Archive for March, 2011

Blogs & Tweets

March 31st, 2011

Interesting Nature commentary on the usefulness of tweeting and blogging from scientific conferences. It points to a helpful paper (see below) summarizing guidelines for blogging etiquette.


Nature Methods 8, 273 (2011) doi:10.1038/nmeth0411-273


Faire parler l’invisible

March 30th, 2011

For those reading french, I recommend this BIOFUTUR special issue dedicated to environmental genomics. I coordinated this series of paper describing recent metagenomics studies  of various ecosystems, including oceans and forest and agrosystem soils, but also buffalo dropping!!! .

Bacterial Community Variation in Human Body Habitats Across Space and Time

March 27th, 2011

Personally, my favorite talk at the last 6th Annual DOE JGI Users Meeting at Walnut Creek was Rob Knight‘s contribution on ‘Spatially and Temporally Resolved Studies of the Human Microbiome‘. Rob was creative and integrative. Displaying the biogeography of bacterial communities on the human body using UniFrac and QUIME was astounding.

A series of large-scale sequencing analyses of  the variable region 2 (V2) of the bacterial 16S ribosomal RNA (rRNA) gene conducted by Rob and his collaborators have shown that the community composition is mainly determined by body habitat (gut, mouth, skin, hair, nostril, …). Within these ecological niches, interpersonal variability is striking, whereas individuals exhibit minimal temporal variability. Several skin locations harbor more diverse communities than the gut and mouth, and skin locations (e.g. your different face zones) varie in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time. According to Rob, these trends may ultimately reveal how microbiome changes cause or prevent disease. For more details, read their recent papers, including Costello et al. (2009).

Let’s do it on the bacterial communities associated with trees.

Fig. 16S rRNA gene surveys reveal hierarchical partitioning of human-associated bacterial diversity. Communities clustered using PCoA of the unweighted UniFrac distance matrix. Each point corresponds to a sample colored by body habitat (from Costello et al. 2009).

Costello et al. (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time. Science 326, 1694-1697.

Caporaso et al.(2010)QIIME allows analysis of high-throughput community sequencing data. Nature Methods doi:10.1038/nmeth.f.303

Upcoming New Phytologist Symposia

March 26th, 2011

26th NPS: Bioenergy trees

INRA Nancy, France: 17–19 May 2011

• Organisers: Francis Martin, Andrea Polle, Gerald Tuskan, Gail Taylor, Michele Morgante

27th NPS: Stoichiometric flexibility in terrestrial ecosystems under global change

Biosphere 2, Arizona, USA: 25—28 September 2011

• Organisers: Rich Norby, Amy Austin, Gaius Shaver, Yiqi Luo, Jeff Dukes, Travis Huxman

28th NPS: Functions and ecology of the plant microbiome

Hotel Aldemar, Rhodes, Greece: 18–21 May 2012

• Organisers: Paul Schulze‐Lefert, Jeff Dangl

29th NPS: Stomata

Manchester, UK, July 2012

• Organisers: Alistair Hetherington and Ian Woodward

30th NPS: Immunomodulation by plant‐associated organisms

California, USA, 17—19 September 2012

• Organisers: Sophien Kamoun, Brian Staskawicz


Botrytis/Sclerotinia Post-Genome Workshop 2011

March 25th, 2011

A Sweet Deal: Mycoheterotrophy

March 23rd, 2011

neottieIn her latest blog post, ‘Stygian Orchids Sucking on the Broom Bush Roots — And Shedding Chloroplast Genes‘, Jennifer Frazer discussed mycoheterotrophy, one of the most fascinating plant-fungus interactions, a ‘ménage à trois’ between a beautiful orchid (here the Western Underground Orchid, Rhizanthella gardneri), its associated mycorrhizal mycelium and their sugar tree provider. In this case, Melaleuca uncinata, the broom bush. The majority of mycoheterotrophic plants studied thus far cheat one of the most widespread mutualisms on earth – the mycorrhizal symbiosis. Mycoheterotrophic plants obtain all of their carbon needs through symbiotic associations with fungi, and, while achlorophyllous, they are not directly parasitic on other plants. Mycoheterotrophic orchids use the sugar from associated mycorrhizal fungi, and thus the carbon from nearby autotrophic plants. These ‘intimate’ associations are not only botanical curiosities, but topical biological systems scrutinized by scientists aiming to understand evolution of plants and fungi (Selosse & Cameron, 2010).

Read more …  Virtual Special New Phytologist Issue on Mycoheterotrophy

Photo: The Bird’s-nest Orchid, Neottia nidus-avis (Chantelouve, Vallon de la Malsanne, Oisans) © F Martin

BGI Joins Earth Microbiome Project

March 22nd, 2011

A GenomeWeb Daily News Post

BGI (Beijing Genomics Institute) will provide a range of services and support for the Earth Microbiome Project (EMP), an effort to sample, sequence, and analyze microbial communities from all over the globe.

The multi-disciplinary EMP effort, the largest sequencing project yet undertaken, will conduct metagenomics studies of 200,000 samples of microbes from soil, air, sea, and freshwater systems from around the world to produce a global Gene Atlas.

BGI said today that it will lead the effort to identify sample collections in Asia, and it will provide DNA extraction, amplification, sequence library construction, and sequencing for metagenomics projects. The Shenzhen, China-based institute also will use its computational resources to develop the bioinformatics pipeline that will provide the analysis framework for the vast amount of data the EMP will produce.

The EMP effort also includes Argonne National Laboratory, the University of Chicago, the University of Colorado-Boulder, Lawrence Berkley National Laboratory, and the US Department of Energy’s Joint Genome Institute. BGI also said that it will host the First International Earth Microbiome Project Conference in Shenzhen this June.

See also:



    March 20th, 2011

    At the Fungal Genome Tools workshop (26th FGC), Jason Stajich announced the release of FungiDB 1.0 beta. This pre-release version of FungiDB is available for early community review. Please explore the site and contact Jason with your feedback.


    March 20th, 2011

    Mushroom Hunting in Alaska

    March 13th, 2011


    Amongst the scheduled symposia:

    • Fungal Population Genomics
    • Molecular Ecology and Biodiversity of Arctic and Boreal Fungi
    • Mechanisms of Fungal-Plant Interactions: Perspectives from the Interface of Ecology, Evolutionary Biology, and Genomics

    I will contribute a talk to the latter symposium.

    Infos and registration: see 79th Mycological Society of America web site.

    Surviving the Ant Gut

    March 12th, 2011

    leaf-cutting-ant-1403Leaf-cutting ants of the genera Acromyrmex and Atta (Family Formicidae: Subfamily Myrmicinae: Tribe Attini) live in mutualistic symbiosis with the basidiomycete Leucocoprinus gongylophorus (Agaricaceae). The ants cultivate the mycobiont mycelium in ‘fungal gardens’ where they brought freshly cut and chew leaves. They apply fecal droplets to the leaf pulp before depositing this mixed substrate to the top of the garden. The fecal fluid contains a large range of hydrolytic enzymes (proteases, pectinases, carbohydrate degrading enzymes) able to efficiently degrade the plant cell wall and cell material. Released carbohydrates serve as a primary source of nutrient for the fungus which then differenciate clusters of a unique tissular structure so-called the ‘gongylidia‘. This massive hyphal swelling are the main food source of the farming leaf-cutting ants. In ant agriculture,the attine ants actively propagate, nurture and defend the basidiomycete cultivar. This mutualistic symbiosis is thought to have originated in the basin of the Amazon rainforest some 50–65 million years ago. The molecular mechanisms driving this ant-fungus mutualism are poorly know.

    In their study published in BMC Biology, Schiøtt et al. showed that the pectinolytic enzymes present in the ant fecal droplets are produced by the fungus. The genes encoding the hydrolytic enzymes are  induced in the gongylidia mycelium, ingested by the feeding ants, transported throughout the ant gut before being released in fecal fluids on the top of the fungal garden. It is suggested by the authors that the fungal enzymes evolved to survive the harsh conditions of the ant gut. The on-going sequencing of the genome of Leucocoprinus gongylophorus will undoubtly provide novel insights on the evolution from saprotrophism to this unique mutualistic symbiosis.


    Figure by Schiøtt et al. BMC Biology 2010 8:156   doi:10.1186/1741-7007-8-156

    Schiøtt et al. (2010 Leaf-cutting ant fungi produce cell wall degrading pectinase complexes reminiscent of phytopathogenic fungi. BMC Biology 2010, 8:156

    Recommended reading: Fungus-Ant mutualism

    Photo: ©,59,AN.html


    March 11th, 2011

    Fungal Biology Reviews

    Keynote and Plenary Papers from IMC9

    Now available for FREE on SciVerse ScienceDirect!

    Great keynote paper: “The poetry of mycological accomplishment and challenge” by John Taylor.


    March 5th, 2011


    Scientific Program is available

    Download the Program Book with concurrent session schedules and abstracts


    © 26th FGC cover art: Amritha S. Wickramage, University of Arizona

    A Nature chain retraction for Arabidopsis secreted defense metabolites

    March 5th, 2011

    arabidopsis_ed_smallThose of you working on rhizospheric compounds and plant-microbe  interactions should read a recent Nature retraction note by Vivanco’s and Ausubel’s labs and related comments in Retraction Watch. The withdrawn paper reported the identification of ten antimicrobial compounds exuded by Arabidopsis thaliana roots to mediate pathogen resistance. Antimicrobial activity was directed against specific pathovars of the bacterial phytopathogen Pseudomonas syringae but not against the pathovar Pseudomonas syringae pv. tomato strain DC3000 that is a highly virulent pathogen of Arabidopsis.

    The authors retracted their Nature Letter after a key reference by Walker et al. was retracted from the scientific literature; The validity of the use of the ten compounds as markers of the Arabidopsis defence response being now in doubt.

    Photo: ©

    Metagenomics Tutorials

    March 3rd, 2011

    stFor those in the lab and elsewhere willing to follow recent tutorials on metagenomics tools:

    – METAREP Human Microbiome Project Virtual Jamboree Tutorial: presented at the Human Microbiome Project (HMP) Virtual Jamboree by Johannes Goll on January 19, 2011.

    – “Climbing Mt. Metagenome“: – a talk Titus Brown gave at JGI on assembling very large, diverse metagenomes.

    See also the JVCI blog post ‘Virtual Comparative Metagenomics