Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru; Kaneko, Kunihiko; Futamata, Hiroyuki

doi:10.1264/jsme2.me13034

Cited by 18 publications

(15 citation statements)

References 69 publications

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“… Kato et al (2005 , 2008 ) constructed model microbial consortia composed of 4–5 bacterial strains, in which all members stably coexisted for long period of time, and demonstrated that existence of both positive and negative interspecies interactions among the members make these consortia stable. The construction of model consortia is a specific and beneficial feature of microbiological research fields, which will also be effective for proof-of-concept studies for theories in the field of macro-ecology ( Haruta et al, 2009 , 2013 ).…”

Section: Introductionmentioning

confidence: 99%

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium

Kato¹,

Yoshida²,

Yamaguchi³

et al. 2014

Front. Microbiol.

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Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.

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Section: Introductionmentioning

confidence: 99%

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium

Kato¹,

Yoshida²,

Yamaguchi³

et al. 2014

Front. Microbiol.

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“…strains YN07 and chemo52. Almost all of the kinetic parameters for phenol of the individual strains were similar to those from the soil bioreactor as described previously (Haruta et al, 2013 ). The K S -values varied within one order of magnitude (from 1 to 10 μM), whereas the K I -values varied within two orders of magnitude (from 100 to 1000 μM).…”

Section: Resultsmentioning

confidence: 93%

“…In a soil bioreactor fed with phenol we previously observed a unique phenomenon where the kinetic parameters shifted toward higher K S and lower K I -values (Futamata et al, 2005 ; Haruta et al, 2013 ). In the present study, to understand this unique phenomenon, SMEs were constructed using isolated strains exhibiting different phenotypic features.…”

Section: Discussionmentioning

confidence: 98%

Interspecies interactions are an integral determinant of microbial community dynamics

et al. 2015

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This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.

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“…In this article, we review various mathematical approaches developed for simulating microbial community dynamics. While a number of published studies have offered insightful perspectives on this subject (e.g., [12][13][14][15][16][17][18]), the present review is unique in the following aspects. First, instead of being confined to specific applications, we cover a wide range of frameworks developed for modeling diverse systems such as biofilms, biogeochemical cycling (in soil or ocean), human microbiota, biotechnology processes, etc.…”

Section: Introductionmentioning

confidence: 99%

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

et al. 2014

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Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.

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Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

Cited by 18 publications

References 69 publications

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium

Interspecies interactions are an integral determinant of microbial community dynamics

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

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