Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation

Abstract

Here, we investigated how different plant biomass, and—for one substrate—pH, drive the composition of degrader microbial consortia. We bred such consortia from forest soil, incubated along nine aerobic sequential - batch enrichments with wheat straw (WS1, pH 7.2; WS2, pH 9.0), switchgrass (SG, pH 7.2), and corn stover (CS, pH 7.2) as carbon sources. Lignocellulosic compounds (lignin, cellulose and xylan) were best degraded in treatment SG, followed by CS, WS1 and WS2. In terms of composition, the consortia became relatively stable after transfers 4 to 6, as evidenced by PCR-DGGE profiles obtained from each consortium DNA. The final consortia differed by ~40 % (bacteria) and ~60 % (fungi) across treatments. A ‘core’ community represented by 5/16 (bacteria) and 3/14 (fungi) bands was discerned, next to a variable part. The composition of the final microbial consortia was strongly driven by the substrate, as taxonomically-diverse consortia appeared in the different substrate treatments, but not in the (WS) different pH one. Biodegradative strains affiliated to Sphingobacterium kitahiroshimense, Raoultella terrigena, Pseudomonas putida, Stenotrophomonas rhizophila (bacteria), Coniochaeta ligniaria and Acremonium sp. (fungi) were recovered in at least three treatments, whereas strains affiliated to Delftia tsuruhatensis, Paenibacillus xylanexedens, Sanguibacter inulus and Comamonas jiangduensis were treatment-specific.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-015-0683-7) 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.…”

“…In order to obtain bacteria with high lignocellulose degradation capacity, we performed an enrichment experiment [28–30] using two sugarcane related substrates—bagasse (B) and straw (St)—and a soil inoculum obtained from a sugarcane plantation, which generated a total of 18 flasks including controls with substrate and no inoculum. Briefly, 10 g of soil inoculum was used to prepare a soil suspension by adding to 90 mL of sodium chloride 0.90% and 10 g of sterile gravel in 250-mL flasks.…”

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

“…Ten randomly taken soil samples of 10 g each were collected from a forest (0 to 10 cm depth) in Groningen, The Netherlands (53.41 N; 6.90 E) in September 2013. Selection of the stable soil-derived microbial consortia has been reported before (Brossi et al 2015). Briefly, cell suspensions were prepared by adding 10 g of mixed soil to 250-ml flasks containing 10 g of sterile gravel in 90 ml of 0.9 % saline solution (NaCl).…”

“…To overcome this hurdle, extracellular enzymes may be harvested from the microbial consortia and applied directly onto the plant biomass (Gladden et al 2011a; Park et al 2012). Enrichments of lignocellulolytic microbes from soils have been performed with switchgrass (SG), wheat straw (WS) and corn stover (CS) as the sole sources of carbon (DeAngelis et al 2013; Jiménez et al 2014a; Brossi et al 2015). Such plant biomass is known to not only contain recalcitrant polysaccharides, but also (easily degradable) small soluble substrates (e.g.…”

“…(1) enriching biodegrader soil-derived microbial consortia on wheat straw, switchgrass and corn stover (Brossi et al 2015) and then (2) re-using the partially degraded substrate as the carbon source for a second growth step with the same microbial consortia. We hypothesised that the once-used plant biomass specifically selected for microbes with high capacities to degrade the more complex plant polysaccharides as well as lignin.…”