Category Archives: microbe

NSF Poststdoc opportunity for Research using biological collections

Earlier this year the NSF released a postdoc opportunity for research to use Biological Collections. In particular these can be strain collections and stock collections. The US Culture Collection Network is a Research Coordination Network which brings together many collaborating culture collections. You can find many of the U.S. living collections there include fungal centers like the Phaff Yeast Collection and Fungal Genetics Stock Center. The Gilbertson Mycological Herbarium at U Arizona under Elizabeth Arnold‘s leadership has developed a rich collection of endophyte fungi which would be another excellent environment to work with these resources. Kyria Boundy-Mills who is the curator of the Phaff collection has also expressed interest in either hosting or helping working with a postdoc on this. There is tremendous biodiversity of the fungi available in these and other culture collections so seems like a great chance to tap into these.
This would be a great opportunity to link work in the 1000 Fungal genomes project and sampling from culture collections (not just sequencing, but growing and characterizing growth, carbon source utilization and integrating that with predictions made from genome comparisons). If this is something interesting to you – do get in touch with some of the curators at these collections, but also my lab and I expect many other labs would be interested hosting someone to work on these questions that take advantage of these living collections of fungi.
Proposals are to be submitted by potential post docs. Submitter must be a US citizen or US permanent resident. The next deadline is November 3, 2015Funding total for the program is $8 million, 40 awards anticipated, up to two years. Here’s some key text from the solicitation:

Competitive Area 2. Postdoctoral Research Fellowships Using Biological Collections.

Biological research collections represent the documented scientific history of life on Earth, and the U.S. museum community alone curates over a billion specimens ranging from bacteria to plants, insects and vertebrates, as well as fossils. Across the globe, collections represent critical infrastructure and support essential research activities in biology and its related fields. Scientists, government agencies, industry and citizens utilize collections to document and understand evolution and biodiversity, study global change, formulate advice on conservation planning, educate the general public, improve interactions between sciences, and devise new practical applications from science to every day life. New technologies supported by NSF in digitization, such as the Advancing Digitization of Biodiversity Collections (ADBC) program, are making collections and their associated data, whether they are physical specimens, text, images, sounds, or data tables, searchable in online databases. Despite this clear progress in improving access to physical specimens and their associated metadata, collections remain under-utilized for answering contemporary questions about fundamental aspects of biological processes. Thus, collections are poised to become a critical resource for developing transformative approaches to address key questions in biology and potentially develop applications that extend biology to physical, mathematical, engineering and social sciences. This postdoctoral track seeks transformative approaches that use biological collections in highly innovative ways to address grand challenges in biology. Priority may be given to applicants who integrate biological collections and associated resources with other types of data in an effort to forge new insight into areas traditionally funded by BIO. Examples of key questions in biology of interest include, but are not limited to, links between genotype and phenotype, evolutionary developmental biology, comparative approaches in functional and developmental neurobiology, and the biophysics of nanostructures. Using collections as a resource for grand challenge questions in biology is expected to present new opportunities to advance understanding of biological processes and systems, inspiring new discoveries in areas with relevance to other disciplines with overlapping interests in biological systems. Applicants must document access to the selected collection(s) in the research and training plan.

Few fungi+host papers

Three papers on some cool fungi that interact with hosts and I recommend them for a good read.

One is coverage of by Ed Yong on rice blast (Magnaporthae orzyae) on paper from Nick Talbot and Gero Steinberg‘s lab on appressorium development in Science this week.

A paper from my lab on role of an expansion of copy number of a chitin-binding domain in the amphibian pathogen B. dendrobatidis.

New Scientist also provides a nice summary of tripartite symbiosis paper on Metarhizium, insects, and plants from Mike Bidochka’s lab.

Fear of Fungi!

The cover of Nature today highlights an article from Matthew Fisher and colleagues on the major impact that Fungi as emerging infectious diseases are playing on threatening diversity of ecosystems and agricultural productivity.

Fisher, M., Henk, D., Briggs, C., Brownstein, J., Madoff, L., McCraw, S., & Gurr, S. (2012). Emerging fungal threats to animal, plant and ecosystem health Nature, 484 (7393), 186-194 DOI: 10.1038/nature10947

Still time to sign up for EMBO Comparative Genomics meeting

[via Teun Boekhout]

This year looks like another great lineup of speakers for the EMBO Comparative Genomics of Microorganisms: ‘Understanding the Complexity of Diversity’ 15-20 Oct 2011 Sant Feliu de Guixols, Spain.

Andrew Allen J. Craig Venter Institute US
Anders Blomberg Göteborg University SE
Chris Bowler École Normale Supérieure FR
Gertraud Burger University of Montreal CA
Bernard Dujon Institut Pasteur FR
Toni Gabaldón CRG, Barcelona ES
Ursula Goodenough Washington University US
Michael Gray Dalhousie University CA
Joseph Heitman Duke University US
Christiane Hertz-Fowler University of Liverpool UK
Regine Kahmann Max Planck Institute DE
Patrick Keeling University of British Columbia CA
Nicole King UC, Berkeley US
Edda Klipp Humboldt University DE
Veronique Leh Louis University of Strasbourg FR
Jan Pawlowski University of Geneva CH
Jure Piskur Lund University SE
Tom Richards University of Exeter UK
Andrew J. Roger Dalhousie University CA
David Roos University of Pennsylvania US
Iñaki Ruiz-Trillo University of Barcelona ES
Joseph Schacherer University of Strasbourg FR
Artur Scherf Institut Pasteur FR
Joey Spatafora Oregon State University US
Nicholas Talbot University of Exeter UK
Kevin Verstrepen University of Leuven BE
Eric Westhof University of Strasbourg FR
Patrick Wincker Genoscope FR
Ken Wolfe Smurfit Institute of Genetics IE
Alexandra Z. Worden University of California US

Some comments from former participants:

Comments from 2009 meeting

Overall rating

Based on responses from 80% of participants:

Excellent 50%; Very Good 44%; Good 6%.



It is hard to improve the meeting. It’s a good mixture of conference and workshop with a lot of input from expert of adjacent field.

I strongly support the idea the meeting is organized in the future at a regular basis.

Very high quality, open minded with presentations ranging from pure genomics to implementation in the field of ecology; plenty of novelties. Plenty of time to discuss and to establish potential collaborations

I hope to have the possibility to go in the future to this meeting. We learn a lot, and also the size is well, the students have the possibility to talk of discuss with senior

Great work!

Thanks to the organizers for an extremely interesting and productive meeting.

Great meeting. This is a unique meeting because it brings together a group of scientists that dont normally interact with each other. Thus, great opportunities for cross-interactions. This meeting has the potential to fill a very unique niche. I enjoyed meeting new people from diverse fields. I plan to attend again and encourage my colleagues to do so.

This meeting was a great match to my interests but also challenged me to think outside of my normal sphere.  I applaud the organizers and the participants in making this a useful meeting.

The meeting was very well organized and at a very good location. I enjoyed it very much.

I hope this meeting continues as it was a valuable forum for the field of comparative genomics.

This meeting is unique in its broad organism focus. Please keep supporting it.

Origins and evolution of pathogens An article in PLoS Pathogens by Morris et al describe a hypothesis about the evolution and origins of plant pathogens applying the parallel theories to the emergence of medically relevant pathogens. The authors highlight the importance of understanding the evolution of organisms in the context of emerging pathogens like Puccinia Ug99 for our ability to design strategies to protect human health and food supplies.  Both bacterial and fungal pathogens of plants are discussed but I (perhaps unsurprisingly) focus on the fungi here. Continue reading Origins and evolution of pathogens

New species of Cryptococcus found in seawater

A paper in IJSEM describes a new species in the Cryptococcus basidiomycete yeast lineage. The name is proposed as Cryptococcus keelungensis sp. nov. for a strain isolated from the sea surface microlayer. Its identity as a Cryptococcus sp was determined by sequencing of 26S rDNA D1/D2 and ITS loci and molecular phylogenetics. This is quite diverged from the human pathogen Cryptococcus neoformans and C. gattii as the new species falls in the order Filobasidiales while C. neoformans is classified in the order Tremellales. Interestingly, based on the phylogeny in the paper it seems to be relatively close to newly discovered Cryptococcus himalayensis.

See also:

C.-F. Chang, C.-F. Lee, S.-M. Liu (2008). Cryptococcus keelungensis sp. nov., an anamorphic basidiomycetous yeast isolated from the sea-surface microlayer of the north-east coast of Taiwan INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58 (12), 2973-2976 DOI: 10.1099/ijs.0.65773-0

Bats beware of white nose

An outbreak of a fungal infection called “white-nose syndrome” is killing bats in the Northeastern US.  This New Scientist article mentions the outbreak briefly and an NPR story and recent Boston Globe story also gives it some coverage.  Sounds like we still don’t know much about the causal agent or how it is killing the bats at this time, but some researchers, including Elizabeth Buckles at Cornell University, Vishnu Chaturvedi at NY State Dept of Health, and Jon Reichard at Boston University are working on it.

This is of course old news if you read what Hyphoid Logic has been saying.

That there is a previously undescribed cold loving fungus sounds very interesting, there have been some recent discoveries of psychrophilic fungi like Cryptococcus laurentii and Rhodotorula himalayensis so it would be interesting to learn more when the researchers publish some of these results.

Some more links

Thanks Kathyrn B for reminder about this story.

Phytophthora work highlighted

A link to the story about Matteo Garbelotto‘s work on Phytophthora ramorum and showing that the source in California is likely from ornamentals from a nursery. The work is to appear soon in Molecular Ecology but alas is not available yet.

A recent paper on updated Phytophthora phylogeny from Jamie Blair and co-authors is also out in FGB. They used genome sequences to determine additional markers for multi-locus sequencing and then sequenced and built trees from 82 taxa. 

Some links

I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., Dölz, F., Telle, S., Wöstemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterial–fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

Tracking honeybee decline

HoneybeeAn early access to article in Science A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder (direct link since DOI is not updated yet) using the current favorite buzzword, metagenomics, of course, describes some early work to try and discover what is killing the honeybees. It is early access and non-free and ScienceExpress is not part of our subscription here so I’ve not actually had a chance to read it yet, but the gist of the reporting about it suggest that a virus is to blame. This is in line with what Joe DeRisi and collaborators found using their Virus chip based on some news reports earlier this year, but no scientific article yet to follow this up.

Some links to today’s SFChronicle article and an article “Stung” from the New Yorker in August that alluded to this Science article.