Publication

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

Jiménez, DJ., de Lima Brossi, M. J., 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

APA

Jiménez, DJ., de Lima Brossi, M. J., Schuckel, J., Kracun, S. K., Willats, W. G. T., & van Elsas, J. D. (2016). Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. Applied Microbiology and Biotechnology, 100(24), 10463-10477. https://doi.org/10.1007/s00253-016-7713-3

Author

Jiménez, Diego Javier ; de Lima Brossi, Maria Julia ; Schuckel, Julia ; Kracun, Stjepan Kresimir ; Willats, William George Tycho ; van Elsas, Jan Dirk. / Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. In: Applied Microbiology and Biotechnology. 2016 ; Vol. 100, No. 24. pp. 10463-10477.

Harvard

Jiménez, DJ, de Lima Brossi, MJ, Schuckel, J, Kracun, SK, Willats, WGT & van Elsas, JD 2016, 'Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches', Applied Microbiology and Biotechnology, vol. 100, no. 24, pp. 10463-10477. https://doi.org/10.1007/s00253-016-7713-3

Standard

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. / Jiménez, Diego Javier; de Lima Brossi, Maria Julia; Schuckel, Julia; Kracun, Stjepan Kresimir; Willats, William George Tycho; van Elsas, Jan Dirk.

In: Applied Microbiology and Biotechnology, Vol. 100, No. 24, 12.2016, p. 10463-10477.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Jiménez DJ, de Lima Brossi MJ, Schuckel J, Kracun SK, Willats WGT, van Elsas JD. Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. Applied Microbiology and Biotechnology. 2016 Dec;100(24):10463-10477. https://doi.org/10.1007/s00253-016-7713-3


BibTeX

@article{ea2f1dcc4cfa49af8c4c555c9d046494,
title = "Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches",
abstract = "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.",
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",
author = "Diego Javier Jim{\'e}nez and {de Lima Brossi}, {Maria Julia} and Julia Schuckel and Kracun, {Stjepan Kresimir} and Willats, {William George Tycho} and {van Elsas}, {Jan Dirk}",
year = "2016",
month = "12",
doi = "10.1007/s00253-016-7713-3",
language = "English",
volume = "100",
pages = "10463--10477",
journal = "Applied Microbiology and Biotechnology",
issn = "0175-7598",
publisher = "SPRINGER",
number = "24",

}

RIS

TY - JOUR

T1 - Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

AU - Jiménez, Diego Javier

AU - de Lima Brossi, Maria Julia

AU - Schuckel, Julia

AU - Kracun, Stjepan Kresimir

AU - Willats, William George Tycho

AU - van Elsas, Jan Dirk

PY - 2016/12

Y1 - 2016/12

N2 - 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.

AB - 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.

KW - Enzyme cocktails

KW - Metagenomics

KW - Metasecretome

KW - Microbial consortia

KW - Plant biomass

KW - THERMOPHILIC BACTERIAL CONSORTIA

KW - COMPLETE GENOME SEQUENCE

KW - WHEAT-STRAW

KW - LIGNOCELLULOSIC BIOMASS

KW - CELLULOSE DEGRADATION

KW - FUNGAL PRETREATMENT

KW - ENZYMES

KW - SOIL

KW - SWITCHGRASS

KW - COMMUNITIES

U2 - 10.1007/s00253-016-7713-3

DO - 10.1007/s00253-016-7713-3

M3 - Article

VL - 100

SP - 10463

EP - 10477

JO - Applied Microbiology and Biotechnology

JF - Applied Microbiology and Biotechnology

SN - 0175-7598

IS - 24

ER -

ID: 38524955