$1.8 million grant from the National Science Foundation
Scientists at the Georgia Institute of Technology have obtained a five-year, $1.8 million grant from the National Science Foundation (NSF) to examine how complex microbial systems use their genetic diversity to respond to human-induced change.
The task is essential because microbial communities carry out crucial functions in the environment, breaking down pollution, recycling nutrients – and serving as main sources of nitrogen and carbon.
Inspite of the significance of microbes, few among the thousands of species that comprise a standard microbial community have been examined thoroughly. The comparatively unidentified organisms inside these communities might have genes which could assist in tackling crucial ecological, energy and various obstacles.
Huge Amount of Diversity
“We are all dependent on these microbes,” said Kostas Konstantinidis, an assistant professor in Georgia Tech’s School of Civil and Environmental Engineering and the grant’s principal investigator. “There are many different species and a huge amount of diversity out there. This project will allow us to look at the details of how this diversity is generated, how redundant it is and how these microbes are changing in response to perturbations in the environment.”
The funding, from the NSF’s “Dimensions of Biodiversity” program, will assist a collaborative work involving Konstantinidis and two other Georgia Tech researchers: Eberhardt Voit and Jim Spain. Voit holds the David D. Flanagan Chair in Biological Systems within the Department of Biomedical Engineering at Georgia Tech and Emory University, and is a Georgia Research Alliance Eminent Scholar. Spain is a professor in the School of Civil and Environmental Engineering.
Investigation to Concentrate on Lake Lanier
The investigation will at first concentrate on Lake Lanier, a large man-made lake situated near Atlanta. Over and above the experimental work, the study calls for considerable mathematical modeling of the complex microbial communities.
“We want to see how the microbial communities of the lake change over time, and how the perturbations affect that,” said Konstantinidis, who holds the Carlton S. Wilder Chair in Environmental Engineering at Georgia Tech. “We then want to extend our understanding to other ecosystems, such as the Gulf of Mexico.”
The scientists will create mesocosms in the research laboratory with microbial populations from Lake Lanier. They will give food to these populations’ pollutants such as hydrocarbons, anti-biotics and pesticides to find out how they react and how they cope with substances to which they might not have been exposed.
Genes to Break Down Pollutants
“Sometimes they may not have the genes to break down the pollutants and may not encode the right enzymes,” Konstantinidis said. “But if you give them enough time, these microbes somehow innovate. We want to understand the genetic mechanisms that allow the microbes to break down a compound that they are seeing for the first time.”
The grant will allow the Georgia Tech researchers to expand knowledge of “rare” microbes, largely unknown organisms that may harbor useful genes.
“We think these unusual microbes may be the key ones,” Konstantinidis said. “Though they may be low in abundance, the whole community may depend on them. When you have a new pollutant, these rare microbes may become more important by providing the genetic diversity needed.”
Extending this understanding will be challenging, however, because few species can be cultured in the laboratory. That difficulty is leading Konstantinidis and his team to develop new tools that allow studying the organisms in the field, without culturing them under laboratory settings. Addressing those challenges may lead to the creation of additional techniques that could benefit other areas of biology, engineering and medicine.
Microbial DNA and Decoding It
“One of the most common techniques is to take the microbial DNA and decode it,” he explained. “From the DNA, we can tell what the organism is and what it may be doing in the environment.”
However, studying DNA brings yet another set of problems. The genes are rarely restored in one piece based upon these genomic methods, and quite often consist of parts of the genome or are infected by DNA from other species.
“Bioinformatics is a big issue for us, because that is how we can put the pieces together,” Konstantinidis explained. “We have to make sense of pieces of DNA from perhaps thousands of organisms. This is where biology, computing and engineering are merging to find clever ways to accomplish such tasks.”
Global Climate Change Trigger Increased Respiration
Part of examining the way the microbial community reacts to change will comprise examining the consequences of increasing temperatures. Will global climate change trigger increased respiration among the microbes and for that reason increase carbon dioxide output, or will temperature change lead the microorganisms to maintain carbon, pulling CO2 out of the atmosphere?
“A big part of the scientific community is working on questions like this to get a better understanding and better model of how microbial systems will respond,” Konstantinidis said.
Modeling will be crucial to understand not only how microbial communities will react to broad climate changes, but also the way they may respond to such dramatic perturbations as large oil spills.
Putting It All Together
“From small experiments in the lab, the goal is to eventually model whole ecosystems – how Lake Lanier works or how the Gulf of Mexico works in terms of the microbes that are there,” he said. “We want to have a more predictive model of how these communities that are so diverse will respond to a perturbation like an oil spill or rising temperatures. With so many thousands of organisms from different species, we need modeling to put it all together.”