Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers

Abstract

Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.

Authors:
; ;
Publication Date:
Research Org.:
University of Wisconsin-Madison, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1423380
Alternate Identifier(s):
OSTI ID: 1510508
Grant/Contract Number:  
BER DE-FC02-07ER64494; FC02-07ER64494
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 9; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Media SA
Country of Publication:
Switzerland
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; microbial enrichment; lignocellulose; xylan; lignin; Pseudomonas; Sphingobacterium

Citation Formats

Carlos, Camila, Fan, Huan, and Currie, Cameron R. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Switzerland: N. p., 2018. Web. doi:10.3389/fmicb.2018.00364.
Copy to clipboard
Carlos, Camila, Fan, Huan, & Currie, Cameron R. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Switzerland. https://doi.org/10.3389/fmicb.2018.00364
Copy to clipboard
Carlos, Camila, Fan, Huan, and Currie, Cameron R. Thu . "Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers". Switzerland. https://doi.org/10.3389/fmicb.2018.00364.
Copy to clipboard
@article{osti_1423380,
title = {Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers},
author = {Carlos, Camila and Fan, Huan and Currie, Cameron R.},
abstractNote = {Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.},
doi = {10.3389/fmicb.2018.00364},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {Switzerland},
year = {2018},
month = {3}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fmicb.2018.00364
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

TABLE 1 TABLE 1: | Description of the metagenomic samples used in this study.
All figures and tables (6 total)
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases
journal, February 2016

  • Terrón-González, Laura; Martín-Cabello, Guadalupe; Ferrer, Manuel
  • Applied and Environmental Microbiology, Vol. 82, Issue 8
  • DOI: 10.1128/AEM.03811-15

Versatile and open software for comparing large genomes
journal, January 2004

  • Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
  • Genome Biology, Vol. 5, Issue 2, R12
  • DOI: 10.1186/gb-2004-5-2-r12

Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance
journal, November 2016

Natural paradigms of plant cell wall degradation
journal, June 2009

Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation
journal, October 2015

  • de Lima Brossi, Maria Julia; Jiménez, Diego Javier; Cortes-Tolalpa, Larisa
  • Microbial Ecology, Vol. 71, Issue 3
  • DOI: 10.1007/s00248-015-0683-7

Diversity meets decomposition
journal, June 2010

  • Gessner, Mark O.; Swan, Christopher M.; Dang, Christian K.
  • Trends in Ecology & Evolution, Vol. 25, Issue 6
  • DOI: 10.1016/j.tree.2010.01.010

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria
journal, January 2015

  • Salvachúa, Davinia; Karp, Eric M.; Nimlos, Claire T.
  • Green Chemistry, Vol. 17, Issue 11
  • DOI: 10.1039/C5GC01165E

Biological valorization of low molecular weight lignin
journal, December 2016

Development and characterization of a thermophilic, lignin degrading microbiota
journal, December 2017

Construction of a stable microbial community with high cellulose-degradation ability
journal, January 2002

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens
journal, January 2016

  • Pritchard, Leighton; Glover, Rachel H.; Humphris, Sonia
  • Analytical Methods, Vol. 8, Issue 1
  • DOI: 10.1039/C5AY02550H

Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
journal, March 2010

  • DeAngelis, Kristen M.; Gladden, John M.; Allgaier, Martin
  • BioEnergy Research, Vol. 3, Issue 2
  • DOI: 10.1007/s12155-010-9089-z

Ethanol for a Sustainable Energy Future
journal, February 2007

Differential expression of cellulases and xylanases by Cellulomonas flavigena grown on different carbon sources
journal, September 2007

  • Sánchez-Herrera, Leticia M.; Ramos-Valdivia, Ana C.; de la Torre, Mayra
  • Applied Microbiology and Biotechnology, Vol. 77, Issue 3
  • DOI: 10.1007/s00253-007-1190-7

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia
journal, December 2016

  • Mello, Bruno L.; Alessi, Anna M.; McQueen-Mason, Simon
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep38781

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia
journal, October 2017

  • Jiménez, Diego Javier; Dini-Andreote, Francisco; DeAngelis, Kristen M.
  • Trends in Microbiology, Vol. 25, Issue 10
  • DOI: 10.1016/j.tim.2017.05.012

Fuelling the future: microbial engineering for the production of sustainable biofuels
journal, March 2016

  • Liao, James C.; Mi, Luo; Pontrelli, Sammy
  • Nature Reviews Microbiology, Vol. 14, Issue 5
  • DOI: 10.1038/nrmicro.2016.32

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

Isolation of bacterial strains able to metabolize lignin and lignin-related compounds
journal, June 2016

  • Tian, J. -H.; Pourcher, A. -M.; Peu, P.
  • Letters in Applied Microbiology, Vol. 63, Issue 1
  • DOI: 10.1111/lam.12581

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches
journal, July 2016

  • Jiménez, Diego Javier; de Lima Brossi, Maria Julia; Schückel, Julia
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 24
  • DOI: 10.1007/s00253-016-7713-3

Preferential Utilization of Aromatic Compounds over Glucose by Pseudomonas putida CSV86
journal, March 2006

Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost
journal, March 2017

  • Ravi, Krithika; García-Hidalgo, Javier; Gorwa-Grauslund, Marie F.
  • Applied Microbiology and Biotechnology, Vol. 101, Issue 12
  • DOI: 10.1007/s00253-017-8211-y

Microbial degradation of aromatic compounds — from one strategy to four
journal, October 2011

  • Fuchs, Georg; Boll, Matthias; Heider, Johann
  • Nature Reviews Microbiology, Vol. 9, Issue 11, p. 803-816
  • DOI: 10.1038/nrmicro2652

Carbon Source-Dependent Inducible Metabolism of Veratryl Alcohol and Ferulic Acid in Pseudomonas putida CSV86
journal, February 2017

  • Mohan, Karishma; Phale, Prashant S.
  • Applied and Environmental Microbiology, Vol. 83, Issue 8
  • DOI: 10.1128/AEM.03326-16

A novel lignin degradation bacterial consortium for efficient pulping
journal, July 2013

Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment
journal, February 2016

  • Korenblum, Elisa; Jiménez, Diego Javier; van Elsas, Jan Dirk
  • Microbial Biotechnology, Vol. 9, Issue 2
  • DOI: 10.1111/1751-7915.12338

Renewable fuels from biomass: Technical hurdles and economic assessment of biological routes
journal, February 2015

  • Klein-Marcuschamer, Daniel; Blanch, Harvey W.
  • AIChE Journal, Vol. 61, Issue 9
  • DOI: 10.1002/aic.14755

Cellulose-binding polypeptides from Cellulomonas fimi: endoglucanase D (CenD), a family A beta-1,4-glucanase.
journal, April 1993

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
journal, February 2016

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 11, Issue 1
  • DOI: 10.1186/s40793-016-0138-x

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters
journal, December 2015

  • Jia, Yangyang; Wilkins, David; Lu, Hongyuan
  • Applied and Environmental Microbiology, Vol. 82, Issue 5
  • DOI: 10.1128/AEM.03360-15

Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil
journal, September 2016

Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity
journal, May 2016

  • Cortes-Tolalpa, Larisa; Jiménez, Diego Javier; de Lima Brossi, Maria Julia
  • Applied Microbiology and Biotechnology, Vol. 100, Issue 17
  • DOI: 10.1007/s00253-016-7516-6

Features of promising technologies for pretreatment of lignocellulosic biomass
journal, April 2005

Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8
journal, January 2013

  • Shi, Yan; Chai, Liyuan; Tang, Chongjian
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-1

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability
journal, March 2016

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance
journal, January 2011

  • Goldfarb, Katherine C.; Karaoz, Ulas; Hanson, China A.
  • Frontiers in Microbiology, Vol. 2
  • DOI: 10.3389/fmicb.2011.00094

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting
journal, April 2017

  • Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.00644

Xylanases of Cellulomonas flavigena: expression, biochemical characterization, and biotechnological potential
journal, January 2017

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil
journal, September 2015

  • Kato, Souichiro; Chino, Kanako; Kamimura, Naofumi
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14295

Lignocellulose degradation mechanisms across the Tree of Life
journal, December 2015

IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016

  • Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw929

Characterization of pyrene degradation by Pseudomonas sp. strain Jpyr-1 isolated from active sewage sludge
journal, July 2013

Metasecretome analysis of a lignocellulolytic microbial consortium grown on wheat straw, xylan and xylose
journal, December 2015

  • Jiménez, Diego Javier; Maruthamuthu, Mukil; van Elsas, Jan Dirk
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0387-8

Defining the functional traits that drive bacterial decomposer community productivity
journal, March 2017

  • Evans, Rachael; Alessi, Anna M.; Bird, Susannah
  • The ISME Journal, Vol. 11, Issue 7
  • DOI: 10.1038/ismej.2017.22

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data
journal, July 2015

Coexistence among Epiphytic Bacterial Populations Mediated through Nutritional Resource Partitioning
journal, January 1994

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Degradation profile of nixtamalized maize pericarp by the action of the microbial consortium PM-06
    journal, June 2019

    • Serrano-Gamboa, José Germán; Rojas-Herrera, Rafael Antonio; González-Burgos, Araceli
    • AMB Express, Vol. 9, Issue 1
    • DOI: 10.1186/s13568-019-0812-7

    Characterization of Silver fir Wood Decay Classes Using Sugar Metabolites Detected with Ion Chromatography
    journal, January 2019

    • Di Lella, Stefania; Tognetti, Roberto; La Porta, Nicola
    • Journal of Wood Chemistry and Technology, Vol. 39, Issue 2
    • DOI: 10.1080/02773813.2018.1508301

    Experimental Microbiomes: Models Not to Scale
    journal, July 2019

    Degradation profile of nixtamalized maize pericarp by the action of the microbial consortium PM-06
    journal, June 2019

    • Serrano-Gamboa, José Germán; Rojas-Herrera, Rafael Antonio; González-Burgos, Araceli
    • AMB Express, Vol. 9, Issue 1
    • DOI: 10.1186/s13568-019-0812-7
      Sort by:
      [ × clear filter / sort ]

      Figures / Tables found in this record:

      TABLE 1 (p. 3)table
      FIGURE 1 (p. 4)figure
      FIGURE 2 (p. 5)figure
      TABLE 2 (p. 5)table
      FIGURE 3 (p. 6)figure
      FIGURE 4 (p. 7)figure
        [ × clear filter / sort ]
        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.

        Similar Records in DOE PAGES and OSTI.GOV collections: