Posts Tagged ‘ecology’

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).


28th NPS

July 15th, 2011

Graveyards on the Move

August 28th, 2010

Cemetery_4Zombie Ants‘, ‘Graveyards on the Move‘ … fungi can make the headlines of newspapers, such as The Guardian, and blog posts (Ancient Zombie Ants, Fungal Parasites & Zombie Ants, Genetics and Behavior, Cordyceps and Nature’s parasitic relationship with it). They referred to the parasitoid Cordyceps fungi (Ascomycota, Pezizomycotina, Sordariomycete, Hypocreales) — a genus that includes about >600 described species. All Cordyceps species are endoparasitoids, mainly on insects and other arthropods.

Jason’s recent tweet  ‘A fun blog post & paper review on Cordyceps entitled “fungal parasites & zombie ants“‘ reminded me one of the more stunning sections of the 2006 BBC’s documentary series Planet Earth showing an ant being preyed on by Cordyceps — you can check out this segment narrated by Sir David Attenborough on YouTube — . Fruiting body of the infecting cordyceps erupting from the ant head and the mushrooming bodies of dead insects are frightening, but so beautiful.

The fungus Ophiocordyceps unilateralis, which is pan-tropical in distribution, causes infected worker ants to leave their nest and die under leaves in the understory of tropical rainforests. Cordyceps spores glue to foraging Carpenter ants (Camponotus leonardi), germinate on the insect cuticule and the fungal hyphae then grows inside the ant body where it releases chemicals that affect host behaviour. Some ants leave the colony and wander off to find fresh leaves on their own, while others fall from their tree-top havens on to leaves nearer the ground. The final stage of the parasitic infection (which may last 3 to 6 days) is the most macabre. In their last hours, infected ants — the zombies — move towards the underside of the leaf they are on and clamp their mandibles in a “death grip” around the central vein, immobilising themselves and locking the fungus in position. Very high densities of dead ants can occur underside of leaves leading to patches. Spores are too large to be wind dispersed and instead fall directly to the ground where they produce secondary spores that infect foraging Carpenter ants as they walk over them.

In a study published last year in PLoS OneMaj-Britt Pontoppidan and her colleagues have shown that the Cordyceps parasitoid not only affects individual ants, but they can also structure the entire host population of a tropical forest in Thailand in terms of its distribution in time and space, and then influence their own distribution: the ‘parasite’s ‘extended phenotype‘. It appeared that the dead ant bodies weren’t randomly distributed in the Thai rainforest floor. Instead they were in large aggregations (the so-called ‘graveyards‘) of up to 26/m2, separated by corpse-free zones. The dead ants had locked onto the undersides of leaves – an example of how the fungus influences its host’s behaviour. The distribution of dead ants appeared to be related to temperature and absolute humidity – things which could influence the survival of fungal spores and thus the chances of an individual ant picking up the infection.

Ant death-grip leaf scars have been documented on 48 Ma fossil leaves, indicating the antiquity of this behaviour (Hughes et al. (2010) Biology Letters online).

Fungal parasites and symbionts play an important role in structuring host plant populations. This study  showed that they also affect animal populations … what about human behavior? (see: the Human Afflicting Strain of Cordyceps Fungus).

BTW, Thanks to its medicinal properties, mushroom hunters in Tibet can earn $900 dollars for an ounce of cordyceps.

Pontoppidan M-B, Himaman W, Hywel-Jones NL, Boomsma JJ, Hughes DP (2009) Graveyards on the Move: The Spatio-Temporal Distribution of Dead Ophiocordyceps-Infected Ants. PLoS ONE 4: e4835. doi:10.1371/journal.pone.0004835

Hughes, DP,  Wappler , T & Lanadeira, CC (2010) Ancient death-grip leaf scars reveal ant-fungal parasitism. Biology Letters. Published online before print August 18, 2010, doi:10.1098/rsbl.2010.0521


Photo: Cambridge Graveyards, UK © F Martin & A carpenter ant (Camponotus leonardi) whose body has been consumed by the fungus Ophiocordyceps © David P Hughes


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.

Unexpected high fungal diversity in forest soils

August 28th, 2009

hetraieSoil fungi play a major role in ecological and biogeochemical processes in forest ecosystems. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). Within the framework of our metagenomics project aimed to assess the microbial diversity in temperate forests, we surveyed the fungal diversity in six different forest soils at the Breuil-Chenue long-term observatory using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). The paper reporting this study is now online on the New Phytologist Early View pages.

No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units (MOTU). Most MOTUs (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant MOTUs showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp.

This study, together with two other surveys exploring the diversity of fungal communities in  Quercus macrocarpa phyllosphere (Jumpponen & Jones, 2009) and the diversity of arbuscular mycorrhiza fungi in a boreonemoral forest (Öpik et al., 2009), validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will likely accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

Buée et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, doi: 10.1111/j.1469-8137.2009.03003.x

Jumpponen & Jones (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, doi: 10.1111/j.1469-8137.2009.02990.x

Öpik et al. (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, doi: 10.1111/j.1469-8137.2009.02920.x