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Bioremediation 3.0 – The New Frontier in Environmental Biotechnology

Bioremediation 3.0 – The New Frontier in Environmental Biotechnology


The solutions to our industrial waste and pollution challenges exist in nature.  Microorganisms have evolved for millennia to consume, degrade, or bind waste and toxins around them, deriving energy from creating circular ecosystems. Leveraging biology in this way is not new. The use of biological processes to treat contaminated wastewater dates back to the Romans, circa 600 B.C. More dedicated and engineered intentional uses are over a century old with an early emphasis on the use of activated sludge. We like to call this first era of biological treatment of a waste stream Bioremediation 1.0. 

In the late 1960s bioremediation was first applied to treat an environmental contaminant, namely petroleum hydrocarbon releases in soil, and we define this as the advent of Bioremediation 2.0. Even in this second era of bioremediation genetic modification and molecular tools were featured. Believe it or not, it has been over 50 years from when Dr. Ananda Chakrabarty of GE genetically transformed the bacterium Pseudomonas putida and received a patent in a landmark case that went to the US Supreme Court. As Bioremediation 2.0 moved from addressing petroleum hydrocarbons to chlorinated solvents, molecular tools for identifying specific microorganisms and functional genes became commonplace in the cleanup of contaminated soil and groundwater.  The documentation of Dehalococcoides spp. in the mid-1990s, as being capable of complete dehalogenation of chlorinated ethenes and the characterization and sequencing of its various reductive dehalogenase genes, was a driving force in this change.

While progress towards treating a variety of contaminants has been great in the last few decades, many compounds that are contaminating the environment or preventing waste streams from being converted to value streams are recalcitrant to biological processes. These are usually synthetic chemicals that nature has had little time to develop methods to break down and derive energy. Perhaps the most notable of these are the ubiquitous and very problematic per- and polyfluorinated alkyl substances, or PFAS which the media are portraying as “Forever Chemicals”.  

The good news is we aspire to collaborate with nature to turn these forever chemicals into has-been chemicals as the era we call Bioremediation 3.0 is ushered in. This is where things get really exciting. In just the last ten to twenty years we’ve had enormous leaps forward in the ability to read,  write and edit DNA simultaneously with dramatic increases in computing power. Consider that it originally took 13 years and over $1 billion to sequence the human genome. Today, less than 20 year later, it can be done in hours for less than $1000! This explosion in technology around synthetic biology, or SynBio for short, left Moore’s Law in the dust in about 2008; that is, SynBio is advancing much faster in terms of cost and scale than even most digital technologies. The genetic transformation of organisms is now positioned such that many keen observers predict a revolution that will dwarf what has been accomplished in digital technology. The potential now exists to read nature’s programming in microorganisms and to discover or write new programming tailored to accomplish Allonnia’s mission: To leverage the power of biotechnology and engineered systems to create transformative solutions for a waste-free world. Welcome to Bioremediation 3.0.

So, while it becomes abundantly clear this is a gateway to breaking down the barriers in biodegradation and biostabilization, we have other frontiers to approach in our collective vision.  

This is just the beginning. Allonnia has selected specific areas for development where current technologies are inadequate and where advanced biological solutions have a high probability of success.  A few examples are listed:

  • Detoxification of produced water from oil and gas operations
  • Binding of rare earth elements from waste or from ore to help secure a domestic supply chain 
  • Biosensors for contaminant detection and process monitoring and optimization
  • Upcycling of plastics, including polyurethane and nylon 
  • Biodegradation of legacy and emerging contaminants; e.g., PFAS, 1,4 dioxane.

At Allonnia we are guided by our core philosophy that Waste is a Failure of Imagination. Now is the moment to develop and deploy powerful transformative biological solutions at scale, leapfrogging less sustainable, and often sub-optimal mechanical and chemical systems. We are building an ecosystem of like-minded partners, individuals and regulators to realize this goal.  Connect with us if you share in this vison.  

Thank you!

We look forward to keeping you updated

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