Posts Tagged ‘soil’

Fungal Carbon Sequestration

March 29th, 2013


By  K. E. Clemmensen, A. Bahr, O. Ovaskainen, A. Dahlberg, A. Ekblad, H. Wallander, J. Stenlid, R. D. Finlay, D. A. Wardle, B. D. Lindahl


Abstract. Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using 14 C bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance]

Read also the linked Commentary by Kathleen K. Treseder and Sandra R. HoldenFungal Carbon Sequestration.

Photo: One of the investigated island situated in the two adjacent lakes Uddjaure and Hornavan in the Northern boreal zone of Sweden (from Björn Lindahl’s home page).


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 Although a bit outdated now, some of its message is still true.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).

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:


    Soil Biodiversity & Ecosystem Services

    February 21st, 2011


    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.


    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.