Who eats the tough stuff DNA stable isotope probing (SIP) of bacteria and fungi degrading 13C-labelled lignin and cellulose in forest soils

Sampling

Decomposition and storage of plant-derived carbon has become a hot topic in environmental research. Since carbon dioxide has been detected as one of the most relevant drivers of global climate change, its potential storage and fate in soils has become key for predicting climate scenarios. Unfortunately, studies with a focus on the decomposition and driving factors are still lacking for precise modelling of the fluxes in a changing world. The main actors of carbon degradation in soils have not been fully identified, especially in regard to bacteria very little is known about their contribution to degradation of persistent carbon components. In the present study, the active microbial community involved in degrading 13C-labelled cellulose and lignin in forest soils was identified using a DNA stable isotopic probing (SIP) approach. Microbial activity assessed by measurements of 13CO2 increased with labelled substrate addition, during a 28 days incubation period. Within the vast microbial communities, bacterial and fungal members specialized in degrading cellulose (e.g. Devosia (Rhizobiales), Sebacinales), lignin (e.g. Sphingopyxis (Sphingomonadales), Paucibacter (Burkholderiales), Xylariales, Auriculariales, Helotiales), and both substrates (e.g. Caulobacter (Caulobacterales), Schizoporaceae, Orbiliales) have been identified. Over the course of the experiment, a successional shift from early degrading colonizers (e.g. Brevundimonas (Caulobacterales), Trichosporonales, Hymenochaetales, Gomphales) to late stage beneficiary microorganisms (e.g. Sphingopyxis (Sphingomonadales), Devosia (Rhizobiales), Orbiliales) became evident. These results provide novel insights into the degradation processes of woody plant debris in soil, disentangling the active microbial degraders from the beneficiaries, within the vast complexity of the soil microbiome.

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1