1
|
Khrennikov A, Iryama S, Basieva I, Sato K. Quantum-like environment adaptive model for creation of phenotype. Biosystems 2024; 242:105261. [PMID: 38964651 DOI: 10.1016/j.biosystems.2024.105261] [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: 06/03/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
The textbook conceptualization of phenotype creation, "genotype (G) + environment (E) + genotype & environment interactions (GE) ↦ phenotype (Ph)", is modeled with open quantum systems theory (OQST) or more generally with adaptive dynamics theory (ADT). The model is quantum-like, i.e., it is not about quantum physical processes in biosystems. Generally such modeling is about applications of the quantum formalism and methodology outside of physics. Macroscopic biosystems, in our case genotypes and phenotypes, are treated as information processors which functioning matches the laws of quantum information theory. Phenotypes are the outputs of the E-adaptation processes described by the quantum master equation, Gorini-Kossakowski-Sudarshan-Lindblad equation (GKSL). Its stationary states correspond to phenotypes. We highlight the class of GKSL dynamics characterized by the camel-like graphs of (von Neumann) entropy: in the process of E-adaptation phenotype's state entropy (disorder) first increases and then falls down - a stable and well-ordered phenotype is created. Traits, an organism's phenotypic characteristics, are modeled within the quantum measurement theory, as generally unsharp observables given by positive operator valued measures (POVMs. This paper is also a review on the methods and mathematical apparatus of quantum information biology.
Collapse
Affiliation(s)
- Andrei Khrennikov
- Linnaeus University, International Center for Mathematical Modeling in Physics and Cognitive Sciences Växjö, SE-351 95, Sweden.
| | - Satoshi Iryama
- Tokyo University of Science, Faculty of Science and Technology, Department of Information Sciences, Noda City, Chiba 278-8510, Japan
| | - Irina Basieva
- Linnaeus University, International Center for Mathematical Modeling in Physics and Cognitive Sciences Växjö, SE-351 95, Sweden
| | - Keiko Sato
- Tokyo University of Science, Faculty of Science and Technology, Department of Information Sciences, Noda City, Chiba 278-8510, Japan
| |
Collapse
|
2
|
Laura M, Jo P. No acetogen is equal: Strongly different H 2 thresholds reflect diverse bioenergetics in acetogenic bacteria. Environ Microbiol 2023; 25:2032-2040. [PMID: 37209014 DOI: 10.1111/1462-2920.16429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Acetogens share the capacity to convert H2 and CO2 into acetate for energy conservation (ATP synthesis). This reaction is attractive for applications, such as gas fermentation and microbial electrosynthesis. Different H2 partial pressures prevail in these distinctive applications (low concentrations during microbial electrosynthesis [<40 Pa] vs. high concentrations with gas fermentation [>9%]). Strain selection thus requires understanding of how different acetogens perform under different H2 partial pressures. Here, we determined the H2 threshold (H2 partial pressure at which acetogenesis halts) for eight different acetogenic strains under comparable conditions. We found a three orders of magnitude difference between the lowest and highest H2 threshold (6 ± 2 Pa for Sporomusa ovata vs. 1990 ± 67 Pa for Clostridium autoethanogenum), while Acetobacterium strains had intermediate H2 thresholds. We used these H2 thresholds to estimate ATP gains, which ranged from 0.16 to 1.01 mol ATP per mol acetate (S. ovata vs. C. autoethanogenum). The experimental H2 thresholds thus suggest strong differences in the bioenergetics of acetogenic strains and possibly also in their growth yields and kinetics. We conclude that no acetogen is equal and that a good understanding of their differences is essential to select the most optimal strain for different biotechnological applications.
Collapse
Affiliation(s)
- Munoz Laura
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Philips Jo
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| |
Collapse
|
3
|
Manzoni S, Chakrawal A, Ledder G. Decomposition rate as an emergent property of optimal microbial foraging. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1094269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Decomposition kinetics are fundamental for quantifying carbon and nutrient cycling in terrestrial and aquatic ecosystems. Several theories have been proposed to construct process-based kinetics laws, but most of these theories do not consider that microbial decomposers can adapt to environmental conditions, thereby modulating decomposition. Starting from the assumption that a homogeneous microbial community maximizes its growth rate over the period of decomposition, we formalize decomposition as an optimal control problem where the decomposition rate is a control variable. When maintenance respiration is negligible, we find that the optimal decomposition kinetics scale as the square root of the substrate concentration, resulting in growth kinetics following a Hill function with exponent 1/2 (rather than the Monod growth function). When maintenance respiration is important, optimal decomposition is a more complex function of substrate concentration, which does not decrease to zero as the substrate is depleted. With this optimality-based formulation, a trade-off emerges between microbial carbon-use efficiency (ratio of growth rate over substrate uptake rate) and decomposition rate at the beginning of decomposition. In environments where carbon substrates are easily lost due to abiotic or biotic factors, microbes with higher uptake capacity and lower efficiency are selected, compared to environments where substrates remain available. The proposed optimization framework provides an alternative to purely empirical or process-based formulations for decomposition, allowing exploration of the effects of microbial adaptation on element cycling.
Collapse
|
4
|
Tsiantis N, Banga JR. Using optimal control to understand complex metabolic pathways. BMC Bioinformatics 2020; 21:472. [PMID: 33087041 PMCID: PMC7579911 DOI: 10.1186/s12859-020-03808-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole populations. Most of these studies have assumed a single-criteria approach. Such optimality principles have been justified from an evolutionary perspective. In the context of the cell, previous studies have shown how dynamics of gene expression in small metabolic models can be explained assuming that cells have developed optimal adaptation strategies. Most of these works have considered rather simplified representations, such as small linear pathways, or reduced networks with a single branching point, and a single objective for the optimality criteria. RESULTS Here we consider the extension of this approach to more realistic scenarios, i.e. biochemical pathways of arbitrary size and structure. We first show that exploiting optimality principles for these networks poses great challenges due to the complexity of the associated optimal control problems. Second, in order to surmount such challenges, we present a computational framework which has been designed with scalability and efficiency in mind, including mechanisms to avoid the most common pitfalls. Third, we illustrate its performance with several case studies considering the central carbon metabolism of S. cerevisiae and B. subtilis. In particular, we consider metabolic dynamics during nutrient shift experiments. CONCLUSIONS We show how multi-objective optimal control can be used to predict temporal profiles of enzyme activation and metabolite concentrations in complex metabolic pathways. Further, we also show how to consider general cost/benefit trade-offs. In this study we have considered metabolic pathways, but this computational framework can also be applied to analyze the dynamics of other complex pathways, such as signal transduction or gene regulatory networks.
Collapse
Affiliation(s)
- Nikolaos Tsiantis
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo, Spain
- Department of Chemical Engineering, University of Vigo, 36310 Vigo, Spain
| | - Julio R. Banga
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo, Spain
| |
Collapse
|
5
|
Geyrhofer L, Brenner N. Coexistence and cooperation in structured habitats. BMC Ecol 2020; 20:14. [PMID: 32122337 PMCID: PMC7053132 DOI: 10.1186/s12898-020-00281-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Background Natural habitats are typically structured, imposing constraints on inhabiting populations and their interactions. Which conditions are important for coexistence of diverse communities, and how cooperative interaction stabilizes in such populations, have been important ecological and evolutionary questions. Results We investigate a minimal ecological framework of microbial population dynamics that exhibits crucial features to show coexistence: Populations repeatedly undergo cycles of separation into compartmentalized habitats and mixing with new resources. The characteristic time-scale is longer than that typical of individual growth. Using analytic approximations, averaging techniques and phase-plane methods of dynamical systems, we provide a framework for analyzing various types of microbial interactions. Population composition and population size are both dynamic variables of the model; they are found to be decoupled both in terms of time-scale and parameter dependence. We present specific results for two examples of cooperative interaction by public goods: collective antibiotics resistance, and enhanced iron-availability by pyoverdine. We find stable coexistence to be a likely outcome. Conclusions The two simple features of a long mixing time-scale and spatial compartmentalization are enough to enable coexisting strains. In particular, costly social traits are often stabilized in such an environment—and thus cooperation established.
Collapse
Affiliation(s)
- Lukas Geyrhofer
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Naama Brenner
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
6
|
Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, Allison SD. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. THE ISME JOURNAL 2020; 14:1-9. [PMID: 31554911 PMCID: PMC6908601 DOI: 10.1038/s41396-019-0510-0] [Citation(s) in RCA: 265] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 06/07/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Ashish A Malik
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Jennifer B H Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Adam C Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| |
Collapse
|
7
|
Romero-Olivares AL, Meléndrez-Carballo G, Lago-Lestón A, Treseder KK. Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay. Front Microbiol 2019; 10:1914. [PMID: 31551941 PMCID: PMC6736569 DOI: 10.3389/fmicb.2019.01914] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/05/2019] [Indexed: 11/29/2022] Open
Abstract
Earth’s temperature is rising, and with this increase, fungal communities are responding and affecting soil carbon processes. At a long-term soil-warming experiment in a boreal forest in interior Alaska, warming and warming-associated drying alters the function of microbes, and thus, decomposition of carbon. But what genetic mechanisms and resource allocation strategies are behind these community shifts and soil carbon changes? Here, we evaluate fungal resource allocation efforts under long-term experimental warming (including associated drying) using soil metatranscriptomics. We profiled resource allocation efforts toward decomposition and cell metabolic maintenance, and we characterized community composition. We found that under the warming treatment, fungi allocate resources to cell metabolic maintenance at the expense of allocating resources to decomposition. In addition, we found that fungal orders that house taxa with stress-tolerant traits were more abundant under the warmed treatment compared to control conditions. Our results suggest that the warming treatment elicits an ecological tradeoff in resource allocation in the fungal communities, with potential to change ecosystem-scale carbon dynamics. Fungi preferentially invest in mechanisms that will ensure survival under warming and drying, such as cell metabolic maintenance, rather than in decomposition. Through metatranscriptomes, we provide mechanistic insight behind the response of fungi to climate change and consequences to soil carbon processes.
Collapse
Affiliation(s)
- Adriana L Romero-Olivares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Germán Meléndrez-Carballo
- Department of Electronics and Telecommunications, Ensenada Center for Scientific Research and Higher Education, Ensenada, Mexico
| | - Asunción Lago-Lestón
- Department of Medical Innovation, Ensenada Center for Scientific Research and Higher Education, Ensenada, Mexico
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
8
|
Pulkkinen K, Pekkala N, Ashrafi R, Hämäläinen DM, Nkembeng AN, Lipponen A, Hiltunen T, Valkonen JK, Taskinen J. Effect of resource availability on evolution of virulence and competition in an environmentally transmitted pathogen. FEMS Microbiol Ecol 2019; 94:4962392. [PMID: 29659817 DOI: 10.1093/femsec/fiy060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 01/21/2023] Open
Abstract
Understanding ecological and epidemiological factors driving pathogen evolution in contemporary time scales is a major challenge in modern health management. Pathogens that replicate outside the hosts are subject to selection imposed by ambient environmental conditions. Increased nutrient levels could increase pathogen virulence by pre-adapting for efficient use of resources upon contact to a nutrient rich host or by favouring transmission of fast-growing virulent strains. We measured changes in virulence and competition in Flavobacterium columnare, a bacterial pathogen of freshwater fish, under high and low nutrient levels. To test competition between strains in genotype mixtures, we developed a quantitative real-time PCR assay. We found that a virulent strain maintained its virulence and outcompeted less virulent strains independent of the nutrient level and resource renewal rate while a less virulent strain further lost virulence in chemostats under low nutrient level and over long-term serial culture under high nutrient level. Our results suggest that increased outside-host nutrient levels might maintain virulence in less virulent strains and increase their contribution to epidemics in aquaculture. The results highlight a need to further explore the role of resource in the outside-host environment in maintaining strain diversity and driving evolution of virulence among environmentally growing pathogens.
Collapse
Affiliation(s)
- Katja Pulkkinen
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| | - Nina Pekkala
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland.,Centre of Excellence in Biological Interactions, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä,Finland
| | - Dorrit M Hämäläinen
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| | - Aloysius N Nkembeng
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| | - Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, P. O. Box 1627, (Neulaniementie 2), University of Eastern Finland, Kuopio, Finland
| | - Teppo Hiltunen
- Department of Microbiology, P. O. Box 56, (Viikinkaari 9), University of Helsinki, Helsinki, Finland
| | - Janne K Valkonen
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland.,Centre of Excellence in Biological Interactions, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä,Finland
| | - Jouni Taskinen
- Department of Biological and Environmental Science, P. O. Box 35, (Survontie 9), University of Jyväskylä, Jyväskylä, Finland
| |
Collapse
|
9
|
de Oliveira VM, Amado A, Campos PR. The interplay of tradeoffs within the framework of a resource-based modelling. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
10
|
Gygli SM, Borrell S, Trauner A, Gagneux S. Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev 2018; 41:354-373. [PMID: 28369307 DOI: 10.1093/femsre/fux011] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/17/2017] [Indexed: 11/12/2022] Open
Abstract
Antibiotic-resistant Mycobacterium tuberculosis strains are threatening progress in containing the global tuberculosis epidemic. Mycobacterium tuberculosis is intrinsically resistant to many antibiotics, limiting the number of compounds available for treatment. This intrinsic resistance is due to a number of mechanisms including a thick, waxy, hydrophobic cell envelope and the presence of drug degrading and modifying enzymes. Resistance to the drugs which are active against M. tuberculosis is, in the absence of horizontally transferred resistance determinants, conferred by chromosomal mutations. These chromosomal mutations may confer drug resistance via modification or overexpression of the drug target, as well as by prevention of prodrug activation. Drug resistance mutations may have pleiotropic effects leading to a reduction in the bacterium's fitness, quantifiable e.g. by a reduction in the in vitro growth rate. Secondary so-called compensatory mutations, not involved in conferring resistance, can ameliorate the fitness cost by interacting epistatically with the resistance mutation. Although the genetic diversity of M. tuberculosis is low compared to other pathogenic bacteria, the strain genetic background has been demonstrated to influence multiple aspects in the evolution of drug resistance. The rate of resistance evolution and the fitness costs of drug resistance mutations may vary as a function of the genetic background.
Collapse
Affiliation(s)
- Sebastian M Gygli
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| |
Collapse
|
11
|
Ketola T, Mikonranta L, Mappes J. Evolution of bacterial life-history traits is sensitive to community structure. Evolution 2016; 70:1334-41. [DOI: 10.1111/evo.12947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/20/2016] [Accepted: 04/30/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Tarmo Ketola
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
| | - Lauri Mikonranta
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
| | - Johanna Mappes
- Department of Biological and Environmental Science, Centre of Excellence in Biological Interactions; University of Jyvaskyla; P. O. Box 35 Jyväskylä 40014 Finland
| |
Collapse
|
12
|
Samani P, Bell G. Experimental evolution of the grain of metabolic specialization in yeast. Ecol Evol 2016; 6:3912-22. [PMID: 27516854 PMCID: PMC4972220 DOI: 10.1002/ece3.2151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/27/2022] Open
Abstract
Adaptation to any given environment may be accompanied by a cost in terms of reduced growth in the ancestral or some alternative environment. Ecologists explain the cost of adaptation through the concept of a trade‐off, by which gaining a new trait involves losing another trait. Two mechanisms have been invoked to explain the evolution of trade‐offs in ecological systems, mutational degradation, and functional interference. Mutational degradation occurs when a gene coding a specific trait is not under selection in the resident environment; therefore, it may be degraded through the accumulation of mutations that are neutral in the resident environment but deleterious in an alternative environment. Functional interference evolves if the gene or a set of genes have antagonistic effects in two or more ecologically different traits. Both mechanisms pertain to a situation where the selection and the alternative environments are ecologically different. To test this hypothesis, we conducted an experiment in which 12 experimental populations of wild yeast were each grown in a minimal medium supplemented with a single substrate. We chose 12 different carbon substrates that were metabolized through similar and different pathways in order to represent a wide range of ecological conditions. We found no evidence for trade‐offs between substrates on the same pathway. The indirect response of substrates on other pathways, however, was consistently negative, with little correlation between the direct and indirect responses. We conclude that the grain of specialization in this case is the metabolic pathway and that specialization appears to evolve through mutational degradation.
Collapse
Affiliation(s)
- Pedram Samani
- Biology Department McGill University Montreal QCH3A 1B1 Canada; University of Montana 32 Campus Drive Missoula 59812 Montana
| | - Graham Bell
- Biology Department McGill University Montreal QC H3A 1B1 Canada
| |
Collapse
|
13
|
Giordano N, Mairet F, Gouzé JL, Geiselmann J, de Jong H. Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies. PLoS Comput Biol 2016; 12:e1004802. [PMID: 26958858 PMCID: PMC4784908 DOI: 10.1371/journal.pcbi.1004802] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/08/2016] [Indexed: 02/03/2023] Open
Abstract
Microbial physiology exhibits growth laws that relate the macromolecular composition of the cell to the growth rate. Recent work has shown that these empirical regularities can be derived from coarse-grained models of resource allocation. While these studies focus on steady-state growth, such conditions are rarely found in natural habitats, where microorganisms are continually challenged by environmental fluctuations. The aim of this paper is to extend the study of microbial growth strategies to dynamical environments, using a self-replicator model. We formulate dynamical growth maximization as an optimal control problem that can be solved using Pontryagin’s Maximum Principle. We compare this theoretical gold standard with different possible implementations of growth control in bacterial cells. We find that simple control strategies enabling growth-rate maximization at steady state are suboptimal for transitions from one growth regime to another, for example when shifting bacterial cells to a medium supporting a higher growth rate. A near-optimal control strategy in dynamical conditions is shown to require information on several, rather than a single physiological variable. Interestingly, this strategy has structural analogies with the regulation of ribosomal protein synthesis by ppGpp in the enterobacterium Escherichia coli. It involves sensing a mismatch between precursor and ribosome concentrations, as well as the adjustment of ribosome synthesis in a switch-like manner. Our results show how the capability of regulatory systems to integrate information about several physiological variables is critical for optimizing growth in a changing environment. Microbial growth is the process by which cells sustain and reproduce themselves from available matter and energy. Strategies enabling microorganisms to optimize their growth rate have been extensively studied, but mostly in stable environments. Here, we build a coarse-grained model of microbial growth and use methods from optimal control theory to determine a resource allocation scheme that would lead to maximal biomass accumulation when the cells are dynamically shifted from one growth medium to another. We compare this optimal solution with several cellular implementations of growth control, based on the capacity of the cell to sense different physiological variables. We find that strategies maximizing growth in steady-state conditions perform quite differently in dynamical conditions. Moreover, the control strategy with performance close to the theoretical maximum exploits information of more than one physiological variable, suggesting that optimization of microbial growth in dynamical rather than steady environments requires broader sensory capacities. Interestingly, the ppGpp alarmone system in the enterobacterium Escherichia coli, known to play an important role in growth control, has structural similarities with the control strategy approaching the theoretical maximum. It senses a discrepancy between the concentrations of precursors and ribosomes, and adjusts ribosome synthesis in an on-off fashion. This suggests that E. coli is adapted for environments with intermittent, rapid changes in nutrient availability.
Collapse
Affiliation(s)
- Nils Giordano
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d’Hères, France
- Inria, Grenoble - Rhône-Alpes research centre, Montbonnot, Saint Ismier Cedex, France
| | - Francis Mairet
- Inria, Sophia-Antipolis Méditerranée research centre, Sophia-Antipolis Cedex, France
| | - Jean-Luc Gouzé
- Inria, Sophia-Antipolis Méditerranée research centre, Sophia-Antipolis Cedex, France
| | - Johannes Geiselmann
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique (CNRS UMR 5588), Saint Martin d’Hères, France
- Inria, Grenoble - Rhône-Alpes research centre, Montbonnot, Saint Ismier Cedex, France
- * E-mail: (JG); (HdJ)
| | - Hidde de Jong
- Inria, Grenoble - Rhône-Alpes research centre, Montbonnot, Saint Ismier Cedex, France
- * E-mail: (JG); (HdJ)
| |
Collapse
|
14
|
Kaiser C, Franklin O, Richter A, Dieckmann U. Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils. Nat Commun 2015; 6:8960. [PMID: 26621582 PMCID: PMC4697322 DOI: 10.1038/ncomms9960] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 10/21/2015] [Indexed: 11/21/2022] Open
Abstract
The chemical structure of organic matter has been shown to be only marginally important for its decomposability by microorganisms. The question of why organic matter does accumulate in the face of powerful microbial degraders is thus key for understanding terrestrial carbon and nitrogen cycling. Here we demonstrate, based on an individual-based microbial community model, that social dynamics among microbes producing extracellular enzymes (‘decomposers') and microbes exploiting the catalytic activities of others (‘cheaters') regulate organic matter turnover. We show that the presence of cheaters increases nitrogen retention and organic matter build-up by downregulating the ratio of extracellular enzymes to total microbial biomass, allowing nitrogen-rich microbial necromass to accumulate. Moreover, increasing catalytic efficiencies of enzymes are outbalanced by a strong negative feedback on enzyme producers, leading to less enzymes being produced at the community level. Our results thus reveal a possible control mechanism that may buffer soil CO2 emissions in a future climate. Microbial decomposers in soil provide the largest ecosystem flux of CO2 to the atmosphere, but interactions at the microscale are poorly understood. Here, the authors use a computer modelling approach to show that social interactions among microbes buffer changing environmental conditions.
Collapse
Affiliation(s)
- Christina Kaiser
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, A-2361 Laxenburg, Austria.,Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Oskar Franklin
- Ecosystem Services and Management Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, A-2361 Laxenburg, Austria.,Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Ulf Dieckmann
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, A-2361 Laxenburg, Austria
| |
Collapse
|
15
|
Hummert S, Bohl K, Basanta D, Deutsch A, Werner S, Theissen G, Schroeter A, Schuster S. Evolutionary game theory: cells as players. MOLECULAR BIOSYSTEMS 2015; 10:3044-65. [PMID: 25270362 DOI: 10.1039/c3mb70602h] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In two papers we review game theory applications in biology below the level of cognitive living beings. It can be seen that evolution and natural selection replace the rationality of the actors appropriately. Even in these micro worlds, competing situations and cooperative relationships can be found and modeled by evolutionary game theory. Also those units of the lowest levels of life show different strategies for different environmental situations or different partners. We give a wide overview of evolutionary game theory applications to microscopic units. In this first review situations on the cellular level are tackled. In particular metabolic problems are discussed, such as ATP-producing pathways, secretion of public goods and cross-feeding. Further topics are cyclic competition among more than two partners, intra- and inter-cellular signalling, the struggle between pathogens and the immune system, and the interactions of cancer cells. Moreover, we introduce the theoretical basics to encourage scientists to investigate problems in cell biology and molecular biology by evolutionary game theory.
Collapse
Affiliation(s)
- Sabine Hummert
- Fachhochschule Schmalkalden, Faculty of Electrical Engineering, Blechhammer, 98574 Schmalkalden, Germany
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Lipson DA. The complex relationship between microbial growth rate and yield and its implications for ecosystem processes. Front Microbiol 2015; 6:615. [PMID: 26136742 PMCID: PMC4468913 DOI: 10.3389/fmicb.2015.00615] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 06/03/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- David A. Lipson
- Department of Biology, San Diego State UniversitySan Diego, CA, USA
| |
Collapse
|
17
|
Litchman E, Edwards KF, Klausmeier CA. Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future. Front Microbiol 2015; 6:254. [PMID: 25904900 PMCID: PMC4389539 DOI: 10.3389/fmicb.2015.00254] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/15/2015] [Indexed: 11/17/2022] Open
Abstract
Trait-based approaches provide a mechanistic framework to understand and predict the structure and functioning of microbial communities. Resource utilization traits and trade-offs are among key microbial traits that describe population dynamics and competition among microbes. Several important trade-offs have been identified for prokaryotic and eukaryotic microbial taxa that define contrasting ecological strategies and contribute to species coexistence and diversity. The shape, dimensionality, and hierarchy of trade-offs may determine coexistence patterns and need to be better characterized. Laboratory measured resource utilization traits can be used to explain temporal and spatial structure and dynamics of natural microbial communities and predict biogeochemical impacts. Global environmental change can alter microbial community composition through altering resource utilization by different microbes and, consequently, may modify biogeochemical impacts of microbes.
Collapse
Affiliation(s)
- Elena Litchman
- W.K. Kellogg Biological Station – Michigan State UniversityHickory Corners, MI, USA
- Department of Integrative Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Kyle F. Edwards
- Department of Oceanography, University of Hawai’i at ManoaHonolulu, HI, USA
| | - Christopher A. Klausmeier
- W.K. Kellogg Biological Station – Michigan State UniversityHickory Corners, MI, USA
- Department of Plant Biology, Michigan State University, East LansingMI, USA
| |
Collapse
|
18
|
Mechanistic links between cellular trade-offs, gene expression, and growth. Proc Natl Acad Sci U S A 2015; 112:E1038-47. [PMID: 25695966 DOI: 10.1073/pnas.1416533112] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Intracellular processes rarely work in isolation but continually interact with the rest of the cell. In microbes, for example, we now know that gene expression across the whole genome typically changes with growth rate. The mechanisms driving such global regulation, however, are not well understood. Here we consider three trade-offs that, because of limitations in levels of cellular energy, free ribosomes, and proteins, are faced by all living cells and we construct a mechanistic model that comprises these trade-offs. Our model couples gene expression with growth rate and growth rate with a growing population of cells. We show that the model recovers Monod's law for the growth of microbes and two other empirical relationships connecting growth rate to the mass fraction of ribosomes. Further, we can explain growth-related effects in dosage compensation by paralogs and predict host-circuit interactions in synthetic biology. Simulating competitions between strains, we find that the regulation of metabolic pathways may have evolved not to match expression of enzymes to levels of extracellular substrates in changing environments but rather to balance a trade-off between exploiting one type of nutrient over another. Although coarse-grained, the trade-offs that the model embodies are fundamental, and, as such, our modeling framework has potentially wide application, including in both biotechnology and medicine.
Collapse
|
19
|
Vulin C, Di Meglio JM, Lindner AB, Daerr A, Murray A, Hersen P. Growing yeast into cylindrical colonies. Biophys J 2014; 106:2214-21. [PMID: 24853750 PMCID: PMC4052359 DOI: 10.1016/j.bpj.2014.02.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/28/2014] [Accepted: 02/25/2014] [Indexed: 10/27/2022] Open
Abstract
Microorganisms often form complex multicellular assemblies such as biofilms and colonies. Understanding the interplay between assembly expansion, metabolic yield, and nutrient diffusion within a freely growing colony remains a challenge. Most available data on microorganisms are from planktonic cultures, due to the lack of experimental tools to control the growth of multicellular assemblies. Here, we propose a method to constrain the growth of yeast colonies into simple geometric shapes such as cylinders. To this end, we designed a simple, versatile culture system to control the location of nutrient delivery below a growing colony. Under such culture conditions, yeast colonies grow vertically and only at the locations where nutrients are delivered. Colonies increase in height at a steady growth rate that is inversely proportional to the cylinder radius. We show that the vertical growth rate of cylindrical colonies is not defined by the single-cell division rate, but rather by the colony metabolic yield. This contrasts with cells in liquid culture, in which the single-cell division rate is the only parameter that defines the population growth rate. This method also provides a direct, simple method to estimate the metabolic yield of a colony. Our study further demonstrates the importance of the shape of colonies on setting their expansion. We anticipate that our approach will be a starting point for elaborate studies of the population dynamics, evolution, and ecology of microbial colonies in complex landscapes.
Collapse
Affiliation(s)
- Clément Vulin
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Ariel B Lindner
- Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine, Université Paris Descartes, Paris, France
| | - Adrian Daerr
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France
| | - Andrew Murray
- Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique and Université Paris Diderot, Paris, France; The Mechanobiology Institute, National University of Singapore, Singapore.
| |
Collapse
|
20
|
Waldherr S, Oyarzún DA, Bockmayr A. Dynamic optimization of metabolic networks coupled with gene expression. J Theor Biol 2014; 365:469-85. [PMID: 25451533 DOI: 10.1016/j.jtbi.2014.10.035] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 11/24/2022]
Abstract
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization techniques. However, metabolic adaptations driven by changes in gene expression cannot be analyzed by steady state models, as these do not account for temporal changes in biomass composition. Here we present a dynamic optimization framework that integrates the metabolic network with the dynamics of biomass production and composition. An approximation by a timescale separation leads to a coupled model of quasi-steady state constraints on the metabolic reactions, and differential equations for the substrate concentrations and biomass composition. We propose a dynamic optimization approach to determine reaction fluxes for this model, explicitly taking into account enzyme production costs and enzymatic capacity. In contrast to the established dynamic flux balance analysis, our approach allows predicting dynamic changes in both the metabolic fluxes and the biomass composition during metabolic adaptations. Discretization of the optimization problems leads to a linear program that can be efficiently solved. We applied our algorithm in two case studies: a minimal nutrient uptake network, and an abstraction of core metabolic processes in bacteria. In the minimal model, we show that the optimized uptake rates reproduce the empirical Monod growth for bacterial cultures. For the network of core metabolic processes, the dynamic optimization algorithm predicted commonly observed metabolic adaptations, such as a diauxic switch with a preference ranking for different nutrients, re-utilization of waste products after depletion of the original substrate, and metabolic adaptation to an impending nutrient depletion. These examples illustrate how dynamic adaptations of enzyme expression can be predicted solely from an optimization principle.
Collapse
Affiliation(s)
- Steffen Waldherr
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Diego A Oyarzún
- Department of Mathematics, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alexander Bockmayr
- DFG Research Center Matheon, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| |
Collapse
|
21
|
Allison SD. Modeling adaptation of carbon use efficiency in microbial communities. Front Microbiol 2014; 5:571. [PMID: 25389423 PMCID: PMC4211550 DOI: 10.3389/fmicb.2014.00571] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022] Open
Abstract
In new microbial-biogeochemical models, microbial carbon use efficiency (CUE) is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e., become less sensitive) to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus, the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.
Collapse
Affiliation(s)
- Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine Irvine, CA, USA ; Department of Earth System Science, University of California Irvine Irvine, CA, USA
| |
Collapse
|
22
|
Hall AR, Angst DC, Schiessl KT, Ackermann M. Costs of antibiotic resistance - separating trait effects and selective effects. Evol Appl 2014; 8:261-72. [PMID: 25861384 PMCID: PMC4380920 DOI: 10.1111/eva.12187] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/06/2014] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance can impair bacterial growth or competitive ability in the absence of antibiotics, frequently referred to as a ‘cost’ of resistance. Theory and experiments emphasize the importance of such effects for the distribution of resistance in pathogenic populations. However, recent work shows that costs of resistance are highly variable depending on environmental factors such as nutrient supply and population structure, as well as genetic factors including the mechanism of resistance and genetic background. Here, we suggest that such variation can be better understood by distinguishing between the effects of resistance mechanisms on individual traits such as growth rate or yield (‘trait effects’) and effects on genotype frequencies over time (‘selective effects’). We first give a brief overview of the biological basis of costs of resistance and how trait effects may translate to selective effects in different environmental conditions. We then review empirical evidence of genetic and environmental variation of both types of effects and how such variation may be understood by combining molecular microbiological information with concepts from evolution and ecology. Ultimately, disentangling different types of costs may permit the identification of interventions that maximize the cost of resistance and therefore accelerate its decline.
Collapse
Affiliation(s)
- Alex R Hall
- Institute of Integrative Biology, ETH Zürich Zürich, Switzerland ; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Zürich, Switzerland ; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Daniel C Angst
- Institute of Integrative Biology, ETH Zürich Zürich, Switzerland ; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Zürich, Switzerland ; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Konstanze T Schiessl
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Zürich, Switzerland ; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Zürich, Switzerland ; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| |
Collapse
|
23
|
Østman B, Lin R, Adami C. Trade-offs drive resource specialization and the gradual establishment of ecotypes. BMC Evol Biol 2014; 14:113. [PMID: 24885598 PMCID: PMC4067365 DOI: 10.1186/1471-2148-14-113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. RESULTS We present a model to study the effects of trade-offs on specialization and adaptive radiation in asexual organisms based solely on competition for limiting resources, where trade-offs are stronger the greater an organism's ability to utilize resources. In this model resources are perfectly substitutable, and fitness is derived from the consumption of these resources. The model contains no spatial parameters, and is therefore strictly sympatric. We quantify the degree of specialization by the number of ecotypes evolved and the niche breadth of the population, and observe that these are sensitive to resource influx and trade-offs. Resource influx has a strong effect on the degree of specialization, with a clear transition between minimal diversification at high influx and multiple species evolving at low resource influx. At low resource influx the degree of specialization further depends on the strength of the trade-offs, with more ecotypes evolving the stronger trade-offs are. The specialized organisms persist through negative frequency-dependent selection. In addition, by analyzing one of the evolutionary radiations in greater detail we demonstrate that a single mutation alone is not enough to establish a new ecotype, even though phylogenetic reconstruction identifies that mutation as the branching point. Instead, it takes a series of additional mutations to ensure the stable coexistence of the new ecotype in the background of the existing ones. CONCLUSIONS Trade-offs are sufficient to drive the evolution of specialization in sympatric asexual populations. Without trade-offs to restrain traits, generalists evolve and diversity decreases. The observation that several mutations are required to complete speciation, even when a single mutation creates the new species, highlights the gradual nature of speciation and the importance of phyletic evolution.
Collapse
Affiliation(s)
- Bjørn Østman
- Department of Microbiology and Molecular Genetics, Michigan State University, MI 48824 East Lansing, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, 48824 East Lansing, USA
| | - Randall Lin
- California Institute of Technology, CA 91125 Pasadena, USA
| | - Christoph Adami
- Department of Microbiology and Molecular Genetics, Michigan State University, MI 48824 East Lansing, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, 48824 East Lansing, USA
| |
Collapse
|
24
|
Frank SA. Microbial metabolism: optimal control of uptake versus synthesis. PeerJ 2014; 2:e267. [PMID: 24795846 PMCID: PMC3940620 DOI: 10.7717/peerj.267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 01/20/2014] [Indexed: 11/20/2022] Open
Abstract
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of resources through the multiple species that create a microbial community. This article analyzes a simple mathematical model of the tradeoff between uptake and synthesis. Key factors include the influx rate from external sources relative to the outflux rate, the rate of internal decay within cells, and the cost of synthesis. Aspects of demography also matter, such as cellular birth and death rates, the expected time course of a local resource flow, and the associated lifespan of the local population. Spatial patterns of genetic variability and differentiation between populations may also strongly influence the evolution of metabolic regulatory controls of individual species and thus the structuring of microbial communities. The widespread use of optimality approaches in recent work on microbial metabolism has ignored demography and genetic structure.
Collapse
Affiliation(s)
- Steven A Frank
- Department of Ecology and Evolutionary Biology, University of California , Irvine , CA , USA
| |
Collapse
|
25
|
Abstract
Mutant lineages may cause cancer-like overgrowths in microbial populations. Theory predicts that microbial regulatory controls may be designed to limit the origin and competitive potential of rogue lineages. A new study shows how a Salmonella species protects itself against overgrowths.
Collapse
|
26
|
de Vargas Roditi L, Boyle KE, Xavier JB. Multilevel selection analysis of a microbial social trait. Mol Syst Biol 2013; 9:684. [PMID: 23959025 PMCID: PMC3779802 DOI: 10.1038/msb.2013.42] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/24/2013] [Indexed: 01/11/2023] Open
Abstract
The study of microbial communities often leads to arguments for the evolution of cooperation due to group benefits. However, multilevel selection models caution against the uncritical assumption that group benefits will lead to the evolution of cooperation. We analyze a microbial social trait to precisely define the conditions favoring cooperation. We combine the multilevel partition of the Price equation with a laboratory model system: swarming in Pseudomonas aeruginosa. We parameterize a population dynamics model using competition experiments where we manipulate expression, and therefore the cost-to-benefit ratio of swarming cooperation. Our analysis shows that multilevel selection can favor costly swarming cooperation because it causes population expansion. However, due to high costs and diminishing returns constitutive cooperation can only be favored by natural selection when relatedness is high. Regulated expression of cooperative genes is a more robust strategy because it provides the benefits of swarming expansion without the high cost or the diminishing returns. Our analysis supports the key prediction that strong group selection does not necessarily mean that microbial cooperation will always emerge.
Collapse
Affiliation(s)
- Laura de Vargas Roditi
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Kerry E Boyle
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Joao B Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
27
|
Raymond B, Bonsall MB. Cooperation and the evolutionary ecology of bacterial virulence: TheBacillus cereusgroup as a novel study system. Bioessays 2013; 35:706-16. [DOI: 10.1002/bies.201300028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ben Raymond
- School of Biological Sciences; Royal Holloway University of London; Egham UK
| | - Michael B. Bonsall
- Department of Zoology; University of Oxford; Oxford UK
- St. Peter's College; Oxford UK
| |
Collapse
|
28
|
Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking. Appl Environ Microbiol 2011; 78:1345-52. [PMID: 22194284 DOI: 10.1128/aem.06585-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.
Collapse
|
29
|
Abstract
George Williams defined an evolutionary unit as hereditary information for which the selection bias between competing units dominates the informational decay caused by imperfect transmission. In this article, I extend Williams' approach to show that the ratio of selection bias to transmission bias provides a unifying framework for diverse biological problems. Specific examples include Haldane and Lande's mutation-selection balance, Eigen's error threshold and quasispecies, Van Valen's clade selection, Price's multilevel formulation of group selection, Szathmáry and Demeter's evolutionary origin of primitive cells, Levin and Bull's short-sighted evolution of HIV virulence, Frank's timescale analysis of microbial metabolism and Maynard Smith and Szathmáry's major transitions in evolution. The insights from these diverse applications lead to a deeper understanding of kin selection, group selection, multilevel evolutionary analysis and the philosophical problems of evolutionary units and individuality.
Collapse
Affiliation(s)
- S A Frank
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
| |
Collapse
|
30
|
Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosystems 2011; 105:147-53. [DOI: 10.1016/j.biosystems.2011.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/12/2011] [Accepted: 05/12/2011] [Indexed: 01/22/2023]
|
31
|
Ernebjerg M, Kishony R. Dynamic phenotypic clustering in noisy ecosystems. PLoS Comput Biol 2011; 7:e1002017. [PMID: 21445229 PMCID: PMC3060162 DOI: 10.1371/journal.pcbi.1002017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 01/29/2011] [Indexed: 11/18/2022] Open
Abstract
In natural ecosystems, hundreds of species typically share the same environment and are connected by a dense network of interactions such as predation or competition for resources. Much is known about how fixed ecological niches can determine species abundances in such systems, but far less attention has been paid to patterns of abundances in randomly varying environments. Here, we study this question in a simple model of competition between many species in a patchy ecosystem with randomly fluctuating environmental conditions. Paradoxically, we find that introducing noise can actually induce ordered patterns of abundance-fluctuations, leading to a distinct periodic variation in the correlations between species as a function of the phenotypic distance between them; here, difference in growth rate. This is further accompanied by the formation of discrete, dynamic clusters of abundant species along this otherwise continuous phenotypic axis. These ordered patterns depend on the collective behavior of many species; they disappear when only individual or pairs of species are considered in isolation. We show that they arise from a balance between the tendency of shared environmental noise to synchronize species abundances and the tendency for competition among species to make them fluctuate out of step. Our results demonstrate that in highly interconnected ecosystems, noise can act as an ordering force, dynamically generating ecological patterns even in environments lacking explicit niches.
Collapse
Affiliation(s)
- Morten Ernebjerg
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| |
Collapse
|
32
|
Abstract
Microbial secretions manipulate the environment and communicate information to neighbours. The secretions of an individual microbe typically act externally and benefit all members of the local group. Secreting imposes a cost in terms of growth, so that cheaters that do not secrete gain by sharing the benefits without paying the costs. Cheaters have been observed in several experimental and natural settings. Given that cheaters grow faster than secretors when in direct competition, what maintains the widely observed patterns of secretion? Recent theory has emphasized the genetic structure of populations, in which secretors tend to associate spatially with other secretors, reducing direct competition and allowing highly secreting groups to share mutual benefits. Such kin selection can be a powerful force favouring cooperative traits. Here, I argue that, although kin selection is a factor, the combination of mutation and demographic processes dominate in determining the relative fitness of secretors versus cheaters when measured over the full cycle of microbial life history. Key demographic factors include the local density of microbes at which secretion significantly alters the environment, the extent to which secretion enhances microbial growth and maximum local density, and the ways in which secretion alters colony survival and dispersal.
Collapse
Affiliation(s)
- Steven A Frank
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA.
| |
Collapse
|
33
|
A mixture of "cheats" and "co-operators" can enable maximal group benefit. PLoS Biol 2010; 8. [PMID: 20856906 PMCID: PMC2939026 DOI: 10.1371/journal.pbio.1000486] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022] Open
Abstract
Is a group best off if everyone co-operates? Theory often considers this to be so (e.g. the "conspiracy of doves"), this understanding underpinning social and economic policy. We observe, however, that after competition between "cheat" and "co-operator" strains of yeast, population fitness is maximized under co-existence. To address whether this might just be a peculiarity of our experimental system or a result with broader applicability, we assemble, benchmark, dissect, and test a systems model. This reveals the conditions necessary to recover the unexpected result. These are 3-fold: (a) that resources are used inefficiently when they are abundant, (b) that the amount of co-operation needed cannot be accurately assessed, and (c) the population is structured, such that co-operators receive more of the resource than the cheats. Relaxing any of the assumptions can lead to population fitness being maximized when cheats are absent, which we experimentally demonstrate. These three conditions will often be relevant, and hence in order to understand the trajectory of social interactions, understanding the dynamics of the efficiency of resource utilization and accuracy of information will be necessary.
Collapse
|