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How a Bioremediation Project Works

Which Contaminants Can Microbes Break Down? A Fit Chart

A plain-English chart of nine contaminant families, from fuels to PFAS to metals: which ones soil microbes can break down, and the evidence for each.

Elm Dirt Science Team

On this page (8 sections)
  1. How to read the chart
  2. The chart
  3. The PFAS row
  4. What the chart leaves out
  5. Fire sites hit three rows
  6. Where Elm Dirt fits
  7. From chart to plan
  8. Sources

Soil microbes can break down many organic contaminants, including fuels, benzene and its relatives, and some solvents and pesticides, while nothing breaks down a metal and PFAS have no established biological remedy. PAHs, dioxins, PCBs and chlorinated compounds sit in between: biology can help under the right conditions, on thinner evidence. The chart sorts nine contaminant families and names the evidence for each row.

How to read the chart

A good fit means biology is routinely used and has a long field record, and a partial fit means it works for some compounds in the group or needs specialist organisms and conditions. Early-stage rows have lab findings with no established field method yet, while not degraded marks a contaminant that is an element, so biology can only move it or change its form.

Even “degraded” comes in degrees, and the goal is complete breakdown to carbon dioxide and water. Partial breakdown leaves intermediates, and some are more toxic than the starting compound [16], so a serious project samples for them.

The chart

Contaminant family Fit What biology can do Main caveat Evidence
Petroleum hydrocarbons (diesel, fuel oils) Good Aerobic microbes use these as food. Landfarming and biopiles are used on diesel, fuel oils, and oily sludge [1][2]. Heavier fractions work best in soil treatment. Light volatile fractions are better handled by vapor extraction [1]. A 365-day field study found added microbes gave the highest diesel removal [3].
Benzene, toluene, and other non-halogenated VOCs Good Aerobic treatment has handled benzene, acetone, toluene, and phenol [2]. Mixing soil can make contaminants evaporate before microbes eat them [4]. Evaporation is not degradation. EPA technical paper [2].
PAHs Partial Lighter PAHs degrade readily in soil studies. Heavier ones are slower and may need partner organisms. EPA places PAHs among compounds with a more limited performance record [2]. In a 25-day soil study an added bacterium removed 63% of naphthalene, 81% of phenanthrene, and 38% of benzo[a]pyrene [5]. A bacterium-fungus pair mineralized 53% of benzo[a]pyrene in soil over 100 days [6].
Chlorinated solvents (TCE, PCE, vinyl chloride) Partial, specialist Specific anaerobic organisms strip chlorine step by step. Aerobic vinyl chloride degraders also exist [7]. Dechlorination can stall at an intermediate compound [2]. A field pilot reached below 5 µg/L in groundwater within 200 days after adding a dechlorinating culture [8].
Pesticides and herbicides Partial Many individual compounds have degraders in the literature. EPA lists pesticides among compounds with a more limited record [2]. Breakdown products must be tracked. A soil bacterium degraded chlorpyrifos in a lab water system, and the products included chlorpyrifos oxon [9].
PCBs Limited Biology has a limited record on PCBs. Biodegradability falls as chlorine content rises [10]. EPA lists PCBs among the limited-record group [2]. EPA technical paper [2].
Dioxins and furans Partial, research White-rot fungi have degraded them in controlled treatment of excavated soil. The published result is on excavated soil treated under controlled conditions. 96% PCDD/F removal in 72 days in solid-state fungal treatment [11]. See our white-rot fungi guide.
PFAS Early-stage Laboratory studies show some bacteria remove fluorine from certain PFAS. PFAS are described as extremely resistant to microbial degradation [12]. Products can include shorter-chain PFAS that persist [13]. Laboratory studies [12][13][14].
Heavy metals Not degraded Microbes and plants can change a metal’s form, bind it, or move it into plant tissue. FRTR states bioremediation is not applicable to inorganic contaminants [16]. See what microbes can and cannot do with metals.

The PFAS row

Marketing runs furthest ahead of the science on PFAS, so here is exactly what the literature shows.

A 2023 critical review covers the microbial transformation routes and enzymes found so far and calls these compounds extremely resistant to microbial breakdown [12]. In a 2012 study, two Pseudomonas strains stripped fluorine from fluorotelomer alcohols, and the products included perfluorinated carboxylic acids, which are persistent PFAS in their own right [13], so the compound changed while nothing was remediated. A 2024 chapter describes Acidimicrobium sp. strain A6 releasing fluoride from PFOA and PFOS in lab incubations [14], and the original 2019 report on that organism has since drawn a published correspondence from other researchers [18], so the work is still early.

For soil, EPA researchers ran bench-scale tests of sorbents, biochar among them, for holding PFAS in place. Granular activated carbon did slightly better than the rest [15]. A sorbent keeps PFAS where they are and destroys none of it.

Microbial PFAS breakdown is still emerging research. What field work can do today is bind PFAS with carbon amendments and measure leaching over time, which is our approach.

What the chart leaves out

  • Oxygen, temperature, moisture, pH and nutrients decide whether any row plays out on your ground. Cold slows biodegradation, and in northern climates it can stall for part of the year [16].
  • Compounds that have sat in soil for years become harder for microbes to reach [17], so fresh spills respond faster than aged contamination.
  • Real sites rarely have one compound, and a mixture such as fuel plus metals needs two plans.
  • A “good fit” row still gets confirmed by sampling before and after.

Fire sites hit three rows

A derailment or industrial fire rarely leaves one contaminant. Burned cargo and buildings tend to leave dioxins and furans, PAHs and other semivolatiles, and sometimes PFAS from firefighting foam. Those fall in three different rows of the chart, so a fire site needs a separate plan for each, with sampling across all of them. Our soil-restoration pilot in East Palestine, Ohio is set up that way.

Where Elm Dirt fits

Peer-reviewed research shows Pseudomonas putida can degrade chlorpyrifos [9] and Comamonas testosteroni can degrade PAHs in soil [5]. Both are among the 291 microbial species identified in Elm Dirt’s Plant Juice by independent lab analysis (Biome Makers). Our products carry bacteria and fungi together, the pairing behind the strongest published benzo[a]pyrene result [6]. Biology takes months to a year or more, confirmed by lab testing.

From chart to plan

The chart is for a first conversation. A treatability study on your soil turns it into a plan, and it is the first thing we would set up. Start with us here.

Sources

  1. Federal Remediation Technologies Roundtable. Remediation Technologies Screening Matrix, section 4-13: Landfarming. Link. Accessed 2026-10-01.
  2. U.S. EPA. Engineering Issue: In Situ and Ex Situ Biodegradation Technologies for Remediation of Contaminated Sites. EPA/625/R-06/015, October 2006. Link. Accessed 2026-10-01.
  3. Szulc A, Ambrożewicz D, Sydow M, et al. The influence of bioaugmentation and biosurfactant addition on bioremediation efficiency of diesel-oil contaminated soil: feasibility during field studies. Journal of Environmental Management 132:121-128, 2014. doi:10.1016/j.jenvman.2013.11.006.
  4. U.S. EPA. A Citizen’s Guide to Bioremediation. EPA 542-F-12-003, September 2012. Link. Accessed 2026-10-01.
  5. Lu Q, Sun X, Jiang Z, Cui Y, Li X, Cui J. Effects of Comamonas testosteroni on dissipation of polycyclic aromatic hydrocarbons and the response of endogenous bacteria for soil bioremediation. Environmental Science and Pollution Research 29(54):82351-82364, 2022. doi:10.1007/s11356-022-21497-z.
  6. Boonchan S, Britz ML, Stanley GA. Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures. Applied and Environmental Microbiology 66(3):1007-1019, 2000. doi:10.1128/AEM.66.3.1007-1019.2000.
  7. Chen G, Rosolina S, Padilla-Crespo E, et al. Natural attenuation potential of vinyl chloride and butyl acrylate released in the East Palestine, Ohio train derailment accident. Environmental Science & Technology 58(40):17743-17755, 2024. doi:10.1021/acs.est.4c04198.
  8. Major DW, McMaster ML, Cox EE, et al. Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environmental Science & Technology 36(23):5106-5116, 2002. doi:10.1021/es0255711.
  9. Pradeep V, Subbaiah UM. Repeated batch and continuous degradation of chlorpyrifos by Pseudomonas putida. Journal of Environmental Science and Health Part B 50(5):346-360, 2015. doi:10.1080/03601234.2015.1000180.
  10. Federal Remediation Technologies Roundtable. Remediation Technologies Screening Matrix, section 3.4: Ex Situ Biological Treatment for Soil, Sediment, and Sludge. Link. Accessed 2026-10-01.
  11. Kaewlaoyoong A, Cheng CY, Lin C, Chen JR, Huang WY, Sriprom P. White rot fungus Pleurotus pulmonarius enhanced bioremediation of highly PCDD/F-contaminated field soil via solid state fermentation. Science of the Total Environment 738:139670, 2020. doi:10.1016/j.scitotenv.2020.139670.
  12. Berhanu A, Mutanda I, Taolin J, Qaria MA, Yang B, Zhu D. A review of microbial degradation of per- and polyfluoroalkyl substances (PFAS): biotransformation routes and enzymes. Science of the Total Environment 859:160010, 2023. doi:10.1016/j.scitotenv.2022.160010.
  13. Kim MH, Wang N, McDonald T, Chu KH. Biodefluorination and biotransformation of fluorotelomer alcohols by two alkane-degrading Pseudomonas strains. Biotechnology and Bioengineering 109(12):3041-3048, 2012. doi:10.1002/bit.24561.
  14. Jaffé PR, Huang S, Park J, Ruiz-Urigüen M, Shuai W, Sima M. Defluorination of PFAS by Acidimicrobium sp. strain A6 and potential applications for remediation. Methods in Enzymology 696:287-320, 2024. doi:10.1016/bs.mie.2024.01.013.
  15. Barth E, McKernan J, Bless D, Dasu K. Investigation of an immobilization process for PFAS contaminated soils. Journal of Environmental Management 296:113069, 2021. doi:10.1016/j.jenvman.2021.113069.
  16. Federal Remediation Technologies Roundtable. Remediation Technologies Screening Matrix, section 3.1: In Situ Biological Treatment for Soil, Sediment, and Sludge. Link. Accessed 2026-10-01.
  17. Alexander M. Aging, bioavailability, and overestimation of risk from environmental pollutants. Environmental Science & Technology 34(20):4259-4265, 2000. doi:10.1021/es001069+.
  18. Liu J, Edwards E, Van Hamme J, et al. Correspondence on “Defluorination of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonate (PFOS) by Acidimicrobium sp. Strain A6.” Environmental Science & Technology 57(48):20440-20442, 2023. doi:10.1021/acs.est.3c06681.

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