Soil Microbiome

[[soil|The soil]] microbiome is the community of bacteria, archaea, fungi, protozoa, viruses, and other microorganisms inhabiting soil. By any measure of biological diversity, the soil microbiome is among the most extraordinary biological communities on Earth.

The scale

A few characteristic numbers:

• A single gram of healthy soil typically contains:
  • 10⁸–10⁹ bacterial cells (1 billion)
  • 4,000–50,000 distinct bacterial species
  • 10⁷–10⁸ archaeal cells
  • 100+ meters of fungal hyphae
  • 10⁴–10⁵ protozoa
  • 10⁹–10¹⁰ virus particles
  • Various nematodes, microarthropods, and other small fauna
• An acre of healthy topsoil typically supports tens of tons of microbial biomass — substantially exceeding the biomass of all the visible plants and animals living above [[soil|the soil]].
• [[soil|The soil]] microbiome contains more [[genetic-diversity|genetic diversity]] than any other terrestrial environment. Most of this diversity has not been cultured in the laboratory and is known only through DNA-sequencing surveys.

What the microbiome does

A non-exhaustive map of functions:

• Nutrient cycling. Microbes drive [[soil|the soil]] cycling of nitrogen, phosphorus, sulfur, carbon, and other elements. Specific examples:
  • [[nitrogen-fixation|Nitrogen fixation]] — by rhizobial bacteria in legume root nodules and by free-living diazotrophs.
  • Nitrification — by nitrifying bacteria converting ammonia to nitrate.
  • Denitrification — by anaerobic bacteria converting nitrate to N₂ gas.
  • Phosphorus solubilization — bacteria and fungi releasing phosphorus from mineral and organic forms.
  • Sulfur cycling — multiple microbial groups oxidizing and reducing sulfur compounds.
• Organic matter dynamics. Microbes are the principal decomposers of plant residues, animal residues, and microbial biomass itself. The same microbes also build the stable [[soil-organic-matter|soil organic matter]] — the microbial efficiency-matrix stabilization hypothesis holds that most stable SOM is microbial necromass.
• Plant-nutrient mediation. Plant roots release substantial carbon (10–40% of total photosynthetic fixation in some species) as exudates that feed the rhizosphere microbiome; in return, the rhizosphere community substantially mediates plant nutrient uptake. The substantial [[mycorrhizal-fungi|mycorrhizal symbiosis]] is the most-studied example.
• Aggregate structure. Microbial polysaccharides, fungal hyphae, and proteins like [[glomalin]] bind soil particles into stable aggregates — the principal physical-structural function of healthy soil.
• Pathogen suppression. Diverse healthy microbiomes substantially suppress plant pathogens through competition, antibiosis, and induction of plant defense responses. The principle of suppressive soils has been recognized since the early 20th century; the molecular mechanisms are now substantially understood.
• Greenhouse-gas regulation. The microbiome regulates fluxes of CO₂, methane, and N₂O between soil and atmosphere. Healthy soils are typically net carbon sinks; degraded soils are typically net sources.
• Bioremediation. Microbial communities degrade petroleum hydrocarbons, certain pesticides, and various other contaminants. See [[hemp-phytoremediation]].

How the microbiome is structured

Several characteristic features:

• Spatial organization. The microbiome is not uniformly distributed. Microbial activity is concentrated in hotspots — the rhizosphere (around plant roots), the detritusphere (around decomposing residues), the drilosphere (around earthworm burrows), and the surfaces of soil aggregates. Most of [[soil|the soil]] volume is comparatively microbially inactive.
• Niche specialization. Different microbes specialize in different substrates, conditions, and ecological roles. Bacterial communities differ between rhizosphere and bulk soil; fungal communities differ between forest, grassland, and cropland soils; archaeal communities differ between aerobic surface and anaerobic deeper layers.
• Fungal-to-bacterial ratio. A useful indicator. Forest and perennial-grassland soils typically have substantial fungal biomass relative to bacterial; tilled cropland soils typically have substantially lower fungal:bacterial ratios. The shift toward bacterial dominance is one of the principal signatures of agricultural disturbance.
• Diversity and function. Healthy soil microbiomes are typically diverse, with substantial functional redundancy (multiple species can perform each principal function). Degraded soils are typically less diverse, with reduced functional capacity.

How agriculture affects it

The principal mechanisms by which [[industrial-agriculture|conventional agriculture]] disrupts [[soil|the soil]] microbiome:

• Tillage mechanically breaks fungal hyphae and disrupts microbial habitat structure. Cumulative tillage substantially reduces fungal biomass and shifts community structure toward bacteria.
• Synthetic nitrogen suppresses [[nitrogen-fixation|biological nitrogen fixation]] and mycorrhizal symbiosis (because plants reduce carbon allocation to symbionts when nutrients are abundant in solution).
• Pesticides and fungicides directly kill non-target microbes; the broader effects on microbiome composition are substantial and incompletely characterized.
• Bare-soil periods without continuous plant root inputs starve the rhizosphere microbial community.
• Monoculture reduces the diversity of root exudates, which selects for less diverse microbiomes.
• Compaction produces anaerobic conditions and favors anaerobic microbial communities (which differ substantially in function from the aerobic communities of well-structured soil).

How the microbiome rebuilds

The principal regenerative practices substantially rebuild [[soil|the soil]] microbiome:

• Continuous living roots through [[cover-cropping|cover cropping]], perennial integration, reduced fallow.
• Reduced tillage allows fungal networks to extend and persist.
• Diverse plant communities support diverse microbiomes through diverse exudates.
• Organic-matter inputs feed microbial growth.
• Compost teas and microbial inoculants can supplement (with substantial caveats about effectiveness).
• Patience. Microbiome restoration typically requires 3–10+ years of consistent regenerative management.

What this gives the platform

The soil microbiome is the substrate under nearly every agricultural and ecological function [[0mn1one|the platform]]‘s land work would depend on. The contemporary scientific recovery of the microbiome — driven substantially by molecular methods that have only become routine since the 2000s — provides the principal scientific foundation under [[regenerative-agriculture|regenerative agriculture]]. The platform takes microbiome health as one of the principal indicators of whether its land work is succeeding.

See also

Auto-generated from this entry’s typed relations: frontmatter, grouped by relation type so the editorial signal isn’t flattened.

• Subset of: [[soil]]
• Parallels: [[soil-food-web]]

Sources

1. Diana H. Wall (ed.). Soil Ecology and [[ecosystem-services|Ecosystem Services]]. Oxford, 2012. Source class: book / scholarly survey.
2. Noah Fierer. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology, 2017. Source class: peer-reviewed scholarly review.
3. David R. Montgomery & Anne Biklé. The Hidden Half of Nature. W.W. Norton, 2016. Source class: book / accessible engagement.
4. Jeff Lowenfels & Wayne Lewis. Teaming with Microbes. Timber Press, 2010 (rev. 2022). Source class: book / accessible practitioner-oriented engagement.

Lenses still to grow

• The rhizosphere as substantial sub-topic.
• Mycorrhizal symbiosis in cellular detail.
• Nitrogen-fixing bacteria in detail.
• The microbial-necromass-stable-SOM hypothesis as continuing scientific framework.
• Compost teas and inoculants as continuing practitioner question.