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

TL;DR

This paper presents a low-cost, open-source bioreactor system for tracking microbial lignin degradation over time, using fungi and computational methods to identify metabolic intermediates.

Contribution

A novel semiautomated bioreactor system and computational workflow for lignin metabolism annotation in fungi.

Findings

The bioreactor system successfully detected lignin degradation intermediates like 4-hydroxybenzoic acid and vanillic acid over 25 days.

A computational workflow annotated enzymatic functions in P. chrysosporium and T. reesei related to lignin metabolism.

The system demonstrated flexibility for biotechnological applications in biodegradation and waste valorization.

Abstract

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 Phanerochaete chrysosporium and Trichoderma reesei 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 P. chrysosporium and T. reesei, 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.

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