Engineered exploitation of microbial potential.

We are at a critical point in our history, faced with the challenges induced by our own large‐scale activities, over many years, which are leading to dramatic changes in our climate and an urgent need for remedial measures. Added to these concerns is the continual growth in populations and the pressure this puts on resources and environmental quality. These multiple stresses have stimulated the need to improve efficiencies in current technologies and the search for alternatives for sustainable energy, securing reliable water supplies, treating waste and the generation of sustainable products. One of the positive features of this alarming situation is the increasing awareness among microbiologist and non‐experts alike, of the potential of microorganisms as providers of some of the remedies. For instance, issues of environmental quality and energy have impacted on the waste industry in such a way it is now seen to be a resource opportunity, and anaerobic digestion is considered to be the way forward for treatment and sustainable energy generation.

With such high hopes riding on microbial potential, it is reassuring to know that in recent decades we have invested significant funding in techniques for improving our knowledge of the microbial world. This includes increasingly elaborate and sophisticated molecular methods for detecting unculturable populations and rapid sequencing for improving genetic understanding. However, we are now at a critical point whereby we urgently need to translate this vast mountain of knowledge and microbial system insights into solutions to the demanding global challenges. Furthermore, if new or even established microbial technologies are going to have any significant impact on climate change or any other of our global problems, they must be effective at very large scales and importantly, be controllable. Control of microbial potential en masse is in fact an engineering challenge.

Manipulation of microbial biomass on a large scale and in a controlled manner is by no means an easy task. However, mankind has had some notable successes in harnessing the potential of microbial processes, most notably the effective exploitation of microbial communities in municipal sewage systems and agriculture. Although such systems are very effective and have served us well for generations, they do not represent examples of where key insights from new genetic information have been exploited to develop novel environmental technologies for solving mankinds' problems. This has yet to be achieved. Furthermore, the successes in terms of harnessing of microbial potential were achieved by Victorian engineers and agriculturalists, not microbiologists. The kind of opportunity today for such life‐changing exploitation would be the identification of microbial gene sequences/strains that enable problematic CO2 to be converted directly by algae into methane or even clean fuels. However, even if we could isolate or generate such strains the challenge of effective exploitation would have to be resolved, most probably by engineers. This is because in order to harness light, algae have to grow on the surface of ponds and such two‐dimensional growth leads to self‐shading. The solutions to such issues require effective collaboration with good engineers to develop algae holding systems or bioreactors, which enable maximal light exposure in three dimensions, reducing the foot‐print and improving yield. Other scenarios whereby cross‐disciplinary collaboration will eventually lead to more effective microbial exploitation include hybrid approaches for treating trace levels of contaminants (such as hormones) in drinking water, by employing a combination of high affinity nanofilters, which concentrate the contaminant, making it bio‐available to catabolic strains.

Encouragingly, there are signs that microbiologists are beginning to open their minds in terms of developing new physical technologies for exploiting cells en masse, in a more controlled manner. These approaches include novel approaches for moving bacteria through soil and manipulating biofilm formation by electrokinetics (Andrews ), stimulating biodegradation by manipulating bacterial genomes in situ employing ultrasound (Song ), and the application of nanomaterials for in situ detection and stimulating cell activity (Chien ). Although early days, such novel approaches provide hope that the microbial potential can be engineered and more reliably harnessed on a large scale. This will require a new generation of microbiologists who have more cross‐disciplinary training, who embrace the opportunities that physical and engineered techniques offer, and who have the imagination to consider complementary approaches for the limited array of microbial cell manipulation methods we traditionally employ (e.g. pH, temperature, concentration). This is very good news as the quicker we realize that sequencing more genomes is not the only option for resolving our problems, the quicker we can generate some effective solutions. Such critical advances will be accelerated by employing more systems biology approaches, linking information from the cell to the whole community, an approach which again will require multidisciplinary training, in this instance computing science and mathematics.

The Victorians may have not realized when they developed sewage and clean water systems the extent they had harnessed the potential of microbial communities to solve their problems. However, what they achieved and what we need to learn again is that the solution to many of our current problems is going to come from effective engineering of microbial systems, as this is the only way to control more effectively and provide the scale‐up required to have significant global impacts.