1
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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 PMCID: PMC11102524 DOI: 10.1038/s41467-024-48591-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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2
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Bloxham B, Lee H, Gore J. Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches. PLoS Comput Biol 2024; 20:e1012049. [PMID: 38739654 PMCID: PMC11135710 DOI: 10.1371/journal.pcbi.1012049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/29/2024] [Accepted: 04/02/2024] [Indexed: 05/16/2024] Open
Abstract
How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.
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Affiliation(s)
- Blox Bloxham
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hyunseok Lee
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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3
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Ho PY, Nguyen TH, Sanchez JM, DeFelice BC, Huang KC. Resource competition predicts assembly of gut bacterial communities in vitro. Nat Microbiol 2024; 9:1036-1048. [PMID: 38486074 DOI: 10.1038/s41564-024-01625-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024]
Abstract
Microbial community dynamics arise through interspecies interactions, including resource competition, cross-feeding and pH modulation. The individual contributions of these mechanisms to community structure are challenging to untangle. Here we develop a framework to estimate multispecies niche overlaps by combining metabolomics data of individual species, growth measurements in spent media and mathematical models. We applied our framework to an in vitro model system comprising 15 human gut commensals in complex media and showed that a simple model of resource competition accounted for most pairwise interactions. Next, we built a coarse-grained consumer-resource model by grouping metabolomic features depleted by the same set of species and showed that this model predicted the composition of 2-member to 15-member communities with reasonable accuracy. Furthermore, we found that incorporation of cross-feeding and pH-mediated interactions improved model predictions of species coexistence. Our theoretical model and experimental framework can be applied to characterize interspecies interactions in bacterial communities in vitro.
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Affiliation(s)
- Po-Yi Ho
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- School of Engineering, Westlake University, Hangzhou, China.
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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4
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Zhu M, Mu H, Dai X. Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion. iScience 2024; 27:108818. [PMID: 38299113 PMCID: PMC10828813 DOI: 10.1016/j.isci.2024.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/02/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and persist during stress. The global strategy that integrates the growth control and stress response remains to be explored. Here, we find that a moderate induction of (p)ppGpp reduces growth rate but significantly enhances the stress tolerance of E. coli, resulting from a global resource re-allocation from ribosome synthesis to the synthesis of stress-responsive proteins. Strikingly, the activation of stress response by (p)ppGpp is still largely retained in the absence of RpoS. In addition, (p)ppGpp induction could activate the catabolism of alanine and arginine, facilitating the adaption of bacteria to nutrient downshift. Our work demonstrates that the activation of stress response by (p)ppGpp could occur in an RpoS-independent manner and (p)ppGpp enables bacteria to integrate the control of growth and stress response in a seesaw fashion, thus acting as an important global regulator of the bacterial fitness landscape.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
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5
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Narla AV, Hwa T, Murugan A. Dynamic coexistence driven by physiological transitions in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575059. [PMID: 38260536 PMCID: PMC10802591 DOI: 10.1101/2024.01.10.575059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.
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Affiliation(s)
| | - Terence Hwa
- Department of Physics, University of California, San Diego
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6
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Yu XA, McLean C, Hehemann JH, Angeles-Albores D, Wu F, Muszyński A, Corzett CH, Azadi P, Kujawinski EB, Alm EJ, Polz MF. Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics. THE ISME JOURNAL 2024; 18:wrad013. [PMID: 38365244 PMCID: PMC10811730 DOI: 10.1093/ismejo/wrad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.
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Affiliation(s)
- Xiaoqian Annie Yu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Craig McLean
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jan-Hendrik Hehemann
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David Angeles-Albores
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Eric J Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Martin F Polz
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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7
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Narla AV, Hwa T, Murugan A. Dynamic coexistence driven by physiological transitions in microbial communities. ARXIV 2024:arXiv:2401.02556v1. [PMID: 38259349 PMCID: PMC10802671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.
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Affiliation(s)
| | - Terence Hwa
- Department of Physics, University of California, San Diego
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8
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Gralka M. Searching for Principles of Microbial Ecology Across Levels of Biological Organization. Integr Comp Biol 2023; 63:1520-1531. [PMID: 37280177 PMCID: PMC10755194 DOI: 10.1093/icb/icad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.
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Affiliation(s)
- Matti Gralka
- Systems Biology lab, Amsterdam Institute for Life and Environment (A-LIFE), Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV, The Netherlands
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9
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Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
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Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
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10
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Takano S, Vila JCC, Miyazaki R, Sánchez Á, Bajić D. The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies. Mol Biol Evol 2023; 40:msad187. [PMID: 37619982 PMCID: PMC10476156 DOI: 10.1093/molbev/msad187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Microbial strategies for resource use are an essential determinant of their fitness in complex habitats. When facing environments with multiple nutrients, microbes often use them sequentially according to a preference hierarchy, resulting in well-known patterns of diauxic growth. In theory, the evolutionary diversification of metabolic hierarchies could represent a mechanism supporting coexistence and biodiversity by enabling temporal segregation of niches. Despite this ecologically critical role, the extent to which substrate preference hierarchies can evolve and diversify remains largely unexplored. Here, we used genome-scale metabolic modeling to systematically explore the evolution of metabolic hierarchies across a vast space of metabolic network genotypes. We find that only a limited number of metabolic hierarchies can readily evolve, corresponding to the most commonly observed hierarchies in genome-derived models. We further show how the evolution of novel hierarchies is constrained by the architecture of central metabolism, which determines both the propensity to change ranks between pairs of substrates and the effect of specific reactions on hierarchy evolution. Our analysis sheds light on the genetic and mechanistic determinants of microbial metabolic hierarchies, opening new research avenues to understand their evolution, evolvability, and ecology.
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Affiliation(s)
- Sotaro Takano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Jean C C Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
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11
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Lee H, Bloxham B, Gore J. Resource competition can explain simplicity in microbial community assembly. Proc Natl Acad Sci U S A 2023; 120:e2212113120. [PMID: 37603734 PMCID: PMC10469513 DOI: 10.1073/pnas.2212113120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 06/16/2023] [Indexed: 08/23/2023] Open
Abstract
Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using the harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.
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Affiliation(s)
- Hyunseok Lee
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Blox Bloxham
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
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12
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Martinez JA, Delvenne M, Henrion L, Moreno F, Telek S, Dusny C, Delvigne F. Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages. PLoS Comput Biol 2022; 18:e1010674. [PMID: 36315576 PMCID: PMC9648842 DOI: 10.1371/journal.pcbi.1010674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/10/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial consortia are an exciting alternative for increasing the performances of bioprocesses for the production of complex metabolic products. However, the functional properties of microbial communities remain challenging to control, considering the complex interaction mechanisms occurring between co-cultured microbial species. Indeed, microbial communities are highly dynamic and can adapt to changing environmental conditions through complex mechanisms, such as phenotypic diversification. We focused on stabilizing a co-culture of Saccharomyces cerevisiae and Escherichia coli in continuous cultures. Our preliminary data pointed out that transient diauxic shifts could lead to stable co-culture by providing periodic fitness advantages to the yeast. Based on a computational toolbox called MONCKS (for MONod-type Co-culture Kinetic Simulation), we were able to predict the dynamics of diauxic shift for both species based on a cybernetic approach. This toolbox was further used to predict the frequency of diauxic shift to be applied to reach co-culture stability. These simulations were successfully reproduced experimentally in continuous bioreactors with glucose pulsing. Finally, based on a bet-hedging reporter, we observed that the yeast population exhibited an increased phenotypic diversification process in co-culture compared with mono-culture, suggesting that this mechanism could be the basis of the metabolic fitness of the yeast. Being able to manipulate the dynamics of microbial co-cultures is a technical challenge that need to be addressed in order to get a deeper insight about how microbial communities are evolving in their ecological context, as well as for exploiting the potential offered by such communities in an applied context e.g., for setting up more robust bioprocesses relying on the use of several microbial species. In this study, we used continuous cultures of bacteria (E. coli) and yeast (S. cerevisiae) in order to demonstrate that a simple nutrient pulsing strategy can be used for adjusting the composition of the community with time. As expected, during growth on glucose, E. coli quickly outcompeted S. cerevisiae. However, when glucose is pulsed into the culture, increased metabolic fitness of the yeast was observed upon reconsumption of the main side metabolites i.e., acetate and ethanol, leading to a robust oscillating growth profile for both species. The optimal pulsing frequency was predicted based on a cybernetic version of a Monod growth model taking into account the main metabolic routes involved in the process. Considering the limited number of metabolic details needed, this cybernetic approach could be generalized to other communities.
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Affiliation(s)
- J. Andres Martinez
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Matheo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Lucas Henrion
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Fabian Moreno
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Samuel Telek
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
| | - Christian Dusny
- Microscale Analysis and Engineering, Department of Solar Materials, Helmholtz-Centre for Environmental Research- UFZ Leipzig, Leipzig, Germany
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liége, Gembloux, Belgium
- * E-mail:
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