News

Postdoc and Student Opportunities

Weʻre recruiting 3 postdoctoral researchers to work on projects funded by the National Science Foundation, and the Gordon and Betty Moore Foundation, two are focused on the diversity, evolution and ecology of Basidiomycete yeasts in Hawaiʻi, and the second is focused on examining the roles of microbiomes in experimental food webs. In all cases, the trainee would have substantial latitude to develop independent lines of inquiry tailored to their specific skillset and interests.

Salary for Postdocs is contingent on experience, but will exceed NIH guidelines. Initial appointment is for one year, with the possibility for renewal.

Potential applicants should contact Anthony Amend Amend@hawaii.edu with a cover letter, CV, and contact information for three references. 

Project 1: Phylogenomics of Pucciniomycotina Yeasts in divergent Hawaiian habitats. 

The main goals of this project are to 1) develop novel and high-throughput isolation strategies to characterize novel yeast diversity from divergent and unusual Hawaiian habitats, 2) examine yeasts in animal guts, and the potential for co-cladogenesis between yeasts and hosts, 3) leverage the environmental heterogeneity of Hawaiian climates to understand the evolution of yeast environmental specificity/generalism, and larger global diversity patterns.

Yeast mutualisms play critical and documented roles in conservation of Hawaiian plants and animals, and there is the opportunity for project personnel to develop conservation research pursuits leveraging yeast systems. We also have ongoing research into yeast degradation of plastics. There are three years of funding for a graduate student, and up to three years of funding for a Postdoc on this project. Graduate students would likely apply via the Botany Department at UHM https://manoa.hawaii.edu/lifesciences/graduate/

• Genomics, phylogenomics, excellent sterile technique, and facility with macro-ecological and biogeographic analyses will be useful for personnel on this project.

Start date for the Postdoc is January 2025, with some flexibility pending circumstances.

Start date for the graduate student is Fall 2025.

Project 2: Developing a marine fungal model system focused on the Basidiomycete yeast Malassezia.

This fungus is frequently detected in marine fungal datasets, and may play a critical role in marine fungal C cycling. Attempts to further understand the ecology and evolution of this yeast have been hindered by the difficulty involved in its cultivation.  The Postdoc on this project will leverage existing visualization and molecular tools to develop novel cultivation and metagenomic strategies to better understand the functional role of this yeast. This postdoc is part of a large collaborative project, and will have the opportunity for extended stays colleagues in Woods Hole, Duke, University of Michigan, and/or University of Washington to participate in training and research activities.  The postdoc will be able to make use of our marine lab, research cruise infrastructure, and global collaboration network to contribute to other pressing questions in marine fungal biology. There are two years of funding for a Postdoc on this project.

• Comparative genomics, fluorescence microscopy, experience isolating fastidious micro-organisms, and microfluidics-engineering/fabrication will serve this researcher well.  

Project 3: Mechanisms of microbial community influence on food web efficiency.

Food webs determine the organization and interaction of life in all terrestrial and aquatic ecosystems. Within food chains, energy is transferred among trophic levels from producers to apex predators in a largely unidirectional and energy-inefficient manner, such that ~90% of available energy is lost to entropy between any two levels. Our earlier work showed that host microbiomes are shaped by food chain hierarchies in a well-studied Hawaiian watershed, and based on these results we developed a simple model food web experimental system based on tank bromeliads in which we have axenic cultures and genomes for mosquito hosts and their microbial symbionts. The postdoc on this project will leverage these tools to understand the genomic/genetic mechanisms underlying microbial constraints on food web efficiency.

• A foundation in genomics, genetics, food web ecology, and microbial community analysis will be important on this project. Familiarity with insects and insect mutualisms would be a bonus.

Start date for the Postdoc is early 2025, with some flexibility pending circumstances.

Summer 2024 Updates!!

So many good things to report!

Let’s start with people… Aloha oe to Bryson and Giullia! And welcome to Postdoc Samira, a recent emigre from the Aime lab at Perdue, and Rayne (who survived our Mycology class this spring), excited to have you both around to help with Bromeliad food web work!

Syrena Whitner is *KILLING* it and received both the MSA Climate Change award AND a travel award to present at IMC in Maastricht.

We had a phenomenal time in Asilomar at the 2nd occasional marine fungi meeting. Having not been to a conference since 2019, it was so great to see familiar faces and catch up on great science. Stay tuned for updates and initiatives from CA.

Lots of fun(gal) updates!

So, it’s been a minute since we’ve updated the website… here’s what you missed.

Big e komo mai to Quinn Moon, Giulia Marenco Di Moriondo, and Reese Tsubota who have stepped in to help with culturing and with our phytoplankton pathogen studies.  Glad you’re here!

Ronja received funding to present at SACNAS in Puerto Rico later this month, depending on the recovery situation there.

Syrena got funding for and presented at the Gordon Conference on Marine Microbes in Switzerland!  

Anthony took a new position in the Pacific Biosciences Research Center, a unit within the School of Ocean and Earth Science and Technology.  The biggest change is that has assumed leadership of the Integrated Center of Environmental Microbiomes and Human Health, a Center of Biomedical Excellence funded by the NIH.  

In funding news, NSF gave the thumbs up on our Rules of Life proposal to study the role of Microbes in food web efficiency and complexity.  This 5 year grant is in collaboration with Nicole Hynson, Peter Sadowski and Matt Medeiros, and will use experimental microcosms to gain a mechanistic understanding of microbial roles in food webs.  We’ve started characterizing Bromeliad invertebrate and microbial communities to build up our understanding of this simple food web. Stay tuned for more on this.

Oh, yeah, we published a bunch of papers, check it out:

Amend, A. S., Swift, S. O., Darcy, J. L., Belcaid, M., Nelson, C. E., Buchanan, J., … & Hynson, N. A. (2022). A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes. Proceedings of the National Academy of Sciences, 119(33), e2204146119.

Read more about this here

Darcy, J. L., Amend, A. S., Swift, S. O., Sommers, P. S., & Lozupone, C. A. (2022). specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. Environmental microbiome, 17(1), 1-12.

Tipton, L., Zahn, G. L., Darcy, J. L., Amend, A. S., & Hynson, N. A. (2022). Hawaiian fungal amplicon sequence variants reveal otherwise hidden biogeography. Microbial ecology, 83(1), 48-57.

Boekhout, T., Amend, A. S., El Baidouri, F., Gabaldón, T., Geml, J., Mittelbach, M., … & Yurkov, A. (2021). Trends in yeast diversity discovery. Fungal Diversity, 1-47.

SO. MUCH. NEWS.

This last year was quite a blur…Here’s what happened:

Departures:

Post-doc Fouad El Baidouri left us for a researcher position with the Neafsy Lab at Harvard/Broad. Gone, but not forgotten! 

Dr. Andre Boraks successfully defended his PhD and is off to work with the International Conservation Fund of Canada.  A hui hou!

Joani Villiunas is heading downhill to work on glowing squid in the McFall-Ngai lab.

Sean Swift has moved on to persue his PhD in the Craig Nelson lab.

Anthony’s on sabbatical through January 2022 

Welcome to the lab:

Undergraduates Bryson Gonzalez, Chloe Twitchell, Max Gatlin and Tyler Stynes have been hard at work isolating marine fungi for our growing culture collection.

Isabel McRae is also helping out for the summer while on break from UCLA. 

Congratulations:

Ronja Steinbach for her NOAA EPP MSI award and for receiving the UH Conservation Award to study marine fungal metabolism of plastics!  Great job!

Danyel Yogi for receivig an NSF REL supplement to fund her continuing work with Marine Malassezia.

Read all about it: 

Boraks, A., Plunkett, G. M., Doro, T. M., Alo, F., Sam, C., Tuiwawa, M., … & Amend, A. S. (2021). Scale-dependent influences of distance and vegetation on the composition of aboveground and belowground tropical fungal communities. Microbial Ecology, 81(4), 874-883.

Egan, C. P., Koko, J. H., Muir, C. D., Zahn, G., Swift, S. O., Amend, A. S., & Hynson, N. A. (2021). Restoration of the mycobiome of the endangered Hawaiian mint Phyllostegia kaalaensis increases its resistance to a common powdery mildew. Fungal Ecology, 52, 101070.

Bernard, J., Wall, C. B., Costantini, M. S., Rollins, R. L., Atkins, M. L., Cabrera, F. P., … & Amend, A. S. (2021). Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. The ISME Journal, 15(4), 999-1009.

Tipton, L., Zahn, G. L., Darcy, J. L., Amend, A. S., & Hynson, N. A. (2021). Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography. Microbial Ecology, 1-10.

Chock, M. K., Hoyt, B., & Amend, A. S. (2021). Mycobiome transplant increases resistance to Austropuccinia psidii in an endangered Hawaiian plant. Phytobiomes Journal.

New monograph by Gerry and others on Holarctic Pluteus

Molecular phylogeny and phylogeography of Holarctic species of Pluteus section Pluteus (Agaricales: Pluteaceae), with description of twelve new species.

Congratulations Gerry!