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Abs E, Chase AB, Manzoni S, Ciais P, Allison SD. Microbial evolution-An under-appreciated driver of soil carbon cycling. GLOBAL CHANGE BIOLOGY 2024; 30:e17268. [PMID: 38562029 DOI: 10.1111/gcb.17268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.
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Affiliation(s)
- Elsa Abs
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Philippe Ciais
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, Irvine, California, USA
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2
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Wang Q, Wei S, Silva AF, Madsen JS. Cooperative antibiotic resistance facilitates horizontal gene transfer. THE ISME JOURNAL 2023; 17:846-854. [PMID: 36949153 PMCID: PMC10203111 DOI: 10.1038/s41396-023-01393-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/24/2023]
Abstract
The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.
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Affiliation(s)
- Qinqin Wang
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Shaodong Wei
- National Food Institute, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ana Filipa Silva
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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3
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Jo C, Bernstein DB, Vaisman N, Frydman HM, Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems 2023; 8:e0001721. [PMID: 36802169 PMCID: PMC10134821 DOI: 10.1128/msystems.00017-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/24/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions. IMPORTANCE Microbial communities participate in many essential processes from biogeochemical cycles to the maintenance of human health. The structure and functions of these communities are dynamic properties that depend on poorly understood interactions among different species. Unraveling these interactions is therefore a crucial step toward understanding natural microbiota and engineering artificial ones. Microbial interactions have been difficult to measure directly, largely due to limitations of existing methods to disentangle the contribution of different organisms in mixed cocultures. To overcome these limitations, we developed the BioMe plate, a custom microplate-based device that enables direct measurement of microbial interactions, by detecting the abundance of segregated populations of microbes that can exchange small molecules through a membrane. We demonstrated the possible application of the BioMe plate for studying both natural and artificial consortia. BioMe is a scalable and accessible platform that can be used to broadly characterize microbial interactions mediated by diffusible molecules.
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Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - David B. Bernstein
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Natalie Vaisman
- Department of Biology, Boston University, Boston, Massachusetts, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | | | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
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4
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Dal Co A, Ackermann M, van Vliet S. Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Syst 2023; 14:98-108. [PMID: 36796335 DOI: 10.1016/j.cels.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.
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Affiliation(s)
- Alma Dal Co
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Duebendorf, Switzerland.
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5
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Lerch BA, Smith DA, Koffel T, Bagby SC, Abbott KC. How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods. PLoS Comput Biol 2022; 18:e1010666. [PMID: 36318525 PMCID: PMC9651594 DOI: 10.1371/journal.pcbi.1010666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/11/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing “cheaters” by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single “public goods” can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce. Many organisms produce “public goods”, substances that may directly benefit their competitors as well as themselves. Because goods production is costly, understanding the evolutionary stability of public goods production has been a subject of considerable interest: what keeps cheaters from taking over a population and driving producers to extinction? Here, we ask when partial privatization of public goods (that is, when producers retain some portion of the good for their own exclusive use) is sufficient to stabilize production even in the absence of spatial structure, and how this depends on environmental conditions. We derive lower bounds for the amount of privatization needed to stabilize production and find that these bounds depend critically on environmental conditions. We further investigate the case of two public goods, each needed for the acquisition of the other, and each a resource whose availability limits growth. We find that the ecological dynamics of such colimiting resources can interact, with privatization of one resource subsidizing more-public, or even fully public, production of the other. Finally, we offer the perspective that producers are not “losers” in a race of loss-of-function mutations, but rather can do no better than to produce the resource in a given set of conditions.
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Affiliation(s)
- Brian A. Lerch
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Derek A. Smith
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas Koffel
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, United States of America
| | - Sarah C. Bagby
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen C. Abbott
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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6
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Lee IPA, Eldakar OT, Gogarten JP, Andam CP. Bacterial cooperation through horizontal gene transfer. Trends Ecol Evol 2021; 37:223-232. [PMID: 34815098 DOI: 10.1016/j.tree.2021.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 11/16/2022]
Abstract
Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.
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Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Omar Tonsi Eldakar
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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7
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Abstract
Bioremediation is a sustainable remediation technology as it utilizes microorganisms to convert hazardous compounds into their less toxic or non-toxic constituent elements. This technology has achieved some success in the past decades; however, factors involving microbial consortia, such as microbial assembly, functional interactions, and the role of member species, hinder its development. Microbial consortia may be engineered to reconfigure metabolic pathways and reprogram social interactions to get the desired function, thereby providing solutions to its inherent problems. The engineering of microbial consortia is commonly applied for the commercial production of biomolecules. However, in the field of bioremediation, the engineering of microbial consortia needs to be emphasized. In this review, we will discuss the molecular and ecological mechanisms of engineering microbial consortia with a particular focus on metabolic cross-feeding within species and the transfer of metabolites. We also discuss the advantages and limitations of top-down and bottom-up approaches of engineering microbial consortia and their applications in bioremediation.
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8
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Konstantinidis D, Pereira F, Geissen E, Grkovska K, Kafkia E, Jouhten P, Kim Y, Devendran S, Zimmermann M, Patil KR. Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion. Mol Syst Biol 2021; 17:e10189. [PMID: 34370382 PMCID: PMC8351387 DOI: 10.15252/msb.202010189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness-costly metabolites through natural selection. In this strategy, metabolic cross-feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co-evolved wild-type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B-group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.
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Affiliation(s)
- Dimitrios Konstantinidis
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Filipa Pereira
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Life Science InstituteUniversity of MichiganAnn ArborUSA
| | - Eva‐Maria Geissen
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kristina Grkovska
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Eleni Kafkia
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Paula Jouhten
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Yongkyu Kim
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Brain Research InstituteKorea Institute of Research and TechnologySeoulSouth Korea
| | - Saravanan Devendran
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Michael Zimmermann
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
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9
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10
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Johnson WM, Alexander H, Bier RL, Miller DR, Muscarella ME, Pitz KJ, Smith H. Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities? FEMS Microbiol Ecol 2020; 96:fiaa115. [PMID: 32520336 PMCID: PMC7609354 DOI: 10.1093/femsec/fiaa115] [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: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 11/14/2022] Open
Abstract
Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
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Affiliation(s)
- Winifred M Johnson
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Sciences and Engineering, Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
| | - Raven L Bier
- Stroud Water Research Center, 970 Spencer Rd., Avondale, PA 19311, USA
| | - Dan R Miller
- PureMagic LTD, Rambam 67, Yad Rambam 9979300, Israel
| | - Mario E Muscarella
- Department of Plant Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Kathleen J Pitz
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Heidi Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
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11
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Differences among species in seed dispersal and conspecific neighbor effects can interact to influence coexistence. THEOR ECOL-NETH 2020. [DOI: 10.1007/s12080-020-00468-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Meijer J, van Dijk B, Hogeweg P. Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves. Commun Biol 2020; 3:401. [PMID: 32728180 PMCID: PMC7391776 DOI: 10.1038/s42003-020-1107-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Metabolic exchange is widespread in natural microbial communities and an important driver of ecosystem structure and diversity, yet it remains unclear what determines whether microbes evolve division of labor or maintain metabolic autonomy. Here we use a mechanistic model to study how metabolic strategies evolve in a constant, one resource environment, when metabolic networks are allowed to freely evolve. We find that initially identical ancestral communities of digital organisms follow different evolutionary trajectories, as some communities become dominated by a single, autonomous lineage, while others are formed by stably coexisting lineages that cross-feed on essential building blocks. Our results show how without presupposed cellular trade-offs or external drivers such as temporal niches, diverse metabolic strategies spontaneously emerge from the interplay between ecology, spatial structure, and metabolic constraints that arise during the evolution of metabolic networks. Thus, in the long term, whether microbes remain autonomous or evolve metabolic division of labour is an evolutionary contingency.
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Affiliation(s)
- Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
| | - Bram van Dijk
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
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13
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Wang S, Payne GF, Bentley WE. Quorum Sensing Communication: Molecularly Connecting Cells, Their Neighbors, and Even Devices. Annu Rev Chem Biomol Eng 2020; 11:447-468. [DOI: 10.1146/annurev-chembioeng-101519-124728] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quorum sensing (QS) is a molecular signaling modality that mediates molecular-based cell–cell communication. Prevalent in nature, QS networks provide bacteria with a method to gather information from the environment and make decisions based on the intel. With its ability to autonomously facilitate both inter- and intraspecies gene regulation, this process can be rewired to enable autonomously actuated, but molecularly programmed, genetic control. On the one hand, novel QS-based genetic circuits endow cells with smart functions that can be used in many fields of engineering, and on the other, repurposed QS circuitry promotes communication and aids in the development of synthetic microbial consortia. Furthermore, engineered QS systems can probe and intervene in interkingdom signaling between bacteria and their hosts. Lastly, QS is demonstrated to establish conversation with abiotic materials, especially by taking advantage of biological and even electronically induced assembly processes; such QS-incorporated biohybrid devices offer innovative ways to program cell behavior and biological function.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
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14
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Herren CM. Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities. Proc Biol Sci 2020; 287:20192945. [PMID: 32396806 PMCID: PMC7287355 DOI: 10.1098/rspb.2019.2945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this ‘critical’ level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.
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Affiliation(s)
- Cristina M Herren
- Harvard Data Science Initiative, Harvard University, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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15
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Uppal G, Vural DC. Evolution of specialized microbial cooperation in dynamic fluids. J Evol Biol 2020; 33:256-269. [DOI: 10.1111/jeb.13593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022]
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16
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Short-range interactions govern the dynamics and functions of microbial communities. Nat Ecol Evol 2020; 4:366-375. [DOI: 10.1038/s41559-019-1080-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022]
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17
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Smith RP, Doiron A, Muzquiz R, Fortoul MC, Haas M, Abraham T, Quinn RJ, Barraza I, Chowdhury K, Nemzer LR. The public and private benefit of an impure public good determines the sensitivity of bacteria to population collapse in a snowdrift game. Environ Microbiol 2019; 21:4330-4342. [DOI: 10.1111/1462-2920.14796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Robert P. Smith
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Aimee Doiron
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Rodrigo Muzquiz
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Marla C. Fortoul
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Meghan Haas
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Tom Abraham
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Rebecca J. Quinn
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Ivana Barraza
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Khadija Chowdhury
- Department of Biological Sciences Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
| | - Louis R. Nemzer
- Department of Chemistry and Physics Halmos College of Natural Sciences and Oceanography, Nova Southeastern University Fort Lauderdale FL USA
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18
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Dzianach PA, Dykes GA, Strachan NJC, Forbes KJ, Pérez-Reche FJ. Challenges of biofilm control and utilization: lessons from mathematical modelling. J R Soc Interface 2019; 16:20190042. [PMID: 31185817 PMCID: PMC6597778 DOI: 10.1098/rsif.2019.0042] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.
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Affiliation(s)
- Paulina A. Dzianach
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
- School of Public Health, Curtin University, Perth, Australia
| | - Gary A. Dykes
- School of Public Health, Curtin University, Perth, Australia
| | - Norval J. C. Strachan
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Ken J. Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Francisco J. Pérez-Reche
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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19
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Stump SM, Johnson EC, Klausmeier CA. Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters. J R Soc Interface 2019; 15:rsif.2017.0822. [PMID: 29563243 DOI: 10.1098/rsif.2017.0822] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/27/2018] [Indexed: 12/13/2022] Open
Abstract
Mutualisms are ubiquitous, but models predict they should be susceptible to cheating. Resolving this paradox has become relevant to synthetic ecology: cooperative cross-feeding, a nutrient-exchange mutualism, has been proposed to stabilize microbial consortia. Previous attempts to understand how cross-feeders remain robust to non-producing cheaters have relied on complex behaviour (e.g. cheater punishment) or group selection. Using a stochastic spatial model, we demonstrate two novel mechanisms that can allow cross-feeders to outcompete cheaters, rather than just escape from them. Both mechanisms work through the spatial segregation of the resources, which prevents individual cheaters from acquiring the resources they need to reproduce. First, if microbe dispersal is low but resources are shared widely, then the cross-feeders self-organize into stable spatial patterns. Here the cross-feeders can build up where the resource they need is abundant, and send their resource to where their partner is, separating resources at regular intervals in space. Second, if dispersal is high but resource sharing is local, then random variation in population density creates small-scale variation in resource density, separating the resources from each other by chance. These results suggest that cross-feeding may be more robust than previously expected and offer strategies to engineer stable consortia.
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Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA .,School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA
| | - Evan Curtis Johnson
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Population Biology Graduate Group, University of California, Davis 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological StationBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Department of Plant BiologyBehavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
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20
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Tsoi R, Dai Z, You L. Emerging strategies for engineering microbial communities. Biotechnol Adv 2019; 37:107372. [PMID: 30880142 DOI: 10.1016/j.biotechadv.2019.03.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022]
Abstract
From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.
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Affiliation(s)
- Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Zhuojun Dai
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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21
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Sun Z, Koffel T, Stump SM, Grimaud GM, Klausmeier CA. Microbial cross-feeding promotes multiple stable states and species coexistence, but also susceptibility to cheaters. J Theor Biol 2019; 465:63-77. [DOI: 10.1016/j.jtbi.2019.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/07/2018] [Accepted: 01/08/2019] [Indexed: 01/22/2023]
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22
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Stump SM, Johnson EC, Klausmeier CA. How leaking and overproducing resources affect the evolutionary robustness of cooperative cross-feeding. J Theor Biol 2018; 454:278-291. [DOI: 10.1016/j.jtbi.2018.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/11/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022]
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23
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Stump SM, Johnson EC, Sun Z, Klausmeier CA. How spatial structure and neighbor uncertainty promote mutualists and weaken black queen effects. J Theor Biol 2018; 446:33-60. [PMID: 29499252 DOI: 10.1016/j.jtbi.2018.02.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/17/2018] [Accepted: 02/26/2018] [Indexed: 10/17/2022]
Abstract
The ubiquity of cooperative cross-feeding (a resource-exchange mutualism) raises two related questions: Why is cross-feeding favored over self-sufficiency, and how are cross-feeders protected from non-producing cheaters? The Black Queen Hypothesis suggests that if leaky resources are costly, then there should be selection for either gene loss or self-sufficiency, but selection against mutualistic inter-dependency. Localized interactions have been shown to protect mutualists against cheaters, though their effects in the presence of self-sufficient organisms are not well understood. Here we develop a stochastic spatial model to examine how spatial effects alter the predictions of the Black Queen Hypothesis. Microbes need two essential resources to reproduce, which they can produce themselves (at a cost) or take up from neighbors. Additionally, microbes need empty sites to give birth into. Under well mixed mean-field conditions, the cross-feeders will always be displaced by a non-producer and a self-sufficient microbe. However, localized interactions have two effects that favor production. First, a microbe that interacts with a small number of neighbors will not always receive the essential resources it needs; this effect slightly harms cross-feeders but greatly harms non-producers. Second, microbes tend to displace other microbes that produce resources they need; this effect also slightly harms cross-feeders but greatly harms non-producers. Our work therefore suggests localized interactions produce an accelerating cost of non-production. Thus, the right trade-off between the cost of producing resources and the cost of sometimes being resource-limited can favor mutualistic inter-dependence over both self-sufficiency and non-production.
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Affiliation(s)
- Simon Maccracken Stump
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.
| | - Evan Curtis Johnson
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Population Biology Graduate Group, University of California, Davis, 2320 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Zepeng Sun
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA
| | - Christopher A Klausmeier
- W. K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA; Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824-1312, USA; Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI 48824-1312, USA
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