Pacbio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes

Abstract

Background In forest ecosystems, biological decomposition of deadwood components plays a pivotal role in nutrient cycling and in carbon storage by enriching soils with organic matter. However, deciphering the functional features of deadwood microbiomes is challenging due to their complexity and the limitations of traditional cultivation methods. Our study demonstrates how such limitations can be overcome by describing metagenome composition and function through the analysis of long DNA molecules using the PacBio HiFi platform. Results The accuracy of PacBio HiFi long-read sequencing emerges as a robust tool for reconstructing microbial genomes in deadwood. It outperformed the routine short-read sequencing and genome sequencing of isolates in terms of the numbers of genomes recovered, their completeness, and representation of their functional potential. We successfully assembled 69 bacterial genomes representing seven out of eight predominant bacterial phyla, including 14 high-quality draft MAGs and 7 nearly finished MAGs. Notably, the genomic exploration extends to Myxococcota, unveiling the unique capacity of Polyangiaceae to degrade cellulose. Patescibacteria contributed to deadwood decomposition processes, actively decomposing hemicellulose and recycling fungal-derived compounds. Furthermore, a novel nitrogen-fixing bacteria within the Steroidobacteriaceae family were identified, displaying interesting genomic adaptations to environmental conditions. The discovered diversity of biosynthetic gene clusters highlights the untapped potential of deadwood microorganisms for novel secondary metabolite production. Conclusions Our study emphasizes new contributors to wood decomposition, especially Polyangiaceae and Patescibacteria for complex and easily decomposable organic matter, respectively. The identification of nitrogen-fixing capabilities within the Steroidobacteraceae family introduces novel perspectives on nitrogen cycling in deadwood. The diverse array of observed biosynthetic gene clusters suggests intricate interactions among deadwood bacteria and promises the discovery of bioactive compounds. Long read sequencing not only advances our understanding of deadwood microbial communities but also demonstrates previously undiscovered functional capacities of the deadwood microbiome. Its application opens promising avenues for future ecological and biotechnological exploration of microbiomes.