Though they can’t be seen with the naked eye, microorganisms rule the world. Within the scientific community and beyond, there is a growing recognition that microorganisms influence virtually every aspect of our day-to-day lives including human health and disease, the breakdown of harmful or toxic chemicals, the cycling of nutrients through ecosystems into the food chain, and the production of climatically important gases. The multitude of microorganisms found in aquatic habitats are especially important to us, as they determine the quality and potential use of one of our most precious natural resources; fresh water. Therefore, understanding the diversity, abundance, and activity of the microbial communities occupying freshwater ecosystems is incredibly important.
Due to their small size and lack of identifying morphological features, the study of environmental microorganisms is predominantly based on extracting their genetic material, such as DNA, in order to identify and quantify them in a given habitat. However, as a team of molecular microbial ecologists from the University of Essex, lead by Dr Dave Clark, describe in their WIREs Water article, such workflows were often prohibitively expensive, resulted in insufficient sample sizes, and were often not able to yield the information researchers needed.
Fortunately, the previous two decades have seen enormous progress in the technologies and methodologies involved with the molecular study of microorganisms, such that the field is now in the midst of a “golden age”.
With “high-throughput” technology, researchers are now able to study the ecology of microbial communities in freshwater habitats in exceptional detail, by simultaneously studying the genetic material of millions of microorganisms at once.
Clark and colleagues highlight some notable examples of where modern molecular methods, combined with cutting-edge technology, have provided further insight into the role of microorganisms in freshwater habitats. For example, the authors describe how, after a significant insecticide spill into the River Kennet in 2013, researchers were able to show that microbial genes related to the degradation of the pesticide were up to seven times more abundant downstream of the spillage compared to upstream, indicating that the microbial community had responded to the spill and were actively removing it from the environment.
Following these examples, Clark and colleagues detail some of the most exciting developments and applications of molecular microbiological methods on the horizon. Among these developments, the miniturisation of technologies used to amplify and sequence microbial genetic material (e.g. DNA) provide the tantalising prospect of being able to study microbial communities in the field, in their natural setting, yielding a more realistic picture of their ecology. Moreover, these new, smaller platforms could be combined, effectively creating “automated remote molecular biomonitoring stations”. These remote stations could be left in the environment, where they routinely take samples of the microbial communities, before sending the data to researchers. Such technology could effectively hand environmental scientists an “early warning” system, allowing the detection of environmental disturbances in freshwater habitats, such as pollution events, by closely monitoring the activity of microbial communities.
The rapid progress in the field of molecular microbiology has ensured that, whilst microorganisms are not easily seen, they will never again be ignored!
Kindly contributed by David Clark.