Bacterial and Archaeal Diversity in Soils and Waters of Great Smoky Mountains National Park.

"Three archaeal and 13 bacterial species were observed in fecal samples from four of the park's elk. The microbial species residing in elk digestive tracts showed seasonality. One of the three archaea was seen only in spring samples while a dominant species of archaea was seen at all times in all animals. All archaea found were related to the genus Methanobrevibacter, which produces methane and is commonly found in the rumen environment. Bacterial diversity patterns showed greater richness and yielded pronounced differences between individual elk and seasons.  Bacteria were identified as belonging to species within the phylum Firmicutes (likely spore-forming strains that could survive the lower digestive tract).    
The researcher has also been visiting the Oconaluftee Visitor Center and Kephart Trail areas with his Methods of General Microbiology class since 2002 to collect samples for isolation and identification.  New genera to this study continue to be observed each year as little or no overlap is observed in the species isolated by the students each year. Out of 345 DNA sequence isolates, very few have been identical. To date, they have detected 5 phyla (Firmicutes, Actinobacteria, Bacteroides, Thermus/Deinococcus, and Proteobacteria), 8 classes, 27 orders, 34 families, and 81 genera have been recorded in 13 years of effort, as well as several colonies that could not be classified down to the level of order. The phylum Bacteroides continued to dominate waters and Firmicutes prevailed in soils.  Many taxa are consistantly unique to either soils or water.
An offshoot of this project has been an attempt to culture Pseudomonas aeruginosa from the samples collected from this class. There has been no success in finding this important, opportunistic pathogen.
Research also includes an ongoing examination of soil bacteria from the Purchase Knob, Cataloochee, and Albright Grove ATBI plots, using a variety of culture techniques.  The results of the bacterial cloning revealed radically different pictures of diversity when compared to culturing.  Cloned 16S rDNA was obtained for 178 bacterial species from the three ATBI plots, including six phyla previously undetected in GSMNP (Acidobacteria, OP10, Planctomyces, Verrucomicrobia, Termite Group 1, and Gemmatimonadetes), having no species overlap between molecular identification and clonal studies of the sites.  Ammonia oxidation (amoA) gene diversity will also be compared for both bacteria and archaea using the T-RFLP method. This will give us some initial insight into functional ecology, with an important part of the nitrogen cycle examined.
Cultivated strains (59) from hemlock roots in the Albright Grove include many that are only distantly related to known species (e.g., DNA similarities of 24-45%) and also groups that contain nitrogen-fixing species (Alphaproteobacteria such as the bradyrhizobia and the genus Janibacter within Actinobacteria).  Across Albright (2008 and 2011), Purchase Knob, and Cataloochee plots, Acidobacteria, presumptive nitrogen-fixing species (e.g., Bradyrhizobium), and archaeal ammonia oxidizers appear to be important components of hemlock ecology. Understanding interactions between bacteria, archaea, and hemlock could aid in successfully reforesting areas and restoring benefits to numerous animals dependent on this tree.
It was hypothesized that the exposed slopes and dark soils over Lake Chilhowee might support the growth of thermophilic spore-forming bacteria from the genus Geobacillus. Isolates were collected in 2007 that grew at 70 degrees C from surface samples as well as from depth to a few feet below the surface leaf litter.
One other study that is ongoing has been examining bacterial and fungal diversity at the next sites of native ants (Aphaenogaster rudis). Preliminary work shows that bacterial diversity at sites in and near Albright Grove were too diverse to assess differences between control and experimental plots.

Tags: albright-grove, aphaenogaster-rudis, aphn, appalachian-highlands-network, archeal, bacteria, cataloochee, digestive-tract, ecological-framework-geology-and-soils-soil-quality-soil-function-and-dynamics, ecological-framework-water-water-quality-microorganisms, elk, fecal-samples, firmicutes, great-smoky-mountains-national-park, grsm, oconoluftee, origin-external, pseudomonas-aeruginosa, purchase-knob, ser, soil, southeast-region, studyid-grsm-00052
Organization: Department of the Interior