Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.

Improving the Autofluorescence of Lophira alata Woody Cells via the Removal of Extractives

The autofluorescence phenomenon is an inherent characteristic of lignified cells. However, in the case of Lophira alata (L. alata), the autofluorescence is nearly imperceptible during occasional fluorescence observations. The aim of this study is to investigate the mechanism behind the quenching of lignin's autofluorescence in L. alata by conducting associated experiments. Notably, the autofluorescence image of L. alata observed using optical microscopy appears to be quite indistinct. Abundant extractives are found in the longitudinal parenchyma, fibers, and vessels of L. alata. Remarkably, when subjected to a benzene-alcohol extraction treatment, the autofluorescence of L. alata becomes progressively enhanced under a fluorescence microscope. Additionally, UV-Vis absorption spectra demonstrate that the extractives derived from L. alata exhibit strong light absorption within the wavelength range of 200-500 nm. This suggests that the abundant extractives in L. alata are probably responsible for the autofluorescence quenching observed in the cell walls. Moreover, the presence and quantity of these extractives have a significant impact on the fluorescence intensity of lignin in wood, resulting in a significant decrease therein. In future studies, it would be interesting to explore the role of complex compounds such as polyphenols or terpenoids, which are present in the abundant extractives, in interfering with the fluorescence quenching of lignin in L. alata.

Systems biology-guided understanding of white-rot fungi for biotechnological applications: a review

Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.