Molecular phylogenetic studies of fungi and evolution of fungal life history stategies.
B.Sc. Univ. Minnesota (1979);
Ph.D. Univ.California, Davis (1987);
Postdoctoral, Univ. Tubingen, Germany (1988);
Postdoctoral, Univ. California, Davis (1989);
Postdoctoral, Univ. California, Berkeley (1990-92).
Research in the Berbee laboratory focuses on the diversity and molecular phylogenetics of fungi. Fungi and animals shared a common ancestor over a billion years ago. Since that time, animals evolved into herbivores and predators while fungi became specialized as decay agents and recyclers in the environment; as plant and animal pathogens; and as symbionts contributing as mycorrhizal partners to plant growth. Through a combination of field and laboratory work, students and postdoctoral researchers are finding and culturing fungi and fungus-like organisms, many of them new to science, and then applying microscopic and molecular phylogenetic techniques to place the origin and diversification of the fungi in a phylogenetic context.
1. Deep divergences and ancient lineages of fungi and fungus-like organisms. With funding from Canada’s NSERC and from the US NSF, members of the Berbee lab are collecting new fungi and fungus-like organisms from aquatic environments, growing them in pure culture whenever possible, and combining microscopic and phylogenetic approaches to make inferences about their biology and evolutionary origins (Tsui et al. 2009; Berbee and Taylor 2010; Marshall and Berbee 2011; Sekimoto et al. 2011). Including our newly discovered organisms as well as taxa from culture collections, they are sequencing genes that allow reconstruction of patterns of evolutionary origin of the fungus life style among evolutionarily divergent fungi and fungus-like organisms (Marshall and Berbee 2010; James and Berbee 2012).
2. Ascomycete evolution, breeding systems and systematics. With more than 30,000 known species, the ascomycetes are diverse and ecologically important. With the support of NSERC, students in the Berbee lab are reconstructing patterns of evolution in the ascomycetes. They are concentrating on the Pleosporales, a well-defined group including many species with adaptations to specialized habitats. Like whales and seals, some fungi in this group originated on land but then returned to the water. Over 60 species in the order Pleosporales produce helicoid asexual spores many adapted for dispersal in water and colonization of aquatic habitats. Our analyses are showing extensive convergence in most morphological characters and molds forming complex, barrel-shaped helical spores to trap air bubbles for floatation arose convergently from three, primarily terrestrial lineages in the Pleosporales (Tsui and Berbee 2006).
The Pleosporales also included many serious pathogens of plants. To track the molecular evolution of changes in breeding systems among these plant pathogens, the Berbee lab is applying molecular amplification of mating type gene DNA. The two opposite mating type genes are the master regulators of sexual reproduction in these fungi. In an outcrossing species, haploid individuals with opposite mating types can mate and 50% of their haploid progeny will be of each mating type. Asexual reproduction propagates the parental mating type. In a selfing species, each haploid nucleus in an individual carries the two opposite mating type genes. Working backwards, by examining the distribution of mating type genes in a population, we can distinguish outcrossing from selfing individuals and sexual from asexual populations (Inderbitzin et al. 2005; Inderbitzin et al. 2006; Inderbitzin et al. 2009).
3. Mycorrhizal fungal diversity. Forestry is of great economic importance in British Columbia (BC) and one of the goals of foresters is to develop management strategies that maintain the diversity of forest organisms including fungi. Mycorrhizae are mutually beneficial associations between fungi and roots of plants and they are required for healthy forests. Our studies show that BC fungi are diverse and that many have yet to be described (Allen et al. 2003; Wright et al. 2009; Harrower et al. 2011). Even though fungi are clearly important to tree health, which fungi are important for particular trees in particular regions of the province remains largely unknown. With funding from NSERC, and with the support of the Vancouver Mycological Society and graduate and undergraduate students conducting research projects, we are exploring the diversity of fungi in BC and contributing to a DNA sequence barcode database that will facilitate identification of our mushroom species. With these data, we will be able to correlate the occurrence of particular fungi with tree species, with geographical regions, and with tree growth rates. This research helps lay the groundwork for development of conservation management strategies for fungi and for the plant community that requires fungal partnerships.
Biology 209: Biology of Nonvascular Plants
Biology 323: Structure and Reproduction of Fungi
Biology 448: Directed studies
Biology 525: Phylogenetics Workshop. To be offered in June, 2013
Jaclyn Dee (PhD Student)
Tanay Bose (MSc Student)
Ludovic LeRenard (PhD Student)
Anna Bazzicalupo (PhD Student, beginning Sept 2012)
Deep divergences and ancient lineages
James TY, Berbee ML (2012) No jacket required - new fungal lineage defies dress code. Bioessays 34 (2):94-102. doi:10.1002/bies.201100110
Marshall WL, Berbee ML (2011) Facing unknowns: living cultures (Pirum gemmata gen. nov., sp nov., and Abeoforma whisleri, gen. nov., sp nov.) from invertebrate digestive tracts represent an undescribed clade within the unicellular opisthokont lineage Ichthyosporea (Mesomycetozoea). Protist 162 (1):33-57. doi:10.1016/j.protis.2010.06.002
Sekimoto S, Rochon D, Long JE, Dee JM, Berbee ML (2011) A multigene phylogeny of Olpidium and its implications for early fungal evolution. BMC Evol Biol 11. doi:doi:10.1186/1471-2148-11-331
Berbee ML, Taylor JW (2010) Dating the molecular clock in fungi - how close are we? Fungal Biology Reviews 24:1-16
Marshall WL, Berbee ML (2010) Population-Level Analyses Indirectly Reveal Cryptic Sex and Life History Traits of Pseudoperkinsus tapetis (Ichthyosporea, Opisthokonta): A Unicellular Relative of the Animals. Mol Biol Evol 27 (9):2014-2026. doi:10.1093/molbev/msq078
Inderbitzin P, Mehta YR, Berbee ML (2009) Phylogenetic studies of Pleospora species with Stemphylium anamorphs based on four loci; lack of separation of Pleospora herbarum and five new lineages. Mycologia 101:329-339
Inderbitzin P, Shoemaker RA, O'Neill NR, Turgeon BG, Berbee ML (2006) Systematics and mating systems of two fungal pathogens of opium poppy: the heterothallic Crivellia papaveracea and a homothallic species with a Brachycladium papaveris asexual state. Canadian Journal of Botany 84 (8):1304-1326
Inderbitzin P, Harkness J, Turgeon BG, Berbee ML (2005) Lateral transfer of mating system in Stemphylium. Proc Natl Acad Sci USA 102 (32):11390-11395
Tsui CKM, Berbee ML (2006) Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences. Mol Phylogen Evol 39 (3):587-597
Mycorrhizal fungal diversity
Harrower E, Ammirati JF, Cappuccino AA, Ceska O, Kranabetter JM, Kroeger P, Lim S, Taylor T, Berbee ML (2011) Cortinarius species diversity in British Columbia and molecular phylogenetic comparison with European specimen sequences. Botany 89 (11):799-810. doi:DOI: 10.1139/B11-065
Wright SHA, Berch SM, Berbee ML (2009) The effect of fertilization on the below-ground diversity and community composition of ectomycorrhizal fungi associated with western hemlock (Tsuga heterophylla). Mycorrhiza 19 (4):267-276. doi:doi:10.1007/s00572-008-0218-x
Allen TR, Millar T, Berch SM, Berbee ML (2003) Culturing and direct DNA extraction find different fungi from the same ericoid mycorrhizal root. New Phytol 160:255-272. doi:doi.org/10.1046/j.1469-8137.2003.00885.x