Vilgalys Mycology Lab – Duke University

Congrats to Jessie Uehling, who recently passed her prelims.  Jessie is a 2nd year Genetics Program student  with  interests in molecular biology and genomics of bacterial-fungal interactions.  For her Ph.D. research, Jessie has chosen to study bacterial-fungal symbioses.  Our lab recently discovered a very unusual bacterial endosymbiont (Glomeribacter sp.) that lives inside endophytic fungi that colonize plant roots and soil.   The genome of the Glomeribacter endosymbiont is greatly reduced (2.5 mb) relative to its free-living relatives in the genus Burkholderia (typcially around 9 mb).  Jessie is working with our collaborators from Oak Ridge National Labs (Jessy Labbe) and INRA (Aurelie Deveaux) to investigate the molecular mechnaisms of fungal-bacterial symbiosis.

Jessie in field in Bastrop, TX

Before coming to Duke, Jessie earned her M.S. at  Humbodlt State in the lab of Terry Henkel working on biodiversity and ecology of Clavulina species (rare and unique guild of ectomycorrhizal fungi associated with remote forest regions of Guyana).

Now into her second year as a Ph.D. student, Jessie is already a productive junior scientist with over 10 published papers arising from her MS thesis on the evolutionary systematics and ecology of mycorrhizal fungi.   Good luck with your next phase, “ABD” (All but Dissertation!).

2013 was a great year for  Fungi.   Epic rains that started in June and lasted thru August sustained huge  fruitings of  chanterelles and other mushrooms across North Carolina and the southeastern US.   This increase in fungal fruiting is  fueling a growing interest in   fungi as well.   Everywhere, people are really getting into mushroom picking, growing, and just learning about their biology.  I was fortunate to teach several mycological classes this year, including a field course at Mountain Lake Biological Station,  a mushroom workshop at the North Carolina Botanical Gardens and another on cultivation with Bountiful Backyards (Durham, NC),  as well as the regular classes that I teach at Duke in mycology and microbiology.  This year’s Mycology class (Bio540) did a great job learning the basics of fungal identification while also keeping up with the latest advances in fungal biology.  The capstone of this class, however, was a banquet at the end of the semester featuring some of the student’s favorite mushroom recipes!

Several members of our lab group will be moving on to different pastures soon!

Greg, Patty and Aldo Bonito are Australia bound

Greg Bonito joined the lab in 2003 as a Ph.D. student to study the molecular systematics of Tuber.   For the last 3 years, Greg has been the lead postdoc for our PMI project with Oak Ridge National Laboratory to study fungal endophyte communities associated with cottonwood (Populus trichocarpa and P. deltoides).   Greg recentliy accepted a Research Scientist position at the Royal Botanic Gardens in Melbourne, Australia.  Way to go!

Soledad Benitez is expecting her baby in December, and will be leaving for South Dakota in January.

Soledad Benitez came in 2009 to join our NSF-sponsored project with Jim Clark (in Duke’s Nicholas School of the Environment) to study ecology of forest pathogens.   The project is using next-gen community sequencing to test elements of the Janzen-Connell hypothesis that has invoked host-specific herbivores and pathogens as agents for maintaining forest tree diversity.  Soledad and her husband Wirat are expecting their second child in December, after which they plan to move to South Dakota. (update: Baby boy Ananda Pipatpongpinyo was born December 2nd. 2013. Family all healthy, happy and at home now.)

Lindsey Becker plans to continue with field research

Lindsey Becker has been working with Soledad on the forest pathogen project, helping to collect and process thousands of plant samples and managing our extensive culture collection.  We’ll be missing Lindsey, and wish her well in her future career!

The Joint Genome Institute recently approved funding for a Community Sequencing Project to sequence the genomes of fungi and their endosymbiotic bacteria.  Recently, several lineages of bacteria were discovered living within the mycelium of early diverging terrestrial plant-associated fungi including the Glomeromycota, Mortierellomycotina, and Mucormycotina.  The endocellular bacteria appear within the fungal mycelium as obligate and in some cases facultative endobacteria. Genomic analyses indicate that these bacteria have reduced genome sizes compared to free-living relatives, and that these ancient fungal endosymbionts can influence fungal reproduction and metabolism.    The bacterial lineages residing within  the hyphae of these fungal lineages include Mollicutes (gram-positive bacteria in the Firmicutes), Stenotrophomonas (gram-negative gamma-proteobacteria), Burkholderia (gram-negative beta-proteobacteria) and Brevundimonas (gram-negative alpha-proteobacteria)

The new CSP will support genome sequencing  of early diverging plant-associated fungi and their endosymbiotic bacteria, and will provide new insights into plant microbiomes and will allow for a novel comparative genomic and evolutionary perspective on fungal-bacterial symbioses. Our focus is on fungi that are ubiquitous in terrestrial soils and plant-dominated ecosystems.

The CSP is led by Greg Bonito from Duke, and includes an international cast of collaborators including Paula Bonfante, Stefano Ghignone, Alessandro Desiro, Alessandra Salvioli (Turin Univeresity, Italy), Christopher Schadt, Jesse Labbe, Dale Pelletier, Gerald Tuskan, Tim Tschaplinski, Steven Brown, David Weston (Oak Ridge National Laboratory), Amy Schaefer (University of Washington), Teresa Pawlowska, Stephan Mondo (Cornell University), Francis Martin (INRA-France).

DOB crew visiting with  Jeff Mitton

This summer our Dimentions of Ectomycorrhizal Diversity project has been busy sampling pine forests across North America.  We are using next-gen sequencing methods to survey fungal diversity associated with pine forests.   This year,   we  streamlined our protocols for soil sampling so that we could visit more sites.

In  June, our Dimentions crew visited  Colorado and Wyoming to sample over 12 pine forests.  To identify sites for this trip we visited with  pine geneticist Jeff Mitton at the University of Colorado, who shared his extensive knowledge of pines and helped us identify good monodominant sites for sampling.  In Wyoming, we vistied with mycologist Steve Miller, who also showed us some great sites in the Medicine Bow National Forest.

Species sampled: Pinus ponderosa (ponderosa pine), P. contorta (lodgepole pine), P.flexilis (limber pine), P. aristata (bristlecone pine), and P. edulis (pinon pine), as well as Picea englemannii (englemann spruce).   

Renee Johansen is a Ph.D. student at the Univ. of Auckland and Landcare Research in Auckland, New Zealand, and is visiting our lab for 8 months on a Fulbright scholarship.  Renee is using next-gen sequencing to characterize mycorrhizal fungal communities associated with European marram grass (Ammophila sp.),  an invasive species that competes with native dune plants in NZ and in North America.

Here are some links to articles and videos about Renee’s research:

http://www.facebook.com/photo.php?fbid=584972848188844&set=pb.172168626135937.-2207520000.1367891543.&type=3&theater

http://www.youtube.com/watch?v=dz0qzoIsVMs&feature=youtube_gdata_player

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