In a bid to overcome the limitations of what scientists found previously from culture-dependent studies, new research shows stable isotope probing, coupled with next-generation sequencing techniques, can be used to identify which organisms living in the complex microbial soil community are involved in the decomposition of lignin, cellulose, and hemicellulose--three major polymers that make up wood.

Researchers from the lab of Bill Mohn (Microbiome Insights co-founder) at University of British Colombia labelled the lignin, cellulose, and hemicellulose of wood samples with a carbon isotope and allowed the process of decomposition to proceed in experimental microcosms. Subsequent amplicon and shotgun sequencing of the microbial communities in the microcosms: first, identified the organisms present without the use of cultures; and second, by measuring the total assimilation of the carbon isotope into the DNA of the sequenced amplicons, identified which species were involved in decomposition. This method greatly improves the understanding of the species and genes involved in this essential process — an insight not possible with standard culturing methods.

Forest soil decomposition of wood is a major global carbon sink, making it important for the study of climate change. To date, researchers knew microbes must be involved in helping fungi, the main drivers of wood decomposition, in the task of recycling this material but were limited in the ability to identify those involved.  This was mostly due to the fact that many bacteria cannot be grown on cultures in the lab. This new approach not only removes this barrier but also, due to the ability of metagenomics to work with pooled samples, provides a glimpse of the entire community in the sample —providing a more natural representation of the forest communities.

The researchers found that bacteria, specifically Gram-negative types from the families Comamonadaceae and Caulobacteraceae, were more involved in lignin degradation, with fungi taking on a prominent cellulose degrading role. Interestingly too, most species incorporated a carbon label from a single lignocellulosic polymer, strongly suggesting specialization among the microbes involved.  Furthermore, they found that variations in the community compositions across different soil types and soil layers constrained the degrading activity. According to the researchers involved: “the relationship between these communities and process rates should receive continuing study to refine our understanding of soil carbon stabilization and terrestrial carbon cycling models.” Additionally, the newly discovered sets of  gene clusters involved in the degradation process provide “a trove of potentially novel enzymes for biotechnological applications.”

This study was recently covered in Chemistry World.