Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

Abstract

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium preenriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10 −9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

“…3A ). Similarly, Kang et al ( 25 ) reported these observations. Based on these results, we infer that a random reassembly of polymer-degrading bacterial populations could be more frequent in systems with reduced microbial loads and diversity.…”

“…In previous studies, the enrichment of LMC has been successfully achieved using top-down approaches ( 14 , 31 – 34 ). Here, a combined strategy was set up, coupling dilution-to-stimulation and dilution-to-extinction methods ( 25 , 35 ), to assemble an MELMC capable of growing in a mixture of agricultural plant residues ( Fig. 1 ).…”

“…The reduction of diversity/complexity by the extinction method has been used to facilitate the isolation of heterotrophic soil microorganisms ( 40 ), to evaluate the impact of diversity in plant root colonization by fungi ( 41 ), and to analyze the transformation of pharmaceutical compounds in wastewater bioreactors ( 42 ). Interestingly, Kang et al ( 25 ) used this dual approach (i.e., dilution to stimulation/extinction) to select a minimal bacterial consortium able to degrade keratin, allowing them to identify the key players in the degradation process. In our study, beta diversity analyses ( Fig.…”

“…Recently, top-down enrichment strategies have been used to select low-diversity, efficient, stable, and resilient microbial communities with a desired metabolic function ( 25 ). To highlight, Gilmore et al ( 10 ) designed a minimal microbial consortium able to produce methane from lignocellulose.…”

An evolutionary algorithm for designing microbial communities via environmental modification

“…In addition to yielding a growing understanding of the composition of various microbial ecosystems [6][7][8], recent advances in DNA sequencing and synthetic biology have enabled new efforts to engineer synthetic multispecies consortia for a variety of applications [9][10][11]. For example, multispecies systems have been designed to degrade complex substrates or pollutants [12][13][14][15], as well as to produce biofuels and molecules for human consumption [15][16][17][18]. Advances such as these portend the advent of new applications in synthetic ecology, in which communities of microbes can be readily designed for a vast number of useful outputs.…”