Welcome to the Kennedy Lab!
Our lab is broadly interested in the ecology of plant-microbe interactions. Much of our work has focused on symbioses between forest trees and ectomycorrhizal fungi, but has increasingly involved other groups of fungi as well as bacteria. Our research questions integrate multiple biological disciplines: mycology and microbiology, ecology and evolution, and molecular biology and biochemistry. Though field sampling and experiments along with greenhouse and growth chamber studies, we seek to mechanistically understand how biotic and abiotic factors influence both the structure and functioning of microbial and plant communities.
What's new in the lab?
Three new studies from diverse lab collaborations are published. The first examines the dynamics of fungal necromass decomposition in soil and wood in the boreal forests surrounding Lake Itasca. It is François's first pub as a post-doc in Minnesota and the first publication ever for Erin Andrews, a star undergrad from Kennedy lab - congrats both! The second is a taxonomic analysis of the Pseudoomphalina kalchbrenneri complex in North America. Collections from the IDENT experiment at Cloquet, MN are part of the newly described species, P. anticostica. The final is the result of a large team effort led by Amy Zanne to highlight the value of using a functional trait-based perspective in studies of plant-associated fungi. It introduces a novel database, Fun^Fun, that contains a large number of fungal traits, ranging from gene content to spore coloration.
Peter started his Fulbright fellowship in Medellin, Colombia. He will be working with researchers at the Universidad Nacional de Colombia (Alvaro Duque) and the Universidad de Antioquia (Aida Vasco-Palacios) studying links between below- and abovegroud biodiversity in Colombian forests.
Our multi-year experimental research on the "Gadgil Effect" was recently accepted for publication at New Phytologist - congrats Chris and Craig!
Welcome to Eduardo Perez Pazos and Lang DeLancey - new graduate students in the Kennedy lab. Eduardo is coming from Mexico City, Mexico, where he completed his undergraduate and master's studies at the National Autonomous University (UNAM). Lang, who wil be co-advised with Sarah Hobbie, is coming from the University of Michigan. Both are joining the EBB graduate program.
Our lab's collaboration (and first study!) of arbuscular mycorrhizal fungal communities in the Forest and Biodiversity (FAB) plots at Cedar Creek was published in FEMS Microbiology Ecology - congrats to lead author Jake Grossman (now at the Harvard Forest Arnold Arboretum)!
A number of excellent presentations were made by Kennedy lab members at the 2019 MSA meeting in Minneapolis - great job Lotus, François, and Joe!
Peter began his year-long sabbatical. In Merida Mexico, Peter will be working with Dr. Juan Dupuy Rada at the Centro de Investigacion Ciencia de Yucatan (CICY) studying links between soil fungal and plant community diversity in tropical dry forests (part of a larger collaboration with UMN professor Jennifer Powers).
Toko Mori, an outstanding curatorial assistant in the Bell Herbarium fungal collections, will be moving to Philadelphia, Pennsylvania with her family. She has done a fanatistic job over the last two years of organizing and accessioning hundreds of fungal collections, particularly those of Patrick Leacock and David McLaughlin. Best of luck in your new endeavors Toko!
Lotus successfully defended her Ph.D. with a fantastic public seminar in the Bell Museum of Natural History - so proud of the first Ph.D. to come from the Kennedy lab! Lotus will be starting a post-doc at the University of California Riverside in Jason's Stajich's lab in the fall doing more outstanding genomics-enabled research on fungi.
Craig is the recipient of a DOE-supported graduate student research fellowship to work in the lab of Jennifer Pett-Ridge at Lawerence Livermore National Laboratory this coming fall 2019 and spring 2020. He will be examining the effects of forest mycorrhizal type on fungal necromas decompositon C and N dynamics using a combination of techniques, including NanoSIMS and stable isotope probing (SIP) analyses. Congrats Craig!
The lab gathered to say goodbye to Amanda Certano. Amanda is starting a new position as a research scientist at CoreBiome. Her work as the lab technician over the last three years has been truly outstanding - she will missed dearly, but we all are excited to see her move on to a fantastic new opportunity!
Joe was awarded a second UROP to continue his studies of fungal ecology (this time with lots of mycorrhizal seedling bioassays) in the Kennedy lab - congrats Joe!
Two new grants were funded through the Itasca Biological Laboratories Seed-to-Root Program! In collaboration with Lee Frelich (Forest Resources) and Yue-Hua Hu (Xishuangbanna Tropical Research Institute), Peter will lead the installation of a new 16 ha ForestGeo plot at Itasca. Peter will also be collaborating with fellow PMB faculty member Trinity Hamilton to use on-site long-read sequencing to studying microbial diversity in Lake Itasca and surrounding aquatic environments.
Welcome to François Maillard, who is a new post-doc joining the Schilling and Kennedy labs. François completed his Ph.D. research in France studying organic matter decomposition in forest ecosystems. With dual expertise in microbial community profiling and physiology, François will be working on range of decomposition-related projects co-targeted by the Schilling and Kennedy labs.
Two new papers from the lab have been accepted for publication in Ecology Letters - the first is looking at fungal necromass decomposition dynamics in the SPRUCE experiment and the second examines global patterns of the ecological factors controlling fine root decomposition. A super congrats to the lead authors, Chris and Craig, respectively!
Peter visited Kew Royal Botanical Gardens and gave a talk at the British Mycological Fall Meeting. Walking the still lush grounds of Kew gardens in unseasonally sunny and dry conditions and chatting with all kinds of different scientists was a real pleasure. Many thanks to Martin Bidartondo!
Welcome to Dr. Yue-Hua Hu, a research professor at the Xishuangbanna Tropical Research Institute in China. Dr. Hu is an expert in plant community ecology, but has recently begun working on soil and phyllosphere fungal communities. He will be visiting the Kennedy lab for a full year.
Peter was invited to give a plenary talk at the Mexican Mycological Congress in Xalapa, Mexico. It was a fantastic experience, thanks to Roberto Garibay-Orijel and all the congress organizers!
The genomes of Suillus continue to roll out, including the first species from the host Pseudotsuga - S. lakei. Others that have come out in 2017 and 2018 include S. ampliporus and S. paluster (on Larix) and S. tomentosus, S. subalutaceus, S. bovinus, and S. occidentalis (on Pinus). Really excited to continue our phylogenomics and comparative genomics work with members of the Suillus Consortium. If you are interested in joinng contact Nhu Nguyen.
Luke McCormack is moving to a new position as a staff scientist at the Morton Arboretum in Illinois. Many congrats on the new position - looking forward to seeing your great work continue there.
Lotus and Caroline both won outstanding student poster prizes at the International Mycological Congress for their work on rRNA copy number and microbial distance-decay patterns, respectively. Excellent work - congrats!
Two new papers for the lab are coming out in Soil Biology and Biochemistry. The first is led by Lauren Cline and explores the effect of organic nitrogen addition on fungal community richness and composition in oak and pine forests at Cedar Creek (spoiler alert: it is surprising similar to the effects of inorganic nitrogen). The second is led by Amanda Certano (her first first author paper!) and looks at the decomposition of fungal necromass with contrasting morphologies (diffuse v. rhizomorphic). See the publications page for more details.
A pair of Rhizopogon genomes generated by Amanda Certano and the JGI team have been released - R. truncatus and R. vulgaris. This is an exciting collaboration with Joey Spatafora and Francis Martin as part of the 1KFG: Deep Sequencing of Ecologically-relevant Dikarya project.
Chris Fernandez and Louis Mielke are both moving into new positions at UMN and in Sweden, respectively - the Kennedy lab has been greatly enriched by your collective presence for many years, thanks for everything.
Lotus won a UMN Doctoral Dissertation Fellowship (DDF) to fund the final year of her thesis research - super congrats!!
Louis Mielke returned to the lab to help build a pipeline for getting fungal collections into the Bell Museum herbarium. We have added over 200 new collections since then and are working closely with Patrick Leacock to accesion his many collections from his master's and Ph.D. theses at UMN. Thanks to Toko Mori for fantastic efforts getting Patrick's collections organized.
Joe Gagne was awarded a UROP to study fungal effects on decomposition at Cedar Creek this summer - congrats Joe!
Luke and Peter are starting a new set of projects with a team of researchers at Clemson University to study the effects of mycorrhizal colonization on fine root decomposition - a big thanks to NSF for funding!
Peter visited Norway and got to see both UiO and NMBU - thanks to Havard and Line for a fantastic visit. (Peter also attended the 2018 NEFOM meeting in Uppsala and talked about using open source fungal databases to enhance ecological inference - thanks to Karina Clemmensen and the other NEFOM organizers for the invitation).
Lotus's first thesis chapter on the unusual host associations of Suillus subaureus came out in New Phytologist - well done!
Both Lauren Cline and Erin Andrews will be moving into new positions starting in January. Both of you are amazing scientists - thanks for all of your many contributions to the Kennedy lab!
Our new paper on how melanin in mycorrhizal fungal necromass affects microbial decomposer structure (both fungi and bacteria) is accepted in Journal of Ecology - congrats Chris!
Our commentary of the new paper by Leho Tedersoo and colleagues about the use of PacBio for metabarcoding of fungi is accepted at New Phytologist - congrats Zewei and Lauren!
Lauren, Chris, Craig, Luke, and Caroline all presented at ESA 2017 in Portland, OR. A great showcase of the diversity of research in our lab. Lotus presented her work at ICOM9 in Prague, Czech Republic and was awarded the Harley medal for outstanding student presentation - congrats Lotus!
A sad and happy good bye to two great members of the Kennedy lab - Obi Wamuo and Caroline Daws. Obi was a superstar undergrad in the lab this summer and Caroline was an oustanding first year grad student. All the best at U Chicago and Stanford, respectively.
Just had a great visit for our collaborators in Norway from University of Olso and Norwegian Life Sciences University. Havard, Line, Ynvgild, Luis, and Sunil all visited the SPRUCE site in northern Minnesota and learned Chris' jedi ways with fungal necromass generation first hand.
Our collaboration with the Knights lab comparing closed reference, open reference, and de novo clustering for fungal HTS datasets is accepted at New Phytologist - check it out here. Congrats to Lauren and Zewei on the Kennedy lab side and Gabe on the Knights lab side - a truly team effort.
Amanda is making great progress on generating Suillus genomes - our first from the lab, S. tomentosus, is officially out. A very fun collaboration with Nhu Nguyen (U Hawaii), Sunny Liao (U Florida), and Rytas Vilgalys (Duke U) - thanks NSF!
Lauren's lead on the effects of fungal wood endophytes of decomposer community structure and functioning is accepted at Functional Ecology - congrats Lauren!
Nico Benucci for Michigan State is visiting the lab to help harvest the first round of our truffle competition experiment. Not only is he an expert on truffles, but he is a great cook too! Thanks so much for coming across the lake for a really fun and productive visit.
Our first efforts to do high throughput sequencing with PacBio are submitted to the UMGC - thanks to Chris for his GenoFest win and Ben Auch for lots of help with library prep.
Erin submits a UROP to fund summer research on fungal necromass decomposition - fingers crossed! (March update - UROP funded - congrats Erin, very excited for the summer).
Double congrats to Chris for winning 4 PacBio cells worth of sequencing at the UMGC GenoFest and to Caroline for winning a Crosby fellowship to help cover her field research in summer 2017.
Lotus won "Outstanding Student Oral Presentation" at the MSA meeting in Berkeley this summer - congrats!
Chris and Luke gave presentations at the ESA meeting in an organized oral session of mycorrhizal fungi.
Undegrad and recent grads Michelle, Alex, Eva, Erin, and Louis did lots of excellent research in the lab this summer.
Peter attended a workshop in Santa Barbara focused on building a fungal traits database - stay tuned on updates for that.
It looks FUNGuild is getting more attention as a community resource as evidenced by inclusion talks at both the ESA and MSA meetings (yeah!). 2017 will include greater database coverage - new additions of soft rot fungi and dung saprotrophs this summer - and the linking FUNGuild to the UNITE database.
Collaboration with the Schilling lab at UMN continues - see the lab publications page for the link about functional roles of endophytes as priority wood colonizers!
The first paper of the Suillus-Pinaceae grant is in press at Mycologia - a massive ITS-based Suillus phylogeny - congrats Nhu!
Lots of good stuff happening in the lab recently - a couple of long-term projects just had papers accepted/published (see lab publications page).
Lotus passed her qualifying exam - she is officially onto Ph.D. candidacy!
Michelle Coblens joined the lab as a summer research assistant. She was an undergraduate at Macalester College and is teaming up with Chris on a wide range of fungal ecology projects this summer.
Chris, Louis, and Peter deployed nearly 1000 ingrowth bags into the SPRUCE experiment to look at the dynamics of mycorrhizal fungi necromass decomposition under different global change scenarios.
Chris and Peter got seed grant funding from the Norwegian Centennial Chairs Program to collaborate with Havard Kauserad, Line Nybakken, and Mikael Olson on a new project. Here is the abstract:
This project will investigate how plant-associated symbiotic fungi influence the storage of carbon in boreal forest soils. The work will specifically focus on how changes in soil fertility and climatic conditions influence the decomposition of dead fungal and plant biomass. Researchers at the University of Minnesota (UM), University of Olso (UIO), and Norwegian Life Sciences University (NMBU) will collaborate on a set of field-based observational and experimental studies located in both Norway and the United States. The research will leverage experimental infrastructure present in both countries and involve scientists with synergistic expertise in fungal and plant ecology, ecosystem biogeochemistry, molecular microbial identification, and bioinformatics. Collectively, the project will provide new insights into the role of plant-associated symbiotic fungi in carbon sequestration processes and how changes in resource availability and environmental conditions may mediate the belowground response of boreal forest ecosystems to climate change.
Chris received the Mycological Society of America's Fungal Forest Ecology Post-doc Award to support his current research on the 'Gadgil effect' at Cedar Creek - congrats Chris!
Eva Carlson presented a poser of her UROP project on Quercus fine root morphology at the Univeristy of Minnesota Undergraduate Research Symposium.
Caroline Daws will be joining the lab in the fall as an incoming Ph.D. student in the Ecology, Evolution, and Behavior graduate program - welcome Caroline! Craig See will also be joining the lab as a shared incoming Ph.D. student with Sarah Hobbie in EEB - welcome Craig!
Amanda Certano has rejoined the lab as the technician on the Suillus NSF grant project - welcome back Amanda!
Lauren has just received a NSF post-doc fellowship to study the long-term effects of nitrogen deposition on fungal communities in midwest forests. She will be co-advised with Jessica Gutknecht and use fungal collections at the Bell Museum of Natural History - congrats Lauren!
Nhu has just accepted a tenure-track faculty position at the University of Hawaii - congrats Nhu!
Our collaboration with Francois Rineau and other European colleagues on the protein degradation abilities of ectomycorrhizal fungi was accepted for publication at Applied and Environmental Microbiology. Here is the .pdf - congrats Francois!
Chris' review on the decomposition dynamics of ectomycorrhizal fungal necromass is now out in Soil Biology and Biochemistry. Nice work Chris - excited to launch new necromass work at SPRUCE and beyond.
Eva Carlson won a UROP award to work with Luke, Matt Kaproth, Jeannine Cavender-Bares, and Peter examining variation in root traits across a diverse suite of temperate and tropical Quercus species - congrats Eva!
The book Mycorrhizal Networks has been published, which contains a chapter by Peter, Jen Walker (former post-doc) and Laura Bogar (former undergraduate student) on the ecology of non-networking hosts. In our chapter, we focused on Alnus-Frankia-ECM interactions and if you are unfamiliar with the lab's previous work on the topic, this chapter is a good summary.
Lots of good stuff. Lauren Cline joined the lab as a post-doc - welcome Lauren! Two visiting scholars are also working with the lab - Drs. Luke McCormack and Ying Han. Excited to have both at UMN. The 'Gadgil Effect' review paper lead by Chris was published. Click here to read it. Just a few weeks later, Peter's collaboration with researchers at Oregon State University and the University of British Colombia on vertical niche partitioning among ectomycorrhizal fungi was published. Click here to read it.
Many members of the lab attended ICOM and gave both oral and poster presentations - well done Lotus, Chris, and Nhu!
FUNGuild (an open-access and open-annotation tool to parse community fungal datasets into ecological guilds) is out and in press - click here for the publication.
Congrats to undergrads Louis M, Cher Ling T, and Léonce S-N for successful poster presentations. Lotus received an NSF-GRFP! Congrats Lotus!! Nhu just published a paper on maximizing ecological signal vs. noise in high throughput sequencing datasets. Read it here. Chris just published a commentary in New Phytologist about moving fungal ecology beyond the black box. Read it here.