To accomplish this, UMass Amherst’s Nüsslein, with colleagues from the universities of Texas, Oregon, Michigan State and the University of Sao Paolo recently launched a microbial observatory project to catalog microbial diversity and study effects of local agricultural practices in Brazil’s Rondonia region. The work is funded by an $800,000 four-year grant from the U.S. Department of Agriculture.
In addition to serving as a repository for soils in which as many as 38,000 microbial species may be present in one cubic centimeter, the observatory will catalog the baseline bacterial diversity in three target habitats: pristine rainforest, burned-and-cleared grazing areas, and second-growth rainforest at different time stages, Nüsslein says.
After months of planning, Nüsslein and colleagues began the observatory with the first collecting trip to Rondonia at the end of the recent rainy season. They took a total 450 cores from the top 4 inches (10 cm) of soil in a grid pattern at several locations in each of the three habitat types. Because soils were collected from second-growth forests known to have been cut in 1911, 1972, 1987 and 2001, the microbiologist adds, experiments will be able to assess the rainforest soils’ ability to recover from clearing and burning over time.
The Amazon region is greatly threatened by habitat loss from ranching, where old-growth rainforest is routinely cleared and replaced by a monoculture of African grass for cattle grazing, Nüsslein points out. An estimated 17 percent of the original habitat is already gone. And despite years of research on Amazonian plants and animals, the soil microbial ecosystem underfoot is among the least understood, the microbiologist adds. Thus, a conservatory where samples will be available to other investigators worldwide, plus focused experiments to answer soil ecology questions is needed.
Specifically, Nüsslein and colleagues plan to use three measures of genomic variability and biodiversity in two marker species, the so-called “universalist” Burkholderia and the slow growing Acidobacteria, which have different physiological strategies and thus represent different ecological niches. The researchers will use high-throughput genome sequencing to assess 400,000 ribosomal RNA marker genes at the same time, as well as gene chip arrays to evaluate the status and spatial patterns of known functional genes in these two bacteria genera from each of the three different habitats and across time.
Burkholderia is known as a “DNA hog,” according to Nüsslein, because like “the Borg” from Star Trek, upon meeting a new organic compound, it incorporates new DNA. It can thus live on numerous different food sources or acquire antibiotic resistance, for example. For the microbial observatory, it is useful as a marker of diversity because it retains a record of these encounters in its own DNA.
“We’ll assess the genomic variability of Burkholderia species as one measure of diversity, and follow the shift in Burkholderia diversity from native rainforest via the impact of deforestation to agricultural monoculture,” the microbiologist notes.
By contrast, Acidobacteria are “fastidious” eaters. By surveying their numbers in soil samples, the researchers can assess a different ecozone. Preliminary results are expected in the spring of 2010, when the team heads out to sample again.
One other factor adds to the depth of information to be collected for the microbial observatory: Chemists from Woods Hole Oceanographic Institution funded by the National Science Foundation have for many years studied greenhouse gases in this same Rondonia region in Amazonia. “This will make multiple layers of climate and other ecological data, along with our microbial inventory, available for study,” says Nüsslein. “Altogether we are creating an unusually rich repository of soil ecological information for future research use.”Klaus Nüsslein
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