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Meacock OJ, Mitri S. Environment-Organism Feedbacks Drive Changes in Ecological Interactions. Ecol Lett 2025; 28:e70027. [PMID: 39737705 DOI: 10.1111/ele.70027] [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: 05/01/2024] [Revised: 11/06/2024] [Accepted: 11/09/2024] [Indexed: 01/01/2025]
Abstract
Ecological interactions are foundational to our understanding of community composition and function. While interactions are known to change depending on the environmental context, it has generally been assumed that external environmental factors are responsible for driving these dependencies. Here, we derive a theoretical framework which instead focuses on how intrinsic environmental changes caused by the organisms themselves alter interaction values. Our central concept is the 'instantaneous interaction', which captures the feedback between the current environmental state and organismal growth, generating spatiotemporal context-dependencies as organisms modify their environment over time and/or space. We use small microbial communities to illustrate how this framework can predict time-dependencies in a toxin degradation system, and relate time- and spatial-dependencies in crossfeeding communities. By re-centring the relationship between organisms and their environment, our framework predicts the variations in interactions wherever intrinsic, organism-driven environmental change dominates over external drivers.
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Affiliation(s)
- Oliver J Meacock
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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2
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Silva-Portela RDCB, Minnicelli CF, Freitas JF, Fonseca MMB, Lima Silva DFD, Silva-Barbalho KK, Falcão RM, Bruce T, Cavalcante JVF, Dalmolin RJS, Agnez-Lima LF. Unlocking the transcriptional profiles of an oily waste-degrading bacterial consortium. JOURNAL OF HAZARDOUS MATERIALS 2024; 485:136866. [PMID: 39694004 DOI: 10.1016/j.jhazmat.2024.136866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 11/27/2024] [Accepted: 12/11/2024] [Indexed: 12/20/2024]
Abstract
This study investigates the transcriptional profile of a novel oil-degrading microbial consortium (MC1) composed of four bacterial isolates from Brazilian oil reservoirs: Acinetobacter baumannii subsp. oleum ficedula, Bacillus velezensis, Enterobacter asburiae, and Klebsiella pneumoniae. Genomic analysis revealed an enrichment of genes associated with xenobiotic degradation, particularly for aminobenzoate, atrazine, and aromatic compounds, compared to reference genomes. The consortium demonstrated superior growth and complete oil degradation relative to individual strains. Transcriptional profiling during growth on oil indicated that key subsystems involved membrane transport, stress response, and dehydrogenase complexes, crucial for hydrocarbon uptake. Notably, genes for degrading aromatics, naphthalene, and chloroalkanes were significantly expressed during the initial oil growth phase. The dominant gene expressed was alkane 1-monooxygenase, particularly in the late growth phase. While A. baumannii exhibited the highest transcriptional activity, B. velezensis showed lower activity despite possessing numerous hydrocarbon degradation genes. The synergistic interactions among strains, confirmed by complementary gene expression patterns, position MC1 as a promising bioremediation agent for hydrocarbon-contaminated environments. However, more than collaboration, competition for nutrient uptake and resistance to stress drive gene expression and adaptation in the presence of oil as the carbon source.
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Affiliation(s)
| | | | - Júlia Firme Freitas
- Department of Cell Biology and Genetics, Federal University of Rio Grande do Norte, Natal 59078900, Brazil
| | | | | | | | - Raul Maia Falcão
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal 59078900, Brazil
| | - Thiago Bruce
- Department of Cell Biology and Genetics, Federal University of Rio Grande do Norte, Natal 59078900, Brazil
| | | | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal 59078900, Brazil; Department of Biochemistry, Federal University of Rio Grande do Norte, Natal 59078900, Brazil
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3
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O'Connor MR, Thoma CJ, Dodge AG, Wackett LP. Phenotypic Plasticity During Organofluorine Degradation Revealed by Adaptive Evolution. Microb Biotechnol 2024; 17:e70066. [PMID: 39724398 DOI: 10.1111/1751-7915.70066] [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: 08/23/2024] [Revised: 11/02/2024] [Accepted: 11/20/2024] [Indexed: 12/28/2024] Open
Abstract
A major factor limiting the biodegradation of organofluorine compounds has been highlighted as fluoride anion toxicity produced by defluorinating enzymes. Here, two highly active defluorinases with different activities were constitutively expressed in Pseudomonas putida ATCC 12633 to examine adaption to fluoride stress. Each strain was grown on α-fluorophenylacetic acid as the sole carbon source via defluorination to mandelic acid, and each showed immediate fluoride release and delayed growth. Adaptive evolution was performed for each recombinant strain by serial transfer. Both strains adapted to show a much shorter lag and a higher growth yield. The observed adaptation occurred rapidly and reproducibly, within 50 generations each time. After adaption, growth with 50-70 mM α-fluorophenylacetic acid was significantly faster with more fluoride release than a preadapted culture due to larger cell populations. Genomic sequencing of both pre- and postadapted strain pairs revealed decreases in the defluorinase gene content. With both defluorinases, adaption produced a 56%-57% decrease in the plasmid copy number. Additionally, during adaption of the strain expressing the faster defluorinase, two plasmids were present: the original and a derivative in which the defluorinase gene was deleted. An examination of the enzyme rates in the pathway suggested that the defluorinase rate was concurrently optimised for pathway flux and minimising fluoride toxicity. The rapid alteration of plasmid copy number and mutation was consistent with other studies on microbial responses to stresses such as antibiotics. The data presented here support the idea that fluoride stress is significant during the biodegradation of organofluorine compounds and suggest engineered strains will be under strong selective pressure to decrease fluoride stress.
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Affiliation(s)
- Madeline R O'Connor
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, USA
| | - Calvin J Thoma
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, USA
| | - Anthony G Dodge
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, USA
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology Institute, University of Minnesota, Twin Cities, USA
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4
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Al-Tameemi Z, Rodríguez-Verdugo A. Microbial diversification is maintained in an experimentally evolved synthetic community. mSystems 2024; 9:e0105324. [PMID: 39404341 PMCID: PMC11575400 DOI: 10.1128/msystems.01053-24] [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: 08/05/2024] [Accepted: 09/11/2024] [Indexed: 11/20/2024] Open
Abstract
Microbial communities are incredibly diverse. Yet, the eco-evolutionary processes originating and maintaining this diversity remain understudied. Here, we investigate the patterns of diversification for Pseudomonas putida evolving in isolation and with Acinetobacter johnsonii leaking resources used by P. putida. We experimentally evolved four experimental replicates in monoculture and co-culture for 200 generations. We observed that P. putida diversified into two distinct morphotypes that differed from their ancestor by single-point mutations. One of the most prominent mutations hit the fleQ gene encoding the master regulator of flagella and biofilm formation. We experimentally confirmed that fleQ mutants were unable to swim and formed less biofilm than their ancestor, but they also produced higher yields. Interestingly, the fleQ genotype and other mutations swept to fixation in monocultures but not in co-cultures. In co-cultures, the two lineages stably coexisted for approximately 150 generations. We hypothesized that A. johnsonii modulates the coexistence of the two lineages through frequency-dependent selection. However, invasion experiments with two genotypes in monoculture and co-culture did not support this hypothesis. Finally, we conducted an evolutionary "replay" experiment to assess whether the presence or absence of A. johnsonii influenced the coexistence of morphotypes at the population level. Interestingly, A. johnsonii had a stabilizing effect on the co-culture. Overall, our study suggests that interspecies interactions play an important role in shaping patterns of diversification in microbial communities. IMPORTANCE In nature, bacteria live in microbial communities and interact with other species, for example, through the exchange of resources leaked into the external environment (i.e., cross-feeding interactions). The role that these cross-feeding interactions play in shaping patterns of diversification remains understudied. Using a simple bacterial system in which one species cross-feeds resources to a second species (commensal species), we showed that the commensal species diversified into two subpopulations that persisted only when the cross-feeder partner was present. We further observed loss-of-function mutations in flagellar genes that were fixed in monocultures but not in co-cultures. Our findings suggest that cross-feeding species influence patterns of diversification of other species. Given that nutrient leakage is pervasive in microbial communities, the findings from this study have the potential to extend beyond our specific bacterial system. Importantly, our study has contributed to answering the larger question of whether species evolved differently in isolation versus when interacting with other species.
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Affiliation(s)
- Zahraa Al-Tameemi
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
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5
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Letten AD, Yamamichi M, Richardson JA, Ke PJ. Microbial Dormancy Supports Multi-Species Coexistence Under Resource Fluctuations. Ecol Lett 2024; 27:e14507. [PMID: 39354904 DOI: 10.1111/ele.14507] [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: 02/12/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 10/03/2024]
Abstract
The ability for microbes to enter dormant states is adaptive under resource fluctuations and has been linked to the maintenance of diversity. Nevertheless, the mechanism by which microbial dormancy gives rise to the density-dependent feedbacks required for stable coexistence under resource fluctuations is not well understood. Via analysis of consumer-resource models, we show that the stable coexistence of dormancy and non-dormancy strategists is a consequence of the former benefiting more from resource fluctuations while simultaneously reducing overall resource variability, which sets up the requisite negative frequency dependence. Moreover, we find that dormants can coexist alongside gleaner and opportunist strategies in a competitive-exclusion-defying case of three species coexistence on a single resource. This multi-species coexistence is typically characterised by non-simple assembly rules that cannot be predicted from pairwise competition outcomes. The diversity maintained via this three-way trade-off represents a novel phenomenon that is ripe for further theoretical and empirical inquiry.
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Affiliation(s)
- Andrew D Letten
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Japan
| | - James A Richardson
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Po-Ju Ke
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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6
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Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [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: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
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Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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7
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Abdoli P, Vulin C, Lepiz M, Chase AB, Weihe C, Rodríguez-Verdugo A. Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders. FEMS Microbiol Ecol 2024; 100:fiae102. [PMID: 39020097 PMCID: PMC11289631 DOI: 10.1093/femsec/fiae102] [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: 01/13/2024] [Revised: 07/02/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024] Open
Abstract
Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.
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Affiliation(s)
- Parmis Abdoli
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Clément Vulin
- Department of Fundamental Microbiology, University of Lausanne, Biophore, CH-1015 Lausanne, Switzerland
| | - Miriam Lepiz
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, 3225 Daniel Avenue, Suite 207, Heroy Hall, Dallas, TX 75205, United States
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Alejandra Rodríguez-Verdugo
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
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Gupta G, Labrie S, Filteau M. Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening. Microorganisms 2024; 12:1396. [PMID: 39065164 PMCID: PMC11279232 DOI: 10.3390/microorganisms12071396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve Labrie
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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9
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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10
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Zhu S, Hong J, Wang T. Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 2024; 15:800. [PMID: 38280843 PMCID: PMC10821886 DOI: 10.1038/s41467-024-45154-w] [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: 07/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.
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Affiliation(s)
- Shiben Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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11
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McNichol SM, Sanchez-Quete F, Loeb SK, Teske AP, Shah Walter SR, Mahmoudi N. Dynamics of carbon substrate competition among heterotrophic microorganisms. THE ISME JOURNAL 2024; 18:wrae018. [PMID: 38366177 PMCID: PMC10942773 DOI: 10.1093/ismejo/wrae018] [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: 09/12/2023] [Revised: 01/06/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
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Affiliation(s)
- Samuel M McNichol
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
| | - Fernando Sanchez-Quete
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Stephanie K Loeb
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd, Lewes, DE 19958, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
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12
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Burkart T, Willeke J, Frey E. Periodic temporal environmental variations induce coexistence in resource competition models. Phys Rev E 2023; 108:034404. [PMID: 37849086 DOI: 10.1103/physreve.108.034404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/13/2023] [Indexed: 10/19/2023]
Abstract
Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic population dynamics model to study how, and under what conditions, a periodic temporal environmental variation can alter an ecosystem's composition and biodiversity. We demonstrate that using timescale separation allows one to qualitatively predict the long-term population dynamics of interacting species in varying environments. We show that the notion of Tilman's R* rule, a well-known principle that applies for constant environments, can be extended to periodically varying environments if the timescale of environmental changes (e.g., seasonal variations) is much faster than the timescale of population growth (doubling time in bacteria). When these timescales are similar, our analysis shows that a varying environment deters the system from reaching a steady state, and stable coexistence between multiple species becomes possible. Our results posit that biodiversity can in part be attributed to natural environmental variations.
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Affiliation(s)
- Tom Burkart
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Jan Willeke
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 München, Germany
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13
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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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14
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Yang D, Kato H, Kawatsu K, Osada Y, Azuma T, Nagata Y, Kondoh M. Reconstruction of a Soil Microbial Network Induced by Stress Temperature. Microbiol Spectr 2022; 10:e0274822. [PMID: 35972265 PMCID: PMC9602341 DOI: 10.1128/spectrum.02748-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023] Open
Abstract
The microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.
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Affiliation(s)
- Dailin Yang
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kazutaka Kawatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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15
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Reyes-González D, De Luna-Valenciano H, Utrilla J, Sieber M, Peña-Miller R, Fuentes-Hernández A. Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia. ROYAL SOCIETY OPEN SCIENCE 2022; 9:212008. [PMID: 35592760 PMCID: PMC9066302 DOI: 10.1098/rsos.212008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/25/2022] [Indexed: 05/03/2023]
Abstract
Microbial ecosystems are composed of multiple species in constant metabolic exchange. A pervasive interaction in microbial communities is metabolic cross-feeding and occurs when the metabolic burden of producing costly metabolites is distributed between community members, in some cases for the benefit of all interacting partners. In particular, amino acid auxotrophies generate obligate metabolic inter-dependencies in mixed populations and have been shown to produce a dynamic profile of interaction that depends upon nutrient availability. However, identifying the key components that determine the pair-wise interaction profile remains a challenging problem, partly because metabolic exchange has consequences on multiple levels, from allocating proteomic resources at a cellular level to modulating the structure, function and stability of microbial communities. To evaluate how ppGpp-mediated resource allocation drives the population-level profile of interaction, here we postulate a multi-scale mathematical model that incorporates dynamics of proteome partition into a population dynamics model. We compare our computational results with experimental data obtained from co-cultures of auxotrophic Escherichia coli K12 strains under a range of amino acid concentrations and population structures. We conclude by arguing that the stringent response promotes cooperation by inhibiting the growth of fast-growing strains and promoting the synthesis of metabolites essential for other community members.
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Affiliation(s)
- D. Reyes-González
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
| | - H. De Luna-Valenciano
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
- Systems Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - J. Utrilla
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
| | - M. Sieber
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - R. Peña-Miller
- Systems Biology Program, Center for Genomic Sciences, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - A. Fuentes-Hernández
- Synthetic Biology Program, Center for Genomic Sciences, Universidad Autónoma de México, 62220 Cuernavaca, Mexico
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16
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Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment. THE ISME JOURNAL 2022; 16:1453-1463. [PMID: 35079136 PMCID: PMC9038690 DOI: 10.1038/s41396-022-01189-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/19/2021] [Accepted: 01/06/2022] [Indexed: 01/07/2023]
Abstract
Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri. We inoculated the co-cultures onto agar surfaces and allowed them to expand (i.e. range expansion) while fluctuating environmental conditions that alter the dependency between the two strains. We alternated between anoxic conditions that induce a mutualistic interaction and oxic conditions that induce a competitive interaction. We observed co-occurrence of both strains in rare and highly localized clusters (referred to as “spatial jackpot events”) that persist during environmental fluctuations. To resolve the underlying mechanisms for the emergence of spatial jackpot events, we used a mechanistic agent-based mathematical model that resolves growth and dispersal at the scale relevant to individual cells. While co-culture composition varied with the strength of the mutualistic interaction and across environmental fluctuations, the model provides insights into the formation of spatially resolved substrate landscapes with localized niches that support the co-occurrence of the two strains and secure co-culture function. This study highlights that in addition to spatial patterns that emerge in response to environmental fluctuations, localized spatial jackpot events ensure persistence of strains across dynamic conditions.
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17
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Malik AA, Bouskill NJ. Drought impacts on microbial trait distribution and feedback to soil carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ashish A. Malik
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
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18
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Shibasaki S, Mobilia M, Mitri S. Exclusion of the fittest predicts microbial community diversity in fluctuating environments. J R Soc Interface 2021; 18:20210613. [PMID: 34610260 PMCID: PMC8492180 DOI: 10.1098/rsif.2021.0613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/09/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species' ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Mauro Mobilia
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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19
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Gupta G, Ndiaye A, Filteau M. Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. Front Microbiol 2021; 12:700752. [PMID: 34646243 PMCID: PMC8503676 DOI: 10.3389/fmicb.2021.700752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022] Open
Abstract
Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Amadou Ndiaye
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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20
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Abstract
Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.
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21
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A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations. Nat Commun 2021; 12:3662. [PMID: 34135315 PMCID: PMC8209047 DOI: 10.1038/s41467-021-23439-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
It has long been known that bacteria coordinate their physiology with their nutrient environment, yet our current understanding offers little intuition for how bacteria respond to the second-to-minute scale fluctuations in nutrient concentration characteristic of many microbial habitats. To investigate the effects of rapid nutrient fluctuations on bacterial growth, we couple custom microfluidics with single-cell microscopy to quantify the growth rate of E. coli experiencing 30 s to 60 min nutrient fluctuations. Compared to steady environments of equal average concentration, fluctuating environments reduce growth rate by up to 50%. However, measured reductions in growth rate are only 38% of the growth loss predicted from single nutrient shifts. This enhancement derives from the distinct growth response of cells grown in environments that fluctuate rather than shift once. We report an unexpected physiology adapted for growth in nutrient fluctuations and implicate nutrient timescale as a critical environmental parameter beyond nutrient identity and concentration. Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.
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22
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Nev OA, Lindsay RJ, Jepson A, Butt L, Beardmore RE, Gudelj I. Predicting microbial growth dynamics in response to nutrient availability. PLoS Comput Biol 2021; 17:e1008817. [PMID: 33735173 PMCID: PMC8009381 DOI: 10.1371/journal.pcbi.1008817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 03/30/2021] [Accepted: 02/17/2021] [Indexed: 01/04/2023] Open
Abstract
Developing mathematical models to accurately predict microbial growth dynamics remains a key challenge in ecology, evolution, biotechnology, and public health. To reproduce and grow, microbes need to take up essential nutrients from the environment, and mathematical models classically assume that the nutrient uptake rate is a saturating function of the nutrient concentration. In nature, microbes experience different levels of nutrient availability at all environmental scales, yet parameters shaping the nutrient uptake function are commonly estimated for a single initial nutrient concentration. This hampers the models from accurately capturing microbial dynamics when the environmental conditions change. To address this problem, we conduct growth experiments for a range of micro-organisms, including human fungal pathogens, baker's yeast, and common coliform bacteria, and uncover the following patterns. We observed that the maximal nutrient uptake rate and biomass yield were both decreasing functions of initial nutrient concentration. While a functional form for the relationship between biomass yield and initial nutrient concentration has been previously derived from first metabolic principles, here we also derive the form of the relationship between maximal nutrient uptake rate and initial nutrient concentration. Incorporating these two functions into a model of microbial growth allows for variable growth parameters and enables us to substantially improve predictions for microbial dynamics in a range of initial nutrient concentrations, compared to keeping growth parameters fixed.
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Affiliation(s)
- Olga A. Nev
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Richard J. Lindsay
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Alys Jepson
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Lisa Butt
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Robert E. Beardmore
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Ivana Gudelj
- Biosciences and Living Systems Institute, University of Exeter, Exeter, United Kingdom
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23
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Defrenne CE, Abs E, Longhi Cordeiro A, Dietterich L, Hough M, Jones JM, Kivlin SN, Chen W, Cusack D, Franco ALC, Khasanova A, Stover D, Romero‐Olivares AL. The Ecology Underground coalition: building a collaborative future of belowground ecology and ecologists. THE NEW PHYTOLOGIST 2021; 229:3058-3064. [PMID: 33616944 PMCID: PMC7986216 DOI: 10.1111/nph.17163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Camille E. Defrenne
- Climate Change Science Institute and Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTN37830USA
| | - Elsa Abs
- Department of Ecology and Evolutionary BiologyUniversity of California Irvine321 SteinhausIrvineCA92697USA
| | - Amanda Longhi Cordeiro
- Department of Ecosystem Science and SustainabilityColorado State UniversityCampus Delivery 1476Fort CollinsCO80523USA
| | - Lee Dietterich
- Department of Ecosystem Science and SustainabilityColorado State UniversityCampus Delivery 1476Fort CollinsCO80523USA
| | - Moira Hough
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZ85721USA
| | - Jennifer M. Jones
- The Kellogg Biological StationMichigan State UniversityHickory CornersMI48824USA
| | - Stephanie N. Kivlin
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTN37996USA
| | - Weile Chen
- College of Life SciencesZhejiang UniversityHangzhouZhejiang310027China
| | - Daniela Cusack
- Department of Ecosystem Science and SustainabilityColorado State UniversityCampus Delivery 1476Fort CollinsCO80523USA
| | | | - Albina Khasanova
- Department of Integrative BiologyUniversity of Texas at AustinAustinTX78712USA
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24
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Nguyen J, Lara-Gutiérrez J, Stocker R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol Rev 2020; 45:6041721. [PMID: 33338228 PMCID: PMC8371271 DOI: 10.1093/femsre/fuaa068] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
From the homeostasis of human health to the cycling of Earth's elements, microbial activities underlie environmental, medical and industrial processes. These activities occur in chemical and physical landscapes that are highly dynamic and experienced by bacteria as fluctuations. In this review, we first discuss how bacteria can experience both spatial and temporal heterogeneity in their environments as temporal fluctuations of various timescales (seconds to seasons) and types (nutrient, sunlight, fluid flow, etc.). We then focus primarily on nutrient fluctuations to discuss how bacterial communities, populations and single cells respond to environmental fluctuations. Overall, we find that environmental fluctuations are ubiquitous and diverse, and strongly shape microbial behavior, ecology and evolution when compared with environments in which conditions remain constant over time. We hope this review may serve as a guide toward understanding the significance of environmental fluctuations in microbial life, such that their contributions and implications can be better assessed and exploited.
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Affiliation(s)
- Jen Nguyen
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juanita Lara-Gutiérrez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
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25
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Rapid evolution destabilizes species interactions in a fluctuating environment. ISME JOURNAL 2020; 15:450-460. [PMID: 33024292 DOI: 10.1038/s41396-020-00787-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Positive species interactions underlie the functioning of ecosystems. Given their importance, it is crucial to understand the stability of positive interactions over evolutionary timescales, in both constant and fluctuating environments; e.g., environments interrupted with periods of competition. We addressed this question using a two-species microbial system in which we modulated interactions according to the nutrient provided. We evolved in parallel four experimental replicates of species growing in isolation or together in consortia for 200 generations in both a constant and fluctuating environment with daily changes between commensalism and competition. We sequenced full genomes of single clones isolated at different time points during the experiment. We found that the two species coexisted over 200 generations in the constant commensal environment. In contrast, in the fluctuating environment, coexistence broke down when one of the species went extinct in two out of four cases. We showed that extinction was highly deterministic: when we replayed the evolution experiment from an intermediate time point we repeatably reproduced species extinction. We further show that these dynamics were driven by adaptive mutations in a small set of genes. In conclusion, in a fluctuating environment, rapid evolution destabilizes the long-term stability of positive pairwise interactions.
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26
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Bär J, Boumasmoud M, Kouyos RD, Zinkernagel AS, Vulin C. Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application. Sci Rep 2020; 10:16084. [PMID: 32999342 PMCID: PMC7528005 DOI: 10.1038/s41598-020-72979-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Populations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through antibiotic challenges and secure population survival. This heterogeneity can be studied in complex environmental or clinical samples by spreading the bacteria on agar plates and monitoring time to growth resumption in order to infer their metabolic state distribution. We present ColTapp, the Colony Time-lapse application for bacterial colony growth quantification. Its intuitive graphical user interface allows users to analyze time-lapse images of agar plates to monitor size, color and morphology of colonies. Additionally, images at isolated timepoints can be used to estimate lag time. Using ColTapp, we analyze a dataset of Staphylococcus aureus time-lapse images including populations with heterogeneous lag time. Colonies on dense plates reach saturation early, leading to overestimation of lag time from isolated images. We show that this bias can be corrected by taking into account the area available to each colony on the plate. We envision that in clinical settings, improved analysis of colony growth dynamics may help treatment decisions oriented towards personalized antibiotic therapies.
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Affiliation(s)
- Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. .,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092, Zurich, Switzerland. .,Department of Environmental Microbiology, 8600, Eawag, Dubendorf, Switzerland.
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27
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Abreu CI, Andersen Woltz VL, Friedman J, Gore J. Microbial communities display alternative stable states in a fluctuating environment. PLoS Comput Biol 2020; 16:e1007934. [PMID: 32453781 PMCID: PMC7274482 DOI: 10.1371/journal.pcbi.1007934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/05/2020] [Accepted: 05/07/2020] [Indexed: 12/24/2022] Open
Abstract
The effect of environmental fluctuations is a major question in ecology. While it is widely accepted that fluctuations and other types of disturbances can increase biodiversity, there are fewer examples of other types of outcomes in a fluctuating environment. Here we explore this question with laboratory microcosms, using cocultures of two bacterial species, P. putida and P. veronii. At low dilution rates we observe competitive exclusion of P. veronii, whereas at high dilution rates we observe competitive exclusion of P. putida. When the dilution rate alternates between high and low, we do not observe coexistence between the species, but rather alternative stable states, in which only one species survives and initial species’ fractions determine the identity of the surviving species. The Lotka-Volterra model with a fluctuating mortality rate predicts that this outcome is independent of the timing of the fluctuations, and that the time-averaged mortality would also lead to alternative stable states, a prediction that we confirm experimentally. Other pairs of species can coexist in a fluctuating environment, and again consistent with the model we observe coexistence in the time-averaged dilution rate. We find a similar time-averaging result holds in a three-species community, highlighting that simple linear models can in some cases provide powerful insight into how communities will respond to environmental fluctuations. The effect of environmental fluctuations on community structure and function is a fundamental question in ecology. A significant body of work suggests that fluctuations increase diversity due to a variety of proposed mechanisms. In this study, we compare the effects of constant and fluctuating dilution regimes on simple microbial communities with two or three species. We find that in all cases, the outcome in a fluctuating environment is the same as that in a constant environment in which the fluctuations are time-averaged. This surprising result highlights that in some communities, ecological stable states may be predicted by averaging environmental parameters, rather than by the variation itself.
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Affiliation(s)
- Clare I. Abreu
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (CIA); (JG)
| | - Vilhelm L. Andersen Woltz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (CIA); (JG)
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28
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Phenotypic variation in spatially structured microbial communities: ecological origins and consequences. Curr Opin Biotechnol 2020; 62:220-227. [DOI: 10.1016/j.copbio.2019.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023]
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Gorter FA, Manhart M, Ackermann M. Understanding the evolution of interspecies interactions in microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190256. [PMID: 32200743 DOI: 10.1098/rstb.2019.0256] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microbial communities are complex multi-species assemblages that are characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength of interspecies interactions have important consequences for emergent community-level properties such as productivity and stability. It is not well understood how interspecies interactions change over evolutionary timescales. Here, we review the empirical evidence that evolution is an important driver of microbial community properties and dynamics on timescales that have traditionally been regarded as purely ecological. Next, we briefly discuss different modelling approaches to study evolution of communities, emphasizing the similarities and differences between evolutionary and ecological perspectives. We then propose a simple conceptual model for the evolution of interspecies interactions in communities. Specifically, we propose that to understand the evolution of interspecies interactions, it is important to distinguish between direct and indirect fitness effects of a mutation. We predict that in well-mixed environments, traits will be selected exclusively for their direct fitness effects, while in spatially structured environments, traits may also be selected for their indirect fitness effects. Selection of indirectly beneficial traits should result in an increase in interaction strength over time, while selection of directly beneficial traits should not have such a systematic effect. We tested our intuitions using a simple quantitative model and found support for our hypotheses. The next step will be to test these hypotheses experimentally and provide input for a more refined version of the model in turn, thus closing the scientific cycle of models and experiments. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Florien A Gorter
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael Manhart
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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Turner CB, Buskirk SW, Harris KB, Cooper VS. Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection. Mol Ecol 2020; 29:138-148. [PMID: 31725941 PMCID: PMC6952539 DOI: 10.1111/mec.15307] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 02/01/2023]
Abstract
Natural environments are rarely static; rather selection can fluctuate on timescales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments, coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.
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Affiliation(s)
- Caroline B Turner
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sean W Buskirk
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Katrina B Harris
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Guo S, He F, Tang T, Tan L, Cai Q. Intra-annual fluctuations dominating temporal dynamics of benthic diatom assemblages in a Chinese mountainous river. ANNALES DE LIMNOLOGIE - INTERNATIONAL JOURNAL OF LIMNOLOGY 2020; 56:22. [DOI: 10.1051/limn/2020020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding temporal dynamics of community may provide insights on biological responses under environmental changes. However, our knowledge on temporal dynamics of river organisms is still limited. In the present study, we employed a multivariate time-series modeling approach with a long-term dataset (i.e. 72 consecutive months) to investigate temporal dynamics of benthic diatom communities in four sites located in a Chinese mountainous river network. We hypothesized that: (1) there are multi-scale temporal dynamics within the diatom community; (2) intra-annual fluctuations dominate the community dynamics; (3) diatom species composing the community respond distinctly to environmental changes. We found that intra-annual fluctuations with periodicities <12 months explained 8.1–16.1% of community variation. In contrast, fluctuations with periodicities of 13–36 months and 37–72 months only accounted for 1.1–5.9% and 2.8–9.7% of variance in diatom community dynamics, respectively. Taxa correlating significantly to each significant RDA axis (namely, RDA taxa group) displayed distinct temporal dynamics. Conductivity, total nitrogen, and pH were important to most RDA taxa groups across the four sites while their effects were group-specific. We concluded that intra-annual dynamics dominated temporal variation in diatom communities due to community responses to local environmental fluctuations. We suggest that long-term monitoring data are valuable for identifying multiple-scale temporal dynamics within biological communities.
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