regions: Evidence from long‐term experiments at Rothamsted Research, United Kingdom

Garnett, T et al. 2017. Grazed and Confused. Food Climate Research Network

Liang, c et al 2017 the importance of anabolism in microbial control over soil carbon storage

Kallenbach et al. 2016. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls 

Eisenhauer et al. 2017. root biomass and exudates link plant diversity with soil bacterial and fungal biomass

Zhalnina1, K et al. 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

Johnson, D.C. et al 2015. Development of soil microbial communities for promoting sustainability in agriculture and a global carbon fix.

Johnson, D.C. 2017. The influence of soil microbial community structure on carbon and nitrogen partitioning in plant/soil ecosystems

Li et al. 2017. Soil carbon sequestration potential in semi-arid grasslands in the Conservation Resever Program.

Derner, J.D. et al. 2017. Carbon sequestration and rangelands: A synthesis of land management and precipitation effects

Tiwari, S et al. 2015. Methanotrophs and CH4 sink: Effect of human activity and ecological perturbations

Rigby et al. 2017. Role of atmospheric oxidation in recent methane growth.

Worden, J. R. et al 2017 Reduced biomass burning emissions reconcile conflicting estimates of the post-2006 atmospheric methane budget

Hristov, A et al. 2017. Discrepancies and Uncertainties in Bottom-up Gridded Inventories of Livestock Methane Emissions for the Contiguous United States

Prinn, R.G. 2014. Ozone, hydroxyl radical, and oxidative capacity. Massachusetts Institute of Technology

6 thoughts on “It’s the Soil Biology, Stupid!

  1. You make some interesting and well-informed comments about soil microbiology and the contribution to soil organic matter. You may be surprised to hear that some of us at rothamsted are very interested in the relationship between soil organic carbon and microbes. I hope to be publishing an important paper on this early next year

    Liked by 1 person

  2. The best place to store water is in the soil.
    With SoiLife Soil Health Programs on light, medium and heavy clay loams, we have been able to store up to 200 litres per cubic metre of pasture, tree crop soils in two years.
    We are excited.

    Liked by 1 person

  3. Love this piece. It’s refreshing to see the paradigm shift in our understanding of the fundamental importance of soil biology recognized and the resulting need to re-examine our existing opinions. Unfortunately, many in respected roles within science, government and agriculture will have a difficult time recognizing that much of their career has been misguided. It does open up opportunities for those who perceive this paradigm shift and apply it.
    It also great hope for solutions to some of our problems.
    Thanks for this article.

    Liked by 1 person

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