Tag Archives: fungus

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.

Will you always be able to satisfy that chocolate craving?

Crinipellis_perniciosa_mushroomNPR had a story this weekend on Cocoa plantation collapse and the ecological aftermath of the changes the witches’ broom fungus Moniliophthora perniciosa has wreaked. The genome sequence project for this Homobasidiomycete fungus (also known as Crinipellis perniciosa, phylogenetic relationships discussed by Aime and Philips-Mora 2005) is underway at the Laboratory Genomica e Expressao at UNICAMP, Brazil.  The witches’s broom (not this witches’ broom) is named because of the bristly form it induces in the cacao plants.

The genome project will hopefully improve the diagnosis and treatment work that is needed.  Beyond the insatiable need for chocolate, the NPR story does talk about the impact on farmers, the economy, and the environment with the loss of these cacao plantations.

Some links:

I was also browsing some articles on other fungi that inhabit cacao plants and saw a recent survey that includes fungi that produce mycotoxins.

Amphibian skin bacteria shown to fight off Batrachochytrium dendrobatidis.

A year ago researchers at James Madison University discovered that, Pedobacter cryoconitis, a bacteria first found on the skin of red backed salamanders, was found to prevent the growth of the chytrid B. dendrobatidis, which is currently decimating frog populations.

(Mountain Yellow-Legged Frog from wikipedia)

The newest research on the subject is being presented this year at ASM by Brianna Lam who worked with other biologists from both San Francisco State University and JMU.

Lam’s research indicates that adding pedobacter to the skin of mountain yellow-legged frogs would lessen the effects of Batrachochytrium dendrobatidis (Bd), a lethal skin pathogen that is threatening remaining populations of the frogs in their native Sierra Nevada habitats.

Lam first conducted petri dish experiments that clearly showed the skin bacteria repelling the deadly fungus. She then tested pedobacter on live infected frogs, bathing some of them in a pedobacter solution. The frogs bathed in pedobacter solution lost less weight than those in a control group of infected frogs that were not inoculated.

In addition to the lab experiments, the JMU and SFSU researchers have studied the yellow-legged frogs in their natural habitats and discovered that some populations with the lethal skin disease survive while others go extinct. The populations that survived had significantly higher proportions of individuals with anti-Bd bacteria. The results strongly suggest that a threshold frequency of individuals need to have anti-Bd bacteria to allow a population to persist with Bd. (from Eureka alert)

The research above is really interesting and I am curious as to how the bacteria is actually killing the chytrid. The only other research I can think of where chytrids were being killed was a BBC news article that wrote about scientists bathing frogs in chloramphenicol.

Penicillium marneffei project

P.marneffeiWe’re excited that a Penicillium marneffei grant to Mat Fisher and collaborators has been funded by the Welcome Trust. It includes a collaboration with Bignell Lab at Imperial College, our lab, JCVI, and Univ of Melbourne. This project will explore functional and comparative genomics approaches to studying the fungus which primarily infects immune compromised individuals in south-east asia where it is found associated with bamboo rats

Scientists at Imperial College London have received almost £350 000 from the Wellcome Trust, the UK’s largest medical research charity, to study Penicillium marneffei, the only Penicillium fungus to cause serious disease in humans. The researchers aim to find out what makes this particular fungus pathogenic.

Read the rest of the release.

Trichoderma reesei genome paper published

TrichodermaThe Trichoderma reesei genome paper was recently published in Nature Biotechnology from Diego Martinez at LANL with collaborators at JGI, LBNL, and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol or other biofuels production.  The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production.

The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger number of glucoside hydrolases which is a collection of carbohydrate degrading enzymes great for making simple sugars out of complex ones. In fact, several plant pathogens compared (Fusarium graminearum and Magnaporthe grisea) and the sake fermenting Aspergillus oryzae all have more members of this family than does.  T. reesei has almost the least (36) copies of a cellulose binding domain (CBM) of any of the filamentous ascomycete fungi.  They used the CAZyme database (carbohydrate active enzymes) database which has done a fantastic job building up profiles of different enzymes involved in carhohydrate degradation binding, and modifications.

Whether T. reesei is really the best cellulose degrading fungus is definitely an open question.  That it works well in the industrial culture that it has been utilized in is important, but there may be other species of fungi with improved cellulase activity and who may in fact have many more copies of cellulases.  So it will be good to add other fungi to the mix with quantitative information about degradation to try and glean what are the most important combination of enzymes and activities.

One technical note.  The comparison of copy number differences employed in the paper is a simple enough Chi-Squared, work that I’ve done with Matt Hahn and others include a gene family size comparison approach that also taked into account phylogenetic distances and assumes a birth-death process of gene family size change.  It would be great to apply the copy number differences through this or other approaches that just evaluate gene trees for these domains to see where the differences are significant and if they can be polarized to a particular branch of the tree.

So will this genome sequence lead to cheaper, better biofuel production? Certainly it provides an important toolkit to start systematically testing individual cellulase enzymes. It’s hard to say how fast this will make an impact, but the work of JBEI and a host of other research groups and biotech companies are going to be able to systematically test out the utility of these individual enzymes.

There is also evolutionary work by other groups on the evolution of these Hypocreales fungi trying to better define when biotrophic and heterotrophic transitions occurred to sample fungi with different lifestyles that might have different cellulase enyzmes that may not have been observed. Defining the relationships of these fungi and when and how many times transitions to lifestyles occurred to choose the most diverse fungi may be an important part of discovering novel enzymes.

Also see

Martinez, D., Berka, R.M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S.E., Chapman, J., Chertkov, O., Coutinho, P.M., Cullen, D., Danchin, E.G., Grigoriev, I.V., Harris, P., Jackson, M., Kubicek, C.P., Han, C.S., Ho, I., Larrondo, L.F., de Leon, A.L., Magnuson, J.K., Merino, S., Misra, M., Nelson, B., Putnam, N., Robbertse, B., Salamov, A.A., Schmoll, M., Terry, A., Thayer, N., Westerholm-Parvinen, A., Schoch, C.L., Yao, J., Barbote, R., Nelson, M.A., Detter, C., Bruce, D., Kuske, C.R., Xie, G., Richardson, P., Rokhsar, D.S., Lucas, S.M., Rubin, E.M., Dunn-Coleman, N., Ward, M., Brettin, T.S. (2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology DOI: 10.1038/nbt1403

Podospora genome published

P.anserinaThe genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons among filamentous Sordariomycete fungi. The authors primarily focused on comparative genomics of Podospora to Neurospora crassa, the next closest model filamentous species.  Within the Sordariomycetes there are now a very interesting collection of closely related species which can be useful for applying synteny and phylogenomics approaches.

The analyses in the manuscript focused on these differences between Neurospora and Podospora identifying some key differences in carbon utilization contrasting the coprophillic (Podospora) and plant saprophyte (Neurospora).  There are several observations of gene family expansions in the Podospora genome which could be interpreted as additional enzyme capacity to break down carbon sources that are present in dung.

The genome of Neurospora has be shaped by the action of the genome defense mechanisms like RIP that has been on interpretation of the reduced number of large gene families and paucity of transposons. The authors report a surprising finding that in their analysis that despite sharing orthologs of genes that are involved in several genome defense, they in fact find fewer repetitive sequences in Podospora while it still fails to have good evidence of RIP.

Overall, these data suggest that P. anserina has experienced a fairly complex history of transposition and duplications, although it has not accumulated as many repeats as N. crassaP. anserina possesses all the orthologues of N. crassa factors necessary for gene silencing, including RIP, meiotic MSUD and also vegetative quelling, a post transcriptional gene silencing mechanism akin to RNA interference

I think this data and observations interleaves nicely with the work our group is exploring on evolution of genome of several Neurospora species which have different mating systems. The fact that the gene components that play a role in MSUD and a RIP are found in Podpospora but yet the degree of RIP and the lack of any observed meiotic silencing suggests some interesting occurrences on the Neurospora branch to be explored.  The potentially different degrees of RIP efficiency and types of mating systems (heterothallic and pseudohomothallic) among the Neurospora spp may also provide a link to understanding how RIP evolved and its role on N. crassa evolution.

Senescence in Podospora

Another aspect of Podopsora biology that isn’t touched on, is the use of the fungus as a model for senescence.  The fungus exhibits maternal senescence which involves targeted changes in the mitochondria that leads to cell death.  The evolutionary and molecular basis for this process has been of interest to many research groups and the genome sequence can provide an additional toolkit for identifying the factors involved in the apoptosis process in this filamentous fungi. Whether it will help find a real link for aging research in other eukaryotes remains to be seen, but it is a good model system for some aspects of how aging and damage to mtDNA are linked.

Espagne, E., Lespinet, O., Malagnac, F., Da Silva, C., Jaillon, O., Porcel, B.M., Couloux, A., Aury, J., et al (2008). The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biology, 9(5), R77. DOI: 10.1186/gb-2008-9-5-r77

More RIP without sex?

In followup to the Aspergillus RIP paper discussion, Jo Anne posted in the comments that her paper published in FGB about RIP in another asexual species of fungi also found that evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).

Continue reading More RIP without sex?

RIPing in an asexual fungus

ResearchBlogging.orgA.niger conidiophoreA paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi.  RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae.  However, I think this study is the first to describe RIP in a putatively asexual fungus.  The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium.  A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi.   Continue reading RIPing in an asexual fungus

Ireland’s blight and Puccinia update

Hyphoid logic points out that it is appropriate to discuss about the oomycete Phytophthora infestans on St. Patrick’s Day and mentions a NYT article “The fungus that conquered Europe” that is worth a look.

It is also worth thinking about another blight, well rust, that is spreading through the middle east and could threaten wheat crops worldwide. New Scientist has excellent coverage of Puccinia graminis strain Ug99 which is spreading faster than expected due to a cyclone that spread the rust spores into Iran two years earlier than expected.

Related posts from last year. “Fungus could cause a food shortage”, “Puccinia black stem rust disease spreading”

Ectomycorrhizal fungus Laccaria bicolor genome

Today, I would like to share the news about the publication of the Laccaria bicolor genome. This is the first mycorrhizal symbiotic genome published in the Nature journal. The title is “The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis”.

The team consisteing of more than 60 researchers from 16 institutions have revealed the interaction between plant and fungi.

For complete publication and additional news.