Semiautomated Monitoring of Longitudinal Microbial Metabolic Dynamics: A Study Case for Lignin Degradation

This study introduces a low-cost, open-source, semiautomated bioreactor system, developed using Arduino and Raspberry Pi, for longitudinal microbial culture studies. The system protocol includes detailed instructions for custom-designed components, specifications for easily purchasable parts, and open-source code for a web-based control interface. It was validated for sterility and tested in a case study involving the cultivation of <i>Phanerochaete chrysosporium</i> and <i>Trichoderma reesei</i> to assess their metabolic profile, both in isolation and coculture, for lignin degradation. Using mass spectrometry coupled with gas chromatography, several lignin degradation intermediates were annotated, including 4-hydroxybenzoic acid, vanillic acid, and ferulic acid, along with their temporal detection over 25 days. Additionally, we developed an annotation workflow to search for enzymatic functions producing these compounds in the genomes of <i>P. chrysosporium</i> and <i>T. reesei</i>, providing multiple layers of evidence to describe, for the first time, a computational annotation for lignin metabolism in these fungi. The results highlighted the production of lignin breakdown intermediates by the two fungal species, with annotations of the respective enzymatic functions, while also demonstrating the bioreactor's flexibility and suitability for diverse biotechnological applications, particularly in the field of biodegradation and waste valorization.