Postdoctoral Research Associate Position- Doyle Lab, Louisiana State University

The Doyle Lab at Louisiana State University is recruiting a postdoctoral research associate to be involved in a project to understand the role of soil microbiota in the dieback of Phragmites australis along the Gulf Coast and research to develop approaches leveraging native soil microbes for restoration efforts. The postdoctoral research associate will be expected to play a part in designing and conducting field, mesocosm, greenhouse, and laboratory experiments, analyzing data, writing manuscripts, presenting results at meetings and conferences, and mentoring undergraduates. Prior experience with microbiome data collection and statistical analysis is required. Ability to carry out strenuous work in a hot and humid climate in coastal marsh habitats will be necessary. Demonstrated experience carrying out microbiome studies, preferably in the context of plant-soil-microbe interactions, is required. Preference will be given to those with a background in mycology and/or experience working with fungal and bacterial cultures. Excellent interpersonal, oral and written communication skills and a willingness and ability to interact and collaborate with other scientists are essential to the success of the research. A valid Louisiana State driver’s license and ability to drive is required at the time of appointment. A start date in March is preferred.

Please contact Vinson Doyle if you have any questions at: vdoyle@agcenter.lsu.edu

Applications should be submitted here

Mycology Colloquium

Hi there! We are planning to have monthly meetings to highlight and offer opportunities to present research!

We encourage you to volunteer and share your research with us!

Do you want to check the recording of previous Mycology Colloquiums? Check our YouTube channel or check them here!

Submit an abstract, title and other info to the following Google Form and we will get in contact with you!

https://docs.google.com/forms/d/e/1FAIpQLSdaoCtuXZapMIqCy5l67rrzve_ro9qOpx1P8ZeSPFRIJwhW9Q/viewform?usp=sf_link

Bioinformatics Resources

Hi there!

This section will list resources for bioinformatics that we thought might be useful!

If you have additional bioinformatics resources you would like us to share send us an email at students.msa@gmail.com.

1. Introduction to Bioinformatics and Computational Biology

This is a GitHub for the Harvard course of Intro to Bioinformatics and Computational Biology! This resource was set up by: Xiaole Shirley Liu, Joshua Starmer, Martin Hemberg, Ting Wang, Feng Yue, Ming Tang, Yang Liu, Jack Kang, Scarlett Ge, Jiazhen Rong, Phillip Nicol and Maartin De Vries.

2. A ggplot2 Tutorial for Beautiful Plotting in R

This is a tutorial for the ggplot2 package on R. The tutorial was set up by Cédric Scherer, check the following Tweet for more info of the tutorial https://twitter.com/CedScherer/status/1335918784729800704?s=20.

Graduate Student at Whitman Lab

The Whitman Lab at the University of Wisconsin-Madison are recruiting a new graduate student (MS or PhD) to join their Soil Ecology lab starting as soon as summer or fall of 2021!

“Students will work with Dr. Thea Whitman as an advisor to develop a project investigating the effects of wildfires on soil microbial ecology and organic matter biogeochemistry. The ideal candidates would have a strong interest in soil ecology and experience in at least some of the following: field or laboratory research, microbiology, soil science, biogeochemistry, ecology, statistical analyses, or bioinformatics (Python or R).

Students will be enrolled in the Soil Science graduate research program (or can potentially be advised through Plant Pathology, the Microbiology Doctoral Training Program, Agroecology, Environment and Resources, or Environmental Chemistry and Technology) at the University of Wisconsin-Madison, and the position will be a 50% Research Assistantship that will include a stipend of $2,068/month. Health care benefits are included in the appointment. UW- Madison has a strong culture of collaboration across fields, and the selected graduate students will interact with researchers from diverse fields, including microbiology, geography, forest ecology, agronomy, and environmental studies.

Applications should be submitted to twhitman@wisc.edu by February 26, 2021, and include a letter describing your interest in the position, a CV, a record of grades (e.g., copy of transcript), and the name and contact information for three references. Successful applicants will need to apply to the Soil Science graduate program through the UW Madison graduate school and be accepted (requires TOEFL scores (if applicable), official transcripts, and letters of recommendation; does not require GRE scores).”

Check Dr. Whitman’s lab website for more info! https://whitmanlab.soils.wisc.edu/

Research Position with the USDA

About this Position:

This position is with the USDA Forest Service, Northern Research Station (NRS). They are seeking for a Research Biologist with an emphasis on mycology, located in Madison, WI. This is a full-time permanent position and the selected candidate will be eligible for a full benefit package including health/life insurance, retirement benefits, vacation and sick leave.

The position will be part of the Center for Forest Mycology Research (CFMR) in the Northern Research Station (NRS Research Work Unit 16). The CFMR is a nationally and internationally recognized source for mycological knowledge and includes a large fungal herbarium and culture collection. The mission of the CFMR is to advance the science of mycology as relates to high-priority fungi critical for forest health and management. The person selected for this position will be responsible for developing research tools and coordinating research teams that address specific solutions to problems that involve high-priority fungi for restoring or maintaining healthy ecosystems. The incumbent is expected to undertake research that will apply mycology, plant pathology and related fields to benefit the health and resiliency of forest resources. Further, the incumbent will be expected to engage CFMR stakeholders and other researchers to define forest health-related research needs in the CFMR over both short and long terms.

Qualification Requirements

Those who are interested must meet the qualification requirements for the GS-­‐0401 series that is covered by the U.S. Office of Personnel Management (OPM) Qualification Standards for General Schedule Positions–GS-­‐12-­‐0401: Research Biologist. The OPM Qualification Standards Handbook Manual is available for the review at any federal personnel office OR on the Internet at http://www.opm.gov/qualifications/SEC-­‐IV/A/gs-­‐admin.asp. Specialized knowledge of mycology will be needed for this position, with a Ph.D. in a field relating to mycology, such as plant pathology, botany, biology, etc., or equivalent experience.

TO APPLY FOR THIS POSITION:
• Go to USAJOBS https://www.usajobs.gov/
o You must set up or have an existing USAJOBS profile.
o Search/locate the announcement number, once available.
o Select position(s) and location(s) you are interested in and begin the application process.
o You must complete and submit your application by the closing date specified on the announcement.

Check more details at https://msafungi.org/research-position-northern-research-station-madison-wi/

Carolina Piña-Páez

caro - Carolina Piña Páez

Carolina Piña Páez grew up in Hermosillo, Sonora, México. She is currently doing research on the Madrean Sky Islands of Arizona and Mexico. Her advisor is Joey Spatafora. 

Tell us about your project! 

My project combines fieldwork and laboratory experiments to unravel past climate change cycles’ effects on Rhizopogon and their hosts (Pinaceae) in the Madrean Sky Islands of the Southwestern US and Northwestern Mexico. Specifically, I’m studying how Rhizopogon salebrosus has migrated with its hosts and how isolation and environment is shaping its evolutionary trajectory.

What awards would you like to brag about?

I’ve been fortunate to have received scholarships from multiple mushroom societies from North America:

  • 2019 Ben Woo Scholarship – Puget Sound Mycological Society
  • 2019 Anita Summers award – Botany and Plant Pathology, Oregon State University
  • 2018 Oregon Mycological Society award
  • 2018 Sonoma County Mycological Association scholarship
  • 2016-2020 CONACYT scholarship recipient for PhD studies
  • 2013 Henry Pavelek Memorial Scholarship – North American Truffling Society

What are your career goals/plans for after you’re done your current position?

My ultimate career goal is to become a professor at a university. I’d love to teach classes in combination with research and fieldwork.  Probably the next step for me is a postdoc position. I’m particularly interested in how recombination impacts genetic diversity.

What is your favorite fungus and why?

It has to be a truffle! Rhizopogon is the closest to my heart, as it was my first truffle but also it’s the protagonist of my PhD project. Rhizopogon salebrosus sporocarps feed a lot of small mammals in the forest, as well as playing a crucial role in seedling establishment after disturbance (like the fires that the West Coast is experiencing right now).

What is your favorite fact/thing about fungi?

Their ability to survive and acquire food from many different sources. Just think about all the different trophic modes present in the Kingdom Fungi! 

Who is your mycology role model?

Jim Trappe

Any great stories from field work?

In 2018, we were in Mexico sampling truffles and collecting soil for greenhouse experiments.  Tláloc was generous, and we had a great year collecting with more than 200 Rhizopogon specimens found. We isolated some cultures in the airbnb, and the soil samples were triple-bagged— as indicated by the USDA—we had a transportation permit, everything was seemingly in order.  The original plan was that Aldo Saldaña, my friend and collaborator, would take us to the airport in Tucson. When we were crossing the border in Nogales, AZ, there was something wrong with the permit…they said that the samples needed to be sent to El Paso, TX, where they could potentially be destroyed!  I asked if there was a possibility that Aldo could take the samples back to México, buying some time, so we could fulfill the requirement that was missing (a heads up email to the border patrol 22 days prior the border crossing). They allowed Aldo to take the samples back, and problem 1 was resolved! Then, we had to figure out how to get to the airport, since our ride was now going back to Mexico with our samples. We walked to the closest gas station in the pouring rain and we experienced the fury of the monsoon. Finally,  we were able to book a shuttle back to Tucson. Once safe at home in Oregon, I sent the infamous email to the US Customs & Border Patrol Agriculture Specialist. Then a return trip a month later meant that I was able to cross the samples without issue.

What do you like to do in your free time? What are your hobbies?

Cooking is one of my biggest passions, I also enjoy beadwork and to learn new weaving techniques.

Anything else you’d like to share with us?

I’m actively looking for a Post doc position, if you’re looking for a new postdoc, send me an email: pinapaec@oregonstate.edu.

PhD Fellowships Plant Pathology at Purdue University

The Department of Botany and Plant Pathology at Purdue has a new PhD training program in Quantitative Plant Pathology (QP3), funded by the USDA and Purdue Research Foundation. QP3 provides funding for students to earn their PhDs in one of 13 plant pathology labs at Purdue: https://ag.purdue.edu/btny/Pages/researchprofiles.aspx. We are searching for talented students who are eager to make a difference through plant pathology.

Plant pathogens cause over $75 billion in crop loss worldwide and threaten to further impact food supply as climate variability and agricultural intensification worsen.  Plant pathologists need skills to analyze big data, develop epidemiological models, or develop models of plant-pathogen interactions on a cellular and molecular scale. The QP3 program will comprehensively train the next generation of plant pathologists in basic studies of molecular plant-microbe interactions as well as applied areas in disease diagnosis, epidemiology and disease management.

First semester students work in three different plant pathology labs to gain experience prior to choosing the laboratory in which to do their PhD. Students can take coursework across a range of plant pathology and quantitative biology courses and participate in a peer-mentoring program. In addition to scientific training, QP3 provides leadership and internship opportunities to prepare students for a variety of scientific careers. With a range of plant pathology faculty and unique imaging and diagnostic resources, Purdue University is uniquely positioned to offer this innovative doctoral training program.

To be eligible, applicants must have:

1.    Undergraduate GPA higher than 3.0

2.    Experience in plant pathology or plant biology (lab, field, academic or industry)

3.    Letter of recommendation from advisor of plant pathology/biology experience

4.    Not previously enrolled in BTNY graduate program at Purdue

The application deadline for QP3 is Dec. 15. Applicants apply to the BPP department through the Purdue Graduate School: https://www.purdue.edu/gradschool/, and list ‘plant pathology’ as their area of interest.

Questions can be directed to Dr. Anjali Iyer-Pascuzzi, asi2@purdue.edu.

P. cinnamomi Genetics Post-Doc

The Manosalva laboratory at UCR is recruiting for a highly motivated postdoc to work on different projects recently funded by USDA grants to understand P. cinnamomi (Pc) genetic and phenotypic diversity, host adaptation, and to develop molecular diagnostics tools. Phytophthora species’overall economic damage to crops in the United States (US) is estimated to be in the tens of billions of dollars, including the costs of control measures. Phytophthora cinnamomi, a widely distributed devastating soil-borne oomycete pathogen, causes Phytophthora Root Rot (PRR) in over 5,000 plant species including many of importance in agriculture, forestry, horticulture, and nursery industry. Avocado PRR remains the common hindrance to avocado production worldwide. This pathogen affects approximately 60-75% of California (CA) avocado growers causing losses of $40 million annually. Despite the importance of this devastating pathogen, the mechanisms explaining the genetic and phenotypic variability as well as host adaptation are completely unknown. Moreover, the recent identification of fungicide resistant Pc isolates that are also more virulent in avocado argues for the development of new strategies for Pc management.

Description. The successful candidate will lead existing and new projects focused on elucidating the molecular basis of pathogen genotypic and phenotypic diversity by integrating molecular, biochemical, genomic,
transcriptomic, and comparative genomics approaches. The appointed will also oversee the P. cinnamomi lab collection and will also participate in the pathogen yearly surveys with other members of the Manosalva research
team. This candidate will work with and assist US collaborators on the development of isolate/clade/phenotypicspecific DNA- and protein-based diagnostic tools that will allow us to monitor the spread and distribution of more virulent and fungicide resistant isolates as well as to detect the emergence or introductions of new P. cinnamomi isolates, which can be detrimental for agriculture, forestry, natural communities, and biodiversity. This position entails laboratory, greenhouse, and field work. The appointee will analyze data, write progress reports, and publications in a timely manner as well as work and train graduate and undergraduate students in the lab.

Minimum qualifications
• A Ph.D. in plant pathology, microbiology, or related areas.
• Experience working with oomycete or fungal pathogens (basic laboratory culture and greenhouse inoculation methods).
• Demonstrated skills and experience analyzing Next Generation Sequencing data.
• Experience with execution of bioinformatic pipelines for genome and transcriptome sequencing analyses.
• Extensive experience with DNA- and RNA-based techniques including nucleic acid isolation and qPCR.
• Strong publication records.
• Excellent communication and writing skills, since this position involves preparing research progress reports and assisting the PI in publications and grant writing activities.
• Work independently and in a collaborative multidisciplinary environment. The appointee will interact with a big research team of ~14 Co-Project Directors with different areas of expertise including Horticulturist, Plant Pathologist, Plant Breeders, Engineers, Bioinformaticians, Farm Advisors, and Extension Faculties.

Preferred qualifications
• Candidates with dual background in Phytophthora spp. biology and genomics will be strongly considered.
• Experience/knowledge related to plant-oomycete molecular interactions and effectoromics will be a plus.
• Experience working with pathogen diagnostic tools such as mitochondrial haplotypes, qPCR, and recombinase polymerase amplification (RPA) will be a plus.
• Knowledge of Linux and computer programing languages will be a plus.

UCR is a world-class research university with an exceptionally diverse undergraduate student body. Its mission is explicitly linked to providing routes to educational success for underrepresented and first-generation college students. A commitment to this mission is a preferred qualification.

How to Apply/Contact: The position could commence as early as November 1st, 2020 but no later than January 15th, 2021. Screening will start on September 21th and will continue until the position is filled. Salary will be competitive and commensurate with qualifications and experience. Candidates should apply directly to Dr. Patricia Manosalva via email by submitting a single PDF file containing: cover letter and curriculum vitae
(CV) indicating how you meet the minimum qualifications and listing the contact information of three references to patricia.manosalva@ucr.edu. The subject of the email should be “Postdoctoral Scholar in Phytophthora cinnamomi”.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, protected veteran status, or any other characteristic protected by law.

Switchgrass Microbiome Post-Doc

Switchgrass is a cellulosic bioenergy crop that is being tested for performance on non-arable (marginal) lands. We seek an excellent Postdoc to conduct microbiome research to understand the drivers and consequences of switchgrass rhizosphere communities, and to coordinate plant, fungal, and bacteria-based team research activities across labs. The position will be located on the Michigan State University (MSU) main campus (East Lansing), but will frequently travel to execute collaborative projects at MSU’s Kellogg Biological Station (Hickory Corners) and present GLBRC microbiome results at meetings.

Check the following link for information on requirements, application instructions and more https://careers.msu.edu/en-us/job/503845/research-associatefixed-term.

Diversity Advancement Graduate Assistantship

BPP Diversity Advancement Graduate Assistantship 

Oregon State University – Department of Botany and Plant Pathology

“The Department of Botany and Plant Pathology (BPP) is pleased to invite applicants for the BPP Diversity Advancement Graduate Assistantship. BPP provides funding for a graduate assistantship to increase the ethnic and cultural diversity in plant sciences, to promote diversification of the academic environment in BPP and OSU, and to prepare students for their future careers in academics and industry. This assistantship is intended to create opportunities that enhance the inclusion of graduate students from nontraditional backgrounds who have expressed interests in a career in the plant sciences.”

Check information about qualifications, assistantship details, application requirements and deadlines at https://bpp.oregonstate.edu/bpp/botany-plant-pathology-diversity-advancement-graduate-assistantship.

For more information contact the BPP Graduate Studies Committee at 541-737-5362 or Bruce McCone at mccuneb@science.oregonstate.edu.