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

Jiménez, DJ., Brossi, M. J. D. L., Schuckel, J., Kracun, S. K., Willats, W. G. T. & van Elsas, J. D., Dec-2016, In : Applied Microbiology and Biotechnology. 100, 24, p. 10463-10477 15 p.

Research output: Contribution to journalArticleAcademicpeer-review

  • Diego Javier Jiménez
  • Maria Julia de Lima Brossi
  • Julia Schuckel
  • Stjepan Kresimir Kracun
  • William George Tycho Willats
  • Jan Dirk van Elsas

The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (similar to 59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, beta-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.

Original languageEnglish
Pages (from-to)10463-10477
Number of pages15
JournalApplied Microbiology and Biotechnology
Volume100
Issue number24
Publication statusPublished - Dec-2016

    Keywords

  • Enzyme cocktails, Metagenomics, Metasecretome, Microbial consortia, Plant biomass, THERMOPHILIC BACTERIAL CONSORTIA, COMPLETE GENOME SEQUENCE, WHEAT-STRAW, LIGNOCELLULOSIC BIOMASS, CELLULOSE DEGRADATION, FUNGAL PRETREATMENT, ENZYMES, SOIL, SWITCHGRASS, COMMUNITIES

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