Khalid Hameed receives Presidential Service Award. Congratulations Khalid!

Congratulations to Professor Khalid Hameed for receiving the President’s Volunteer Service award.  Khalid received this award for his volunteer work with US AID Farmer-to-Farmer program to support mushroom cultivation in the developing world.  He and Van Cotter recently presented a summary of this work at the recent MASMC conference.

MASMC 2017 Poster – Mushroom Cultivation Support Farmer-to-Farmer Program

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Endosymbiotic bacteria of Mortierella: part of the core Populus microbiome

We recently published two papers arising from our first Populus endophyte genomes.  Here are some links along with the news release prepared for the DOE

Uehling J, Gryganskyi A, Hameed K, Tschaplinski T, Misztal PK, Wu S, Desirò A, Vande Pol N, Du Z, Zienkiewicz A, Zienkiewicz K, Morin E, Tisserant E, Splivallo R, Hainaut M, Henrissat B, Ohm R, Kuo A, Yan J, Lipzen A, Nolan M, Labutti K, Barry K, Goldstein AH, Labbe J, Schadt C, Tuskan G, Grigoriev I, Martin F, et al. 2017. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens. Environmental Microbiology …. doi:10.1111/1462-2920.13669.

Li Z, Yao Q, Dearth SP, Entler MR, Castro Gonzalez HF, Uehling JK, Vilgalys RJ, Hurst GB, Campagna SR, Labbé JL, Pan C. 2017. Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system. Environmental Microbiology …. doi:10.1111/1462-2920.13605.

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98 Suillus X 10 Pinaceae


Prepare to mass-inoculate!

As part of our NSF-funded study on coevolution of mycorrhizal fungi in the genus Suillus with members of the plant family Pinaceae, we just finished setting up a spore-print bioassay pairing 30 Suillus species with 10 different host trees from the conifer family Pinaceae.    The seedlings will be harvested after 2-3 months to test for mycorrhizal specificity with different groups of confier hosts.  Molina & Trappe (1982) first demonstrated  strong patterns of mycorrhizal specificity (compatible/incompatible) for 27 species of ectomycorrizal fungi grown with 7 species of Pinaceae hosts.  In our experiments, we are investigating molecular-based interactions that result in mycorrhizal compatibility  between Suillus with different species white pines (Pinus subg. Strobus), hard pines (subg. Pinus), Douglas fir (Pseudotsuga spp.), larch (Larix sp.) and spruce (Picea sp.).  See Liao et al. (2106) for more on molecular genetics of mycorrhizal compatibility/incompatibility!

Why 98 and 10?  That’s exactly how many seedlings (980) fit inside two of our R-chambers in the Duke Phytotron (plus uninoculated control plants).    Our team has collected spore prints and cultures from over 500 collections of Suillus from pine forests around the world.  It was hard deciding which spore prints to test!


–Molina, R., and J. M. Trappe. 1982. Patterns of ectomycorrhizal host specificity and potential among Pacific Northwest conifers and fungi. Forest Science 28:423–458.
–Liao, H.-L., Y. Chen, and R. Vilgalys. 2016. Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus. PLoS Genet 12:e1006348.

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Suillus metatranscriptomics paper published in PLOS Genetics

oct_2016Our first  paper on compatibility/incompatibility in Suillus is finally out!  Suillus species are members of the bolete family that fruit in association with different members of the conifer family Pinaceae. Here’s what we report in this paper:
1. We tested 5 species of Suillus for ability to develop ectomycorrhizae on white pines (Pinus sect. Strobus) vs. hard pines (sect. Pinus).  Pairings between individual species of Suillus and Pinus were scored as ‘compatible’ or ‘incompatible’.
2. RNASeq analysis reveals that all of the Suillus species were able to germinate with  different pine hosts, but they (and their host) express different sets of genes during compatible vs. incompatible responses.
3. A distinct set of ‘core genes’ are expressed by both fungal and plant partners during compatible vs. incompatible interactions.

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Sept 23-25: Mushroom Hunting in Vermont—Lithuanian Style

img_0581Last week we went hunting for fungi in Vermont at Camp Neringa, a Lithuanian summer camp where I used to go as a kid.  The foray got a write up by author Laima Vince in the Huffington Post.  Even found some Suillus!




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Sept 17-18: Alex Smith Foray Report (Univ. Michigan Biological Field Station)


Alexander H. Smith – Dean of American Mycology

Mycologists and their students from  the Great Lakes region meet each fall for the A. H. Smith foray.  Alex Smith was my academic grandfather, widely known as the dean of  modern American mushroom taxonomy, and who taught mycology at Univ. of Michigan for 50 years.  This year’s Smith Foray took place in Smith’s favorite collecting site at the University of Michigan Field Station, located on Douglas Lake at the north end of Michigan’s lower peninsula.  The Foray was hosted by the Tim James lab at the Univ. of Michigan, with over 80 mycologists participating including several  Duke Mycology Alumni including Tim, Anne Pringle (Univ. Wisconsin), and Greg Bonito (Michigan State Univ.).  As you can see, we had excellent collecting!


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Aug 1-4, 2016: Sierra truffles and Suilli

This pre-conference field trip to the southern Sierra’s was a repeat performance of an earlier pre-meeting foray that took place in 1996 prior to the 1st International Conference on Mycorrhizae.   That conference was hosted by Tom Bruns and his colleagues from UC Berkeley, who also hosted this year’s Mycological Society meetings.

Using the Lake Shore Resort at Huntington Lake as our base camp, we collected fungi from the Sierra National Forest between 2000-3000 m.   The area is located between Yosemite and King’s Canyon National Parks.  This snowmelt-driven mountain ecosystem  is a famous evolutionary hotspot with many highly endemic plants and fungi, including a rich abundance of truffles and classic secotioid fungal species that represent ‘missing links’ in mushroom evolution (the “Secotioid Syndrome” described  by Harry Thiers,  1984, Mycologia 76:1–8).  I was also thrilled to find several species of Suillus for our ongoing genomics work, including S. megaporinus, a bizarre little bolete with a highly upturned pileus that closes back on itself to reveal a fully exposed pore surface (an ‘inverse truffle’).   These forests are full of so many beautiful trees that I could not stop photographing them, including Abies magnifica, Abies concolor, Pinus jeffreyi, Pinus lambertiana, Pinus monticola, Pinus contorta, Calocedrus decurrens and Sequoiadendron giganteum.  We also saw many beautiful mycoheterotophic species, including Pterospora and Sarcodes spp.  The foray organizers, Dan Luoma and Joyce Eberhardt did an amazing job transporting our eager group to and from the mountains.  We are all very grateful for their work to organize this fine little expedition prior to the MSA meetings!

Here are some of the cool fungi we found:

Here are some shots of the amazing forests and plants that we saw in the Sierras:

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Undergraduate Assistant Positions available:  Genetics of plant-fungal interactions.


We have several openings for independent study and paid research assistants for projects that study interactions between plants and their symbiotic mycorrhizal fungi.   We are using molecular-based methods to study interactions between symbiotic fungi with with native tree species (pines, oaks, and cottonwoods). Duties include assistance with fieldwork (planting, watering, harvesting) and laboratory experiments (culturing, DNA sequencing).  Training will be provided.  If you are interested in growing and knowing plants and fungi, then we are interested in you.  We are looking for a reliable person able to work up to 20 hrs per week.  The position is available during the academic year, and during summer.  More information about the lab and our research is at

Application: email a brief statement of interest (mentioning relevant skills/background), and a 1 page vitae in (pdf format preferred) plus names of 2 references to Rytas Vilgalys,  Interviews will begin immediately until the position is filled.

Contact: Rytas Vilgalys (Biology Department),

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Summer 2016 – Fungi of Mountain Lake Biological Station

Just finished an excellent 3-week field mycology class at the Mountain Lake Biological Station (9-29 July, 2016).  MLBS is operated by the University of Virginia Biology Department, and is located in a remote part of the southern Appalachian mountains near Pembroke, VA.  This year’s class and I spent three weeks exploring the rich forests and fungal communities that surround the Station.  Weather was perfect with daily rain showers and cool temps to stimulate fruiting.  Notable highlights included abundant fruiting of several classic southern Appalachian fungi including Russula earlei, Boletinellus merulioides, Amanita jacksonii, and dozens of boletes including Boletus separans,  B. nobilis, and Suillus subaureus.  Together with the 6 students in the class, we made over 300 beautiful collections of fungi.

During this time I gave a seminar at the Station, with an update on our NSF DOB pine microbiome survey data for two forest plots close to MLBS. VA1: Pinus strobus, Poverty Hollow, Mongomery Co., VA.  VA2: P. strobus, White Pine Lodge, Giles Co., VA.  At each site, we collected fruit bodies and soil samples, and were able to identify a list of most common fungi occurring as OTUs in soil under white pines.  Many of these are the same charismatic macrofungi that we observed fruiting all over the station.  The most abundantly detected OTU is a species of Lecanicillium, which is the asexual form of the genus Cordyceps.

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Postdoc position available: Mycorrhizal Genomics, Bioinformatics

The Vilgalys Lab at Duke University seeks a postdoctoral researcher in the area of fungal genomics, bioinformatics, and molecular evolution.  The selected candidate will contribute to ongoing studies on comparative genomics of ectomycorrhizal  fungi (Suillus spp.) and their symbiotic interaction with pines and related trees  (Pinaceae). We are especially interested in candidates with prior experience in bioinformatics and comparative genomics including phylogenomics, as well as molecular plant-pathology.  The postdoc chosen for this position will have opportunities to interact with collaborating institutions in the US and abroad.  Duke University offers an excellent working environment, with modern facilities and competitive salaries.  Demonstrated expertise must include a track record of peer-reviewed publications.  Interested applicants should send a cv, research statement, and names of 3 references (preferably in a single pdf) to Dr. Rytas Vilgalys,   The position is available immediately and will remain open until a suitable candidate has been hired. For more information on the Vilgalys Lab see:

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