Archive for October, 2011

Academic Tweeting

October 31st, 2011

Available now: a guide to using Twitter in university research, teaching, and impact activities by the London School of Economics and Social Sciences

Download the PDF for more on:

  • Building your following and managing your profile
  • Using Twitter to maximise the impact of your research project
  • Making the most of Twitter alongside your own blog
  • Using course accounts with students
  • A step by step guide to adding a Twitter feed to Moodle
  • Extra resources and links to blog posts and articles on academic blogging and impact


Root hair development

October 30th, 2011

The root epidermis of Brachypodium distachyon and Oryza sativa comprise hair (H) cells and nonhair (N) cells (imaged using cryo-scanning electron microscopy). The morphology of cells in the root hair zone of (a, b) B. distachyon and (c, d) O. sativa is shown. Blue and red colours highlight H cells in B. distachyon and O. sativa, respectively. Bars, 100 μm.

Liked the paper by Chul Min Kim & Liam Dolan (2011) Root hair development involves asymmetric cell division in Brachypodium distachyon and symmetric division in Oryza sativa. New Phytologist DOI: 10.1111/j.1469-8137.2011.03839.x



Observations on the Animalcula

October 30th, 2011

A great day for Open Access in scientific publishing: the Royal Society has announced that its world-famous historical journal archive – whith the first edition of The Philosophical Transactions of the Royal Society appearing in 1665 – has been made permanently free to access online. Nestling amongst these prestigious archive, you will find Isaac Newton’s first published scientific papergeological work by a young Charles Darwin, and a series of accounts of  Antonij van Leeuwenhoek’s early observations using the cutting-edge instrument of these Old Times, the Microscope, including the first ‘Observations on the Animalcula Found Upon Duckweed‘ … 300 years before metagenomics.

Van Leeuwenhoek A (1712) Some Further Microscopical Observations on the Animalcula Found Upon Duckweed. Phil. Trans. 28: 160-164.


Metatranscriptomics of Forest Soil Ecosystems

October 29th, 2011


Forest soils (including litter, humus and coarse woody debris) host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon sequestration, and biogeochemical cycles. Among these microbial communities, fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, humus saprobes, white- and brown-rot wood decayers, parasites and mycorrhizal symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga) remains unexplored using high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled mycorrhizal, wood decomposer, humus and litter saprobes are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, wood and litter decay and trophic mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum. The number of available fungal genomes has expanded dramatically in recent months, and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities.

Within the framework of the DOE Joint Genome Institute Community Sequencing Program, we have therefore embarked in a challenging large-scale metatranscriptomics project to explore the interaction of forest trees with communities of soil fungi, including ectomycorrhizal symbionts that dramatically affect tree growth, and saprotrophic soil fungi impacting carbon sequestration in forests. We are going to sequence the metatranscriptome of soil fungi (i.e., wood decayers, litter and humus saprotrophs, and ectomycorrhizal symbionts) in woody debris, litter/humus, rhizosphere and ectomycorrhizal roots of ecosystems representative of major Earth biomes, the boreal, temperate and mediterranean forests.

Metatranscriptome samples. A range of forest ecosystems has been selected on the basis of their ecological importance and the availability of metadata linked to these forest sites. In contrast to agricultural soils, forest soils, in particular those of boreal forests with low pH values, are characterised by strong vertical stratification due to the resulting absence of fauna causing mixing. This provides a spatial structure for evaluation of hypotheses concerning functional attributes of taxa occupying spatially distinct horizons.

Sampling will be conducted on selected stands in long-term observatories (LTOs) or national survey sites:

  • Boreal forests: Bonanza Creek (Alaska) and Siljansfors (Sweden).
  • Temperate forests: DOE long term studies at Duke Forest, the post-fire stands at the Bitterroot National Forest and Michigan maple N-deposition sites (USA), a forest-woodland-grassland transect in Rollainville (France), and the Breuil-Chenue plantation (France).
  • Mediterranean forests at Puéchabon near Montpellier (France) and at Aspurz south-western Pyrenees (Spain).

For these soil samples, we will run: (1) Tag-encoded FLX-titanium amplicon pyrosequencing (TEFAP) of the fungal rDNA ITS to survey the existing communities and (2) RNA-Seq of soil samples. For this cDNA profiling, we will sequence ~110Gbp per site for a total of 1 terabase using Illumina HiSeq PE chemistry. Reads produced by RNA-Seq will be used to reconstruct de novo the different fungal metatranscriptomes (best case scenario). In addition, we will use Illumina fragment recruitment, a process of aligning sequencing reads to reference genomes. Metatranscriptomic reads will thus be aligned to the >100 genomes of soil fungi available in the JGI MycoCosm. To improve this crucial step, we also propose the gDNA sequencing and RNA-Seq of the 25 most abundant fungal species harvested on the studied sites to serve as the foundation for a reference database for metagenomics of fungi and for a comprehensive survey of the potential soil fungal metabolome. We will annotate the fungal genomes/transcriptomes and soil fungal metagenomes with all these characteristics and will compare the different metagenomes in terms of these characteristics.

These experimental datasets will provide a mechanistic insight into the fungal communities’ structural organization and functioning in forests. In addition, the present metagenomic data will give a comprehensive picture of the organization of the tree-associated microbiome in terms of metabolic pathways, subsystems, molecular functions and biological processes.

Sequencing of new fungal species will be performed in concert with existing large-scale genome studies (e.g., the 1000 Fungal Genomes project), so as to minimize unnecessary redundancies. As such we recognize that this project represents a large effort and great challenge in defining the microbiome of important forest ecosystems and a group of micro-organisms, the soil fungi.


Image (top): Denali Ntl Park, Alaska (© F Martin)

7th Annual DOE JGI User Meeting

October 24th, 2011

The 7th Annual DOE JGI User Meeting ‘Genomics of Energy & Environment’ will be held at the Marriott Hotel in Walnut Creek, California on March 20 – 22, 2012.

Scientists interested in how genomics applies to bioenergy and environmental issues are invited to attend the annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting. This international gathering of researchers with an interest in sequence-based science offers three days of presentations, tours, workshops, and poster sessions.

Topics: Synthetic biology & biodesign, Systems biology/transcriptional networks, Application of single cell genomics in microbial ecology and bioprospecting, Genomic analysis of biofuel traits in maize and switchgrass, Cloud computing as a platform for large scale sequence analysis, Ocean viruses: towards population genomics, understanding virus-host interactions, and accessing the uncultured, Omics in the Arctic: Genome-enabled contributions to carbon cycle and biogeochemical research in high-latitude ecosystems, and Ancient DNA


JGI Fall 2011 Primer

October 24th, 2011

The Fall 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:

  • Tagging enzymes that can take the heat
  • Carbon fixation in the dark ocean
  • Linking fungi to boreal forests
  • Notable publications & more…


International Human Microbiome Congress in Paris

October 23rd, 2011

The next International Human Microbiome Congress, organized by the European consortium MetaHIT will take place in Paris, March 19-21, 2012 at the Palais Brongniart.

In the Valley of the Silver Moon

October 22nd, 2011

Everything goes in circles, everything comes around again, and those, like me, who enjoyed the Laurel Canyon singer-songwriters Crosby, Stills, Nash, Young, and Eagles, will love ‘Gentle Spirit‘ from Jonathan Wilson. Wilson’s album is remarkably evocative of that golden late ‘60s, early ‘70s period. Wilson specialises in vintage gear, and ‘Gentle Spirit‘ sounds like the product of such equipment – warm, wistful, coated in creamed harmonies – but also, crucially, alive.

Darkness Visible: Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

October 20th, 2011

At the Jacques Monod Conference on Integrated Ecological Genomics, scientists from the USA and Europe met in Roscoff earlier this week to discuss how to bridge metagenomics, functional genomics, evolution biology and microbial ecology for a better understanding of marine, soil and gut ecosystems. The meeting was very exciting hosting top-notch speakers: Eugene Koonin, Mary Ann Moran, Tim Vogel, Julia Vorholt, Peter Young, Philippe Vandenkoornuyse, Puri Lopez-Garcia, Antje Boetius, Folker Meyer, Laurence Garzarek, Gurvan Michel, Oded Beja, Patrick Forterre, Forest Rohwer and Rotem Sorek, amongst others.

As a soil microbiologist, I enjoyed very much the presentations on metagenomics of ‘exotic’ ecosystems, such as the Chilean upwelling, the Deap Sea and the seafloor. I’m so envious of those guys from the Tara Oceans Expedition collecting samples throughout the world seas (see Map below).

If you want to learn more about the ‘Microbial Ecology of the Dark Ocean above, at, and below the Seafloor‘, visit Beth Orcutt amazing web site ‘Microbes Are Awesome‘ and read:

Zinger et al. (2011) Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS One 6: e24570.

Orcutt et al. (2010) Microbial Ecology of the Dark Ocean above, at, and below the Seafloor. Microbiology & Molecular Biology Reviews 75: 361–422.

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, et al. (2011) A Holistic Approach to Marine Eco-Systems Biology. PLoS Biol 9: e1001177. doi:10.1371/journal.pbio.1001177.

Poretsky, R. S., S. Gifford, J. Rinta-Kanto, M. Vila-Costa, and M. A. Moran. 2009. Analyzing gene expression from marine microbial communities using environmental transcriptomics. Journal of Visualized Experiments 24, e1086, doi: 10.3791/1086.

Thx Philippe & Oded

Image: © CNRS-Roscoff


Integrated Ecological Genomics

October 18th, 2011

Follow the Jacques Monod Conferences on Integrated Ecological Genomics (Roscoff, 15-19 October) on Twitter: @fmartin1954: #IEG

A lovely fungus

October 12th, 2011

Annegret and Yohann took this photo of our favorite ectomycorrhizal fungus Laccaria bicolor (strain S238N) fruiting near its poplar host. Its whithish mycelium is seen growing on ectomycorrhizal roots.

Image: Fruiting body of Laccaria bicolor S238N (© INRA: A Kohler & Y Daguerre).

Fungal Biology in the Age of Genomics

October 12th, 2011

The special issue of Mycology (Volume 2 Issue 3) dedicated to ‘Fungal Biology in the Age of Genomics‘ has been published and will be free to view until 30 November 2011.

This issue was guest edited by LiJun Ma, Natalie Fedorova, and Joan Bennett.


Table of Contents:

  • Editorial: Fungal Biology in the Age of Genomics by Li-Jun Ma, Joan W Bennett & Natalie D Fedorova
  • Approaches to Fungal Genome Annotation by Brian J. Haas, Qiandong Zeng, Matthew D. Pearson, Christina A. Cuomo & Jennifer R. Wortman
  • Fungal genome resources at NCBI by B. Robbertse & T. Tatusova
  • From genetics to genomics: fungal collections at the Fungal Genetics Stock Center by Kevin McCluskey
  • A brief utilization report on the Illumina HiSeq 2000 sequencer by Lin Liu, Ni Hu, Bo Wang, Minfeng Chen, Juan Wang, Zhijian Tian, Yimin He & Danni Lin
  • Fueling the future with fungal genomics by Igor V. Grigoriev, Daniel Cullen, Stephen B. Goodwin, David Hibbett, Thomas W. Jeffries, Christian P. Kubicek, Cheryl Kuske, Jon K. Magnuson, Francis Martin, Joseph W. Spatafora, Adrian Tsang & Scott E. Baker
  • Dynamics of effectors in host–pathogen interactions by Rays H.Y. Jiang
  • What can the Aspergillus flavus genome offer to mycotoxin research? by Jiujiang Yu, William C. Nierman, Natalie D. Fedorova, Deepak Bhatnagar, Thomas E. Cleveland & Joan W. Bennett