Archive for August, 2012

Back to the Future

August 24th, 2012

I’ve tried to keep this blog reasonably up to date, but I am falling behind. I have said yes to too many things. I’ve tons of news on our projects in fungal genomics that may be of interest to you. I’ll do my best to cope with my backlog over the next few weeks. Let’s start with one of our consortium paper recently published investigating the evolution of the wood decay machinery in forest fungi. An exciting blend of comparative genomics and paleomycology.

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes by Floudas et al. (2012) Science 336: 1715-1719

This is the first paper arising from the JGI Saprotrophic Agaricomycotina Project (SAP). It was published in Science on July 29, 2012. Together with the JGI Mycorrhizal Genome project, the SAP project is aiming to reconstruct the evolution of two major lifestyles, saprotrophism and mutualism, in Fungi. This paper is the first account of a large-scale JGI project, lead by David Hibbett (Clark University), reporting twelve new genomes and involving 71 authors from 13 countries. As mentioned by one of the referee: “this manuscript epitomizes the modern publishing era where a one-hundred page supplement presents most of the information in a dry and matter-of-fact tone, while an extremely well-written and exciting summary functions primarily to advertise its findings to a broad audience“. It truly represents an integrative effort ably deploying the methodologies from multiple disciplines to draw exciting conclusions in fungal evolution.

The Wood Decay Machinery. Plant lignin and (hemi)cellulose are the most abundant biopolymers in terrestrial ecosystems. Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. Fungal-mediated degradation of wood lignocellulose is thus a critical link in the environmental carbon cycle, and is of great economic interest for its potential applications in lignocellulose bioconversion, biofuel production and feedstock improvement. Saprotrophic Agaricomycotina are active and abundant degraders of this lignocellulosic biomass. Two principal modes of decay occur in the Agaricomycotina, termed white rot and brown rot. White rot fungi are capable of efficiently degrading all components of plant cell walls, including the highly recalcitrant lignin fraction. Brown rot fungi modify but do not appreciably remove the lignin, which remains as a polymeric residue following removal of cellulose and hemicellulose. Brown rot residues are highly resistant to further decay and contribute to the fixed carbon pool in humic soils, particularly in cool-temperate and boreal, conifer-dominated ecosystems. Brown rot fungi thus play a significant role in terrestrial carbon sequestration.

Some historical background. In March 2010, we proposed the SAP to the JGI community-based sequencing program for whole-genome sequencing of a suite of wood decayers in the subphylum Agaricomycotina. The principal criteria for target selection included: phylogenetic diversity, functional diversity, ecological importance, availability of (homokaryotic) mycelial cultures and community interest. We proposed a suite of 30 species divided into three Tiers of ten species each. As of today, the genome sequences of >20 species have been released and are used in comparative studies that illustrate the diversity and evolution of wood decay strategies. Comparisons of these multiple genomes enables determination of the essential components of white- and brown-rot decay mechanisms reported in the Science paper. Amazingly enough, JGI teams have been able to sequence and annotate all these genomes in about two years … and the Consortium has been able to mine this massive dataset to generate the paper findings in less than one year thanks to David and Igor’s efficient coordination.

The Major Findings. Comparative analyses of 31 fungal genomes suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the evolution of the lignin degrading white rot fungi took place at the end of the Carboniferous (Paleozoic era). During the Carboniferous, vast swathes of forest covered the land, which would eventually be laid down and become the coal beds characteristic of the Carboniferous system. This phylogenomic reconstruction implies that this evolution may have caused the end of the Carboniferous as it ended the large coal deposits characteristic of that period. Well, I agree that this contention is highly speculative. Only a Time Machine would allow us to get back to the dinosaur era and check if this speculation stands true!!!

As in my previous genomics endeavours, I have personally learned a great deal in the course of this work, and I have enjoyed collaborating with so many expert colleagues.

Other commentaries:

Perspective: Chris Todd Hittinger. Endless Rots Most Beautiful. Science 336: 1649-1650. 2012.

Hibbett’s blog: SAP paper published in Science

Tracking the Remnants of the Carbon Cycle: How an Ancestral Fungus May Have Influenced Coal Formation

INRA: Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

Scientific America: White Rot Fungi Slowed Coal Formation



Photo: Fomitopsis pinicola (Red Banded Polypore) is one of the most conspicuous and widely distributed polypores in coniferous forest regions of the northern hemisphere. F. pinicola is one of the sequenced fungus (see its JGI Portal) (© F Martin).

Les champignons au charbon

August 22nd, 2012

Évolution : un champignon préhistorique serait à l’origine de l’arrêt de la formation du charbon

Voici le communiqué de presse de l’INRA sur notre article dans Science sur l’évolution des mécanismes de dégradation de la lignocellulose chez les champignons du groupe des Agaricomycotina: [“L’apparition, il y a environ 300 millions d’années, d’un champignon capable de détruire efficacement le bois pourrait en partie expliquer l’arrêt de la formation de charbon à base de débris végétaux à cette même période. C’est l’une des conclusions d’une étude menée par des chercheurs de l’Inra, du CNRS et des universités de Lorraine et d’Aix-Marseille dans le cadre d’un consortium international. L’étude a permis également de comprendre le processus de dégradation du bois par les champignons contemporains, ce qui devrait fortement intéresser le secteur des bioénergies.] … en savoir plus

Floudas et al. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719.


Photo: Young fruiting body of  Fomitopsis pinicola (Red Banded Polypore) (© F Martin).


August 20th, 2012

Planning is in full swing for the next International Mycological Congress, IMC10 in Bangkok, Thailand, August 3-8, 2014.

Point your web browser to:

Now, just 24 months to Bangkok 2014, is the time for you to suggest topics for Sessions and Symposia using the form on the website or right here:

Submit your ideas now, the committee will begin choosing topics in just 90 days, on November 1, 2012.

Leka Manoch and Morakot Tanticharoen
Co-Chairs, IMC10 Organizing Committee


myTree of the Month

August 15th, 2012

From Pop Entosa’s site. Pep’s work is focused on an exploration of the medium itself–deconstructing and reconstructing photographic images to create new visual experiences. I like the series dedicated to trees. Multiple shots of each tree were taken while walking in a circle around it, then blended together and reworked to discover what became of the orbit – the tree and its environment.

Morning Glory

August 12th, 2012

Full sun exposure …



August 9th, 2012

This Summer, I’m devoting my free time to write a book on Fungi/Mushrooms (Champignons in french) for the Editions Quae: “200 Clès pour comprendre les champignons” (Mushrooms Facts: 200 Questions & Answers). Mushrooms possess considerable mystique and they have been the subject of numerous papers, accounts and books, and I’m browsing the web to search for documents on these fascinating organisms … and they are great gems, including superbe paintings as follows:

Image from Meyers Blitz-Lexikon ‘Die Schnellauskunft für jedermann in Wort und Bild‘ © Wikimedia Commons

Fungal Fruiting Bodies and Fanatics

August 8th, 2012

In her review of  two recent books, Mushroom (by Nicholas Money) and Mycophilia (by Eugenia Bone) devoted to the standing of mushrooms in nature and in human culture, Linnaea Ostroff wrote a short, but vibrant, description of fungal fruiting bodies and sex in these exciting organisms:

[“Mushrooms are the sex organs of fungi. They are ballistics experts that emerge when the fungus is ready to reproduce, launch spores by the billion, and vanish. Or rather, they puff up and deflate. The sudden appearance of mushroom on a lawn or under a log, like many illusions, is achieved with extensive advance setup and hydraulics. After a spore germinates, it sends filaments out underground in all directions in search of food and other fungi. When two fungal colonies—or three or more, as fungi are substantially less constrained than animals—of the same species meet, their cells merge and their DNA combines in the mushroom version of mating. New spores are produced, and the cells of the future mushroom are organized around them. This process occurs at the tips of the filaments, accounting for mushrooms’ quirk of appearing in rings. When the conditions are right, water rushes in and pressurizes the assembly, swelling the cells and inflating the mushroom. In many species, that takes only a few hours, the spores are soon released, and the mushroom shrivels by sundown. Others survive a week or more, and some tougher forms may last for months.” ]. Read more

‘Mushroom’ by Nicholas P. Money, Oxford University Press, New York, 2011. 221 pp.

Mycophilia. Revelations from the Weird World of Mushrooms by Eugenia Bone, Rodale, New York, 2011. 368 pp..




Soil & Civilization

August 3rd, 2012

I’m reading Edward Hyam’s book entitled ‘Soil and Civilization‘. Published in 1952, that’s a provocative classic described as ‘the first of its kind to cover the vast panorama of human history from a strictly ecological point of view‘. Although a bit outdated now, some of its message is still true. This is an account of the relationship between people and soil. Each has shaped the other for millenia. Hyam describes people as “parasites” leeching th goodness from the soil. Several writers have documented the fall of civilizations throughout history in parallel with the destruction of their soil (see Erosion of Civilizations). These stories are stark reminders not to take soil and soil stewardship for granted — soil is not an inexhaustible resource.

Soil and civilization. 1976. Edward Hyams. New York: Harper & Row. (Originally published in 1952).

JGI Summer 2012 Primer

August 2nd, 2012

The summer edition of the U.S Department of Energy (DOE) Joint Genome Institute (JGI) newsletter The Primer is now available for download:

…featuring articles and images:

Features include:

  • A summary of the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting
  • Comparative Genomics of White Rot Fungi Providing Insight into Selective Ligninolysis
  • The Omics Response to the Deepwater Oil Spill
  • Assembling the Switchgrass Genome
  • Single-cell Genomics @ the DOE JGI
  • Save the Date for the 8th Annual Genomics of Energy & Environment Meeting MARCH 25-29, 2013 in WALNUT CREEK, CA
  • Other Publication Highlights



8th JGI Users Meeting

August 2nd, 2012

Aboveground-belowground interactions

August 1st, 2012

The British Ecological Society, the Biochemical Society and the Society for Experimental Biology are organising a meeting entitled ‘Aboveground-belowground interactions: technologies and new approaches’, which is being held on 8-10 Oct 2012 in London.

The aim of the symposium is to promote cross-disciplinary collaboration by bringing together existing technology users and developers (e.g. biochemists, geneticists, bioinformaticists) who are interested in applying their skills to address research questions at the whole organism and ecological scales with above-belowground researchers working at biochemical, ecological, physiological, and molecular scales who have a desire to learn and apply new research technologies.