Microbial biogeography and what Baas Becking should have said

Compared to the discipline of ecology, the science of microbial ecology is in its infancy. But can the models and principles of general ecology be used in combination with modern molecular methodologies to provide insights into how microbial communities organise and change in space and time?

Eariler this year I received an invitation from the SGM to write a short article on my work on microbial biogeography – being recognised as a pioneer and driver of this new field of microbial ecology (‘how nice’, I thought, ‘of course I would be delighted to help serve the Society…’) – with this article and others to create an issue of Microbiology Today focused around ‘biogeography’ and to tie in with the 100 year anniversary of the death of Alfred Russel Wallace. Wallace was one of the early pioneers of what would become the scientific fields of ecology and evolution, along with others such as von Humboldt, de Candolle, Darwin, and many, many others. What I know of Wallace and indeed his contemporaries like Darwin is vague at best – this is either a reflection on me personally (fair play – I admit I’m not perfect) or has wider reflections on incorporating the history of science into scientific teaching at say the undergraduate level. A third, and probably heretical viewpoint to some, is although such pioneers provided fundamental conceptual beginnings for ecology, evolution and biogeography, over a century later, it is difficult for me to relate their immediate influence and importance on the work I do now – although there are those who will no doubt strongly argue otherwise. To clarify my own viewpoint, we should be aware of what has gone before us – and I applaud people like the comedian and natural history enthusiast Bill Bailey’s efforts to bring Wallace out of the shadow of Darwin – but ultimately for me science should be about moving forward and ever pushing those boundaries for societal and economic benefit.

What is bioegeography?

Getting back on topic with regards to this piece on microbial biogeography – one of my overarching aims has been to bridge the gap between the disciplines of general ecology and microbial ecology. A key conceptual framework in ecology that I, and others, have since adopted is that of biogeography – the study of the distributions of biodiversity over space and time to reveal where organisms live, in what abundance, and why. But first, it is important to appreciate certain facts about the field of microbial ecology in general and then more specifically the diversity and abundance of micro-organisms.

Microbial ecology

Ecology as a science is over 150 years old and over that time ecologists, such as Alfred Russel Wallace, Charles Darwin, Frank Preston, Robert May, Robert MacArthur and Edward Wilson (to name a few from the many), have developed principles and theories on the distribution and abundances of animal and plant species, and the interaction among species, and between species and their environments. In contrast, microbial ecology is in its relative infancy (~30–40 years). A main challenge for microbial ecologists over that shorter time frame has been to develop better (read ‘molecular-based’) techniques to survey microbial communities in their natural habitats. It could be argued that little robust microbial ecological theory exists – Koch’s postulates and Baas Becking’s ‘everything is everywhere, but, the environment selects’ aside – I’ll come back to the latter later on. As such, my fundamental work has and continues to be focused on better understanding and predicting how microbial communities assemble and develop, and how microorganisms are distributed across different spatial and temporal scales; in essence, unravelling the complexity of microbial communities in their natural environments. I have achieved this by exploiting and (importantly) adapting models, theories, and principles from general ecology, coupled with ever improving developments in genomics and bioinformatics. I emphasise ‘adapting’ because it is important not to lose sight of the fact that the biology of animals and plants is different to that of microbes – and even the biology of different microbes can be staggeringly different. Therefore, a simple mapping of ecological theory on to microbial populations and communities is extremely naïve in that respect.

Immense amounts of micro-organisms with a huge diversity

It is well known that microbial ecology has been both driven and limited by the increasing plethora of techniques used to assess micro-organisms and their communities. In many cases this has led to an almost unhealthy obsession for using the latest methodologies, typically at the expense of the research questions being asked. However, these methodological developments are needed to assess the vast diversity and abundance of micro-organisms. Based on current best estimates – there are 1030 microbial individuals on Earth, when compared with 1021 stars in the universe, making the microbial world immense. It is now believed that microbes in our bodies add up to 100 trillion cells, 10 times the number of human cells (good news for those watching their weight – you can take 90% off straight away!). Further, with approximately 109 bacterial individuals in 1 g of soil, you would only need to sample a handful of soil to surpass the current global human population of ~7 billion people. With regards to diversity estimates, it is reported that healthy people can share their bodies with up to ~10,000 species of microbes. In the environment it is estimated that there are 70 species per ml in sewage works, 160 per ml in oceans, and up to 38,000 per g of soil. These current best estimates of microbial abundance and diversity make those for larger organisms pale into comparison. Just the sheer extent of diversity and abundance should be enough of a driver for many to study micro-organisms and their ecology.

Microbes on earth outnumber the stars in the universe by a factor of 9. Stocktrek Images/Thinkstock.

Baas Becking said what?

The adoption and adaption of ecological theory in microbial ecology began to really gain momentum from the middle of the last decade – centred largely on the question of microbial biogeography. Some researchers used the Baas Becking ‘tenet’ of microbiology ‘everything is everywhere, but, the environment selects’ as a battle ground for whether microbial biogeography could exist or not. The increasing amount of papers published since then provides strong evidence for microbial biogeography (whether bacteria, archaea, fungi or protists) and indeed there is evidence for certain scenarios where no biogeographical patterns are found to exist. In retrospect, the Baas Becking tenet now seems a ridiculous statement to base debate on microbial biogeography. It is probably the case that ‘some things are everywhere and some things are not. Sometimes the environment selects and sometimes it doesn’t.’ – admittedly this is not as snappy as the original but it is based on factual truth. Clearly, the question should be what factors are driving patterns of spatial or temporal distribution, as we need to unravel and understand the underlying mechanisms for such patterns of diversity and distribution. Finally, the potential of exploiting theories, models and principles from general ecology, coupled with everimproving molecular methodologies, could well provide invaluable insights into how microbial communities organise and change in space and time. This increased knowledge of microbial community ecology will help us better understand and predict changes in the natural environment, allow improved manipulation of agricultural and industrial processes and give improved protection of human health.

Christopher van der Gast

NERC Centre for Ecology & Hydrology, Maclean Building. Email: [email protected]. He is currently learning more about Alfred Russel Wallace.