Culturability and dynamics of bacterial communities along the Pine Canyon Watershed of Big Bend National Park, TX
Soil bacterial communities are known to play a significant role in ecosystems as they are responsible for, among other things, nutrient cycling, and plant and rhizosphere interactions. Those bacterial communities which persist in arid environments have gained special attention over the past several years as life in these environments is often believed to be limited due to a lack of available water. Since soil bacteria play such a significant role in the environment, understanding how seasonal changes in soil moisture and temperature affect bacterial community structure and function is critical for understanding how soil bacteria contribute to the functioning of arid ecosystems. However, the study of soil bacterial communities has been limited due to difficulties experienced in culturing organisms from the environment. Furthermore, PCR-based, culture-independent techniques have become increasingly popular amongst researchers, but these techniques which impose a bias limiting observations to only the most DNA-dominant bacterial species, species which are not believed to play a large functional role in the ecosystem. Hence, a large and possibly important proportion of the bacterial population could be commonly overlooked.
A year-long, two-part research project on the environmental effects on soil bacterial communities in three sites along the Pine Canyon Watershed of Big Bend National Park began in August 2005. The first part examined the DNA-dominant bacterial community structure using PCR and Denaturing Gradient Gel Electrophoresis along with Fatty Acid Methyl Ester analysis. These techniques revealed a stable DNA-dominant bacterial community structure throughout the summer and winter seasons, and no significant changes in bacterial structure were recorded during a large precipitation event during August 2006. The second study utilized a culture-based approach to examine the functional bacterial communities along the three sites. The culture-based approach revealed that two different assemblages of soil bacteria exist, a culturable-dominant and a culturable-non-dominant. The culturable-dominant assemblage remained relatively stable throughout the seasonal changes and during the precipitation event of August 2006 and consisted largely of bacterial species of the Arthrobacter and Burkholderia genus. However, the culturable-non-dominant assemblage responded to seasonal changes by either increasing or decreasing in population density and increased in density during the precipitation event. The responses observed in the culturable-non-dominant assemblage may provide an explanation towards the difficulty many researchers experience in culturing organisms from the environment. Furthermore, culture-dependant techniques proved to be more sensitive in detecting changes in the bacterial community structure than culture-independent based techniques.
Also, to aide in the collection of data for the second study, computer software was developed using the C# computer language and has been made available at: http://www.biol.ttu.edu/faculty/jzak/dgge_soft.