The interactions between plants and fungi is a widely recognized phenomenon and an example of one of the diverse interactions that may be central to understanding key evolutionary patterns and processes between fungi and their hosts. My research has linked molecular techniques, in combination with field and laboratory experiments, to understand the evolutionary and ecological processes governing the distribution of fungi in plant-fungal interactions including: 1) What are the contributions of historical, biological or ecological factors that promote genetic divergence and speciation?; 2) How do biotic factors affect the distribution and genetic structure of populations? and; 3) What are the patterns and processes affecting fungal diversification?

In the past several years, the research in the my lab has focused mainly on these projects: 1) a project that seeks to identify the routes of introduction, divergence between geographic species, and the processes involved in shaping the genetic history of Armillaria mellea species complex; 2) identify genes encoding for bioluminescence in A. mellea and; 3) using sequence data to reconstruct phylogenies in tandem with morphological analyses to understand the evolutionary history and diversification of a large group of pink-spored fungi (Basidiomycota, Entolomataceae).

« Read Less

• Largent DL, Kluting KL, Anderson NM, Bergemann SE. 2016. Leptonoid species from New South Wales and northeastern Queensland Australia. Mycotaxon 131: 153-176. 
• Kluting KL, Baroni TJ, Bergemann SE (2014) Toward a stable classification of genera within the Entolomataceae:  a phylogenetic re-evaluation of the Rhodocybe-Clitopilus clade.  Mycologia 106: 1127-1142.
• Bergemann SE, Abell-Davis SE, Largent DL  (2014) Entocybe haastii from Watagans National Park, New South Wales, Australia.  Mycotaxon 126: 61-70.
• Largent DL, Bergemann SE, Abell-Davis SE, Kluting KL, Cummings GA (2013) Five Leptonia species from central New South Wales and northeastern Queensland.  Mycotaxon 125: 11-25.
• Hughes KW, Petersen RH, Lodge DJ, Bergemann SE, Baumgartner K, Tulloss RE, Lickey E, Cifuentes J (2013) Evolutionary consequences of putative intra- and interspecific hybridization in agaric fungi.  Mycologia 105: 1577-1594.
• Bergemann SE, Kordesch NC, Van-Sant-Glass W, Metz TA, Garbelotto M (2013) Implications of tanoak decline in forests impacted by Phytophthora ramorum:  girdling decreases the soil hyphal abundance of ectomycorrhizal fungi associated with Notholithocarpus densiflorus.  Madroño 60: 95-106.
• Largent DL, Bergemann SE, Abell-Davis SE, Kluting KL, Cummings GA (2013) Three new species of Inocephalus with cuboid basidiospores from New South Wales and Queensland, Australia.  Mycotaxon 123: 301-319.
• Baumgartner K, Baker BR, Korhonen K, Zhao, Hughes KW, Bruhn J, Bowman TS, Bergemann SE (2012) Evidence of natural hybridization among homothallic members of the basidiomycete Armillaria mellea sensu stricto.  Fungal Biology 116: 677-691.
• Largent DL, Bergemann SE, Cummings GA, Ryan KL, Abell-Davis SE, Moore SE (2011) Pouzarella (Agaricales, Entolomataceae) species from the Barrington Tops National Park (New South Wales) and from northern Queensland Australia. Mycotaxon 117: 435-483.
• Baumgartner K, Trevadon R, Bruhn J, Bergemann SE (2010) Contrasting patterns of genetic diversity and population structure of Armillaria mellea sensu stricto in the eastern and western United States.  Phytopathology 100: 708-718.
• Bonuso E, Zambonelli A, Bergemann SE, Mirco I, Garbelotto M (2010) Multilocus phylogenetic and coalescent analyses identify two cryptic species in the Italian bianchetto truffle, Tuber borchii Vittad.  Conservation Genetics 11: 1453-1466.
• Baumgartner K, Bergemann SE, Fujiyoshi P, Rolshaushen PE, Gubler WD (2009) Microsatellite markers for the grapevine pathogen, Eutypa lata.  Molecular Ecology Resources 9: 222-224
• Baumgartner K, Grubisha LG, Fujiyoshi P, Garbelotto M, Bergemann SE (2009) Microsatellite markers for the diploid basidiomycete fungus Armillaria mellea.  Molecular Ecology Resources 9: 943-946.
• Bergemann SE, Smith MA, Parrent JL, Gilbert GS, Garbelotto M (2009) Genetic population structure and distribution of a fungal polypore, Datronia caperata (Polyporaceae), in mangrove forests of Central America.  Journal of Biogeography 36: 266-279.
• Grubisha LG, Bergemann SE, Bruns TD (2007) Host islands within the California Northern Channel Islands create fine-scale genetic structure in two sympatric species of the symbiotic ectomycorrhizal fungus Rhizopogon.  Molecular Ecology 16: 1811-1822. 
• Guglielmo F, Bergemann SE, Gonthier P, Nicolotti G, Garbelotto M (2007) A multiplex PCR-based method for the detection and early identification of wood rotting fungi in standing trees.  Journal of Applied Microbiology 103: 1490-1507.
• Kennedy PG, Bergemann SE, Hortal S, Bruns TD (2007) Determining the outcome of field-based competition between two Rhizopogon species using real-time PCR.  Molecular Ecology 61: 881-890.
• Peay K, Bruns TD, Kennedy PG, Bergemann SE, Bruns TD (2007) A strong species–area relationship for eukaryotic soil microbes: island size matters for ectomycorrhizal fungi.  Ecology Letters 10: 470-480.
• Bergemann SE, Garbelotto M (2006) High diversity of fungi recovered from the roots of mature tanoak (Lithocarpus densiflorus) in northern California.  Canadian Journal of Botany 84: 1380-1394.

« Read Less

The classic interactions between plants and fungi is a widely recognized phenomenon and an example of one of the diverse interactions that may be central to understanding evolutionary patterns and processes between fungi and their hosts.? My research has linked molecular techniques, in combination with field and laboratory experiments, to understand the evolutionary and ecological processes governing the distribution of plant pathogens and mycorrhizal fungi including: (1) What are the contributions of historical, biological or ecological factors that promote population divergence and speciation? (2) How do biotic interactions affect genetic structure of populations? (3) Are patterns of divergence linked to past ecological or selective pressures?

During the last three years at MTSU, the research in the my lab has focused on three areas: 1) a collaborative project on the worldwide distribution of Armillaria mellea species that seeks to identify the routes of introduction, divergence between geographic species, and the processes involved in shaping the genetic history of A. mellea; 2) the Moorea Biocode Project, a genetic inventory of the fungi of Moorea (French Polynesia) and; 3) the diversity of entolomatoid fungi in western Australia.?

The forest pathogen Armillaria mellea (Basidiomycota, Physalacriaceae) is among the most significant forest pathogens causing root rot in northern temperate forest trees worldwide. A present, we are working on several projects aimed at understanding the evolution history of A. mellea with particular focus on identifying mechanisms of varying levels of variation from worldwide populations.? In one study, we compared levels of genetic within and between eastern US using variable microsatellite markers.? We found evidence of genetic structure consistent with phylogenetic divergence.? Although there were no apparent restrictions to gene flow within each region, Bayesian assignment tests implemented in STRUCTURE identified contrasting patterns of intra-regional genetic diversity: i) western populations formed a single deme and, ii) eastern populations showed population structure, evidenced by three demes or clusters, in the absence of assignment based on geographic origin.? It appears that a potential source of alleles into the southeastern US may be from Mexico.? Our analyses of isolates from self-fertile strains that produce unusual, diploid spores from Africa and Japan indicate a shared history, likely mediated by transport of infected plants, and are the result of hybridization between lineages that originated in Europe and China.? At present there are also several questions that remain unanswered including the major routes of colonization from the ancestral population, and the maintenance of two divergent, mitochondrial haplotypes in western North America.? These questions, along with understanding the evolution of functional gene complexes in A. mellea, will be possible with the draft release of the A. mellea genome (see http://www.jgi.doe.gov/genome projects/pages/projects.jsf?kingdom=Fungi) for more information about the JGI genome project).

The Moorea Biocode project involves the complete genetic inventory (barcoding) of the terrestrial and marine macrobiota in French Polynesia. My current work on the project includes: (1) surveys of macrofungi (i.e., mushroom-forming fungi); (2) analyses of environmental samples (soil, leaves and wood of living plants, decaying litter and wood) for characterization of fungal communities using culture isolation and analysis of DNA clone libraries; (3) analyses of fungal communities associated with invasive plant species; (4) comparisons of endophytic fungal communities associated with dominant plant species across a land-use gradient ranging from agricultural plantations and agroforestry to endemic plant communities; and (5) characterization of mycorrhizal symbionts of an introduced tree species, Pinus caribaea.

The last project is a collaboration with Dr. Dave Largent (former master's advisor at Humboldt State University) to understand the diversity of entolomatoid fungi in western Australia.? At present, we are currently utilizing morphological? and molecular methods to characterize species diversity within the entolomatoid fungi.? Future projects include the integration and development of additional protein coding loci to understand the infrageneric relationships within this entolomatoid fungi.

« Read Less