Molecular Ecology of Leaf Litter Decomposition

PI : Marc Buée ( UMR 1136 « Interactions Arbres/Micro-organismes » )

Co-applicants : Bernd Zeller (BEF) & Francis Martin (IAM)

 

Collaboration : Stéphane Uroz (IAM), Aurélie Deveau (IAM), Eric Gelhaye (IAM), Laurent Saint-André (BEF)

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Context — Terrestrial carbon (C) is largely located in soils and a large part of the sequestered C in forest ecosystems accumulates in soil litter. The decaying leaf litter is colonized by saprotrophic bacteria, but mostly by leaf fungal decayers and ectomycorrhizal fungi. Leaf fungal decayers are the main decomposers of coniferous and deciduous wood and litter. However, ectomycorrhizal species have been found to dominate fungal communities, where there are competing successfully with leaf decomposers for soil space and nutrients. Being supported by carbohydrates from their host plants rather than depending on energy from organic matter, mycorrhizal fungi are very competitive and monopolise nutrients for themselves and their hosts. Mycorrhizal fungi play a major role in the turnover of litter accumulated on the forest floor, that represents potentially the main source of N for plant growth, and then in the nitrogen (N) cycling.

Objectives —

The LeafLitterOmics project proposes an integrated field study of the molecular and biochemical mechanisms driving interactions between organic matter chemistry, microbial community composition and enzyme activities during decomposition.

The proposed project will survey (1) changes in litter chemical composition by spectroscopic and spectrometric techniques, (2) composition of the microbiome by high-throughput rDNA sequencing, and (3) the transcriptome of the most abundant fungal species, during the decomposition of oak litter. These experiments will be designed to define the relationships between activities of decomposer microorganisms, ectomycorrhizal symbionts and litter chemistry.

Approach — This research proposes to molecular genetic analyses of microbial community composition and activity to understand the interactions between leaf decomposers and symbiotic fungi by using in situ leaf litterbags in the field, metagenomics, transcriptomics and chemistry analysis.

(1) To survey changes in the composition of microbial communities (ectomycorrhizal fungi, leaf decomposers, saprotrophic bacteria) during the degradation and stabilization of oak litter by using high-throughput rDNA sequencing;

(2) To assess gene and protein expression of the most abundant ectomycorrhizal symbionts and litter decomposers during their interactions by RNA-Seq. Mass spectrometry proteomics could be investigate in an additional project, in collaboration with the ‘Environmental Molecular Science Laboratory (EMSL)’.

(3) To assess changes in the leaf litter chemistry during the decomposition by spectroscopy.

Key results —

• During autumn 2013, senescent oak leaves have been collected from two French sites: Champenoux forest (54) and Breuil forest (58). Previous data have shown that these two litters presented different concentrations of Ca and Mg, but varied little in their biochemical composition. In January 2014, for each type of litter, thirty bags (“litterbags” 5 × 14.5cm, with a porosity of 1.4 × 1.8 mm) were placed in the Champenoux forest (experimental site of the MOS network).
• The degradationof the twocategories ofoaklitterwas followedin2014(monitoringstill in progress). The kinetic ofdegradation shows, in the early months, agreater loss ofmass in theleaves fromthesite of Champenoux. Leaves from the site ofBreuilshowslowerbiodegradability(Fig.1): loss of 15% DM for leavesof Breuiland 25% for those from Champenoux. During the 12 last months, this tendency was not significant and important heterogeneity of the decaying was observed between the samples.
• In parallel, sub-samplingswere performed (n = 3 per treatment) periodically and stockedat -80° Cfor subsequentmolecular analyzesandNIRS/MIRSmeasurements.
• Spring 2014 and summer 2015 wereimpacted bya severe drought. Consecutively to this lack of water, the degradation ofleaves was relatively slow duringthese periods. For this reason, the sampling of this organic mattershouldcontinueuntil winter 2015-2016.
• In the meantime,a protocol for the extraction ofmetagenomicDNA wassuccessfully optimizedfrom samples ofoaklitter(FRB project, NPDC) to reducetheco-extractionof potentialPCR inhibitors(polyphenolsandorganic matter extractable compounds).

Main findings —

Our preliminary results clearly shown different levels of biodegradation for the two litters of sessile oak. Analyses (in course) of NIRS / MIRS profiles should identify specific chemical determinants related to the relative “recalcitrance” of this organic matter. Furthermore, the study of the fungal species composition should highlight which microbial actors involved in the biodegradation of litter over time. These analyses should partially correct the measured heterogeneity.

Because of the low dynamic degradation of these litters, a last sampling will be programed in February 2016. The final molecular analyses and NIRS / MIRS measurements will be acquire in spring 2016.

This was a joint project with the U.S. DOE Joint Genome Institute (Walnut Creek, CA), the U.S. DOE Environmental Molecular Sciences Laboratory (EMSL) and the Sveriges Lantbruks Universitets (SLU) in Uppsala and Lund. Unfortunately, this joint project was not supported and functional approaches cannot be investigated. However, the development of protocol for eukaryotic mRNA extraction has been developed in our laboratory on soil samples of the same forest site (Figure 2). These metatranscriptomic samples have been recently sequenced by the JGI.

Future perspectives —

The samples (RNA/DNA) will be available, however, for targeted functional analysis of CAZymes, expressed during the succession of microbial species. The analyzes will be performed to correlate NIRS / MIRS profiles and taxonomic data.

A publication on the succession of fungal communities during the oak litter degradation, will be write in the second half of 2016.

 

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Photo caption
Credit :  Marc Buée
Anthina flammea developing on beech leaves