Metabolic modeling of a mutualistic microbial community
Abstract
The rate of production of methane in many environmentsdepends upon mutualistic interactions between sulfate-reducing bacteriaand methanogens. To enhance our understanding of these relationships, wetook advantage of the fully sequenced genomes of Desulfovibrio vulgarisand Methanococcus maripaludis to produce and analyze the firstmultispecies stoichiometric metabolic model. Model results were comparedto data on growth of the co-culture on lactate in the absence of sulfate.The model accurately predicted several ecologically relevantcharacteristics, including the flux of metabolites and the ratio of D.vulgaris to M. maripaludis cells during growth. In addition, the modeland our data suggested that it was possible to eliminate formate as aninterspecies electron shuttle, but hydrogen transfer was essential forsyntrophic growth. Our work demonstrated that reconstructed metabolicnetworks and stoichiometric models can serve not only to predictmetabolic fluxes and growth phenotypes of single organisms, but also tocapture growth parameters and community composition of simple bacterialcommunities.
- Authors:
- Publication Date:
- Research Org.:
- COLLABORATION - U.Washington
- Sponsoring Org.:
- USDOE Director. Office of Science. Biological andEnvironmental Research
- OSTI Identifier:
- 925518
- Report Number(s):
- LBNL-60299
R&D Project: VGTLUW; BnR: KP1501021; TRN: US200809%%781
- DOE Contract Number:
- DE-AC02-05CH11231
- Resource Type:
- Journal Article
- Resource Relation:
- Journal Name: Molecular Systems Biology; Journal Volume: 3; Journal Issue: 92; Related Information: Journal Publication Date: 03/13/2007
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; COMMUNITIES; DESULFOVIBRIO; ELECTRONS; FORMATES; HYDROGEN TRANSFER; LACTATES; METABOLITES; METHANE; PRODUCTION; SIMULATION; SULFATE-REDUCING BACTERIA; Desulfovibrio flux-balance modeling interspecies hydrogentransfer Methanococcus syntrophy
Citation Formats
Stolyar, Sergey, Van Dien, Steve, Hillesland, Kristina Linnea, Pinel, Nicolas, Lie, Thomas J., Leigh, John A., and Stahl, David A.. Metabolic modeling of a mutualistic microbial community. United States: N. p., 2007.
Web. doi:10.1038/msb4100131.
Stolyar, Sergey, Van Dien, Steve, Hillesland, Kristina Linnea, Pinel, Nicolas, Lie, Thomas J., Leigh, John A., & Stahl, David A.. Metabolic modeling of a mutualistic microbial community. United States. doi:10.1038/msb4100131.
Stolyar, Sergey, Van Dien, Steve, Hillesland, Kristina Linnea, Pinel, Nicolas, Lie, Thomas J., Leigh, John A., and Stahl, David A.. Tue .
"Metabolic modeling of a mutualistic microbial community". United States.
doi:10.1038/msb4100131.
@article{osti_925518,
title = {Metabolic modeling of a mutualistic microbial community},
author = {Stolyar, Sergey and Van Dien, Steve and Hillesland, Kristina Linnea and Pinel, Nicolas and Lie, Thomas J. and Leigh, John A. and Stahl, David A.},
abstractNote = {The rate of production of methane in many environmentsdepends upon mutualistic interactions between sulfate-reducing bacteriaand methanogens. To enhance our understanding of these relationships, wetook advantage of the fully sequenced genomes of Desulfovibrio vulgarisand Methanococcus maripaludis to produce and analyze the firstmultispecies stoichiometric metabolic model. Model results were comparedto data on growth of the co-culture on lactate in the absence of sulfate.The model accurately predicted several ecologically relevantcharacteristics, including the flux of metabolites and the ratio of D.vulgaris to M. maripaludis cells during growth. In addition, the modeland our data suggested that it was possible to eliminate formate as aninterspecies electron shuttle, but hydrogen transfer was essential forsyntrophic growth. Our work demonstrated that reconstructed metabolicnetworks and stoichiometric models can serve not only to predictmetabolic fluxes and growth phenotypes of single organisms, but also tocapture growth parameters and community composition of simple bacterialcommunities.},
doi = {10.1038/msb4100131},
journal = {Molecular Systems Biology},
number = 92,
volume = 3,
place = {United States},
year = {Tue Mar 13 00:00:00 EDT 2007},
month = {Tue Mar 13 00:00:00 EDT 2007}
}
-
Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community-level data as a critical input for the networkmore »
-
Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants is accepted for publication in MPMI
Most bacterial symbionts of plants are phenotypically characterized by their parasitic or matualistic relationship with the host; however, the genomic characteristics that likely discriminate mutualistic symbionts from pathogens of plants are poorly understood. This study comparatively analyzed the genomes of 54 plant-symbiontic bacteria, 27 mutualists and 27 pathogens, to discover genomic determinants of their parasitic and mutualistic nature in terms of protein family domains, KEGG orthologous groups, metabolic pathways and families of carbohydrate-active enzymes (CAZymes). We further used all bacteria with sequenced genomesl, published microarrays and transcriptomics experimental datasets, and literature to validate and to explore results of the comparison.more » -
Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments
Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors.