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Title: In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi

Abstract

Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitability. Microbial growth simulations reveal that the fungus Anaeromyces robustus is most suited to pair with either the bacterium Clostridia ljungdahlii or the methanogen Methanosarcina barkeri—both organisms also found in the rumen microbiome. By capitalizing on simulations to screen six alternative organisms, valuable experimental time is saved towards identifying stable consortium members. This approach is also readily generalizable to larger systems and allows one to rationally select partnermore » microbes for formation of stable consortia with non-model microbes like anaerobic fungi.« less

Authors:
 [1];  [1];  [2];  [1]
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  1. Univ. of California, Santa Barbara, CA (United States). Department of Chemical Engineering
  2. Univ. of California, Santa Barbara, CA (United States). Department of Computer Science
Publication Date:
Research Org.:
Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1485152
Grant/Contract Number:  
SC0010352
Resource Type:
Accepted Manuscript
Journal Name:
Processes
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2227-9717
Publisher:
Multidisciplinary Digital Publishing Institute (MDPI)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anaerobic fungi; in silico modeling; microbial consortia; dynamic flux balance analysis; non-model organism; lignocellulose

Citation Formats

Wilken, St., Saxena, Mohan, Petzold, Linda, and O’Malley, Michelle. In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi. United States: N. p., 2018. Web. doi:10.3390/pr6010007.
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Wilken, St., Saxena, Mohan, Petzold, Linda, & O’Malley, Michelle. In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi. United States. https://doi.org/10.3390/pr6010007
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Wilken, St., Saxena, Mohan, Petzold, Linda, and O’Malley, Michelle. Mon . "In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi". United States. https://doi.org/10.3390/pr6010007. https://www.osti.gov/servlets/purl/1485152.
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@article{osti_1485152,
title = {In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi},
author = {Wilken, St. and Saxena, Mohan and Petzold, Linda and O’Malley, Michelle},
abstractNote = {Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitability. Microbial growth simulations reveal that the fungus Anaeromyces robustus is most suited to pair with either the bacterium Clostridia ljungdahlii or the methanogen Methanosarcina barkeri—both organisms also found in the rumen microbiome. By capitalizing on simulations to screen six alternative organisms, valuable experimental time is saved towards identifying stable consortium members. This approach is also readily generalizable to larger systems and allows one to rationally select partner microbes for formation of stable consortia with non-model microbes like anaerobic fungi.},
doi = {10.3390/pr6010007},
journal = {Processes},
number = 1,
volume = 6,
place = {United States},
year = {Mon Jan 15 00:00:00 EST 2018},
month = {Mon Jan 15 00:00:00 EST 2018}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.3390/pr6010007
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Citation Metrics:
Cited by: 12 works
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Figures / Tables:

Table 1 Table 1: Genome-scale models of potential consortia partners for the un-modeled anaerobic gut fungi used in this work.
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    Works referencing / citing this record:

    Biomass-degrading enzymes are catabolite repressed in anaerobic gut fungi
    journal, October 2018

    • Henske, John K.; Gilmore, Sean P.; Haitjema, Charles H.
    • AIChE Journal, Vol. 64, Issue 12
    • DOI: 10.1002/aic.16395
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