Abstract
Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitability. Microbial growth simulations reveal that the fungus Anaeromyces robustus is most suited to pair with either the bacterium Clostridia ljungdahlii or the methanogen Methanosarcina barkeri—both organisms also found in the rumen microbiome. By capitalizing on simulations to screen six alternative organisms, valuable experimental time is saved towards identifying stable consortium members. This approach is also readily generalizable to larger systems and allows one to rationally select partner microbes for formation of stable consortia with non-model microbes like anaerobic fungi.
Highlights
Modern biotechnology is well poised to take advantage of the current shift towards a more sustainable chemical industry [1]
We present a marriage of experimental and computational tools used to identify suitable consortia partners for anaerobic gut fungi
All experiments were conducted in triplicate using 40 mL of M2 media [18] loaded with 2 g of corn stover grass, (4 mm particle size) supplied by the United States Department of Agriculture (USDA)-ARS research center (Madison, WI, USA), in 75 mL serum bottles
Summary
Modern biotechnology is well poised to take advantage of the current shift towards a more sustainable chemical industry [1]. Current industrial techniques used to overcome this barrier include physical, chemical and biological treatment (e.g., milling, acid hydrolysis and enzyme treatment, respectively) [4]. Biological conversion attempts to exploit natural mechanisms to produce chemicals from lignocellulose. Two competing alternatives are being investigated: consolidated bioprocessing and microbial consortia approaches [5]. The former seeks to engineer a single organism to both degrade biomass and produce a high value commodity chemical [6]. The latter seeks to leverage specialist organisms to split the associated metabolic burden between them [7]. Exploiting the natural degradation powers of non-model fungi could prove beneficial in this endeavor
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