What made you decide to become a microbiologist?
You have been studying the molecular biology of biomining bacteria for more than 30 years. How and where did this epic research endeavour all start?
After completing a PhD in the treatment of tannery and fellmongery effluent, I worked at the Leather Industries Research Institute for a couple of years before deciding that I would like to become an academic as I was seeking a more balanced role between teaching and research. If I had continued to work on tannery effluent, I felt that I would have been directly competing with my previous employer and the person who replaced me. I therefore looked around for a new research field and asked myself the question, ‘where does microbiology and mining (at the time I thought this was South Africa’s largest industry) overlap’? This was in the then relatively new field of bioleaching. At about the same time, I was approached by Eric Livesey-Goldblatt, who was manager of the research division of the General Mining Corporation and who had been dabbling in using microorganisms to solubilize uranium at the Buffelsfontein mine. I later discovered that mining has never been SA’s largest industry and that agriculture has always exceeded mining in size but through answering that question had discovered the main field in which I was to work.
What were the driving forces that kept you fascinated with these one-celled rock-eating bacteria all this time?
What originally fascinated me was their unusual physiology. These bacteria can grow in water if provided with air, mineral (containing either iron or sulphur) and trace elements. They produce acid from the mineral and so grow at a pH generally below 2.0 which keeps the iron in solution. In addition, they have a beneficial value in that they are involved in what have become substantial industrial processes (tank and heap leaching of certain metals from ores) and an environmental problem when not controlled in that they are responsible for acid mine drainage. This combination of the microorganisms having an interesting physiology and a significant applied side was highly attractive and difficult to beat. The downside was that the microorganisms are difficult to work with, grow relatively slowly and the yield of cells is low. This also turned out to be an advantage in that not too many people were prepared to put up with these difficulties and this kept international competition manageable.
We know you as a very humble person Doug, but what would you say were your greatest contributions to the field?
Well I was privileged to be involved as a supervisor (together with Prof David Woods) for the MSc of Philippa Norman who worked at General Mining Corporation in the early to mid 1980s and whose work was the basis for what became a multimillion gold-bioleachingprocess known as the Biox® process. Philippa had been an honours student of mine when I was at Wits and had worked on a bioleaching project for her honours year. Another significant contribution was the discovery that Acidithiobacillus ferrooxidans, plays a negligible role in tank bioloeaching processes as our focus (and those of others) had been almost entirely on this species of bacterium up until that time. Then there was our work on plasmids and the horizontal gene pool of these bacteria and the development of genetic systems for some these bacteria. Although we had some successes, the genetic systems are still not satisfactory. I adopted a tactic of identifying what I thought were areas of confusion in the field (such as the direct-indirect leaching debate and the most appropriate method for the development of a microbial bioleaching consortium) and tried to make a contribution to topics such as these by writing targeted reviews. These reviews have attracted much attention and many citations. I also initiated and edited the publication of two books on biomining, one published in 1997 and the second a decade later in 2007. Much of this was covered in an honorary lecture that I was invited to deliver at the International Symposium on Biohydrometallurgy held in Changsha, China towards the end of 2011. I entitled the lecture “Some important developments in the biomining over the past 30 years”.
Much of your work was on evolutionary biology. Since we cannot go back in time, what is the point of speculating on how genetic elements evolved?
Even though there is some speculation as to how genetic elements may have evolved, there is good support for some theories. For example the role of gene duplication in the evolution of genes encoding proteins with new properties. Some of my greatest pleasures have been working with plasmid evolution and trying to understand some of the compromises that these elements have adopted in trying to outcompete related plasmids but without imposing too heavy a burden on the host cells. The way that toxin-antitoxin systems of different types have evolved and the discovery of the apparently different roles that they play on chromosomes and on plasmids has been simply amazing. Of course which roles came first is speculation, but this has not detracted from the fascination of discovering what they do. Although much is known the story is still far from complete and there is likely to be many more surprises.
What are some of the unanswered questions remaining or future trends in the field of biomining bacteria?
There are several unanswered questions that will take some time to go into so I will restrict the answer to just one. A few years ago it was discovered that some bacteria produce nanowires or pilus-like structures that allow the transfer of electrons. For example minerals containing ferric iron are insoluble under aerobic and neutral conditions, but some bacteria are able to use in situ ferric iron as an electron acceptor by producing nanowires that make contact with the mineral and thereby discharge their electrons onto the ferric iron. These nanowires can also be used to connect the metabolism of aerobic bacteria that have access to an electron acceptor but no electron donor to anaerobic bacteria that have an electron donor but no suitable electron acceptor. Nanowires conductive chains can link the metabolism of several microorganisms together over a distance of many centimetres. Although nanowires have not been reported among biomining bacteria as yet, I would be surprised if they are not found to play an important role in heap-leaching processes. They are unlikely to be involved in tank leaching as the tanks are vigorously stirred and this will break any nanowire linkages, but heap leaching is a largely static process.
In your opinion, what has been some of the most exciting developments in microbiology during the course of your career?
Of course the use of recombinant DNA technology was extremely exciting. To be able to work with DNA, be able to read it and examine its expression under various conditions was simply mind-blowing at the time. I was privileged to be involved close to the beginning. When I finished my post-graduate studies, the first DNA restriction endonucleases had purified and that some of them cut at defined palindromic sequences had only recently been discovered. So the techniques were not yet available. However, by the time that I decided to become an academic the first cloning vectors had been made and the necessary enzymes (e.g. a small selection of restriction endonucleases and ligase) were becoming commercially available.
Along the same lines, the development of amplification techniques and DNA sequencing completely revolutionized microbial taxonomy and our understanding of the relationship of microorganisms to each other. Before that microbial taxonomy was very inconsistent partly because unlike higher organisms, microbes did not leave a useable fossil record. One had to arbitrarily decide whether the Gram-negative/Gram-positive divide was more important than say autotrophic/heterotrophic, respiration/fermentation, motility, the ability to make spores etc., when developing the hierarchy for a classification system. DNA sequence information removed much of that uncertainty.
Then the ‘omics’, genomics, proteomics, transcriptomics, metabolomics and the like have added a new range of possibilities.
The ability to study organisms that are not easily cultivated, the sequencing of all microorganisms in a whole sample to identify what organisms are present and the analysis of the metabolic roles that they play based on sequence information are further exciting developments.
People are now moving on to address biological questions at a single cell rather than a population level. Information is being gained that is not obtainable when one works with the averages that one obtains when dealing with a whole population. For example during plasmid conjugation it seems that the initial conjugation is a very rare event but that once the first plasmid transfer has taken place, the plasmid arrives in an unrepressed recipient from which further conjugation readily takes place. This effect is not discernible when one examines conjugation at a population level as opposed to the single cell level.
As you would gather, the rapid development and application of technology has revolutionised the field of microbiology. Of course technology has its limitations and will give wrong answers if we neglect the basics such as cultivation methods, the effect of laboratory media, life cycles and that microorganisms in nature probably live in famine mode for most of the time with brief bursts of feasting if they are fortunate.
Who are the scientists who have had the greatest impact on your career as a researcher?
Prof David Woods had a major impact as a mentor. This was especially during my undergraduate and honours years where I learned a lot from his approach and even more so when I joined UCT as a staff member in 1982. Of course I learned a lot from valued colleagues at the institutions that I have been associated with both as a student and lecturer (Rhodes, Wits, UCT and Stellenbosch) as well as a number of overseas people. However, I could not single out two or three as being more influential than others. I have greatly enjoyed working with many of the research students and others in my laboratory at both UCT and Stellenbosch. The loyal support received from Dr Shelly Deane, my laboratory manager and research associate for more than 20 years, was also highly appreciated.
Is there one highlight to your career that has made everything worthwhile?
There have been many highlights and I cannot single out one. For example my first inaugural lecture when at UCT and the way that I was treated as an invited guest at several international meetings were very special. Several awards and acknowledgements including this SASM gold medal have been highly appreciated. In the early days, there were one or two occasions where after obtaining a good result it felt as though I was walking 30 cm above the ground. I recall thinking I wonder if this is how it feels to be on drugs, but it would take too long to explain the circumstances.
What did you not achieve in your career?
Looking back at my time at both UCT and Stellenbosch which together cover 31 years, both periods were perfect and way beyond what I could have reasonably expected. I have also received more acknowledgements than I deserve and I say that in all seriousness. I do not view myself as a particularly talented researcher or academic and in my view there are many other equally good or better academics who did not receive the same level of recognition. I think that I happened to choose a good research topic, with little competition from others and happened to be in the right place at the right time. Possibly the only disappointment is that I would like for us to have established a genetic transfer system for at least some of the biomining bacteria that is as reliable as those for some other bacteria.
Any advice/lessons learned that you can share with young people aspiring to a career in Microbiology?
I am not competent to speak about all aspects of Microbiology, but for people aspiring to be an academic, find a field that you enjoy and begin working. The exact project that you begin with can be rather simple, but provided you keep your eyes open and read supportive literature, you will be amazed at what you will discover that there is to be researched. New projects will be found at almost any level of sophistication that you can imagine. If you find areas that you cannot research alone either because you lack the skills or access to resources, establish collaborations or visit laboratories where the skills can be learned or access to equipment obtained. The most important thing is to begin working with an enquiring mind, the sophistication will follow.
What are your views on the marriage between Science and Faith?
I am not so sure that I would use the term ‘marriage’ as science and faith address fundamentally different things and may never be fully ‘married’. For example science can attempt to address questions, such as how did the universe come into existence and how might it end? Or what is life and how can one distinguish life from non-life? However, science is unable to address other questions that are hugely important to us as humans. For example, questions such as does the universe, or does life, have a purpose or meaning? Science does not have the tools to begin answering these as they are non-scientific questions. In fact from a scientific perspective the hard answer would be that neither the universe nor life has any purpose or meaning. For those of us who do not accept this answer, one has to look elsewhere for answers and this is where faith comes in. From a western perspective the discussion has been restricted to one largely dominated by the Bible and evolution. The assumption being that what is recorded in the Bible is a scientific account of the origin of things and therefore to the extent evolution is shown to be true, it is inconsistent with the Biblical account and therefore a faith that has a Biblical base can be discarded. However, this does not address the difficult questions of purpose and meaning. In looking for the answer one needs to search for the truth even if this is uncomfortable rather than believing in some theory of one’s own choosing.
Are there highlights in your academic career that are not related to your research?
I really enjoyed my 16.5 years at UCT and there was nothing I would change about that time. Being promoted to a full-professor before I had expected and without having applied was very motivating and the first time that I received an A-rating from the NRF was also special. However, possibly the thing that I have appreciated most was the wonderful spirit of cooperation and collaboration that existed within the Department of Microbiology at the University of Stellenbosch during the 13.5 years that I was Chairperson. It was something that I had hoped for when I accepted the position in 1999 and turned out even better than envisioned. I have both academic and non-academic staff members to thank for that. A fitting culmination was in November 2011 when a wonderful gala dinner was held at the Stellenbosch Institute for Advanced Studies (STIAS) to commemorate the 50th year of existence of the Department. Even though it was not a farewell event, from my perspective it was that and it was truly an occasion that I will remember with appreciation for the rest of my days.
How do you view the role and value of SASM to the microbiology community?
Being the anchor for the organization of regular conferences is almost certainly the SASMs most important role. As a scientist one belongs to various families, such as that of one’s own department, those in one’s region or country and those internationally. If one attends focussed meetings regularly then one develops very close relationships with these families. My experience has been that this applies especially to international colleagues who do related work to one’s own, these people become very close. The role of SASM is different as it is a fairly broad grouping and there may not be many people who work in one’s own narrow field of interest. The scientific stimulation at SASM meetings may therefore be less. Nevertheless, it has been my experience that if the plenary speakers are carefully chosen these lectures can introduce one to new topics or ways of thinking beyond the focussed international meetings that I have found so useful. This expansion of exposure to aspects of microbiology beyond ones narrow interests that I have experienced at SASM conferences has been of great value. The SASM provides a very important forum for learning about who does what in one’s own country and what expertise and skills are available locally. It further allows for local networking and these networks are very important for all sorts of purposes including the identification of people who could serve on committees, as external examiners or as potential new staff and researchers. SASM meetings also provide an important avenue for research students to hone their presentation skills and to recognise that they are part of a larger microbiology community.
Interview questions compiled by Heinrich Volschenk and Marla Tuffin