Acquiring Mastery: My Journey as a Practicing Microbiologist

When I graduated from university, the idea of gaining mastery over Microbiology seemed absurd. In my mind, Microbiology was a scientific discipline, not a craft like guitar-making. I had a friend who is a master luthier and I understood his appreciation of the nuances of wood and grain; how he shapes them to achieve beautiful sounds. Microbiology was not like that. My academic studies taught me that it is done methodically, built upon rigorous research and scientific review. Methods are developed through systematic optimization and testing, and then are thoroughly reviewed before publication. Once published, they are adhered to closely, always referring to the original. There’s no nuance here. Yet I discovered over the next 31 years that the expert application of Microbiology requires Mastery.

After graduation, I decided to dedicate myself to the new field of Bioremediation. I would use microbes to break down toxic compounds and render them harmless. With ambition, verve and a PhD, I began pursuing this dream. Unfortunately, none of my training prepared me to apply my knowledge in the real world. I discovered this when my neighbour asked me to clean up a gasoline spill in his backyard. I knew everything about the microbes and metabolic pathways that break down petroleum products, but I had no idea how to clean up my neighbour’s spill. This is when I realized that knowledge is one thing but practice is quite another. I became determined to learn my craft.

After starting my environmental consultancy, one of my first jobs was to detoxify contaminated soil at the Interfor Squamish sawmill. The site had been closed and about 10,000 cubic yards of soil contaminated with highly toxic pentachlorophenol (PCP) were excavated. Trucking this material to a hazardous waste incinerator carried an exorbitant price and I was tasked with bioremediating this material. Undaunted by my earlier failure, I set about solving this problem.

I knew broadly where to look for microbes that break down PCP, but I needed to identify a source of them for this project. To do that, I needed a method to quantify PCP-degraders in different materials and find a good source. Unfortunately, there was nothing like that in the published literature. I had to create a medium in my own lab, and then test different materials to identify a good source. After doing this, I grew the PCP-degraders in bulk, and then added them to the contaminated soil so they could break down PCP. Within a few years, this site – the largest hazardous site in BC at the time – was fully decontaminated. This was done at a fraction of the cost of trucking. I knew that the method I created was untested, but I demonstrated its effectiveness by cleaning up the soil. To me, this was its true validation.

More challenging projects came my way over the next 10-15 years, and I found that there were never off-the-shelf solutions for any of my problems. My foundations in Microbiology – and in science – were solid, but none of what I had learned at school was readily applicable to my problems. Always, I needed to modify existing methods or develop a new one altogether. This included methods to isolate microbes degrading metal-cyanide complexes, toxic wood extractives, naphthenic acids and other petroleum hydrocarbons; media for selenium-reducers, polythionates oxidizers, etc. Sometimes, these methods required simple adjustments to existing ones, but other times they had to be developed from scratch. Always, the validity of these new methods was confirmed by their effectiveness in solving problems, such as when I detoxified cyanide-contaminated mining waste.

Over time, I grew increasingly confident and relied less and less on published methods and reference books like Methods in Aquatic Bacteriology. My knowledge and self-confidence evolved and my point of reference changed. I didn’t need to consult reference manuals anymore: I trusted my own approach. I was gaining mastery over my subject.

Developing new techniques wasn’t only critical for executing projects, but also winning them. In a competitive bid for then-Houston Lighting & Power, I won a contract to treat selenium from ash pond runoff partly because I could identify sources of selenium reducers. I was facing stiff competition from much bigger companies and I needed to find a winning strategy. I decided to invent a medium to grow selenium-reducers (none existed at the time), obtain sediment samples from the project site and demonstrate that some of them contained selenium-reducers. I won the contract when I showed the results of my test during a bid presentation, the crimson red band of elemental selenium providing indisputable proof that the samples contained selenium reducers.

I was starting to feel that I could address any challenge that came my way. I felt that I could walk blindly into a project and tackle it through my own devices. To me, this became a key test of mastery: could I solve a difficult problem by relying only on my own knowledge and experience? Several new projects came along which proved that I could.

I won a private research contract to uncover a bacterial process to dissolve gold, as an alternative to using cyanide. Several factors made this project exceptionally difficult. First, is the fact that gold is a noble metal: there are very few compounds that react with it, let alone dissolve it. Second, there is considerable secrecy around the subject. Many aspects of the difficult chemistry of gold cyanidation are jealously guarded by gold mining companies. I scoured the scientific literature for reports on biological dissolution of gold, but the only studies I found were of no practical use. Presumably, studies showing promise were never published. I was left entirely to my own devices in figuring out how to proceed.

With a limited basis of knowledge to guide my work, I began from first principles.?Only a few substances can solubilize gold, including cyanide, thiosulphate and sulphide. I looked for microorganisms that produce these compounds and tested them for gold dissolution. None of this worked. The only lead worth pursuing was the curious observation of a transient release of gold during the biological detoxification of cyanide in spent heaps.

I deduced the likely environment that might account for this phenomenon, drawing on my understanding of the geochemistry of mining environments and knowledge of Microbiology. I searched for comparable environments at mine sites and sampled them for microorganisms. My hunches proved correct and I recovered microbes that dissolve gold. In technical terms, gold was dissolved by partially-oxidized sulphur compounds that were produced during the anoxic denitrification of sulphide minerals. This was an extraordinary finding: a completely new process! This discovery was a testament to the mastery I had acquired over my discipline.

At the beginning of my career, I found that my scientific background was solid, but that applying it demanded constant adjustment. I always needed to adapt creatively what I had learned and to work out new methods that could be applied in the given situation. Over the course of years, these various challenges broadened my knowledge and confidence, and I stopped relying on external references. I learned the nuances of the environments I was working in, much like my luthier friend. I developed and learned to trust my inner compass.

Perhaps my journey – the need for constant innovation – reflects the fact that I worked in a new industry, but this isn’t the case. It is the charge of any practitioner in a given field. My surgeon friend has never seen patients presenting themselves as a perfect illustration from Grey’s Anatomy. She has always been confronted with the vagaries of real human bodies. In the end, any practitioner who does not fear tackling difficult challenges will eventually develop mastery over their discipline. It is the inevitable outcome of repeated challenge and success.