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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Highlights from the 13th European Conference on Fungal Genetics

Screen Shot 2016-04-11 at 4.13.49 PM

April 1-6 – 13th European Conference on Fungal Genetics, Paris, France
Just returned from a very stimulating meeting with 800 European fungal biologists at ECFG13.  How can anyone refuse a chance to visit Paris and hear about the latest breaking advances in fungal genomics?  Sunny, Jessy, Greg and I all presented at the congress, and had a chance to meet up with our european colleagues including several former lab members.  And see a little of Paris!

This meeting was held at the Cité des Sciences et de l’Industrie Congress Center of La Villette, located in northeastern part of Paris.  Meeting highlights included outstanding plenary talks by Regina Kahmann (fungal effector biology), Bernard Dujon (yeast genome evolution), and Paola Bonfante (bacterial endosymbiosis in fungi).

At the ECFG13, I was invited to speak at the contributed session on ecological and population genomics of fungi.  Members of our lab also organized a pre-meeting workshop on fungal bacterial interactions and presented several posters.  The abstracts are below

Presentations by the Vilgalys lab at the 13th European Fungal Genetics Conference, Paris, 3-6 Apr 2016

VILGALYS Rytas, LIAO Hui Ling, BONITO Gregory, HAMEED Khalid, GRIGORIEV Igor, SCHADT Christopher, LABBE Jessy, TUSKAN Gerald, TSCHAPLINSKI Timothy, MARTIN Francis
Metagenomic study of plant-fungal interactions between Populus trichocarpa with its rhizosphere fungi
A highly diverse community of fungi occurs within roots of forest trees that includes beneficial (mycorrhizal) mutualists, saprophytes, pathogens, and other guilds whose function is unknown. Several species of endophytic fungi have been found to have a growth-promoting effect on Populus and other plant hosts, though the molecular bases of these effects still are not fully understood. Genome sequencing and targeted metatranscriptome experiments are being undertaken for a key set of Populus root-associated fungi to aid in the understanding of mechanisms involved in plant-fungal interactions. We interrogated the ecological function of two fungal species Mortierella elongata PMI93 and Ilyonectria europeae PMI82 using metagenomic approaches including RNAseq, metabolomics, and proteomics. P. trichocarpa plants were grown from cuttings and inoculated using forest soils (soil bioassay) and also individually inoculated with either PMI93 or PMI82. After 3 months growth, comparative metatranscriptomics reveal that both PMI93 and PMI82 are both most active in the rhizosphere (rhizophytic activites) versus the root systems (endophytic activities). Gene profiles of P. trichocarpa roots showed significant changes in response to inoculation with M. elongata PMI93 but not to Ilyonectria PMI82. Inoculation with M. elongata was found to alter plant-environmental interaction and cell signaling, altering the predominant plant genes for nutrient uptake, extracellular secreted proteins and plasma membrane receptor activities, receptor/kinase transduction followed by transcriptional regulation. Up regulation of genes for specific nutrient hydrolysis/uptake and growth promotion, and down regulation of genes for LRR-receptors/kinases, strongly suggest that M. elongata manipulates plant defense to equilibrate the energy resource for plant growth. The functional activity of Mortierella and Ilyonectria in the root and soil systems will also be discussed.

Transcriptome sequencing sheds light on host-symbiont interactions between zygomycete Mortierella elongata and endosymbiont C. Glomeribacter sp.
Several research groups have recently investigated the ubiquity and dynamics of bacterial endosymbionts living inside of fungal cells. There are a few studies on fungal hosts belonging to Asco- and Basidiomycota, however, the best-studied examples of endosymbiosis in fungi are from plant- associated zygomycetes. Best studied in the Arbuscular Mycorrhizal (AM) fungi, these endosymbionts are thought to be obligate, long-term residents of the intracellular environment where they may contribute to both fungal and plant health, although the direct or indirect nature of these interactions remain has yet to be experimentally evaluated. We isolated a strain of Mortierella elongata AG77 (Zygomycota, Mucormycotina, Mortierellales) from the rhizopshere of Populus deltoides. We found that M. elongata AG77 harbors a strain of Candidatus Glomeribacter sp., and we have assembled and annotated genomes for both the host fungus and its resident endosymbiont. The genome of C. Glomeribacter sp. is similar to other publicly available genomes, but also has unique features potentially suggesting distinct functionality. In an attempt to understand the nature of the interaction between fungal host M. elongata and endosymbiont C. Glomeribacter sp. we used an antibiotic treatment to create a strain cleared of endosymbiont populations for comparative studies. Here we present comparative host fungal transcriptomes in the presence and absence of obligate endosymbiont C. Glomeribacter sp. The following questions were addressed through this work: Does endosymbiont presence affect fungal host functioning? Do host-endosymbiont dynamics of Mortierella-Glomeribacter differ from those of the obligate plant associated AM fungus Gigaspora- Glomeribacter?

LIAO Hui-Ling, CHEN Yuan, BRUNS Tom D., PEAY Kabir G., TAYLOR John W., BRANCO Sara, TALBOT Jennifer M., GREGORIEV Igor, BARRY Kerrie, HOYT David W., NICORA Carrie D., PURVINE Samuel O., CHEN Ko-Hsuan and VILGALYS Rytas
Common and unique (host-specific) genes involved in ectomycorrhzal symbiosis between Pinus and Suillus
Suillus species are members of the boletes (Suillaceae) that form host-specific ectomycorrhizal (EM) associations with conifer tree species in the family Pinaceae. Suillus species play critical roles in the function of forest ecosystems by providing their plant hosts with resources as well as protection from pathogens in exchange for plant-derived sugars. Our research aims at understanding of coevolution and genomics between plants and mutualistic fungi of Suillus. We investigated the genetics of EM symbiosis and host-specificity by cross-inoculation of different Pinus hosts with basidiospores of different Suillus species with varying natural host ranges. We assessed the outcome of these interactions using comparative genomics, metatranscriptomics, metabolomics and proteomics. Several Suillus spp. including S. granulatus, S. pictus, and S. americanus readily form ectomycorrhizae (compatible reaction) with plant hosts belonging to Pinus subgenus Strobus (P. strobus and P. monticola), but were incompatible with other ‘2-needle pine’ hosts belonging to subgenus Pinus (P. taeda, P. banksiana). Meta0mics of inoculated roots revealed that both plants and fungi express distinctive responses during incompatible vs. compatible mycorrhizal pairings. Using RNA-Seq, we identified common and unique patterns of plant-fungal gene expression for compatible/incompatible Pinus-Suillus pairings. Compatible mycorrhizal interactions are further characterized by distinct metabolomic signatures for trehalose, mannitol and arabitol. Functional annotation of highly expressed genes reveals that the Suillus-Pinus respond via similar highly conserved gene regulatory networks involving coordinated responses by both fungal and plant genomes, including G-protein signaling and secretory pathways. Pinus spp. activate a core set of gene products that mediate Suillus-specific recognition, including leucine-rich repeat and pathogen resistance proteins. We are developing the Pinus-Suillus symbiosis as a model for understanding plant-fungal communication and other aspects of EM function. Current studies employ full genome analysis, transcriptomics and metabolomics to investigate molecular mechanisms of EMF-plant co- evolution.

BONITO Gregory, HAMEED Khalid, BUSBY Posy, BENUCCI Gian Nm, TUSKAN Gerald, SCHADT Christopher, VILGALYS Rytas
Using common gardens to study effects of soil origin and host genotype on the Populus and Pinus root mycobiome
Populus is a model woody plant species important ecologically as a pioneer and economically as a biofuel and fiber crop. Nutrition and aboveground biomass of Populus is largely dependent upon belowground root growth and interactions with ectomycorrhizal, arbuscular mycorrhizal and endorrhizal fungi, as well as prokaryotic organisms and other soil fauna. Our research utilizes trap- plant experiments and characterizes fungal communities through next generation amplicon sequencing. In this experiment we chose a panel of Populus trichocarpa DOE-BESC reference genotypes, selected on account of their productivity, lignin type, lignin content, and geographic origin. Cuttings were grown in triplicate in soils collected from four common garden sites in the Pacific Northwest, a natural Populus soil from NC and in sterile sand as control group. Plants were grown for 5 months and then roots were harvested, washed, and fungal communities were characterized by MiSeq amplicon sequencing of the ITS & LSU rDNA. Y-diversity of fungal communities on BESC reference genotypes shows strong biogeographic structuring. Uninoculated control plants were significantly shorter in height (P<0.01) and their microbiome consisted of fewer taxa. Fungal community similarity on Populus roots grown in different soils follows a decay by distance model, although some root-assocated fungal taxa are widespread geographically. Host species and genotypes may influence fungal and bacterial community structure in a context dependent manner, and although particular host-genotype x fungal species interactions were documented, these were most pronounced in soils harboring higher fungal biodiversity and were not related to any particular preselected host character.

STAJICH Jason, SPATAFORA Joseph, GRIGORIEV Igor, MARTIN Francis (4), HENRISSAT, Bernard, 1000 FUNGAL GENOMES PROJECT consortium (including V lab members)
Genome evolution in early diverging fungi from the 1000 fungal genomes perspective
Transitions in morphological complexity, trophism, and lifestyles have occurred throughout the evolution of the fungal kingdom. To examine these changes in the context of genomic changes requires a well-resolved phylogeny of the fungi and a dense sampling of reference genomes. We have made efforts to improve the available diversity of fungal genomes through the 1000 fungal genomes project (1KFG; http://1000.fungalgenomes.org) and other efforts. The first analysis of 350 of these genomes has been use to construct a resolved phylogeny of the fungi with new understanding of the early branching zoosporic (chytrid) and zygomycete fungi. We find support for multiple, early diverging lineages that include zoosporic fungi, two clades of the zygomycetes we have named Zoopagomycota and Mucoromycota which show long standing symbioses with animals and plants respectively. The arbuscular mycorrhizal fungi (Glomeromycota) group with strong support within the Mucoromycota not as separate lineage. Comparison of gene content to reconstruct changes that lead to emergence of complex multicellular forms reveal the likely complex ancestor of the Dikarya fungi. We also examined the multiple evolutionary losses of the flagella inferred from the phylogeny and how that compares to the loss or retention of genes necessary for the flagellar complex and we identify additional genes that show similar retention patterns.


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Postdoctoral position (FILLED): plant-fungal symbiosis and evolution

The Vilgalys Mycology Lab at Duke University seeks a postdoctoral researcher in the area of plant-fungal symbiosis and evolution.  The selected candidate will contribute to ongoing studies on ecology and evolution of forest soil fungi and their interactions with trees including Populus, Pinus and other species.  We are especially interested in linkages between phylogenetic diversity, population structure, and molecular functioning of forest fungi, including their effects on ecosystem processes.

Major Duties/Responsibilities: Design, conduct and interpret laboratory and field based research; lead and contribute to the development of scientific manuscripts and proposals. The postdoc chosen for this position will also have opportunities to interact with collaborating institutions in the US and abroad.  Research is facilitated by state-of-the-art equipment/facilities for microbiology, molecular biology, and genomics, in a professional environment with excellent technical support.

Qualifications Required: Ph.D. degree in mycology, molecular ecology, phylogenomics, or related fields. Applicant should have demonstrated expertise in modern molecular ecology methods including quantitative PCR, DNA sequence analyses, phylogentics, as well as working with the informatics tools for microbiome and metagenomic studies. Demonstrated expertise must include a track record of peer-reviewed publications.

Qualifications Preferred: Priority will be given to applicants with a successful history of interdisciplinary, integrative, and innovative research in this area. Interested applicants should send a cv, research statement, and names of 3 references (preferably in a single pdf) to Dr. Rytas Vilgalys, fungi@duke.edu.   The position is available immediately and will remain open until a suitable candidate has been hired. For more information on the Vilgalys Lab see: http://sites.duke.edu/vilgalyslab/

update Apr 2016:  this position has been filled.

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MASMC 2016 conference at Penn State University April 22-24, 2016

This year’s Middle Atlantic States Mycology Conference will be hosted by the Dave Geiser lab at Penn State University on April 22-24.  MASMC is an annual gathering of mycologists from around Eastern North America (not just the Mid-Atlantic). It is informal, fun and a great opportunity for people (esp. students) to present research results/plans in a relaxed atmosphere.  There will be talks, poster presentations, a tour of Penn State’s world-renowned Mushroom Research Center, a morel hunt, and other fun activities.

Go to masmc2016.wordpress.com and follow @masmc2016 on Twitter for more details!

Contact David Geiser at masmc2016@gmail.com if you have any questions.

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Feb 9: Genetics seminar by Jason Stajich

Just wanted to bring everyone’s attention to the following seminar by Jason Stajich.  Jason is an asst professor at the Univ. of California at Riverside, did both his undergrad and PhD at Duke on comparative fungal genomics.

“Genome evolution in early branching fungi: exploring genomic consequences of changes in lifestyles and morphology.”

Jason Stajich, UC Riverside, Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology

12:30 PM – 1:30 PM; Nanaline Duke 147

Sponsored by University Program in Genetics & Genomics (UPGG)

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Jan 26: Suilloposium!! combo visit by Nhu Nguyen and Peter Kennedy

In January, we hosted a visit by Peter Kennedy and Nhu Nguyen, who with Sunny Liao are coPIs on our recent NSF grant to assemble the first ever genome-based phylogeny for the genus Suillus (see Research Page for more details about the project).   During their visit,  we discussed grant objectives and made plans for future work on this project.  (Update – March 2016 – Congratulations to both Nhu Nguyen and Sunny Liao who both recently accepted faculty positions- Nhu at U of Hawaii, and Sunny at U of Florida! We’re all very excited for their future and the prospects for further work on Suillus.Slide1

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MASMC 2015 a success

Check out the program and highlights from last week’s MASMC&mf conference*.

*MASMC&mf = Middle Atlantic States Mycology Conference (and morel foray)

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Wanted: Undergraduate Assistant –  Genetics of plant-fungal interactions

We have an opening for a part time research assistant to help with several projects on interactions between plants (roots), fungi, and bacteria.  We are using molecular-based methods to study interactions between symbiotic fungi with with native tree species (pines, oaks, and cottonwoods).  Duties include assisting 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 for summer, and may be extended to include the academic year.  More information about the lab and our research is at http://sites.duke.edu/vilgalyslab/

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, fungi@duke.edu. Interviews will begin immediately until the position is filled.


Contact: Rytas Vilgalys (Biology Department), fungi@duke.edu


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2015 Asilomar Fungal Genetics Meetings

Many excellent presentations and great weather at this year’s Fungal Genetics Meetings (March 17-22, 2015).  Here’s a link to the program and abstracts,  and a  link to the #fungal15 twitter feed.  The meetings were well-attended by current and former Duke mycologists.  Some of my highlights included
-opening plenary session talk by Duke’s Nick Buchler on evolution of cell cycle regulation in fungi
-Fungal Biodiversity session chaired by Georgiana May and Linda Kohn, featuring talks by members of the Lutzoni lab
-Contributed session on Environmental Transcriptomics chaired by Cheryl Kuske and myself, and featuring talks by Sunny Liou and Greg Bonito
-sneaking out with the lab group to visit Point Lobos State Park


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