Category Archives: host-microbe

Recent animal-associated fungal genome papers

The genomes of five dermatophyte fungi were sequenced and the analyses of their lifestyles presented in a new paper out in mBio in Martinez et al. 2012. The authors were able to identify gene family changes that associate with lifestyle changes including proteases that can degrade keratin suggesting how these species have adapted to obtaining nutrients from an animal host. The continued finding of fungal-specific kinase families in these fungi, extending the observations from previous studies in Coprinopsis and Paracoccidioides on the FunK1 kinase family, makes me hope we will some day get some molecular information on the specificity of these families in addition to these copy number observations.
Another paper published in Genome Research this summer from Emily Troemel‘s lab and the Broad Institute describes the sequencing of two microsporidia species that are natural parasites of Caenorhabditis.The paper reveals some suprising things about Microsporidia evolution including the presence of a clade-specific nucleoside H+ symporter which is only found in bacteria and some eukaryotes and not in any Fungi. The phyletic distribution suggested it was acquired more recently and couple from lateral gene transfer. This acquisition likely helps the microsporidia cells obtain nucleosides from the host since the parasite cannot synthesize these. There is also evidence of evolution of microsporidia-specific secretion signals in the hexokinases which may be a mechanism for delivery of these enzymes into host cells to catalyze rapid growth once inside the host. Many more gems in this paper including phylogenetic placement of the microsporidia from phylogenomic approaches (also see related recent work from Toni Gabaldon‘s lab).

The superpowers of endophytes

New Scientist has an article entitled “Fungus-powered superplants may beat the heat” on how endophytic fungi from thermotollerant grass – Dichanthelium lanuginosum – can be used to improved drought-, salt-, and cold- tolerance of many other plants including rice. This symbiosis of the endophyte and grass also has additional player in the form of a mycovirus that infects the fungus which we’ve talked about before. The article doesn’t seem to reference any recently published papers but mainly the ongoing work for field trials and the application of these endophytes to speed the adaptations of the plants.

This complicated partnership is a fascinating example of the complex strategies that have evolved among these organisms as part of colonization of new niches. It is also quite likely, they are along for the ride in most plant systems and we are just now beginning to see their diversity and function.

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

Cordyceps on the brain

Cordyceps militaris (Ryan Kepler)I gave a lecture on animal-fungal symbionts and parasites this week so was doing more reading of recent literature on insect-fungi associations. A couple of quick notes worth sharing.

Ophiocordyceps unilateralis was the parasite of the day last week and includes a description of an interesting recent paper looking at the consistency of the symptoms of zombie ants. The article also mentions Carl Zimmer’s post on the same paper in more detail.

You of course have seen the very cool electronic/online Cordyceps monograph at from Joey Spatafora’s lab?

The genome of Cordyceps militaris was sequenced by researchers at the Chinese Academy of Sciences. They find a reduced copy numbers of many gene families suggesting to the authors that the specialized ecology of the fungus may have limited the need for expanded gene families. The do find expanded copy numbers of metalloproteases – a finding we have also seen in human and amphibian associated pathogens as well as by the authors who looked at the insect associated fungus Metarhizium. There is also a reduction in cutinases and genes related to degrading plant cell walls similar to findings in the human associated pathogens Coccidioides suggesting similar genomic routes to specializing on an animal host from a generalist. They also found that this fungus is heterothallic based on genomic identification of the MAT1-1 locus. There are several more interesting findings in the paper including expression profiling of fruiting body via RNA-Seq.
Zheng, P., Xia, Y., Xiao, G., Xiong, C., Hu, X., Zhang, S., Zheng, H., Huang, Y., Zhou, Y., Wang, S., Zhao, G., Liu, X., St Leger, R., & Wang, C. (2011). Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine Genome Biology, 12 (11) DOI: 10.1186/gb-2011-12-11-r116

Microsporidia genomes on the way

New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus.  There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place.  The synteny-based evidence was another way to find a phylogenetic placement for them but it would be helpful to have additional support in the form of additional shared derived characteristics that group Mucormycotina and Microsporidia. There is hope that increased number of genome sequences and phylogenomic approaches can help resolve the placement and more further understand the evolution of the group.

For data analysis, a new genome database for comparing these genomes is online called MicrosporidiaDB. This project has begun incorporating the available genomes and providing a data mining interface that extends from the EuPathDB project.

Dynamics of amphibian pathogen infection cycles
Two papers out this week on the population dynamics and epidemiology of the chytrid pathogen of amphibians, Batrachochytrium dendrobatidis (Bd). This is work from the Vredenburg and Briggs labs that includes several decade-long studies of frog declines and the prevalence of Bd.

See Vance in action swabbing a frog

In the Briggs et al paper, they describe a 5-year study on the fungal load in surviving populations of frogs in Sierra Nevada mountain lakes.  They find that adult frogs that have low enough fungal load escape chytridiomycosis and can actually lose and regain infection. They propose that fungal load dynamics are the reason behind differential survival of various populations of mountain frogs. They conclude that:

“Importantly, model results suggest that host persistence versus extinction does not require differences in host susceptibility, pathogen virulence, or environmental conditions, and may be just epidemic and endemic population dynamics of the same host–pathogen system.”

So they propose that differences in the populations that are coming down with the disease is due only to “density-dependent host–pathogen dynamics” not that some populations are resistant. They go on to provide a detailed model of persistence if the host and pathogen, chance of reinfection, and survival of the host which is derived from the long-term study data.  There are many more interesting findings and models proposed in the paper. It also further reinforces (for me) the need to know more about the molecular basis of the host-pathogen interactions and more about how the fungus persists without a host, lifestyle of how it overwinters, and the details of the microbe-host interactions, and the infection dynamic when zoospores disperse from infected frogs.

The Vrendenburg et al paper adresses the dynamics of population decline in the mountain yellow-legged frogs over a periods of 1-5 and 9-13 year study in 3 different study sites at different sampling intervals.  The authors were able to catalog the species decline and conduct skin swabbing to assess Bd prevalence. They found that the fungus spread quickly as it could detected in virtually all the lakes over the course of a year starting with a 2004 survey. The dramatic declines of frog populations in these lakes followed in the years subsequent to the initial detection. This sadly predicts that most if not all of the mountain lakes will go extinct for the frogs as the current tadpoles develop into frogs in the next 3 years and then fall victim to Bd. Based on their sampling work, the authors were also able to correlate what fungal burden predicted a subsequent decline – in populations where more the ~10,000 zoospores were detected in a swab from frog skin, then the frog population was about to experience a sharp decline.  The take-home from this work is that finding ways to keep the intensity of fungal infections down could provide a meaningful intervention that could prolong the viability of the population.

Briggs, C., Knapp, R., & Vredenburg, V. (2010). Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912886107

Vredenburg, V., Knapp, R., Tunstall, T., & Briggs, C. (2010). Dynamics of an emerging disease drive large-scale amphibian population extinctions Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0914111107