Marsden grant takes microbiology to the extreme

By Matthew Wood 27/09/2010

Dr. Charles Lee is a FRST Postdoctoral Research Fellow at the Department of Biological Sciences at The University of Waikato. His research into the microbial ecology of extreme environments received a significant financial boost on Friday when the 2010 Marsden Fund grants were announced. The Fast-Start grant will support new research into the relationship between the McMurdo Dry Valleys soils and their resident microbial populations. Studying the microscopic life of this frozen desert could shed new light on the long-term glacial history of the valleys, while providing a valuable biological perspective with which to assess current and future environmental change in the Antarctic. Dr. Lee was kind enough to field a few questions from Journeys to the Ice

The McMurdo Dry Valleys, deep sea hydrothermal vents… It sounds like you have a penchant for extreme environments!?

I think it’s mostly a matter of being at the right place at the right time (and being funded at the right time helps, too). Working on extreme environments has its obviously perks (i.e., extreme tourism), but it also comes with a lot of unique challenges. These challenges, both in terms of the fieldwork and lab analyses, are as much of a draw as the excitement and experiences for me, and applying a lot of cutting-edge molecular and bioinformatic tools to these unique habitats has allowed us to answer many longstanding questions, which is of course very satisfying.

What kind of bioinformatic tools do you use in your research?

A lot of our research is based on metagenomic and metatranscriptomic sequencing, and that undoubtedly is the most challenging part when it comes to bioinformatics. Pyrosequencing of PCR amplicons is quickly becoming the most common analysis for studying microbial community structure, and we have made some very significant progress in characterizing and validating this technique through both benchwork and bioinformatic analyses. We’re also interested in analyzing molecular biology data using stringent statistical algorithms and resolving the relationship between biological and abiotic (i.e., geochemistry) data.

Charles Lee

What interests you about the genetics of microscopic life, rather than that of larger organisms?

I tend to look at the components of an ecosystem in terms of total biomass, and if one looks at things that way, it would be foolish not to understand the structure and function of microbial communities as part of studying an ecosystem. This is particularly true in extreme environments such as deep-sea hydrothermal vents, where the entire ecosystem literally relies on the bacteria to harvest energy from the environment. The microbiota of the Antarctic Dry Valleys is interesting in a different way since it is one of the few places on Earth where bacterial and archaeal communities are not heavily influenced by more complex organisms, allowing us to examine how physicochemical factors influence microbial communities.

You also study the geochemical transfers between microbial communities and their environments: do you see yourself as being just as much an Earth scientist as a biologist?

It is very true that I’m becoming more and more of an Earth scientist. Before I started doing Antarctic research I couldn’t tell granite from marble, but identifying geological features has now become an obsession of mine. As I said earlier, the Dry Valleys is one of the few places on Earth where the physical environment and geochemistry predominantly determine the structure and function of microbial communities, so it would be negligent of me to not have some basic understandings of geology.

To use the living biology of an environment to make inferences about the longer term evolution of that environment seems to be a fairly novel approach. In what ways might microbial genetics and geochemistry give you insights into the glacial history of the McMurdo Dry Valleys?

People have long assumed that the microbial ecology of the Dry Valleys is influenced or even determined by ancient organic material, which of course is determined by the glacial history of the location. There’s some evidence that the first part of this statement is not necessarily true, but glacial history is also manifested in a variety of other physicochemical conditions that do influence microbial communities. People have tried to identify such links with more complex organisms such as lichen or micro-invertebrates, but so far nothing solid has been accepted by the wider community. Identifying the connection between microbial ecology and glacial geomorphology is the more risky part of my proposed research, but the potential reward is great. My current hypothesis is that the “rare biosphere” of local microbial communities, which can only be described economically using PCR amplicon pyrosequencing, contains some information on the glacial history.

Lake Vida

Is it likely that the microscopic life of the Dry Valleys is, or soon will be, influenced by anthropogenic climate change?

Anthropogenic climate change will have a greater effect on polar ecosystems than temperate ones due to the fact that even relatively minor changes can lead to phase shift (i.e., ice to water) in the polar regions. The question right now is how quickly will Dry Valley biota respond to climate change, given the cold temperatures and supposedly slow metabolism. We have some very fresh data that shows microbial communities can in fact respond to changes in climatic conditions very rapidly and drastically, which can have catastrophic consequences for the ecosystem.

Do you think the existence of life in such extreme terrestrial environments has implications for the possibility of life elsewhere in the solar system?

NASA has long used the Dry Valleys as an analog for Mars, and many people in the astrobiology community think the type of life found in the Dry Valleys is reflective of the type of life we can find on Mars. My personal view is that the current conditions on other planets may not matter as much as conditions in the past. Working in extreme environments has taught me to never underestimate the resilience of life, but for self-reproducing organisms to emerge from the primordial soup requires some fairly stringent conditions, so I think we may not necessarily be looking in the right places or using the right approaches right now.

Many thanks to Dr. Lee and congratulations to all the recipients of Marsden funding for 2010.


Top — (c) 2010 Charles Lee

Bottom — Lake Vida, Victoria Valley (c) 2003 Matthew Wood


Bonus Video Podcast: The Perito Moreno Glacier Rupture Cycle

The Perito Moreno Glacier is a major tourism drawcard for Argentine Patagonia. Its persistent advance during the 20th century has resulted in a dam and rupture cycle at its terminus in the formerly-glaciated upper reaches of Lago Argentino. The glacier is somewhat of an enigma: nearly all of the other Southern Patagonian Ice Field outlet glaciers are currently receding.