Suillus metatranscriptomics paper published in PLOS Genetics

Our 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 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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2016 ORNL, INRA and Duke fungal genomics meeting

May 24-25, 2016:  We just finished hosting an excellent meeting with our Plant Microbial Interfaces research team, which includes scientists from Oak Ridge National Laboratory and Francis Martin’s mycorrhizal genomics group from INRA.  Two full days of research updates and discussion about future directions for the PMI project, followed by a field trip to Duke Forest to collect sporocarps for genome sequencing.


Francis Martin lecturing on ectomycorrhizae

A highlight of the meeting was a public lecture/seminar by Francis Martin, INRA
‘Unearthing the roots of the mycorrhizal symbioses’

Below is the short talk program from our two day meeting
Rytas Vilgalys: introduction/welcome
Mitch Doktycz: introduction/overview/goals for discussion
Gregory Bonito: Metagenomics of Populus-associated fungal communities based on plant/soil bioassay
Chris Schadt and Allison Veacham: Ongoing and Planned PMI Microbiome, Mycobiome and Metagenomics activities at ORNL
Brian Looney: “Russulaceae as a new addition to the Populus model system”
Jessy Labbé: Ongoing and Planned PMI activities with Populus-fungal interactions
Sunny Liao: Metatranscriptomics of Populus root microbiome interactions: “Phyto-Zero”
Claire Veneault-Fourrey: Fungal mycorrhiza-induced Small Secreted Protein: all effectors of symbiosis?
Francis Martin: Identification of developmental pathways in Laccaria-Populus ectomycorrhiza and other models by RNA-Seq;
Jessie Uehling: Microfluidics approaches for study of fungal-bacterial interactions
Aurélie Deveau: Biofilm formation by the helper-bacteria BBc6 on Laccaria bicolor hyphae
Posy Busby:  leaf endophyte communities and the Populus microbiome
Tim Tschaplinski: Integrating metabolomes of Populus and its fungi
Dan Jacobson: Network analyses integrating everything

After the meetings, visitors were treated to a collecting trip in Duke Forest, including a visit to former FACE research site.

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April: visitors, morels, and MASMC

April is a beautiful time of year in North Carolina and a great time to visit Duke University. This month we hosted several visitors to our lab, and also attended MASMC

Neolecta irregularis

Neolecta irregularis

Apr 14: Alija Mujic (Ph.D., Oregon State University, currently in the Matt Smith lab at Univ. of Florida)
“Out of Western North America: systematics and phylogeography of Rhizopogon subgenus Villosuli based on genome-scale sequence typing”

Alija was one of this semester’s Systematics Discussion Group speakers, presented a research seminar on genome evolution in truffles.  During his visit, Alija joined the microbial ecology class for a field trip to Duke Forest to hunt morels (we found one, also some nice specimens of Neolecta).

IMG_9357Apr 21: Tracey Steinrucken (Fulbright Fellow, Ph.D. student at Hawkesbury Ecological Institute, West Sydney University, Australia).
“Endophytes, Dieback and Invasive Plants”.
Tracey just finished a 9 month Fulbright fellowship in the Mateo Garbelloto lab at UC-Berkeley,  afterward visited our lab for one week before joining our lab group on a road trip to this year’s MASMC conference at Penn State Univ. (see below)

IMG_9364April 21: Dan Jacobson, Oak Ridge National Laboratory
“Discovery of Plant Functions Involved in Microbial Interactions: Pleiotropic and Epistatic Networks for Populus trichocarpa”

Dan is a computational biologist and central coPI for the Plant-Microbial Interfaces (PMI) Genomics SFA (that also supports our lab) through the U.S. Dept. of Energy.  He presented a seminar on the application of network analysis for integrating metagenomic data for the Populus microbiome.


April 24-26:  MASMC – Middle Atlantic States Mycology Conference, Penn State Univ.
We had perfect weather for a roadtrip back into early spring at State College, PA hosted by David Geiser & Co.  MASMC has been the premier mycological reunion held every spring, now 35 years running.  This year’s keynote speaker was Prof. M. Cathie Aime, who presented a knuckle-gripping presentation on fungal diversity of Guyana.  As always, great opportunity to hear what new students are working on, and catching up with the greater family of fungal biologists from all over eastern USA (and much further abroad).  I have to admit, every MASMC is better than the one before it.

IMG_9431April 28: Alejandro Rojas, Ph.D. candidate, Michigan State University
“Oomycete community diversity: the soybean root rot complex”
Alejandro presented his PhD research to the SDG group about nextgen barcoding of oomycete diversity and its application for plant disease surveillance.  He will be joining our lab later this summer as a postdoc.


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Fungi featured in Nat Geographic blog post

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