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.

Keywords: (Hemi) cellulolytic activity; Bacterial–fungal consortia; Bioconversion; Plant biomass.

Fig. 1

Copy numbers (y axis) of (a) bacterial 16S rRNA gene and (b) fungal ITS region across transfers 1, 4, 6 and 9 for all treatments. Transfers and treatments are indicated on the x axis. Error bars represent the standard deviation of the means of three independent replicates. Different lowercase letters (a) refer to differences among the 16S rRNA gene abundances within treatments and uppercase letters (A-C) to differences among ITS1 region abundances across treatments (ANOVA, p < 0.05). Abbreviations: WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2

Fig. 2

Substrate weight loss (%) of different substrates in the transfers 6 and 9. Different lowercase letters (a-d) refer to differences among treatments in T6 and uppercase ones (A-D) to differences among treatments, at T9 (ANOVA, p < 0.01). Abbreviations: WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2

Fig. 3

Degradation rates of lignocellulosic components of substrates in transfer 9. Different letters (a-d) refer to differences among the means of treatments (ANOVA, p < 0.01). Abbreviations: L - lignin, C - cellulose, H - hemicellulose, WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2

Fig. 4

Community fingerprints (PCR-DGGE) of bacterial and fungal communities along transfers 1, 4, 6 and 9 on different substrates; (a) WS1, (b) WS2, (c) SG and (d) CS, for bacterial communities and (e) WS1, (f) WS2, (g) SG and (h) CS, for fungal communities. A, B, C and D represent nMDS and statistical analyses (ANOSIM; global R value) for bacterial communities in the different substrates and E, F, G and H for fungal communities in the different substrates. Abbreviations: WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2

Fig. 5

Community fingerprinting (PCR-DGGE) for (a) bacterial and (b) fungal communities in the final consortia on different substrates and for the original soil inoculum. A and B represent nMDS and statistical analyses (ANOSIM; global R value) for bacterial and fungal communities respectively. To details about B1 - B8 and F1 - F5, see text. Abbreviations: WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2 T9 - transfer 9

Fig. 6

Venn diagram indicating unique and common bacterial and fungal strains across all treatments. Abbreviations: WS1 - wheat straw pH 7.2, WS2 - wheat straw pH 9.0, SG - switchgrass pH 7.2, CS - corn stover pH 7.2