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Faller L, Leite MFA, Kuramae EE. Enhancing phosphate-solubilising microbial communities through artificial selection. Nat Commun 2024; 15:1649. [PMID: 38388537 PMCID: PMC10884399 DOI: 10.1038/s41467-024-46060-x] [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: 08/24/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.
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Affiliation(s)
- Lena Faller
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Utrecht University, Institute of Environmental Biology, Ecology and Biodiversity, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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2
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Thomas JL, Rowland-Chandler J, Shou W. Artificial selection of microbial communities: what have we learnt and how can we improve? Curr Opin Microbiol 2024; 77:102400. [PMID: 38091857 DOI: 10.1016/j.mib.2023.102400] [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: 07/10/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 02/12/2024]
Abstract
Microbial communities are capable of performing diverse functions with important bioindustrial and medical applications. One approach to improving community function is to breed new communities by artificially selecting for those displaying high community function ('community selection'). Importantly, community selection can improve the function of interest without needing to understand how the function arises, just like in classical artificial selection of individuals. However, experimental studies of community selection have had varied and largely limited success. Here, we review a conceptual framework to help foster an understanding of community selection and its associated challenges, and provide broad insights for designing effective selection strategies.
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Affiliation(s)
- Joshua L Thomas
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Jamila Rowland-Chandler
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Wenying Shou
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, United Kingdom.
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3
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Yu SR, Zhang YY, Zhang QG. The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis. Front Microbiol 2023; 14:1257935. [PMID: 37840740 PMCID: PMC10570731 DOI: 10.3389/fmicb.2023.1257935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
The potential for artificial selection at the community level to improve ecosystem functions has received much attention in applied microbiology. However, we do not yet understand what conditions in general allow for successful artificial community selection. Here we propose six hypotheses about factors that determine the effectiveness of artificial microbial community selection, based on previous studies in this field and those on multilevel selection. In particular, we emphasize selection strategies that increase the variance among communities. We then report a meta-analysis of published artificial microbial community selection experiments. The reported responses to community selection were highly variable among experiments; and the overall effect size was not significantly different from zero. The effectiveness of artificial community selection was greater when there was no migration among communities, and when the number of replicated communities subjected to selection was larger. The meta-analysis also suggests that the success of artificial community selection may be contingent on multiple necessary conditions. We argue that artificial community selection can be a promising approach, and suggest some strategies for improving the performance of artificial community selection programs.
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Affiliation(s)
- Shi-Rui Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
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4
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Blanton AG, Perkins S, Peterson BF. In vitro assays reveal inherently insecticide-tolerant termite symbionts. Front Physiol 2023; 14:1134936. [PMID: 37501931 PMCID: PMC10368989 DOI: 10.3389/fphys.2023.1134936] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/30/2023] [Indexed: 07/29/2023] Open
Abstract
Introduction: Termite symbionts are well known for conferring a myriad of benefits to their hosts. Bacterial symbionts are repeatedly associated with increased fitness, nutritional supplementation, pathogen protection, and proper development across insect taxa. In addition, several recent studies link bacterial symbionts to reduced insecticide efficacy. This has important implications both in pest control management and environmental bioremediation efforts. Insects' guts may be a valuable resource for microbes with broad application given their unique niches and metabolic diversity. Though insecticide resistance in termites is considered unlikely due to their life history, the close association of termites with a multitude of bacteria raises the question: is there potential for symbiont-mediated pesticide tolerance in termites? Methods and results: We identified a candidate that could grow in minimal medium containing formulated pesticide. This bacterial isolate was then subjected to continuous culture and subsequently demonstrated improved performance in the presence of pesticide. Isolates subjected to continuous culture were then grown at a range of concentrations from 1-10X the formulation rate. After constant exposure for several generations, isolates grew significantly better. Conclusion: Here we demonstrate that naïve insect hosts can harbor symbionts with inherent insecticide tolerance capable of rapid adaptation to increasing insecticide concentrations overtime. This has broad implications for both pest control and environmental cleanup of residual pesticides.
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5
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Sanchez A, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC, Kuehn S. The community-function landscape of microbial consortia. Cell Syst 2023; 14:122-134. [PMID: 36796331 DOI: 10.1016/j.cels.2022.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.
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Affiliation(s)
- Alvaro Sanchez
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA; Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain.
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Abigail Skwara
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The Unviersity of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
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6
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George AB, Korolev KS. Ecological landscapes guide the assembly of optimal microbial communities. PLoS Comput Biol 2023; 19:e1010570. [PMID: 36626403 PMCID: PMC9831326 DOI: 10.1371/journal.pcbi.1010570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023] Open
Abstract
Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.
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Affiliation(s)
- Ashish B. George
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Carl R. Woese Institute for Genomic Biology and Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (ABG); (KSK)
| | - Kirill S. Korolev
- Department of Physics and Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
- * E-mail: (ABG); (KSK)
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7
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Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y, Tang H. Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. MLIFE 2022; 1:382-398. [PMID: 38818482 PMCID: PMC10989833 DOI: 10.1002/mlf2.12043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/01/2024]
Abstract
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
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Affiliation(s)
- Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Miaoxiao Wang
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyETH ZürichEawagSwitzerland
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yong Nie
- College of EngineeringPeking UniversityBeijingChina
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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8
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Raynaud T, Devers-Lamrani M, Spor A, Blouin M. Community diversity determines the evolution of synthetic bacterial communities under artificial selection. Evolution 2022; 76:1883-1895. [PMID: 35789998 DOI: 10.1111/evo.14558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 01/22/2023]
Abstract
Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function. Working with communities instead of individuals as selection units brings in additional sources of variation in the considered function that can influence the outcome of the artificial selection. In this study, we wanted to assess the effect of manipulating the initial community richness on artificial selection efficiency, defined as the change in the targeted function over time. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their richness (from one to 16 strains). Overall, the selected communities were 16% more productive than the control communities, but a convergence of community composition might have limited the effect of diversity on artificial selection efficiency. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. We propose that applying artificial selection on communities varying for their diversity could be a way to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.
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Affiliation(s)
- Tiffany Raynaud
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Marion Devers-Lamrani
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Aymé Spor
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Manuel Blouin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
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9
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Shuster SM, Keith AR, Whitham TG. Simulating selection and evolution at the community level using common garden data. Ecol Evol 2022; 12:e8696. [PMID: 35342594 PMCID: PMC8928883 DOI: 10.1002/ece3.8696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
A key issue in evolutionary biology is whether selection acting at levels higher than the individual can cause evolutionary change. If it can, then conceptual and empirical studies must consider how selection operates at multiple levels of biological organization. Here, we test the hypothesis that estimates of broad‐sense community heritability, HC2, can be used to predict the evolutionary response by community‐level phenotypes when community‐level selection is imposed. Using an approach informed by classic quantitative genetics, we made three predictions. First, when we imposed community‐level selection, we expected a significant change in the average phenotype of arthropod communities associated with individual tree genotypes [we imposed selection by favoring high and low NMDS (nonmetric multidimensional scaling) scores that reflected differences in arthropod species richness, abundance and composition]. Second, we expected HC2 to predict the magnitude of the community‐level response. Third, we expected no significant change in average NMDS scores with community‐level selection imposed at random. We tested these hypotheses using three years of common garden data for 102 species comprising the arthropod communities, associated with nine clonally replicated Populus angustifolia genotypes. Each of our predictions were met. We conclude that estimates of HC2 account for the resemblance among communities sharing common ancestry, the persistence of community composition over time, and the outcome of selection when it occurs at the community level. Our results provide a means for exploring how this process leads to large‐scale community evolutionary change, and they identify the circumstances in which selection may routinely act at the community level.
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Affiliation(s)
- Stephen M. Shuster
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Center for Adaptable Western Landscapes Northern Arizona University Flagstaff Arizona USA
| | - Arthur R. Keith
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Center for Adaptable Western Landscapes Northern Arizona University Flagstaff Arizona USA
| | - Thomas G. Whitham
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Center for Adaptable Western Landscapes Northern Arizona University Flagstaff Arizona USA
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10
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Xie L, Shou W. Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities. Nat Commun 2021; 12:6799. [PMID: 34815384 PMCID: PMC8611069 DOI: 10.1038/s41467-021-26647-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Microbial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and "reproduce" the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a "community function landscape", we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j ; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/ .
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Affiliation(s)
- Li Xie
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
| | - Wenying Shou
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
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11
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Jacquiod S, Spor A, Wei S, Munkager V, Bru D, Sørensen SJ, Salon C, Philippot L, Blouin M. Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes. Ecol Lett 2021; 25:189-201. [PMID: 34749426 DOI: 10.1111/ele.13916] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Artificial selection of microbiota opens new avenues for improving plants. However, reported results lack consistency. We hypothesised that the success in artificial selection of microbiota depends on the stabilisation of community structure. In a ten-generation experiment involving 1,800 plants, we selected rhizosphere microbiota of Brachypodium distachyon associated with high or low leaf greenness, a proxy of plant performance. The microbiota structure showed strong fluctuations during an initial transitory phase, with no detectable leaf greenness heritability. After five generations, the microbiota structure stabilised, concomitantly with heritability in leaf greenness. Selection, initially ineffective, did successfully alter the selected property as intended, especially for high selection. We show a remarkable correlation between the variability in plant traits and selected microbiota structures, revealing two distinct sub-communities associated with high or low leaf greenness, whose abundance was significantly steered by directional selection. Understanding microbiota structure stabilisation will improve the reliability of artificial microbiota selection.
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Affiliation(s)
- Samuel Jacquiod
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Aymé Spor
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Shaodong Wei
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Victoria Munkager
- Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark
| | - David Bru
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Salon
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Laurent Philippot
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
| | - Manuel Blouin
- Agroécologie laboratory, Université Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Université Bourgogne, Dijon, France
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12
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Closed microbial communities self-organize to persistently cycle carbon. Proc Natl Acad Sci U S A 2021; 118:2013564118. [PMID: 34740965 PMCID: PMC8609437 DOI: 10.1073/pnas.2013564118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/16/2022] Open
Abstract
Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it challenging to determine how changes in composition and the environment impact cycling. Enabled by a new high-precision method to quantify carbon cycling, we show that materially closed microbial ecosystems (CES) provided with only light self-organize to robustly cycle carbon. Studying replicate CES that support a carbon cycle reveals variable community composition but a conserved set of metabolic capabilities. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients. Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.
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13
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The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View. BIOLOGY 2021; 10:biology10070651. [PMID: 34356506 PMCID: PMC8301382 DOI: 10.3390/biology10070651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary This interdisciplinary study, conducted by experts in evolutionary biology, ecology, ecosystem studies, arts, medicine, forensic analyses, agriculture, law, and philosophy of science describe how microbiome studies are convergently affecting the concepts and practices of diverse fields and practices, that now consider microbiomes within their legitimate scope. Consequently, it describes what seems to be an ongoing pluridisciplinary epistemic revolution, with the potential to fundamentally change how we understand the world through an ecologization of pre-existing concepts, a greater focus on interactions, the use of multi-scalar interaction networks as explanatory frameworks, the reconceptualization of the usual definitions of individuals, and a de-anthropocentrification of our perception of phenomena. Abstract Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.
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14
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Chang CY, Vila JCC, Bender M, Li R, Mankowski MC, Bassette M, Borden J, Golfier S, Sanchez PGL, Waymack R, Zhu X, Diaz-Colunga J, Estrela S, Rebolleda-Gomez M, Sanchez A. Engineering complex communities by directed evolution. Nat Ecol Evol 2021; 5:1011-1023. [PMID: 33986540 PMCID: PMC8263491 DOI: 10.1038/s41559-021-01457-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/28/2021] [Indexed: 02/03/2023]
Abstract
Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.
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Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Madeline Bender
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Richard Li
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Madeleine C Mankowski
- Department of Immunobiology and Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Molly Bassette
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Julia Borden
- Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, CA, USA
| | - Stefan Golfier
- Max Planck Institute of Molecular Cell Biology and Genetics, and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Paul Gerald L Sanchez
- European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Heidelberg, Germany
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Xinwen Zhu
- Department of Biomedical Engineering and the Biological Design Center, Boston University, Boston, MA, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Maria Rebolleda-Gomez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.
- Microbial Sciences Institute, Yale University, New Haven, CT, USA.
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15
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Sánchez Á, Vila JCC, Chang CY, Diaz-Colunga J, Estrela S, Rebolleda-Gomez M. Directed Evolution of Microbial Communities. Annu Rev Biophys 2021; 50:323-341. [PMID: 33646814 PMCID: PMC8105285 DOI: 10.1146/annurev-biophys-101220-072829] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes.
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Affiliation(s)
- Álvaro Sánchez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Chang-Yu Chang
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - Sylvie Estrela
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
| | - María Rebolleda-Gomez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, USA; , , , , ,
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16
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Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol 2021; 29:908-918. [PMID: 33812769 DOI: 10.1016/j.tim.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Abstract
Environmental accumulation of anthropogenic pollutants is a pressing global issue. The biodegradation of these pollutants by microbes is an emerging field but is hampered by inefficient degradation rates and a limited knowledge of potential enzymes and pathways. Here, we advocate the view that significant progress can be achieved by harnessing artificial community selection for a desired biological process, an approach that makes use of eco-evolutionary principles. The selected communities can either be directly used in bioremediation applications or further be analyzed and modified, for instance through a combination of systems biology, synthetic biology, and genetic engineering. This knowledge can then inform machine learning and enhance the discovery of novel biodegradation pathways.
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Affiliation(s)
- Erik Borchert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany; University of Kiel, Kiel, Germany
| | - Peter Deines
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
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17
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Whitham TG, Allan GJ, Cooper HF, Shuster SM. Intraspecific Genetic Variation and Species Interactions Contribute to Community Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-123655] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolution has been viewed as occurring primarily through selection among individuals. We present a framework based on multilevel selection for evaluating evolutionary change from individuals to communities, with supporting empirical evidence. Essential to this evaluation is the role that interspecific indirect genetic effects play in shaping community organization, in generating variation among community phenotypes, and in creating community heritability. If communities vary in phenotype, and those phenotypes are heritable and subject to selection at multiple levels, then a community view of evolution must be merged with mainstream evolutionary theory. Rapid environmental change during the Anthropocene will require a better understanding of these evolutionary processes, especially selection acting at the community level, which has the potential to eliminate whole communities while favoring others.
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Affiliation(s)
- Thomas G. Whitham
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Gerard J. Allan
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Hillary F. Cooper
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Stephen M. Shuster
- Department of Biological Sciences and Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, Arizona 86011, USA
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18
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Chang CY, Osborne ML, Bajic D, Sanchez A. Artificially selecting bacterial communities using propagule strategies. Evolution 2020; 74:2392-2403. [PMID: 32888315 PMCID: PMC7942404 DOI: 10.1111/evo.14092] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Accepted: 08/29/2020] [Indexed: 02/06/2023]
Abstract
Artificial selection is a promising approach to manipulate microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both used "propagule" selection strategies, whereby the best-performing communities are used as the inocula to form a new generation of communities. Both experiments were contrasted to a random selection control. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used multiple soil communities as the starting inocula, and the function under selection was the communities' cross-feeding potential. In both experiments, the selected communities reached a higher mean function than the control. In the first experiment, this was caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, this response was fueled by the large initial variance in function across communities, and stopped when the top-performing community "fixed" in the metacommunity. Our results are in agreement with basic expectations from breeding theory, pointing to some of the limitations of community-level selection experiments that can inform the design of future studies.
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Affiliation(s)
- Chang-Yu Chang
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Melisa L. Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA.,Microbial Sciences Institute. Yale University, New Haven, CT, USA.,The Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.,Corresponding author:
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19
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Doulcier G, Lambert A, De Monte S, Rainey PB. Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity. eLife 2020; 9:e53433. [PMID: 32633717 PMCID: PMC7440921 DOI: 10.7554/elife.53433] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.
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Affiliation(s)
- Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
| | - Amaury Lambert
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRSParisFrance
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERMParisFrance
| | - Silvia De Monte
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary BiologyPlönGermany
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20
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Rainey PB, Quistad SD. Toward a dynamical understanding of microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190248. [PMID: 32200735 PMCID: PMC7133524 DOI: 10.1098/rstb.2019.0248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 75231 Paris, France
| | - Steven D. Quistad
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI) UMR8231, ESPCI Paris, CNRS, PSL Research University, 75231 Paris, France
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21
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Sanchez-Gorostiaga A, Bajić D, Osborne ML, Poyatos JF, Sanchez A. High-order interactions distort the functional landscape of microbial consortia. PLoS Biol 2019; 17:e3000550. [PMID: 31830028 PMCID: PMC6932822 DOI: 10.1371/journal.pbio.3000550] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for the management of natural microbiomes and the design of synthetic consortia. Specifically, it is poorly understood whether community functions can be quantitatively predicted from traits of species in monoculture. Inspired by the study of complex genetic interactions, we have examined how the amylolytic rate of combinatorial assemblages of six starch-degrading soil bacteria depend on the separate functional contributions from each species and their interactions. Filtering our results through the theory of biochemical kinetics, we show that this simple function is additive in the absence of interactions among community members. For about half of the combinatorially assembled consortia, the amylolytic function is dominated by pairwise and higher-order interactions. For the other half, the function is additive despite the presence of strong competitive interactions. We explain the mechanistic basis of these findings and propose a quantitative framework that allows us to separate the effect of behavioral and population dynamics interactions. Our results suggest that the functional robustness of a consortium to pairwise and higher-order interactions critically affects our ability to predict and bottom-up engineer ecosystem function in complex communities.
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Affiliation(s)
- Alicia Sanchez-Gorostiaga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Melisa L. Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Juan F. Poyatos
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre (CNB-CSIC), Madrid, Spain
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
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22
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Sanchez-Gorostiaga A, Bajić D, Osborne ML, Poyatos JF, Sanchez A. High-order interactions distort the functional landscape of microbial consortia. PLoS Biol 2019; 17:e3000550. [PMID: 31830028 DOI: 10.1101/333534] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023] Open
Abstract
Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for the management of natural microbiomes and the design of synthetic consortia. Specifically, it is poorly understood whether community functions can be quantitatively predicted from traits of species in monoculture. Inspired by the study of complex genetic interactions, we have examined how the amylolytic rate of combinatorial assemblages of six starch-degrading soil bacteria depend on the separate functional contributions from each species and their interactions. Filtering our results through the theory of biochemical kinetics, we show that this simple function is additive in the absence of interactions among community members. For about half of the combinatorially assembled consortia, the amylolytic function is dominated by pairwise and higher-order interactions. For the other half, the function is additive despite the presence of strong competitive interactions. We explain the mechanistic basis of these findings and propose a quantitative framework that allows us to separate the effect of behavioral and population dynamics interactions. Our results suggest that the functional robustness of a consortium to pairwise and higher-order interactions critically affects our ability to predict and bottom-up engineer ecosystem function in complex communities.
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Affiliation(s)
- Alicia Sanchez-Gorostiaga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Melisa L Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Juan F Poyatos
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre (CNB-CSIC), Madrid, Spain
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
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23
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Raynaud T, Devers M, Spor A, Blouin M. Effect of the Reproduction Method in an Artificial Selection Experiment at the Community Level. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00416] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Petersen IAB, Meyer KM, Bohannan BJM. Meta-Analysis Reveals Consistent Bacterial Responses to Land Use Change Across the Tropics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Arias-Sánchez FI, Vessman B, Mitri S. Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? PLoS Biol 2019; 17:e3000356. [PMID: 31469824 PMCID: PMC6716632 DOI: 10.1371/journal.pbio.3000356] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment.
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Affiliation(s)
- Flor I Arias-Sánchez
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Björn Vessman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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26
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Wright RJ, Gibson MI, Christie-Oleza JA. Understanding microbial community dynamics to improve optimal microbiome selection. MICROBIOME 2019; 7:85. [PMID: 31159875 PMCID: PMC6547603 DOI: 10.1186/s40168-019-0702-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. RESULTS Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. CONCLUSIONS The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
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27
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Xie L, Yuan AE, Shou W. Simulations reveal challenges to artificial community selection and possible strategies for success. PLoS Biol 2019; 17:e3000295. [PMID: 31237866 PMCID: PMC6658139 DOI: 10.1371/journal.pbio.3000295] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/25/2019] [Accepted: 05/13/2019] [Indexed: 02/04/2023] Open
Abstract
Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.
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Affiliation(s)
- Li Xie
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alex E. Yuan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology PhD program, University of Washington, Seattle, Washington, United States of America
| | - Wenying Shou
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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28
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Dussault AC. Functional Biodiversity and the Concept of Ecological Function. HISTORY, PHILOSOPHY AND THEORY OF THE LIFE SCIENCES 2019. [DOI: 10.1007/978-3-030-10991-2_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractThis chapter argues that the common claim that the ascription of ecological functions to organisms in functional ecology raises issues about levels of natural selection is ill-founded. This claim, I maintain, mistakenly assumes that the function concept as understood in functional ecology aligns with the selected effect theory of function advocated by many philosophers of biology (sometimes called “The Standard Line” on functions). After exploring the implications of Wilson and Sober’s defence of multilevel selection for the prospects of defending a selected effect account of ecological functions, I identify three main ways in which functional ecology’s understanding of the function concept diverges from the selected effect theory. Specifically, I argue (1) that functional ecology conceives ecological functions as context-based rather than history-based properties of organisms; (2) that it attributes to the ecological function concept the aim of explaining ecosystem processes rather than that of explaining the presence of organisms within ecosystems; and (3) that it conceives the ecological functions of organisms as use and service functions rather than design functions. I then discuss the extent to which the recently proposed causal role and organizational accounts of ecological functions better accord with the purposes for which the function concept is used in functional ecology.
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29
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Kang D, Herschend J, Al-Soud WA, Mortensen MS, Gonzalo M, Jacquiod S, Sørensen SJ. Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity. BIORESOURCE TECHNOLOGY 2018; 270:303-310. [PMID: 30236907 DOI: 10.1016/j.biortech.2018.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Keratin refers to a group of insoluble and recalcitrant protein materials. Slaughterhouses produce large amount of keratinous byproducts, which are either disposed or poorly valorized through costly thermochemical processes for animal feed formulation. Learning from nature, keratinolytic microbial consortia stand as a cost-efficient and environmental friendly way to valorize this recalcitrant resource. Directed selection was applied to enrich soil-born microbial consortia, using sequential batch cultivations in keratin medium, while measuring enzymes activity and monitoring consortia compositions via 16S rRNA gene amplicon sequencing. A promising microbial consortium KMCG6, featuring mainly members of Bacteroidetes and Proteobacteria, was obtained. It possessed keratinolytic activity with <25% residual substrate remaining, which also displayed a high degradation reproducibility level after long-term cryopreservation. This work represents an advance in the field of α-keratin degradation with potential for practical applications.
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Affiliation(s)
- Dingrong Kang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Applied Medical Sciences, Al-Jouf University, Quryyat, Saudi Arabia
| | - Martin Steen Mortensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Milena Gonzalo
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Agroécologie AgroSup Dijon, INRA, Univ Bourgogne Franche-Comté, France.
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
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Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
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Dussault AC. Functional ecology's non-selectionist understanding of function. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018; 70:1-9. [PMID: 30060909 DOI: 10.1016/j.shpsc.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/26/2018] [Accepted: 05/06/2018] [Indexed: 06/08/2023]
Abstract
This paper reinforces the current consensus against the applicability of the selected effect theory of function in ecology. It does so by presenting an argument which, in contrast with the usual argument invoked in support of this consensus, is not based on claims about whether ecosystems are customary units of natural selection. Instead, the argument developed here is based on observations about the use of the function concept in functional ecology, and more specifically, research into the relationship between biodiversity and ecosystem functioning. It is argued that a selected effect account of ecological functions is made implausible by the fact that it would conflict with important aspects of the understanding of function and ecosystem functional organization which underpins functional ecology's research program. Specifically, it would conflict with (1) Functional ecology's adoption of a context-based understanding of function and its aim to study the functional equivalence between phylogenetically-divergent organisms; (2) Functional ecology's attribution to ecosystems of a lower degree of part-whole integration than the one found in paradigm individual organisms; and (3) Functional ecology's adoption of a physiological or metabolic perspective on ecosystems rather than an evolutionary one.
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Affiliation(s)
- Antoine C Dussault
- Collège Lionel-Groulx, 100, Rue Duquet, Sainte-Thérèse, Québec, J7E 3G6, Canada; Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada.
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Voss JD, Goodson MS, Leon JC. Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species. Zoonoses Public Health 2018; 65:279-290. [PMID: 29430857 DOI: 10.1111/zph.12445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 01/07/2023]
Abstract
We propose the idea of "phenotype diffusion," which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and "obesogens"), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so identification of phenotype diffusion is highly relevant for practitioners (public health officials, physicians and veterinarians) in this field.
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Affiliation(s)
- J D Voss
- Epidemiology Consult Service Division, United States Air Force School of Aerospace Medicine, Wright-Patterson AFB, OH, USA
| | - M S Goodson
- 711th Human Performance Wing, Human Effectiveness Directorate, Wright-Patterson AFB, OH, USA.,UES Inc., Dayton, OH, USA
| | - J C Leon
- Epidemiology Consult Service Division, United States Air Force School of Aerospace Medicine, Wright-Patterson AFB, OH, USA
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Free A, McDonald MA, Pagaling E. Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:131-189. [PMID: 30342721 DOI: 10.1016/bs.aambs.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.
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Affiliation(s)
- Andrew Free
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael A McDonald
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Eulyn Pagaling
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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Suzuki K, Yoshida K, Nakanishi Y, Fukuda S. An equation‐free method reveals the ecological interaction networks within complex microbial ecosystems. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12814] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kenta Suzuki
- Biodiversity Conservation Planning SectionCenter for Environmental Biology and Ecosystem StudiesNational Institute for Environmental Studies Ibaraki Japan
| | - Katsuhiko Yoshida
- Biodiversity Conservation Planning SectionCenter for Environmental Biology and Ecosystem StudiesNational Institute for Environmental Studies Ibaraki Japan
| | - Yumiko Nakanishi
- Institute for Advanced BiosciencesKeio University Yamagata Japan
- RIKEN Center for Integrative Medical Sciences Kanagawa Japan
| | - Shinji Fukuda
- Institute for Advanced BiosciencesKeio University Yamagata Japan
- PRESTO, Japan Science and Technology Agency Saitama Japan
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Baum DA, Vetsigian K. An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory. ORIGINS LIFE EVOL B 2016; 47:481-497. [PMID: 27864699 PMCID: PMC5705744 DOI: 10.1007/s11084-016-9526-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/18/2016] [Indexed: 01/01/2023]
Abstract
Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces. We propose high-throughput screening of a diverse set of conditions in order to identify combinations of "food," energy sources, and mineral surfaces that foster the emergence of surface-associated chemical consortia that are capable of adaptive evolution. Identification of such systems would greatly advance our understanding of the emergence of self-propagating entities and the onset of adaptive evolution during the origin of life.
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Affiliation(s)
- David A Baum
- Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI, 53706, USA. .,Wisconsin Institute for Discovery, University of Wisconsin, 330 N. Orchard Street, Madison, WI, 53706, USA.
| | - Kalin Vetsigian
- Wisconsin Institute for Discovery, University of Wisconsin, 330 N. Orchard Street, Madison, WI, 53706, USA.,Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI, 53706, USA
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Abstract
AbstractExperimental studies of group selection show that higher levels of selection act on indirect genetic effects, making the response to group and community selection qualitatively different from that of individual selection. This suggests that multilevel selection plays a key role in the evolution of supersocial societies. Experiments showing the effectiveness of community selection indicate that we should consider the possibility that selection among communities may be important in the evolution of supersocial species.
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Zomorrodi AR, Segrè D. Synthetic Ecology of Microbes: Mathematical Models and Applications. J Mol Biol 2015; 428:837-61. [PMID: 26522937 DOI: 10.1016/j.jmb.2015.10.019] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/17/2015] [Accepted: 10/21/2015] [Indexed: 12/29/2022]
Abstract
As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.
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Affiliation(s)
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA; Department of Biology, Boston University, Boston, MA; Department of Biomedical Engineering, Boston University, Boston, MA.
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Goodnight CJ. Multilevel selection theory and evidence: a critique of Gardner, 2015. J Evol Biol 2015; 28:1734-46. [PMID: 26265012 DOI: 10.1111/jeb.12685] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 11/28/2022]
Abstract
Gardner (2015) recently developed a model of a 'Genetical Theory of Multilevel Selection, which is a thoughtfully developed, but flawed model. The model's flaws appear to be symptomatic of common misunderstandings of the multi level selection (MLS) literature and the recent quantitative genetic literature. I use Gardner's model as a guide for highlighting how the MLS literature can address the misconceptions found in his model, and the kin selection literature in general. I discuss research on the efficacy of group selection, the roll of indirect genetic effects in affecting the response to selection and the heritability of group-level traits. I also discuss why the Price multilevel partition should not be used to partition MLS, and why contextual analysis and, by association, direct fitness are appropriate for partitioning MLS. Finally, I discuss conceptual issues around questions concerning the level at which fitness is measured, the units of selection, and I present a brief outline of a model of selection in class-structured populations. I argue that the results derived from the MLS research tradition can inform kin selection research and models, and provide insights that will allow researchers to avoid conceptual flaws such as those seen in the Gardner model.
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Affiliation(s)
- C J Goodnight
- Department of Biology, University of Vermont, Burlington, VT, USA
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40
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Blouin M, Karimi B, Mathieu J, Lerch TZ. Levels and limits in artificial selection of communities. Ecol Lett 2015; 18:1040-8. [DOI: 10.1111/ele.12486] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/21/2015] [Accepted: 07/06/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Manuel Blouin
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618); Université Paris-Est Créteil Val-de-Marne (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot); 61 avenue du Général de Gaulle 94010 Créteil France
| | - Battle Karimi
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618); Université Paris-Est Créteil Val-de-Marne (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot); 61 avenue du Général de Gaulle 94010 Créteil France
- Laboratoire Chrono-environnement (UMR 6249); Université de Franche-Comté; 16 route de Gray 25000 Besançon France
| | - Jérôme Mathieu
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618); Université Pierre et Marie Curie Paris06 - Sorbonne (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot); 7 quai Saint Bernard 75005 Paris France
| | - Thomas Z. Lerch
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618); Université Paris-Est Créteil Val-de-Marne (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot); 61 avenue du Général de Gaulle 94010 Créteil France
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Utilities of gossip across organizational levels : Multilevel selection, free-riders, and teams. HUMAN NATURE-AN INTERDISCIPLINARY BIOSOCIAL PERSPECTIVE 2015; 16:278-92. [PMID: 26189751 DOI: 10.1007/s12110-005-1011-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 10/15/2004] [Accepted: 10/15/2004] [Indexed: 10/23/2022]
Abstract
Gossip is a subject that has been studied by researchers from an array of disciplines with various foci and methods. We measured the content of language use by members of a competitive sports team across 18 months, integrating qualitative ethnographic methods with quantitative sampling and analysis. We hypothesized that the use of gossip will vary significantly depending on whether it is used for self-serving or group-serving purposes. Our results support a model of gossip derived from multilevel selection theory that expects gossip to serve group-beneficial rules when rewards are partitioned at the group level on a scale that permits mutual monitoring. We integrate our case study with earlier studies of gossip conducted by anthropologists, psychologists, and management researchers.
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Goldsby HJ, Knoester DB, Kerr B, Ofria C. The effect of conflicting pressures on the evolution of division of labor. PLoS One 2014; 9:e102713. [PMID: 25093399 PMCID: PMC4122366 DOI: 10.1371/journal.pone.0102713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 06/23/2014] [Indexed: 11/18/2022] Open
Abstract
Within nature, many groups exhibit division of labor. Individuals in these groups are under seemingly antagonistic pressures to perform the task most directly beneficial to themselves and to potentially perform a less desirable task to ensure the success of the group. Performing experiments to study how these pressures interact in an evolutionary context is challenging with organic systems because of long generation times and difficulties related to group propagation and fine-grained control of within-group and between-group pressures. Here, we use groups of digital organisms (i.e., self-replicating computer programs) to explore how populations respond to antagonistic multilevel selection pressures. Specifically, we impose a within-group pressure to perform a highly-rewarded role and a between-group pressure to perform a diverse suite of roles. Thus, individuals specializing on highly-rewarded roles will have a within-group advantage, but groups of such specialists have a between-group disadvantage. We find that digital groups could evolve to be either single-lineage or multi-lineage, depending on experimental parameters. These group compositions are reminiscent of different kinds of major evolutionary transitions that occur within nature, where either relatives divide labor (fraternal transitions) or multiple different organisms coordinate activities to form a higher-level individual (egalitarian transitions). Regardless of group composition, organisms embraced phenotypic plasticity as a means for genetically similar individuals to perform different roles. Additionally, in multi-lineage groups, organisms from lineages performing highly-rewarded roles also employed reproductive restraint to ensure successful coexistence with organisms from other lineages.
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Affiliation(s)
- Heather J. Goldsby
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- BEACON Center for Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - David B. Knoester
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Benjamin Kerr
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- BEACON Center for Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
| | - Charles Ofria
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
- BEACON Center for Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
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43
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Ecosystem Evolution is About Variation and Persistence, not Populations and Reproduction. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13752-014-0171-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bouzat JL, Hoostal MJ. Evolutionary Analysis and Lateral Gene Transfer of Two-Component Regulatory Systems Associated with Heavy-Metal Tolerance in Bacteria. J Mol Evol 2013; 76:267-79. [DOI: 10.1007/s00239-013-9558-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 03/23/2013] [Indexed: 11/28/2022]
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Zarraonaindia I, Smith DP, Gilbert JA. Beyond the genome: community-level analysis of the microbial world. BIOLOGY & PHILOSOPHY 2013; 28:261-282. [PMID: 23482824 PMCID: PMC3585761 DOI: 10.1007/s10539-012-9357-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/29/2012] [Indexed: 05/10/2023]
Abstract
The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.
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Affiliation(s)
- Iratxe Zarraonaindia
- Argonne National Laboratory, Institute for Genomic and Systems Biology, 9700 South Cass Avenue, Argonne, IL 60439 USA
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Daniel P. Smith
- Argonne National Laboratory, Institute for Genomic and Systems Biology, 9700 South Cass Avenue, Argonne, IL 60439 USA
| | - Jack A. Gilbert
- Argonne National Laboratory, Institute for Genomic and Systems Biology, 9700 South Cass Avenue, Argonne, IL 60439 USA
- Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 USA
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46
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Bouchard F. How Ecosystem Evolution Strengthens the Case for Functional Pluralism. SYNTHESE LIBRARY 2013. [DOI: 10.1007/978-94-007-5304-4_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Bernstein HC, Carlson RP. Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems. Comput Struct Biotechnol J 2012; 3:e201210017. [PMID: 24688677 PMCID: PMC3962199 DOI: 10.5936/csbj.201210017] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/24/2012] [Accepted: 11/28/2012] [Indexed: 01/29/2023] Open
Abstract
This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.
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Affiliation(s)
- Hans C Bernstein
- Department of Chemical and Biological Engineering & Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
| | - Ross P Carlson
- Department of Chemical and Biological Engineering & Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
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Penn AS, Conibear TCR, Watson RA, Kraaijeveld AR, Webb JS. Can Simpson's paradox explain co-operation in Pseudomonas aeruginosa biofilms? ACTA ACUST UNITED AC 2012; 65:226-35. [PMID: 22469426 DOI: 10.1111/j.1574-695x.2012.00970.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 03/28/2012] [Accepted: 03/28/2012] [Indexed: 11/28/2022]
Abstract
Co-operative behaviours, such as the production of public goods, are commonly displayed by bacteria in biofilms and can enhance their ability to survive in environmental or clinical settings. Non-co-operative cheats commonly arise and should, theoretically, disrupt co-operative behaviour. Its stability therefore requires explanation, but no mechanisms to suppress cheating within biofilms have yet been demonstrated experimentally. Theoretically, repeated aggregation into groups, interleaved with dispersal and remixing, can increase co-operation via a 'Simpson's paradox'. That is, an increase in the global proportion of co-operators despite a decrease in within-group proportions, via differential growth of groups. We investigate the hypothesis that microcolony formation and dispersal produces a Simpson's paradox that explains bacterial co-operation in biofilms. Using the production of siderophores in Pseudomonas aeruginosa as our model system for co-operation, we use well-documented co-operator and siderophore-deficient cheat strains to measure the frequency of co-operating and cheating individuals, in-situ within-microcolony structures. We detected significant within-type negative density-dependant effects that vary over microcolony development. However, we find no evidence of Simpson's paradox. Instead, we see clear within-microcolony spatial structure (cheats occupying the interior portions of microcolonies) that may violate the assumption required for Simpson's paradox that group members share equally in the public good.
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Affiliation(s)
- Alexandra S Penn
- Electronics and Computer Science, University of Southampton, Southampton, UK.
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49
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Abstract
A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only by processes that occur within communities such as drift and individual selection, but also by among-community processes, such as divergent selection owing to random differences among communities in species composition, and group and community-level selection. The effect of these among-community-level processes depends on the pattern of migration among communities. Migrating units may be individuals (migrant pool model), groups of individuals (single-species propagule pool model) or multi-species associations (multi-species propagule pool model). The most interesting case is the multi-species propagule pool model. Although this pattern of migration may a priori seem rare, it becomes more plausible in small well-defined 'communities' such as symbiotic associations between two or a few species. Theoretical models and experimental studies show that community selection is potentially an effective evolutionary force. Such evolution can occur either through genetic changes within species or through changes in the species composition of the communities. Although laboratory studies show that community selection can be important, little is known about how important it is in natural populations.
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Affiliation(s)
- Charles J Goodnight
- Department of Biology, University of Vermont, 120 MLS, Burlington, VT 05401, USA.
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50
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Abstract
Microbial ecology is revealing the vast diversity of strains and species that coexist in many environments, ranging from free-living communities to the symbionts that compose the human microbiome. In parallel, there is growing evidence of the importance of cooperative phenotypes for the growth and behavior of microbial groups. Here we ask: How does the presence of multiple species affect the evolution of cooperative secretions? We use a computer simulation of spatially structured cellular groups that captures key features of their biology and physical environment. When nutrient competition is strong, we find that the addition of new species can inhibit cooperation by eradicating secreting strains before they can become established. When nutrients are abundant and many species mix in one environment, however, our model predicts that secretor strains of any one species will be surrounded by other species. This "social insulation" protects secretors from competition with nonsecretors of the same species and can improve the prospects of within-species cooperation. We also observe constraints on the evolution of mutualistic interactions among species, because it is difficult to find conditions that simultaneously favor both within- and among-species cooperation. Although relatively simple, our model reveals the richness of interactions between the ecology and social evolution of multispecies microbial groups, which can be critical for the evolution of cooperation.
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Affiliation(s)
- Sara Mitri
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
- Oxford Centre for Integrative Systems Biology, Oxford University, Oxford OX1 3QU, United Kingdom; and
| | - João B. Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
- Oxford Centre for Integrative Systems Biology, Oxford University, Oxford OX1 3QU, United Kingdom; and
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