Construction of simplified microbial consortia to degrade recalcitrant materials based on enrichment and dilution-to-extinction cultures

Abstract

The capacity of microbes degrading recalcitrant materials has been extensively explored from environmental remediation to industrial applications. Although significant achievements were obtained with single strains, focus is now going toward the use of microbial consortia because of advantages in terms of functional stability and efficiency. While consortia assembly attempts were made from several known single strains, another approach consists in obtaining consortia from complex environmental microbial communities in search for novel microbial species, genes and functions. However, assembling efficient microbial consortia from complex environmental communities is far from trivial due to large diversity and biotic interactions at play. Here we propose a strategy containing enrichment and dilution-to-extinction cultures to construct simplified microbial consortia (SMC) for keratinous waste management, from complex environmental communities. Gradual dilutions were performed from a keratinolytic microbial consortium, and dilution 10−9 was selected to construct a SMC library. Further compositional analysis and keratinolytic activity assays demonstrated that microbial consortia were successfully simplified, without impacting their biodegradation capabilities. These SMC possess promising potential for efficient keratinous valorization. More importantly, this reasoning and methodology could be transferred to other topics involving screening for simplified communities for biodegradation, thus considerably broadening its application scope.ImportanceMicrobial consortia have got more and more attention and extensive applications due to their potential advantages. However, a high diversity of microbes is likely to hide uncontrollable risks in practice specific to novel strains and complicated interaction networks. Exploring a convenient and efficient way to construct simplified microbial consortia is able to broaden the applied scope of microbes. This study presents the approach based on enrichment and dilution-to-extinction cultures, which gain abundance microbial consortia including some without losing efficiency from the enriched functional microbial community. The microbial interactions at the strain level were evaluated by using compositional identification and correlation analysis, which contribute to revealing the roles of microbes in the degradation process of recalcitrant materials. Our findings provide a systematic scheme to achieve optimizing microbial consortia for biodegradation from an environmental sample, could be readily applied to a range of recalcitrant materials management from environmental remediation to industrial applications.

The plant endosphere world – bacterial life within plants

“…Along these lines, Kong et al (2018) suggested simplified microbial consortia (SMC) comprising core microbial strains identified by microbial community sequencing and network analysis. It has been further demonstrated that the development of SMC from complex microbial communities can be feasible by combining enrichment with the adapted dilution-to-extinction approach to obtain stable and functional microbial consortia (Kang et al, 2019). However, also satellite taxa and rare microbiome taxa have been reported to have important functions (Hol et al, 2015).…”

Top-down engineering of complex communities by directed evolution

“…Based on our simulations, we suggest that (i) ensuring that communities are generationally stable before selection is applied, and (ii) systematically exploring the effect of bottleneck size on between-community variation, will both enhance the effectiveness of both strategies. bottlenecking (also known as dilution-to-extinction [21,22,27,71,82,84] ) is a blunt method for randomly removing "deleterious" taxa, which has the cost of also eliminating potentially beneficial species. Horizontal immigration from the regional pool may create variants that contain new and potentially "beneficial" species, but it has the cost of potentially adding species with deleterious effects.…”

“…Directed evolution can be used to iteratively optimize the function of microbial communities, through sequential rounds of exploration and selection. Previous approaches to engineer communities from the top-down include enrichment (which is often followed by a perturbation such as a bottleneck, to reduce community complexity)[20,[22][23][24]28,82,83] , and selective breeding by artificial selection[1,[31][32][33][34][36][37][38][39][40][41][42] . The directed evolution approach we have studied here combines components of both approaches: the iterative search that is inherent of the latter, with the idea of building stable consortia and exploring compositional variants of the former.…”

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

“…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) have designed a minimal microbial consortium able to produce methane from lignocellulose.…”

“…In previous studies, the enrichment of LMC has been successfully achieved using topdown approaches (14,(31)(32)(33)(34). Here, a combined strategy was set up, coupling dilutionto-stimulation and dilution-to-extinction methods (25,35), to assemble a MELMC capable of growing in a mixture of agricultural plant residues (Fig. 1).…”