Microbial solutions: Sean Carim on combatting pollution with microbes

5 September 2016

For Sean Carim, growing up in Hong Kong played a central role in sparking his interest in science, but not the one you would expect. Environmental issues were an accepted part of life, with battery and shoe factories nearby, poor water quality, and the human impact of chemical mismanagement already becoming evident.

“There are many people going into biology with a focus on medicine or human health, but a lot of these issues are caused by poor environmental health, and this comorbidity will continue to become a bigger factor,” he says. 

This curiosity is channeled through Carim’s very practical view of scientific potential, “Biology makes sense to me, and lends itself well to real-life applications. It’s not ‘just’ plants or theoretical research; I want to see if I can tackle world problems with biology and develop some technology that we need to do it.”

Exploring biology

Carim is currently advancing his studies in microbiology and conducting research on biotechnological solutions to environmental pollution issues as a PhD student at the University of California, Berkeley, but it’s been an interesting ride to get even this far. 

Sean Carim

Initially a neuroscience student, a summer exchange program at MIT introduced him to microbiology and particularly its advantages in terms of applied science and engineering. Already restless and looking for a way into clean production and environmental challenges, it was the logical choice. Berkeley’s requirement for three field rotations before choosing a specialisation likewise was appealing.

The first of these internships was in environmental biochemistry, working on a project making oil pumping cleaner. 

When oil is extracted from offshore oil rigs, ocean water is pumped in to push the oil out, introducing marine microorganisms and sulfates into the oil well. Electrons in the crude oil mix with these organisms, contaminating the oil and the system with hydrogen sulfide, necessitating rigorous cleaning which poses a hazard for downstream workers and oil spills. 

The team’s work scrutinised how to decrease sulfide production in oil reservoirs, including removing sulfates from seawater and building bioreactors to use marine microorganisms and their unique environments as a seawater treatment. Cue tangential conversation on environmental impact and ethics of deep sea oil drilling.

Taming microorganisms

Carim’s second rotation was in a metabolic engineering lab using microorganisms to create high markup chemicals like perfumes, biodegradable plastics, and jet fuel. This form of bioenergy rests on encouraging microbes to eat all parts of a plant better, absorbing its complex carbs into energy, such as sugar cane into ethanol. 

Essentially, as Carim blithely explains, metabolic engineering is about “how to make microbes produce more interesting things,” but also for greener, more environmentally friendly chemical production. 

During his time in this lab, he was introduced to Streptomyces, a common soil microbe which is very difficult to engineer, but capable of producing a wide range of chemicals, including antibiotics. As part of efforts to engineer a strain of Streptomyces which more efficiently consumes plant biomass, Carim worked on getting Streptomyces venezuelae to expand its eating habits to xylos (plant matter). 

In this process, a plant is grown to a specific size before its biomass is harvested and broken down to basic sugars. Microbes are engineered to respond to or process these specific sugars, and are then introduced to them. After the feast, it all goes into the centrifuge, hopefully with the desired chemical to be found in the skimmings.

Engineering solutions

The third rotation proved to be the charm, in a systems biology lab with a strong biochemical engineering emphasis. This lab engages in functional genomics, studying the functional components of each gene in different bacteria, and is developing a new tool to study a wider variety of bacterial genetic function. 

The usual process in doing this involves growing bacteria, harvesting and purifying its entire genomic DNA, breaking it into smaller nucleotide bases via ultrasound, and inserting it into other bacterial DNA. 

Mixing it so each cell gets a different DNA piece ensures that individual bacteria carries random pieces of another genome. Subjecting these bacteria to a range of tests helps researchers understand the functional contribution of each single piece of DNA. The ability to run more tests simultaneously and for cheaper will greatly aid in studying more genomes and advance tailored engineering efforts.

This research is important because bacteria are ubiquitous and do all kinds of biochemical transformations on their own; an eco-friendly and efficient power to harness for a wide array of scientific needs, especially for medical and environmental purposes. 

On a basic level alone, bacteria break down organisms into simpler, more recyclable things, and understanding how they tick will help in targeting infectious strains better. This move away from synthetic processes or later-stage treatment to refocusing on natural processes and capabilities is a perfect blend of Carim’s environmentalism and research background. 

“Science is an increasingly collaborative field now, but this is the ultimate partnership—with the building blocks of nature,” he notes. “If we can better characterise bacteria in our environment, we can understand and model biogeochemical activity, i.e. ‘x will happen because this particular microbe is present’. If there are pollutants in the environment, we can introduce bacteria to degrade and recycle them naturally and safely. If we can identify gene x in genome y has a specific function allowing this chemical transformation, we can add the gene to our chemical engineering toolbox.”

For his own PhD project, Carim is looking to expand functional genomics tools to Streptomyces bacteria. This will require a brand new method, as the bacteria are notoriously difficult to work with and the scale is still daunting, but with high payoffs, such as green chemistry or drought tolerance in plants. 

Ideally, Carim hopes to move straight into industry after completing his doctorate, as the most direct way to make an impact on the world. 

“Academia takes a long view, challenging and hypothesizing what could happen down the road, but industrial applications focus on collaborative approaches to current issues,” he explains. 

This interdisciplinary lens to contemporary scientific challenges also factored into Carim’s decision not to go all in on one specific project. “It could be that pure biology isn’t the way to a cleaner, greener world. Bioengineering, genomics, nanotechnology, and a variety of techniques and approaches should be involved in answering a biology question or developing a tool. There are so many roads to what I want to do, so I have lots to explore still.”

Sean Carim is currently a Croucher Scholar and PhD student in the Department of Microbiology at the University of California, Berkeley. He received his BSc in Biology from The Hong Kong University of Science and Technology in 2015. 

To view Sean’s personal Croucher profile, please click here.