Pseudomonas in Soil Remediation: What the Research Shows

Pseudomonas is a generalist genus with specialist strains. P. putida, P. fluorescens and P. stutzeri have been studied on diesel, chlorinated solvents and organophosphate pesticides, and one P. stutzeri strain held a full-scale groundwater cleanup for four years. The same research shows why a species name alone doesn’t tell you what a microbe can do: most of the abilities below belong to particular strains, and some have been lost in culture.

The organism

Pseudomonas is a genus of Gram-negative bacteria common in soil and water. One review calls it a diversified genus with a series of catabolic pathways and enzymes involved in pesticide degradation [1], which is why it shows up so often in remediation papers. The genus is large, so the useful question is always about a specific species, and often a specific strain.

What the research shows

Where the evidence comes from

• The full-scale field evidence is P. stutzeri strain KC in groundwater, fed weekly with acetate, alkali and phosphorus [6].
• The field evidence in soil is the diesel consortium that included P. putida and P. fluorescens, which shows the consortium worked as a team without isolating any one member’s contribution [3].
• Everything else, including the TCE, chlorpyrifos and fluorotelomer work, comes from the laboratory.

For a genus cited this often, the soil field record is thin.

In a real project

Schoolcraft, Michigan, is the strongest field record in the genus. A team led from Michigan State University installed a row of closely spaced injection and extraction wells near the edge of a carbon tetrachloride plume, added strain KC, and fed it acetate, alkali and phosphorus every week. Removal held at about 98% for four years, strain KC colonized above 100,000 cells per gram, and roughly 18,600 cubic meters of groundwater were treated [6]. Small, transient amounts of chloroform and hydrogen sulfide appeared and cleared when the acetate dose was cut [6]. It worked in the field, and it took a lot of operating to make it work.

Limits, and why strain matters

An ability can sit on a mobile genetic element. The pdt genes behind strain KC’s carbon tetrachloride activity are on an integrative and conjugative element. In a 2024 genome study, most cells in a culture-collection sample had lost that element, and the authors say strain selection has to account for it [8]. A bacterium with the right name can still lack the ability.

Some breakdown needs a helper compound, and P. putida F1 degraded TCE with an enzyme it makes for toluene, so the cells had to be grown on toluene first, and the rate fell quickly [4]. That is cometabolism, and it needs a steady supply of the inducing compound.

A changed compound may not be a destroyed one. The fluorotelomer study found perfluorinated carboxylic acids among the products [7], so we don’t describe it as PFAS remediation. See our contaminant fit chart.

By-products count as well, and the chlorpyrifos study detected chlorpyrifos oxon among the products, which tracking the parent compound alone would miss [5].

Activity ranges are often narrow, and P. putida F1 degraded dichloroethylenes but not tetrachloroethylene or vinyl chloride [4], so a strain that works on one chlorinated compound may fail on the next.

Works with

The diesel field study used eight bacterial taxa together, and the carbon tetrachloride biocurtain depended on engineered feeding and well placement [3][6]. In practice Pseudomonas is one member of a working community supported by oxygen, nutrients and a carbon source. Biostimulation vs. bioaugmentation explains how those supports get chosen, and microbes that eat oil covers its role among oil degraders.

When a proposal names Pseudomonas

• Which species and strain, and how was it identified?
• Is the degradation ability shown for that strain, or only reported for the species?
• Has the ability been checked in the product itself, for example by testing for the relevant genes?
• Does the mechanism need a helper compound, such as the toluene that P. putida F1 needed to degrade TCE [4]?
• Which breakdown products will be sampled?
• What carbon, nutrient and oxygen supply keeps the organism active, and who pays for it over the project?

“It’s a well-known soil bacterium” doesn’t answer any of these. Our guide to evaluating a bioremediation proposal applies the same logic in twelve questions.

Is it in Elm Dirt’s products?

Pseudomonas is in Elm Dirt’s products at the species level: Biome Makers, an independent lab, identified eight Pseudomonas entries in Elm Dirt’s Plant Juice: seven named species (P. putida, P. mendocina, P. alcaligenes, P. oleovorans, P. balearica, P. stutzeri and P. fluorescens) and one identified only to genus.

Peer-reviewed research shows Pseudomonas putida can take part in diesel degradation [3] and degrade chlorpyrifos [5], and Pseudomonas stutzeri can degrade carbon tetrachloride [6]. Each is among the 291 microbial species identified in Elm Dirt’s Plant Juice by independent lab analysis (Biome Makers). Profiles: P. putida, P. stutzeri, P. fluorescens, P. oleovorans and P. mendocina.

The Biome Makers method identifies and counts species. It doesn’t show that the strains in our product carry the genes behind any result above, and that evidence is strain-specific. Elm Dirt has not published product-level degradation data for these compounds. We plan on months to a year or more, verified by independent lab testing.

Related

• Contaminants: petroleum hydrocarbons, chlorinated solvents and VOCs, pesticides and herbicides
• Sites: fuel spills
• Guides: how to evaluate a bioremediation proposal

Open questions

Whether the Pseudomonas strains in any Elm Dirt product carry these degradation genes, or would be active in a given soil at a given dose, takes strain-level testing and a treatability study to answer. Ask us about testing for your project.

Sources

1. Gilani RA, Rafique M, Rehman A, Munis MF, Rehman SU, Chaudhary HJ. Biodegradation of chlorpyrifos by bacterial genus Pseudomonas. Journal of Basic Microbiology 56(2):105-119, 2016. doi:10.1002/jobm.201500336.
2. 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.
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. Wackett LP, Gibson DT. Degradation of trichloroethylene by toluene dioxygenase in whole-cell studies with Pseudomonas putida F1. Applied and Environmental Microbiology 54(7):1703-1708, 1988. doi:10.1128/aem.54.7.1703-1708.1988.
5. 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.
6. Dybas MJ, Hyndman DW, Heine R, et al. Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environmental Science & Technology 36(16):3635-3644, 2002. doi:10.1021/es0114557.
7. 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.
8. Sewell HL, Criddle CS, Woo SG, Kim S, Müller JA, Kaster AK. Pseudomonas stutzeri KC carries the pdt genes for carbon tetrachloride degradation on an integrative and conjugative element. Microbial Physiology (online 16 April 2024). doi:10.1159/000538783.