On this page (12 sections)
Plenty of soil bacteria eat oil, using the hydrocarbons in diesel and crude as food, pulling oxygen from the air and turning the carbon into biomass, carbon dioxide and water. Pseudomonas, Acinetobacter and Rhodococcus turn up again and again in the research. Most public coverage is about marine spills and the specialists that bloom in seawater, so this post covers soil: the organisms, how they work, what a 365-day field study found, and what slows them down.
Why oil makes good food
A review of petroleum biodegradation states that many native microorganisms in water and soil can degrade hydrocarbon contaminants [1]. EPA’s technical paper describes the mechanism: with oxygen available, many microbes degrade hydrocarbons and gain energy and carbon from the reaction. At many fuel sites oxygen limits how much treatment happens, and adding air lets degradation continue [2].
So the first rule for oil in soil is getting oxygen to the oil. Flooded or compacted soil can stall a project full of capable microbes.
The enzymes
The breakdown of a fuel chain starts with enzymes called alkane hydroxylases, and a well-studied system comes from a Pseudomonas putida strain called GPo1. Researchers cloned versions of its alkane hydroxylase from other bacteria and showed most of them allow growth on alkanes, and a Pseudomonas fluorescens strain missing its alkane hydroxylase gene could no longer grow on alkanes of 12 to 16 carbons [3]. A diesel-degrading Acinetobacter calcoaceticus strain from Canadian soil switched on a different hydroxylase gene, alkM, when grown on diesel [4].
The enzymes sit on specific genes, and strains differ in whether they carry them, so a species name alone doesn’t guarantee the ability.
Organisms with published research
| Organism | What the research shows | Scale | In Elm Dirt’s products? |
|---|---|---|---|
| Pseudomonas putida | Member of a bioaugmentation consortium in a 365-day field study of diesel-contaminated soil [5]. A well-studied alkane hydroxylase system comes from its GPo1 strain [3]. | Field consortium, plus laboratory genetics | Yes, identified in Plant Juice. See P. putida. |
| Pseudomonas fluorescens | Same field consortium [5]. Alkane hydroxylase deletion removed growth on C12 to C16 alkanes [3]. | Field consortium, plus laboratory genetics | Yes. See P. fluorescens. |
| Acinetobacter calcoaceticus (strain CA16) | Degraded 82 to 92% of C12 to C18 alkanes in 28 days with diesel as its only carbon source [4]. | Laboratory culture | Yes. See A. calcoaceticus. |
Peer-reviewed research shows each of these species can take part in hydrocarbon degradation, as cited, and each is among the 291 microbial species identified in Elm Dirt’s Plant Juice by independent lab analysis (Biome Makers). Site results still have to be confirmed by lab testing.
The soil field study
The diesel study ran 365 days in the field and compared four treatments: natural attenuation, a biosurfactant, bioaugmentation with a bacterial consortium, and bioaugmentation plus the biosurfactant. Bioaugmentation gave the highest diesel biodegradation, and the biosurfactant made no notable difference [5]. The consortium had eight bacterial taxa, including both Pseudomonas species in the table.
The Exxon Valdez cleanup adds a different kind of evidence. Fertilizer on oiled shorelines significantly increased biodegradation rates, driven mainly by nitrogen concentration, oil loading and how much natural degradation had already happened [8]. That was shoreline sediment, not farm soil, but it shows that feeding the native organisms can matter as much as adding new ones. Biostimulation vs. bioaugmentation sets out when each applies.
Soil, sand and sea
Marine spills have well-known specialists called obligate hydrocarbonoclastic bacteria, Alcanivorax chief among them. When oil reaches seawater, a small group of these genera blooms from low or undetectable levels, and added nutrients can speed that up [7]. In Gulf beach sand after Deepwater Horizon, bacterial gene abundance ran about tenfold higher in oiled sand than clean sand, and the authors isolated oil degraders from 14 genera, including Pseudomonas and Acinetobacter [6].
The soil studies cited here center on more versatile genera such as Pseudomonas, Acinetobacter and Rhodococcus instead of the marine specialists.
Putting them to work
Projects rarely depend on one microbe; they set up conditions that let a community work, and each method below is a way of getting oxygen to the oil. Land treatment, or land farming, tills an 8- to 12-inch layer of soil to promote aerobic biodegradation, usually in a prepared bed with a liner to contain leachate [2]. Biopiles pile excavated soil with amendments and aerate it for a few weeks to a few months [2]. In place, bioventing pushes air into fuel-contaminated subsurface soil and can take a few years, according to EPA [2].
Reading the numbers
Each lab percentage describes a defined setup, and the 82 to 92% alkane removal came from one isolate in a minimal growth medium, with diesel as its only carbon source, over 28 days [4]. The field study measured a whole consortium in real soil over a year [5]. Neither predicts what an organism will do on a given site, though together they show the capability exists and the conditions it was shown under.
What slows oil breakdown in soil
- Oxygen is the most common limit at fuel sites [2].
- Biodegradation slows as soil cools and in northern climates can stop working for part of the year [10].
- The fraction matters, and FRTR says landfarming works best on heavier hydrocarbons such as diesel and fuel oils, while light volatile compounds suit soil vapor extraction better [9]. A mixed spill needs a plan for each fraction.
- Nutrients can set the pace, and at Valdez, nitrogen concentration mainly controlled the degradation rate [8].
- Older contamination is harder for microbes to reach, as explained in how long soil bioremediation takes.
Questions for a diesel or crude oil project
- Which fractions were measured at baseline, and by what lab method?
- Is there an untreated comparison area or natural-attenuation arm, as in the field study?
- How will oxygen reach the oil, and how will that be checked?
- What happens in the cold season?
- When is the first sampling round, and what result would change the plan?
The full list is in our guide to evaluating a bioremediation proposal.
Landowners with a spill
Report and contain the spill first, starting with your state environmental agency. Biology treats the soil that remains after the source is stopped and bulk contamination is removed. See petroleum hydrocarbons and fuel spills.
Limits of the evidence
The evidence here is species-level or strain-level. Strain results describe particular isolates, and the 365-day field study describes one site in one climate. Elm Dirt has not published product-level degradation data for petroleum compounds, and the Biome Makers analysis shows which species are present, not that any strain in our products carries a given enzyme. We plan on months to a year or more for biological work, verified by independent lab testing. If you have a fuel release to deal with, tell us about the site.
Sources
- Das N, Chandran P. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnology Research International 2011:941810. doi:10.4061/2011/941810.
- 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.
- Smits THM, Balada SB, Witholt B, van Beilen JB. Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. Journal of Bacteriology 184(6):1733-1742, 2002. doi:10.1128/JB.184.6.1733-1742.2002.
- Ho MT, Li MSM, McDowell T, MacDonald J, Yuan ZC. Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil. BMC Biotechnology 20(1):39, 2020. doi:10.1186/s12896-020-00632-z.
- 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.
- Kostka JE, Prakash O, Overholt WA, et al. Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Applied and Environmental Microbiology 77(22):7962-7974, 2011. doi:10.1128/AEM.05402-11.
- Yakimov MM, Timmis KN, Golyshin PN. Obligate oil-degrading marine bacteria. Current Opinion in Biotechnology 18(3):257-266, 2007. doi:10.1016/j.copbio.2007.04.006.
- Bragg JR, Prince RC, Harner EJ, Atlas RM. Effectiveness of bioremediation for the Exxon Valdez oil spill. Nature 368:413-418, 1994. doi:10.1038/368413a0.
- Federal Remediation Technologies Roundtable. Remediation Technologies Screening Matrix, section 4-13: Landfarming. Link. Accessed 2026-10-01.
- 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.