Project description:Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step, itself, might require induction. To capture this early gene regulation event, here we integrated fine-scale cryo-sectioning with whole transcriptome sequencing to dissect gene expression at the single hyphal cell scale (tens of μm). We improved spatial resolution 50x, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. By comparing the first 100-μm section with a 100-μm from a later decay stage, it was clear that the early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation, LOX) that were previously and incorrectly assumed to be constitutively expressed. However, this delayed pattern was not universal, with a handful of genes upregulated immediately at the hyphal front.

2022-03-01 | GSE193915 | GEO

Rhodonia placenta

Project description:Localizing gene regulation by RNA-seq reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta

| PRJNA329543 | ENA

Capturing early gene expression dynamics during wood decay by brown rot fungus Rhodonia placenta

Project description:Capturing early gene expression dynamics during wood decay by brown rot fungus Rhodonia placenta

| PRJNA798397 | ENA

Using Rhodopseudomonas palustris as a model bacterium to study fungal-bacterial interactions in wood decayed by the brown rot fungus Rhodonia placenta

Project description:Brown rot fungi play an essential role in carbon cycling by decomposing lignocellulose into substrates usable by themselves and other microbes. Interactions between bacteria and fungi can be competitive or beneficial, but these relationships are not well understood because of a lack of good model systems. To model cross-feeding between fungi and bacteria, wood decayed by the brown rot fungus Rhodonia placenta was used as a carbon source for the phototrophic bacterium Rhodopseudomonas palustris. We found that fungal decay products generated by Rda. placenta could be used by R. palustris for growth, and later decay stages contained more usable substrates than early stages. Mass spectrometry identified a range of aromatic and non-aromatic acids, but after 95 days of bacterial growth, R. palustris only consumed non-aromatic acids over the aromatic lignin monomers. Genes involved with aromatic compound degradation were unimportant for growth and RNA sequencing revealed that aromatic compound degradation genes were repressed on decayed wood extract. Randomly barcoded transposon sequencing failed to identify a solitary catabolic pathway used by R. palustris, suggestive of substrate co-utilization, and surprisingly showed that genes involved with copper toxicity were essential. Finally, we found genes involved with biosynthesis of certain cofactors were non-essential on decayed wood extract, suggesting these nutrients were scavenged, and implicating these resources in supporting microbial communities in the environment. This study helps lay the foundation for a model fungal-bacterial system to study interactions that govern these relationships which will be valuable for understanding ecological interactions and industrially relevant co-culture systems.

2026-06-08 | GSE311457 | GEO

Rhodonia placenta

Project description:Fungus that causes brown rot of wood

| PRJNA19791 | ENA