Posts Tagged ‘microbial ecology’

What is the most abundant deposited fungal genus in GenBank?

October 30th, 2010

chanterelles

Jason Stajich wrote a few Perl and BioPerl scripts to analyze the distribution of fungal species with ribosomal DNA internal transcribed spacer ( ITS) sequences in NCBI GenBank. The whole spreadsheet of the data is public and available here and Jason’s comments are available on his blog post. According to this analysis, soil  Fusarium is the most abundant deposited genus. As stressed by Jason, the analyzed sequences are mainly from Sanger-based studies. The recent released of 454 seq’ing based fungal surveys will certainly change this current picture.

Soil Metagenomics 2010

August 15th, 2010

401px-Braunschweig-burgplatz_1Christoph Tebbe is organizing the next International Symposium on Soil Metagenomics at the Johann Heinrich von Thünen-Institute (vTI) Forum in Braunschweig (Germany) on December 08–10, 2010. An objective of this symposium is to discuss the future applications of next generation sequencing to address the complex soil ecosystems.

Photo: © Burgplatz in Braunschweig, Germany by Matthias Prinke.

ECOFINDERS

May 30th, 2010

CB055265Great news!!! To increase the understanding of the role of soil biodiversity in ecosystem functioning, the European Commission (EC) awarded €7 million to our research project ECOFINDERS. This four year project, coordinated by INRA, aims to support European Union soil policy making by providing the necessary tools to design and implement strategies for sustainable use of soils.

The project will include:

  • Characterisation of the biodiversity of European soils and the normal operating range (NOR) according to soil types, threats, climatic zone and land use,
  • Determination of relationships between soil biodiversity, functioning and ecosystem services,
  • Quantification of the economic values of soil ecosystem services,
  • Evaluation of the impacts of human activities on soil biodiversity, functioning and services,
  • Design of policy-relevant and cost-effective indicators for monitoring soil biodiversity, functioning and ecosystem services.

To reach this overall aim, the project will pursue the following:

  • Describe the diversity of soil organisms (microorganisms and fauna) by using nextgen sequencing,
  • Decipher their interactions through trophic food webs,
  • Determine the role played by soil organisms in soil functioning and major ecosystem services: nutrient retention, carbon storage, water retention, soil structure regulation, resistance to pests and diseases, and regulation of above-ground diversity,
  • Assess the stability and resilience of ecosystems against threats in relation to their biodiversity: soil erosion and physical degradation, decline in organic content, loss of soil biodiversity, and soil contamination.

The 22 consortium partners will:

  • Develop and standardise phenotypic tools and procedures to measure the faunal biodiversity,
  • Design molecular methods to characterise the faunal diversity calibrated upon phenotypic traits,
  • Customise functional tools and methods to determine the functional diversity of fauna,
  • Establish high-throughput molecular assays for assessing microbial and faunal biodiversity,
  • Design, develop and establish a database aimed at mapping the European soil biodiversity and threats,
  • Establish cost-effective bioindicators to measure microbial and faunal diversity, their associated functions and the resulting ecosystem services,
  • Evaluate the economic added-value brought by these bioindicators in assessing the consequences of soil management policy for soil biodiversity and functioning,
  • Implement effective dissemination strategies to transfer the project knowledge and tools to soil stakeholders, notably but not exclusively regional, national and European policy-makers, and inform the general public about the issues associated with the sustainability of soil biodiversity.

My lab will focus on developing 454-based genotyping to survey the microbial communities — hundreds of creeping subterranean bugs will ended up in digits. Our on-going analysis of forest soil metagenomes will likely feed this large scale multi-year project.

You Are What You Eat

May 22nd, 2010

cabbage-noriA nice post from by Karen Schwarzberg and Mike Gurney at Small Things Considered (The Microbe Blog) discussing a paper recently published in Nature by Hehemann et al. which reports that, in at least one particular instance, we do harbor bacteria adapted to the traditional diet of our culture. Porphyranases are glycosyl hydrolases cleaving sulphated polysaccharides of carrageenan and agar from marine algae. These enzymes found in marine bacteria are common in Japanese—and only Japanese—intestinal microbiota. The Japanese can digest their nori (Porphyra) thanks to specific strains of Bacteroides plebeius that they host. The initial acquisition of the β-porphyranase genes by B. plebeius was likely by horizontal transfer from a marine Bacteroidetes.

Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Nature, 464 (7290), 908-912 DOI: 10.1038/nature08937

See also my previous post on the gut metagenomics-inspired poem from the Cuttlefish Poet at The Digital Cuttlefish‘s “You are What you Eat.”

Photo: Cabbage Nori Rolls.© http://blog.fatfreevegan.com/2006/05/cabbage-nori-rolls.html