Microbial Ecology
What kinds of bacteria are out there? What are their roles in the environment? How they do what they do? What are the rules that govern their occurrence and interactions?
To us, people who work in the field of microbial ecology, these questions are an everyday challenge. Answers to these simple, but fundamental questions, are at the heart of our work. In the long term, they will allow us to answer bigger and more important questions. For instance, what are the mechanisms by which microbial communities influence and modify their ecosystem?
As you might suspect by now, microbial ecology is the study of microbes in the environment, their interactions and effects on it. It turns out that microbes are out there in staggering numbers, from to 100 bacterial cells per gram of sediments 2.5 km beneath the sea floor to 1029 cells in the seafloor sediment 1,2. To put it in perspective, that’s around the same number of stars estimated to exist in the observable universe. Certainly, this makes this field of research one of the most challenging.
Moreover, microorganisms are not found in isolation in the environment. Instead, several groups of different bacteria usually occur in each specific habitat, ranging from a few hundreds to several thousands different species 3. We refer to these assemblages of microbes as microbial communities. Microbial ecology focuses heavily on the disentangling the structure and behavior of these communities.
Microbial communities colonize every habitable niche of our planet, from the high altitude wetlands of the Chilean altiplano to the deepest depths of the Pacific Ocean in Mexico 4,5. And those are just two examples. The list of environments in which we detect signs of life, as we know it, is extensive, and keeps growing. Thermal springs, the Arctic ice, corroding mine tailings, sulfurous volcanic vents, the hyper-salty Dead Sea in Israel, you name it. However not all microorganisms can live in these environments. While the vast majority of organisms on earth live under moderate conditions of temperature, acidity, water and oxygen availability, among other conditions, there is a large group of microbes than thrive very happily in quite harsh environmental conditions. We refer to them as Extremophiles, and they are a very useful model to tackle some of the questions exposed above.
Extremophiles
To define a extreme condition we do it in comparison to normal conditions. We do this often based on physical parameters. Temperature, acidity, salinity and so on. As continuous variables, these physical parameters allow us to determine which conditions are extreme, given that they make difficult for organisms not only survive but thrive.
Simply put, extremophiles are organisms with the capacity to live and reproduce under severe, and often, extreme environmental conditions (temperature, acidity, salinity, etc.), conditions that are, for the most of the living organisms on earth, uninhabitable. However, as researchers, we like to classify things, so we have divided extremophiles into categories, depending on how they deal with these conditions. If they barely tolerate these conditions, they are called facultative extremophiles, while obligate extremophiles are those which only live in the extremes of specific physical or chemical parameters. To complicate matters further, depending of the parameter in question, we divide extremophiles into specific categories. Just one example, based on temperature, microorganisms growing between 10ºC to 42ºC are defined as mesophiles, while psychrophiles live below 15ºC, and thermophiles grow a hot temperatures, from 40ºC to up to 100ºC 6. Like these, there are several other categories of extremophiles; halophiles, which live on high salt concentration environments, acidophiles, which thrive in acid, anaerobes, which require anoxic conditions to multiply, etc..
So, why studying the microbial ecology tries to understand the dynamics and effects of these special microbes on the environment?.
Answers, some.
Until here we have established definitions; microbial ecology and extremophiles. The method, and the subject of study. For us, the observers, key answers that can be obtained through the analysis of these microbes are:
How did life on earth begin? Due to the extreme conditions found in early earth, extremophiles could provide us with clues about evolution at the very origin of life.
How do extreme microbial communities impact their environment? Given that, usually, environments were extremophiles thrive have reduced richness, meaning less species compared to habitats with normal conditions, modeling and studying such impacts is potentially easier. These simpler systems are beginning to provide clues to attempt answering similar questions on a bigger scale. How does human activity affect biodiversity in these extreme ecosystems? Despite their characteristics, most of these are fragile environments. Having a better understanding of the biology and ecology of extremophiles could help to better evaluate the potential ecological consequences of environmental changes, at local and global scale.
Of course definitive answers to these topics will take time. Nonetheless, research on extremophiles has steadily increased since the late 60’s, when Thomas D. Brock isolated the first thermophile, Thermus aquaticus, that would lead to a revolution in the field of biotechnology 20 years later. For instance, useful applications derived from research on extremophiles that have changed the way we do biotechnology include, the polymerase chain reaction (PCR), biofuels, biomining and bioremediation 7.
By now it’s easier to understand why a great deal of microbial ecology research has focused on extremophiles. They represent a great opportunity to trace back evolution, to investigate the effects of climate change and human activity in the environment, and walk towards the modeling of bigger ecosystems.
We still have a lot to cover in the quest to answer our initial question, what do bacteria do in the environment?. In the meantime, researchers have cataloged an extraordinary amount of information regarding extremophile diversity, their amazing biological strategies, and the ecological roles they play in these harsh, yet incredibly interesting, environments.
Post by Harold Nuñez, May 23, 2016.
Edited by Raquel Quatrini
References
- Julie A. Huber. Making methane down deep. Science 349, 376-377 (2015). Back to text
- Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & D’Hondt, S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl. Acad. Sci. U.S.A. 109, 16213–16216 (2012). Back to text
- Schloss, P. D., Girard, R., Martin, T., Edwards, J. & Thrash, J. C. The status of the microbial census: an update. (2016). Back to text
- Hasan, N. A. et al. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proc. Natl. Acad. Sci. U.S.A. 112, E2813–9 (2015). Back to text
- Dorador, C., Vila, I., Imhoff, J. F. & Witzel, K.-P. Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in northern Chile: an example of geographical dispersion? FEMS Microbiology Ecology 64, 419–432 (2008). Back to text
- Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001). Back to text
- Coker, J. A. Extremophiles and biotechnology: current uses and prospects. F1000Research 5, 396 (2016). Back to text