Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity

Abstract

Despite multiple research efforts, the current strategies for exploitation of lignocellulosic plant matter are still far from optimal, being hampered mostly by the difficulty of degrading the recalcitrant parts. An interesting approach is to use lignocellulose-degrading microbial communities by using different environmental sources of microbial inocula. However, it remains unclear whether the inoculum source matters for the degradation process. Here, we addressed this question by verifying the lignocellulose degradation potential of wheat (Triticum aestivum) straw by microbial consortia generated from three different microbial inoculum sources, i.e., forest soil, canal sediment and decaying wood. We selected these consortia through ten sequential-batch enrichments by dilution–to–stimulation using wheat straw as the sole carbon source. We monitored the changes in microbial composition and abundance, as well as their associated degradation capacity and enzymatic activities. Overall, the microbial consortia developed well on the substrate, with progressively-decreasing net average generation times. Each final consortium encompassed bacterial/fungal communities that were distinct in composition but functionally similar, as they all revealed high substrate degradation activities. However, we did find significant differences in the metabolic diversities per consortium: in wood-derived consortia cellobiohydrolases prevailed, in soil-derived ones β-glucosidases, and in sediment-derived ones several activities. Isolates recovered from the consortia showed considerable metabolic diversities across the consortia. This confirmed that, although the overall lignocellulose degradation was similar, each consortium had a unique enzyme activity pattern. Clearly, inoculum source was the key determinant of the composition of the final microbial degrader consortia, yet with varying enzyme activities. Hence, in accord with Beyerinck’s, “everything is everywhere, the environment selects” the source determines consortium composition.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-016-7516-6) contains supplementary material, which is available to authorized users.

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation

“…Other studies obtained similar degradation levels (between 40 and 50% average of all three lignocellulosic fractions [28, 29] with more than 20 different identified strains in the community). Here, we could identify a total of seven synthetic communities with optimal degradation levels.…”

“…Furthermore, we used enzymatic and metabolic-profile assessments to determine the degradation potential and metabolic property of the isolated members of the community. Enzymatic assessments are rather simple, powerful, and quantitative approaches for screening purposes and have been effectively used in analyzing lignocellulose degradation capacities [26, 29, 40]. Here, we used this method for screening purposes, focusing only on enzymes from the GH family, which are related to hemicellulose and cellulose degradation.…”

“…Even though the analysis of enriched communities from environmental samples reveals the dominance of few bacterial phyla (e.g., Proteobacteria , Firmicutes , Chloroflexi , and Bacteroidetes ), the number of ecological dominant species (culturable and unculturable) remains high, i.e., > 20 identified strains [18, 25–29]. The complexity of such systems can make it difficult to disentangle the interactive network that ultimately drives the degradation process.…”

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

“…Recently, Cortes-Tolalpa et al (2016) reported that inoculum source is also a key factor that strongly influences the composition of plant biomass-degrading microbial consortia. However, stochastic factors (“first come, first bite”) might also have affected the selection process and so driven the microbial diversity in the consortia.…”

Characterization of a furan aldehyde-tolerantβ-xylosidase/α-arabinosidase obtained through a synthetic metagenomics approach

“…; Cortes‐Tolalpa et al . ). The microbial origin, the genomic context and the annotation of the genes for these selected GHs all suggest that they play an important role in plant biomass degradation (Jiménez et al .…”