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The microbes cleaning up our world

Bioremediation connects fungi transforming herbicides, hydrocarbon-using bacteria, metal-binding biomass and plants accumulating pollutants. Its potential becomes useful when we distinguish transformation, transfer and verified detoxification.

Soil biology · Bioremediation · 7 October 2026

In “The Microbes Cleaning Up Our World”, Dr Sandra Tuszynska, a guest of Dr Elaine’s Soil Food Web School, presents research and experience. Her central message is to understand whole communities: one organism may begin a transformation and others continue processing its products.

What does cleaning up a pollutant mean?

Bioremediation uses organisms and their activity to reduce pollution or exposure. Mycoremediation uses fungi; phytoremediation uses plants and their soil interactions. Several different mechanisms are involved.

• Biosorption: binding to cells or biomass, including dead biomass. The pollutant need not be destroyed; loaded material needs management.
• Bioaccumulation: uptake into organisms, requiring attention to harvest, biomass and food-chain exposure.
• Biotransformation and biodegradation: enzymes change organic molecules, potentially creating intermediates that remain or become more toxic.
• Complete mineralisation: conversion to simple inorganic substances. Disappearance of the parent compound alone does not prove it.
• Bioprecipitation and biomineralisation: solid compounds may reduce metal mobility, but stability can change with pH and redox conditions.
• Bioleaching: microbial activity mobilises metals from solids. The liquid must be collected and treated.

Metals do not biodegrade. Nickel, zinc and uranium are elements; arsenic is a metalloid. Their location, binding or chemical form can change, but fungal uptake does not make them disappear. Binding radionuclides does not neutralise their radioactivity.

Organisms discussed in the presentation

“sp.” means an unidentified species within a genus. Findings for one strain cannot automatically be assigned to every member.

• Microbacterium sp.: a possible reading at 10:18 in the metals section. The slide spelling and pollutant-specific attribution need confirmation.
• Micrococcus sp.: metals at 10:18 and diuron demethylation at 41:34. The strain and diuron study were not independently identified.
• “chigela”, possibly Shigella: an uncertain name at 10:18 with no substantiated specific application; it is not presented as an organism recommended for use.
• Bacillus sp.: metals/metalloids at 10:18, without a species, strain or removal rate.
• Schizophyllum commune: contaminated environments, metals, antiseptics and Fungi Mutarium at 15:50, 45:01, 49:49 and 1:25:15. The antiseptic study identifies AJ11.
• Purpureocillium lilacinum: a possible identification at 18:17, consistent with primary research on stress adaptation in contaminated soils; slide confirmation remains necessary.
• Cladosporium sphaerospermum: melanin and growth under ionising radiation at 20:13, without evidence of eliminating radiation.
• Penicillium citrinum: uranium bioleaching and, separately, binding dissolved uranium to dead biomass at 21:42.
• Pleurotus spp.: ligninolytic enzymes, hydrocarbons and Fungi Mutarium at 26:52, 49:49 and 56:32. Species are not securely identified in each example.
• Phanerochaete: a possible reading in white-rot and persistent-compound sections at 27:29, 28:31 and 49:17; no species is assigned to uncertain transcription.
• Trametes versicolor: diuron and 3,4-DCA transformation supported by primary research, with dyes and polycyclic aromatic hydrocarbons also discussed.
• Ganoderma spp.: lignin-modifying enzymes at 27:29 and 34:58; no specific strain or removal rate.
• Pycnoporus spp.: diuron and other organic pollutants at 43:27–45:01. The independently identified study uses P. sanguineus MCA16; this species is established by the study, not securely by the transcript.
• Mycorrhizal fungi: nickel and zinc responses at 1:23:48–1:25:15, without species identification.
• Microalgae: general binding, accumulation and transformation at 05:35 and 22:09, without species or performance figures.
• Acidophilic bioleaching organisms: iron and sulphur reactions at 12:58. Chemolithotrophy is distinct from photosynthesis.
• Native hydrocarbon-degrading bacteria: oil degradation under suitable conditions, including Exxon Valdez at 52:49–56:07; no species names.
• Phenanthrene- and pyrene-degrading bacteria: reported population increases with mushroom substrate at 58:25–59:29; the exact study was not identified.
• A 14-isolate biofilm community: Tuszynska’s diuron account at 39:15–41:34. Names are not supplied and she leaves possible eukaryotic presence open.

Fungi, metals and radioactive environments

Tuszynska refers to Lea Chavah Traxler’s Schizophyllum research in Chernobyl, including survival and metal adaptation and transport in hyphae. At 16:40 she mentions roughly 8 mm daily spread, presence one metre away after six months and survival for a year. These are different observations, not a fixed growth or cleanup rate.

Mechanisms discussed include restricting entry, export, vacuolar binding and association with glutathione or metallothioneins. These show adaptation, not proof that a field is suitable for food production. Loaded biomass still needs management.

Research on possible P. lilacinum examines particular strains’ peroxide-stress resistance, respiration and polyphosphates. It does not establish that fungi “eat uranium”. Dadachova and colleagues’ melanin research found altered electronic properties and enhanced growth under tested irradiation conditions. Using radiation energy is a different claim from reducing a site’s radionuclide inventory.

P. citrinum illustrates opposite transfers: bioleaching can move metal from rock into liquid; dead biomass can move dissolved uranium onto solids. Restoration requires understanding the entire pathway.

Enzymes and difficult chemical bonds

The 26:16–34:58 section addresses white-rot fungi. Their lignin-modifying abilities motivate research on certain human-made pollutants; chemical similarity alone proves no particular compound’s degradation.

Laccases oxidise some substrates, sometimes with mediators. Lignin and manganese peroxidases participate in oxidative reactions. Oxygenases and cytochrome P450 can mediate hydroxylation and dealkylation; glutathione transferases support conjugation. Siderophores, acids and binding factors affect metals and are not all enzymes. Hydrophobins and biosurfactants can improve contact, which is distinct from complete degradation.

Persistent organic pollutants do not all contain dioxins. Agent Orange combined 2,4-D and 2,4,5-T; TCDD was an unwanted manufacturing contaminant, not the herbicidal active ingredient. Proposed fungal work in Vietnam is a research idea, not an established cleanup protocol.

Diuron: follow the transformation products

Diuron transformation may produce DCPMU, DCPU or 3,4-dichloroaniline. Metabolites need measuring alongside the parent.

Tuszynska describes selecting 14 from 68 soil isolates and transformation in continuous culture within about three days. The complete paper and isolate names are unavailable in the supplied transcript; final products were not tested. This remains her research account, without proof of full detoxification. Montmorillonite inhibited that experiment, which does not establish that all clay soils block degradation.

A Trametes versicolor study reported 83% diuron and 100% 3,4-DCA degradation after seven days’ laboratory incubation. Its separate trickle-bed work does not turn these figures into guaranteed reactor or field performance. P. sanguineus MCA16 removed 56% diuron in forty days, producing DCPU and DCPMU. Crude extracts did not degrade diuron in vitro despite laccase production, so the whole effect cannot be attributed to laccase. The Micrococcus demethylation example remains an unverified presentation reference.

Communities can offer complementary pathways; biodiversity alone does not prove removal of every toxic intermediate.

Antiseptics and Schizophyllum commune

The 45:01–46:20 section concerns chlorhexidine gluconate and benzalkonium chloride. A 2025 study identifies AJ11 from Indian hospital effluent. With 50 mg/L CHG and 100 mg/L BAC, parent chromatographic peaks were no longer detected on days nine and eight respectively, while metabolite peaks appeared.

This is laboratory evidence of transformation. New products show why parent disappearance does not establish a safe final liquid. Real wastewater and toxicity assessment are needed.

Oil: organisms also need suitable conditions

Exxon Valdez illustrates biostimulation, improving conditions for existing organisms. Oxygen, nutrients, temperature and pollutant accessibility matter. Primary research on four Prince William Sound beaches investigated oxygen and nutrients in 2011–2012 while oil persisted more than twenty years after the spill.

The talk also includes Paul Stamets’s oyster-mushroom example and spent-substrate accounts with figures of about 200 ppm, 6,500 to 112 mg/kg in eight months, and 78% in nine weeks. Corresponding primary studies were not securely identified. These remain talk figures, not verified results or targets. Visible plants or mushrooms alone do not prove cleanup.

Plastics and Fungi Mutarium

The 46:44–51:19 section discusses polyethylene, polypropylene, PVC and polystyrene. Questions include actual polymer changes, products and additives’ fate.

Livin Studio and Utrecht University’s Fungi Mutarium was a design and research prototype using nutrient agar and pretreated plastic, with Pleurotus and S. commune mentioned. Its description presents ongoing research. Surface colonisation, weathering or mass loss, polymer breakdown and complete mineralisation are distinct.

We do not propose eating fungi grown on plastic or contaminated substrates. An edible species in clean cultivation does not establish the safety of contaminated biomass.

Hemp and PFAS

At 1:01:44, the talk describes Upland Grassroots and the Mi’kmaq Nation at former Loring Air Force Base in Maine. Research examines Cannabis sativa phytoextraction and, separately, hydrothermal liquefaction of harvested biomass.

Uptake transfers PFAS into tissues; it does not mean the plant breaks carbon–fluorine bonds. Authors do not present a complete solution. Subsequent processing varied by compound, with measured PFOS mass increasing under some conditions. The entire chain needs testing. Other site contaminants mentioned, such as fuel and DDT, were not all shown removed by the hemp trial.

Nickel, zinc and mycorrhizae

In audience questions, Tuszynska describes doctoral work on cellular, mitochondrial and vacuolar responses to nickel and zinc, with more difficult nickel responses under tested conditions. The transcript does not name the fungus. Proposed S. commune uptake work is a future idea without a demonstrated nickel-removal rate.

Harvesting loaded plants or fungi requires controlled management. Spreading contaminated biomass elsewhere can transfer pollution.

Meaning for regenerative agriculture

Organic matter, cover, structure and communities can contribute to wider restoration. God’s Way Ltd projects discussed at 1:04:09–1:05:56 illustrate habitat and soil work; pollutant-removal measurements are not supplied.

Improved biological functioning and chemical decontamination require different, complementary measurements. Microscopy and vigorous crops do not replace pollutant analysis. Tests for selected metals and pathogens do not prove the absence of untested PFAS or pesticides.

A documented project needs baseline pollutants, concentrations, depths and migration pathways; a site-appropriate method; pilots and controls; transformation-product and toxicity checks; management of loaded soil, filters, leachate and biomass; and long-term monitoring of possible remobilisation.

Microorganisms offer remarkable possibilities. Accurate descriptions, suitable applications and measured outcomes turn inspiration into useful knowledge for soil, water and communities.

Video guide

• 05:35: basic mechanisms.
• 10:18: bacteria and metals.
• 15:50: Schizophyllum and radiation tolerance.
• 26:16: white-rot fungi and enzymes.
• 35:28: diuron and communities.
• 45:01: antiseptics.
• 46:44: plastics and Fungi Mutarium.
• 52:49: oil pollution.
• 1:01:44: hemp and PFAS.
• 1:23:48: nickel, zinc and mycorrhizae.

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