1
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Sangha JS, Barrett P, Curtis TP, Métris A, Jakubovics NS, Ofiteru ID. Effects of glucose and lactate on Streptococcus mutans abundance in a novel multispecies oral biofilm model. Microbiol Spectr 2024; 12:e0371323. [PMID: 38376204 PMCID: PMC10986578 DOI: 10.1128/spectrum.03713-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions.IMPORTANCEWe developed a controlled (by removing host factor) dynamic system metabolically representative of early colonization of Streptococcus mutans not measurable in vivo. Hypotheses on factors influencing S. mutans colonization, such as community composition and inoculation sequence and the effect of metabolite concentrations, can be tested and used to predict the effect of interventions such as dietary modifications or the use of toothpaste or mouthwash on S. mutans colonization. The defined in vitro model (species and medium) can be simulated in an in silico model to explore more of the parameter space.
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Affiliation(s)
- Jay S. Sangha
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul Barrett
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, United Kingdom
| | - Thomas P. Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Aline Métris
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, United Kingdom
| | - Nicholas S. Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Irina D. Ofiteru
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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2
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Picot A, Shibasaki S, Meacock OJ, Mitri S. Microbial interactions in theory and practice: when are measurements compatible with models? Curr Opin Microbiol 2023; 75:102354. [PMID: 37421708 DOI: 10.1016/j.mib.2023.102354] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/10/2023]
Abstract
Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence on each other's growth and death. We review here how theoretical approaches are used to extract interaction measurements from experimental data in microbiology, particularly focusing on the generalised Lotka-Volterra (gLV) framework. Though widely used, we argue that the gLV model should be avoided for estimating interactions in batch culture - the most common, simplest and cheapest in vitro approach to culturing microbes. Fortunately, alternative approaches offer a way out of this conundrum. Firstly, on the experimental side, alternatives such as the serial-transfer and chemostat systems more closely match the theoretical assumptions of the gLV model. Secondly, on the theoretical side, explicit organism-environment interaction models can be used to study the dynamics of batch-culture systems. We hope that our recommendations will increase the tractability of microbial model systems for experimentalists and theoreticians alike.
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Affiliation(s)
- Aurore Picot
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shota Shibasaki
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Oliver J Meacock
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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3
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Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
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Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
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4
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Treloar NJ, Braniff N, Ingalls B, Barnes CP. Deep reinforcement learning for optimal experimental design in biology. PLoS Comput Biol 2022; 18:e1010695. [PMID: 36409776 PMCID: PMC9721483 DOI: 10.1371/journal.pcbi.1010695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 12/05/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The field of optimal experimental design uses mathematical techniques to determine experiments that are maximally informative from a given experimental setup. Here we apply a technique from artificial intelligence-reinforcement learning-to the optimal experimental design task of maximizing confidence in estimates of model parameter values. We show that a reinforcement learning approach performs favourably in comparison with a one-step ahead optimisation algorithm and a model predictive controller for the inference of bacterial growth parameters in a simulated chemostat. Further, we demonstrate the ability of reinforcement learning to train over a distribution of parameters, indicating that this approach is robust to parametric uncertainty.
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Affiliation(s)
- Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Nathan Braniff
- Department of Applied Mathematics, University of Waterloo, Waterloo, Canada
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, Canada
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
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5
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Kim J, Armin G, Inomura K. Saturating relationship between phytoplankton growth rate and nutrient concentration explained by macromolecular allocation. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100167. [PMID: 36518172 PMCID: PMC9742995 DOI: 10.1016/j.crmicr.2022.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Phytoplankton account for about a half of photosynthesis in the world, making them a key player in the ecological and biogeochemical systems. One of the key traits of phytoplankton is their growth rate because it indicates their productivity and affects their competitive capability. The saturating relationship between phytoplankton growth rate and environmental nutrient concentration has been widely observed yet the mechanisms behind the relationship remain elusive. Here we use a mechanistic model and metadata of phytoplankton to show that the saturating relationship between growth rate and nitrate concentration can be interpreted by intracellular macromolecular allocation. At low nitrate levels, the diffusive nitrate transport linearly increases with the nitrate concentration, while the internal nitrogen requirement increases with the growth rate, leading to a non-linear increase in the growth rate with nitrate. This increased nitrogen requirement is due to the increased allocation to biosynthetic and photosynthetic molecules. The allocation to these molecules reaches a maximum at high nitrate concentration and the growth rate ceases to increase despite high nitrate availability due to carbon limitation. The produced growth rate and nitrate relationships are consistent with the data of phytoplankton across taxa. Our study provides a macromolecular interpretation of the widely observed growth-nutrient relationship and highlights that the key control of the phytoplankton growth exists within the cell.
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Affiliation(s)
- Jongsun Kim
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
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6
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Calabrese F, Stryhanyuk H, Moraru C, Schlömann M, Wick LY, Richnow HH, Musat F, Musat N. Metabolic history and metabolic fitness as drivers of anabolic heterogeneity in isogenic microbial populations. Environ Microbiol 2021; 23:6764-6776. [PMID: 34472201 DOI: 10.1111/1462-2920.15756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behaviour. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time-resolved stable isotope probing and nanoscale secondary ion mass spectrometry to quantify substrate assimilation by individual cells of Pseudomonas putida, P. stutzeri and Thauera aromatica. Acetate and benzoate at different concentrations were used as substrates. Anabolic heterogeneity was quantified by the cumulative differentiation tendency index. We observed two major, opposing trends of anabolic heterogeneity over time. Most often, microbial populations started as highly heterogeneous, with heterogeneity decreasing by various degrees over time. The second, less frequently observed trend, saw microbial populations starting at low or very low heterogeneity, and remaining largely stable over time. We explain these trends as an interplay of metabolic history (e.g. former growth substrate or other nutrient limitations) and metabolic fitness (i.e. the fine-tuning of metabolic pathways to process a defined growth substrate). Our results offer a new viewpoint on the intra-population functional diversification often encountered in the environment, and suggests that some microbial populations may be intrinsically heterogeneous.
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Affiliation(s)
- Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Schlömann
- Department of Environmental Microbiology, Institute of Biosciences, TU-Bergakademie Freiberg, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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7
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Dynamic Modeling of Carnobacterium maltaromaticum CNCM I-3298 Growth and Metabolite Production and Model-Based Process Optimization. Foods 2021; 10:foods10081922. [PMID: 34441699 PMCID: PMC8391277 DOI: 10.3390/foods10081922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Carnobacterium maltaromaticum is a species of lactic acid bacteria found in dairy, meat, and fish, with technological properties useful in food biopreservation and flavor development. In more recent years, it has also proven to be a key element of biological time–temperature integrators for tracking temperature variations experienced by perishable foods along the cold-chain. A dynamic model for the growth of C. maltaromaticum CNCM I-3298 and production of four metabolites (formic acid, acetic acid, lactic acid, and ethanol) from trehalose in batch culture was developed using the reaction scheme formalism. The dependence of the specific growth and production rates as well as the product inhibition parameters on the operating conditions were described by the response surface method. The parameters of the model were calibrated from eight experiments, covering a broad spectrum of culture conditions (temperatures between 20 and 37 °C; pH between 6.0 and 9.5). The model was validated against another set of eight independent experiments performed under different conditions selected in the same range. The model correctly predicted the growth kinetics of C. maltaromaticum CNCM I-3298 as well as the dynamics of the carbon source conversion, with a mean relative error of 10% for biomass and 14% for trehalose and the metabolites. The paper illustrates that the proposed model is a valuable tool for optimizing the culture of C. maltaromaticum CNCM I-3298 by determining operating conditions that favor the production of biomass or selected metabolites. Model-based optimization may thus reduce the number of experiments and substantially speed up the process development, with potential applications in food technology for producing starters and improving the yield and productivity of the fermentation of sugars into metabolites of industrial interest.
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8
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Jafari SA, Osfouri S, Azin R. Modelling of batch biomethanation process for maximizing income based on values of consumed and produced gases. KOREAN J CHEM ENG 2020. [DOI: 10.1007/s11814-020-0501-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Treloar NJ, Fedorec AJH, Ingalls B, Barnes CP. Deep reinforcement learning for the control of microbial co-cultures in bioreactors. PLoS Comput Biol 2020; 16:e1007783. [PMID: 32275710 PMCID: PMC7176278 DOI: 10.1371/journal.pcbi.1007783] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/22/2020] [Accepted: 03/10/2020] [Indexed: 01/01/2023] Open
Abstract
Multi-species microbial communities are widespread in natural ecosystems. When employed for biomanufacturing, engineered synthetic communities have shown increased productivity in comparison with monocultures and allow for the reduction of metabolic load by compartmentalising bioprocesses between multiple sub-populations. Despite these benefits, co-cultures are rarely used in practice because control over the constituent species of an assembled community has proven challenging. Here we demonstrate, in silico, the efficacy of an approach from artificial intelligence-reinforcement learning-for the control of co-cultures within continuous bioreactors. We confirm that feedback via a trained reinforcement learning agent can be used to maintain populations at target levels, and that model-free performance with bang-bang control can outperform a traditional proportional integral controller with continuous control, when faced with infrequent sampling. Further, we demonstrate that a satisfactory control policy can be learned in one twenty-four hour experiment by running five bioreactors in parallel. Finally, we show that reinforcement learning can directly optimise the output of a co-culture bioprocess. Overall, reinforcement learning is a promising technique for the control of microbial communities.
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Affiliation(s)
- Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, Canada
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
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10
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Ugalde-Salas P, Desmond-Le Quéméner E, Harmand J, Rapaport A, Bouchez T. Insights from Microbial Transition State Theory on Monod's Affinity Constant. Sci Rep 2020; 10:5323. [PMID: 32210303 PMCID: PMC7093443 DOI: 10.1038/s41598-020-62213-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/10/2020] [Indexed: 11/19/2022] Open
Abstract
Microbial transition state theory (MTS) offers a theoretically explicit mathematical model for substrate limited microbial growth. By considering a first order approximation of the MTS equation one recovers the well-known Monod’s expression for growth, which was regarded as a purely empirical function. The harvest volume of a cell as defined in MTS theory can then be related to the affinity concept, giving a new physical interpretation to it, and a new way to determine its value. Consequences of such a relationship are discussed.
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Affiliation(s)
- Pablo Ugalde-Salas
- INRAE, Univ Montpellier, LBE, 102 avenue des Etangs, 11100, Narbonne, France.
| | | | - Jérôme Harmand
- INRAE, Univ Montpellier, LBE, 102 avenue des Etangs, 11100, Narbonne, France
| | - Alain Rapaport
- MISTEA, INRAE, Univ. Montpellier, Montpellier SupAgro, Montpellier, France
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11
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Hou L, Griswold N, Ji J, Hu Z. Specific affinity and relative abundance of methanogens in acclimated anaerobic sludge treating low-strength wastewater. Appl Microbiol Biotechnol 2019; 104:291-302. [PMID: 31732752 DOI: 10.1007/s00253-019-10149-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/20/2019] [Accepted: 09/22/2019] [Indexed: 11/26/2022]
Abstract
Kinetic parameters affecting effluent water quality including half saturation constant (Ks), maximum specific growth rate (μmax), and specific affinity ([Formula: see text], defined as μmax/Ks) were investigated using three types of anaerobic sludge (raw anaerobic digestion sludge referred to as unacclimated sludge, unacclimated sludge after endogenous decay, and sludge acclimated to low-strength wastewater in an anaerobic membrane bioreactor (AnMBR) for 360 days). Long-term acclimation to low-strength wastewater resulted in sludge with high specific affinity (1.6 × 10-3 L/mg COD/day for acclimated sludge compared to 4.1 × 10-4 L/mg COD/day for unacclimated sludge). The μmax values for unacclimated sludge and acclimated sludge were 0.08 and 0.07 day-1, respectively. The Ks values for unacclimated sludge and acclimated sludge were 194 ± 81 mg COD/L and 45 ± 13 mg COD/L, respectively. Although the Ks of unacclimated sludge after endogenous decay increased to 772 ± 74 mg COD/L, μmax increased to 0.35 day-1 as well, resulting in no statistically significant difference of [Formula: see text] between the two types of unacclimated sludge. Overall, [Formula: see text] is a better indicator than μmax or Ks alone for determining effluent water quality, as effluent substrate concentration is approximately inversely proportional to the specific affinity. 16S rRNA sequencing data analysis indicated a high abundance (85.8% of total archaea) of Methanosaeta in the microbial community after long-term acclimation. High [Formula: see text] associated with the enrichment of Methanosaeta appears to ensure successful anaerobic treatment of low-strength wastewater.
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Affiliation(s)
- Liyuan Hou
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO, 65211, USA
| | - Nick Griswold
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO, 65211, USA
| | - Junyuan Ji
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266000, China.
- College of Environmental Science and Engineering, Ocean University of China, 238 Songling Road, Laoshan District, Qingdao, 266100, China.
| | - Zhiqiang Hu
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO, 65211, USA.
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12
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Investment in secreted enzymes during nutrient-limited growth is utility dependent. Proc Natl Acad Sci U S A 2017; 114:E7796-E7802. [PMID: 28847943 DOI: 10.1073/pnas.1708580114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Pathogenic bacteria secrete toxins and degradative enzymes that facilitate their growth by liberating nutrients from the environment. To understand bacterial growth under nutrient-limited conditions, we studied resource allocation between cellular and secreted components by the pathogenic bacterium Pseudomonas aeruginosa during growth on a protein substrate that requires extracellular digestion by secreted proteases. We identified a quantitative relationship between the rate of increase of cellular biomass under nutrient-limiting growth conditions and the rate of increase in investment in secreted proteases. Production of secreted proteases is stimulated by secreted signals that convey information about the utility of secreted proteins during nutrient-limited growth. Growth modeling using this relationship recapitulated the observed kinetics of bacterial growth on a protein substrate. The proposed regulatory strategy suggests a rationale for quorum-sensing-dependent stimulation of the production of secreted enzymes whereby investment in secreted enzymes occurs in proportion to the utility they confer. Our model provides a framework that can be applied toward understanding bacterial growth in many environments where growth rate is limited by the availability of nutrients.
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13
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Roller BRK, Schmidt TM. The physiology and ecological implications of efficient growth. ISME JOURNAL 2015; 9:1481-7. [PMID: 25575305 DOI: 10.1038/ismej.2014.235] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/18/2014] [Accepted: 10/31/2014] [Indexed: 11/09/2022]
Abstract
The natural habitats of microbes are typically spatially structured with limited resources, so opportunities for unconstrained, balanced growth are rare. In these habitats, selection should favor microbes that are able to use resources most efficiently, that is, microbes that produce the most progeny per unit of resource consumed. On the basis of this assertion, we propose that selection for efficiency is a primary driver of the composition of microbial communities. In this article, we review how the quality and quantity of resources influence the efficiency of heterotrophic growth. A conceptual model proposing innate differences in growth efficiency between oligotrophic and copiotrophic microbes is also provided. We conclude that elucidation of the mechanisms underlying efficient growth will enhance our understanding of the selective pressures shaping microbes and will improve our capacity to manage microbial communities effectively.
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Affiliation(s)
- Benjamin R K Roller
- 1] Department of Microbiology and Molecular Genetics, East Lansing, MI, USA [2] Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA [3] Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- 1] Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, USA [2] Ecology and Evolutionary Biology, Ann Arbor, MI, USA [3] Microbiology and Immunology, Ann Arbor, MI, USA
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14
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Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol 2013; 195:4900-14. [PMID: 23974031 PMCID: PMC3807489 DOI: 10.1128/jb.00504-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/20/2013] [Indexed: 12/31/2022] Open
Abstract
The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.
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Affiliation(s)
- Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Jennifer V. Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M. Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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15
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Olivieri G, Russo ME, Maffettone PL, Mancusi E, Marzocchella A, Salatino P. Nonlinear Analysis of Substrate-Inhibited Continuous Cultures Operated with Feedback Control on Dissolved Oxygen. Ind Eng Chem Res 2013. [DOI: 10.1021/ie400782y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giuseppe Olivieri
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio n. 80, 80125 Napoli, Italy
| | - Maria Elena Russo
- Istituto di Ricerche sulla Combustione C.N.R., P.le V. Tecchio n. 80, 80125 Napoli, Italy
| | - Pier Luca Maffettone
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio n. 80, 80125 Napoli, Italy
| | - Erasmo Mancusi
- Dipartimento
di Ingegneria, Università degli Studi del Sannio, Piazza Roma,
21, I 82100 Benevento, Italy
- Chemical
and Food Engineering Department, Universidade Federal de Santa Catarina, 88040-970 Florianópolis, SC, Brazil
| | - Antonio Marzocchella
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio n. 80, 80125 Napoli, Italy
| | - Piero Salatino
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio n. 80, 80125 Napoli, Italy
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Bren A, Hart Y, Dekel E, Koster D, Alon U. The last generation of bacterial growth in limiting nutrient. BMC SYSTEMS BIOLOGY 2013; 7:27. [PMID: 23531321 PMCID: PMC3626568 DOI: 10.1186/1752-0509-7-27] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/12/2013] [Indexed: 11/24/2022]
Abstract
Background Bacterial growth as a function of nutrients has been studied for decades, but is still not fully understood. In particular, the growth laws under dynamically changing environments have been difficult to explore, because of the rapidly changing conditions. Here, we address this challenge by means of a robotic assay and measure bacterial growth rate, promoter activity and substrate level at high temporal resolution across the entire growth curve in batch culture. As a model system, we study E. coli growing under nitrogen or carbon limitation, and explore the dynamics in the last generation of growth where nutrient levels can drop rapidly. Results We find that growth stops abruptly under limiting nitrogen or carbon, but slows gradually when nutrients are not limiting. By measuring growth rate at a 3 min time resolution, and inferring the instantaneous substrate level, s, we find that the reduction in growth rate μ under nutrient limitation follows Monod’s law, μ=μ0sks+s. By following promoter activity of different genes we found that the abrupt stop of growth under nitrogen or carbon limitation is accompanied by a pulse-like up-regulation of the expression of genes in the relevant nutrient assimilation pathways. We further find that sharp stop of growth is conditional on the presence of regulatory proteins in the assimilation pathway. Conclusions The observed sharp stop of growth accompanied by a pulsed expression of assimilation genes allows bacteria to compensate for the drop in nutrients, suggesting a strategy used by the cells to prolong exponential growth under limiting substrate.
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Affiliation(s)
- Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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17
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Olivieri G, Russo ME, Di Donato A, Marzocchella A, Salatino P. Unstable steady state operations of substrate inhibited cultures by dissolved oxygen control. J Biotechnol 2011; 156:302-8. [DOI: 10.1016/j.jbiotec.2011.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 08/09/2011] [Accepted: 09/07/2011] [Indexed: 11/30/2022]
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18
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Zinn M, Durner R, Zinn H, Ren Q, Egli T, Witholt B. Growth and accumulation dynamics of poly(3-hydroxyalkanoate) (PHA) in Pseudomonas putida GPo1 cultivated in continuous culture under transient feed conditions. Biotechnol J 2011; 6:1240-52. [DOI: 10.1002/biot.201100219] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/10/2011] [Accepted: 06/20/2011] [Indexed: 11/06/2022]
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19
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Rutgers M, Dam KV, Westerhoff HV. Control and Thermodynamics of Microbial Growth: Rational Tools for Bioengineering. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388559109040625] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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21
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High hydrogen peroxide concentration in the feed-zone affects bioreactor cell productivity with liquid phase oxygen supply strategy. Bioprocess Biosyst Eng 2007; 31:357-67. [PMID: 17972108 DOI: 10.1007/s00449-007-0170-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 10/12/2007] [Indexed: 10/22/2022]
Abstract
Liquid phase oxygen supply strategy (LPOS), in which hydrogen peroxide (H(2)O(2)) is used to supply oxygen to the bioreactor, leads to low cell productivity despite high specific productivities of relevant metabolites. We hypothesized that high H(2)O(2) concentrations in the feed-zone led to local cell death, which in turn, lead to lower cell productivity. To test the hypothesis, a mathematical model was developed. Bacillus subtilis 168 was used as the model system in this study. The model simulations of cell concentrations in the bioreactor-zone were verified with the experimental results. The feed-zone H(2)O(2) concentrations remained 12-14 times higher than bulk bioreactor concentrations. The high local concentrations are expected to cause local cell killing, which explains the decrease in overall cell production by 50% at 300 rpm compared to conventional cultivation. Further, among the four different feed strategies studied using the model, dissolved oxygen (DO) controlled H(2)O(2) feed strategy caused least local cell killing and improved overall cell production by 34%.
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22
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Seletzky JM, Noak U, Fricke J, Welk E, Eberhard W, Knocke C, Büchs J. Scale-up from shake flasks to fermenters in batch and continuous mode withCorynebacterium glutamicum on lactic acid based on oxygen transfer and pH. Biotechnol Bioeng 2007; 98:800-11. [PMID: 17318907 DOI: 10.1002/bit.21359] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Scale-up from shake flasks to fermenters has been hampered by the lack of knowledge concerning the influence of operating conditions on mass transfer, hydromechanics, and power input. However, in recent years the properties of shake flasks have been described with empirical models. A practical scale-up strategy for everyday use is introduced for the scale-up of aerobic cultures from shake flasks to fermenters in batch and continuous mode. The strategy is based on empirical correlations of the volumetric mass transfer coefficient (k(L) a) and the pH. The accuracy of the empirical k(L) a correlations and the assumptions required to use these correlations for an arbitrary biological medium are discussed. To determine the optimal pH of the culture medium a simple laboratory method based on titration curves of the medium and a mechanistic pH model, which is solely based on the medium composition, is applied. The effectiveness of the scale-up strategy is demonstrated by comparing the behavior of Corynebacterium glutamicum on lactic acid in shake flasks and fermenters in batch and continuous mode. The maximum growth rate (micro(max) = 0.32 h(-1)) and the oxygen substrate coefficient (Y O2 /S= 0.0174 mol/l) of C. glutamicum on lactic acid were equal for shake flask, fermenter, batch, and continuous cultures. The biomass substrate yield was independent of the scale, but was lower in batch cultures (Y(X/S) = 0.36 g/g) than in continuous cultures (Y(X/S) = 0.45 g/g). The experimental data (biomass, respiration, pH) could be described with a simple biological model combined with a mechanistic pH model.
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Affiliation(s)
- Juri M Seletzky
- Biochemical Engineering, RWTH Aachen University, Sammelbau Biologie, Worringerweg 1, 52056 Aachen, Germany
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23
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Rinker KD, Kelly RM. Effect of carbon and nitrogen sources on growth dynamics and exopolysaccharide production for the hyperthermophilic archaeon Thermococcus litoralis and bacterium Thermotoga maritima. Biotechnol Bioeng 2000; 69:537-47. [PMID: 10898863 DOI: 10.1002/1097-0290(20000905)69:5<537::aid-bit8>3.0.co;2-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Batch and continuous cultures were used to compare specific physiological features of the hyperthermophilic archaeon, Thermococcus litoralis (T(opt) of 85 degrees to 88 degrees C), to another fermentative hyperthermophile that reduces S degrees facultatively, that is, the bacterium Thermotoga maritima (T(opt) of 80 degrees to 85 degrees C). Under nutritionally optimal conditions, these two hyperthermophiles had similar growth yields on maltose and similar cell formula weights based on elemental analysis: CH(1.7)O(0. 7)N(0.2)S(0.006) for T. litoralis and CH(1.6)O(0.6)N(0.2)S(0.005) for T. maritima. However, they differed with respect to nitrogen source, fermentation product patterns, and propensity to form exopolysaccharides (EPS). T. litoralis could be cultured in the absence or presence of maltose on an amino acid-containing defined medium in which amino acids served as the sole nitrogen source. T. maritima, on the other hand, did not utilize amino acids as carbon, energy, or nitrogen sources, and could be grown in a similar defined medium only when supplemented with maltose and ammonium chloride. Not only was T. litoralis unable to utilize NH(4)Cl as a nitrogen source, its growth was inhibited at certain levels. At 1 g/L ( approximately 20 mM) NH(4)Cl, the maximum growth yield (Y(x/s(max))) for T. litoralis was reduced to 13 g cells dry weight (CDW)/mol glucose from 40 g CDW/mol glucose in media lacking NH(4)Cl. Alanine production increased with increasing NH(4)Cl concentrations and was most pronounced if growth on NH(4)Cl was carried out in an 80% H(2) atmosphere. In T. maritima cultures, which would not grow in an 80% H(2) atmosphere, alanine and EPS were produced at much lower levels, which did not change with NH(4)Cl concentration. EPS production rose sharply at high dilution rates for both organisms, such that maltose utilization plots were biphasic. Wall growth effects were also noted, because cultures failed to wash out at dilution rates significantly above maximum growth rates determined from batch growth experiments. This study illustrates the importance of effective cultivation methods for addressing physiological issues related to the growth of hyperthermophilic heterotrophs.
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Affiliation(s)
- K D Rinker
- Department of Chemical Engineering, North Carolina State University, PO Box 7905, Raleigh, North Carolina 27695-7905, USA
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24
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Rinker KD, Kelly RM. Effect of carbon and nitrogen sources on growth dynamics and exopolysaccharide production for the hyperthermophilic archaeonThermococcus litoralis and bacteriumThermotoga maritima. Biotechnol Bioeng 2000. [DOI: 10.1002/1097-0290(20000905)69:5%3c537::aid-bit8%3e3.0.co;2-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Vink JPM, van der Zee SEATM. Some physicochemical and environmental factors affecting transformation rates and sorption of the herbicide metamitron in soil. ACTA ACUST UNITED AC 1999. [DOI: 10.1002/(sici)1096-9063(199602)46:2<113::aid-ps321>3.0.co;2-u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Kovárová-Kovar K, Egli T. Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics. Microbiol Mol Biol Rev 1998; 62:646-66. [PMID: 9729604 PMCID: PMC98929 DOI: 10.1128/mmbr.62.3.646-666.1998] [Citation(s) in RCA: 380] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. However, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. For pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. The low quality of experimental data has so far hampered the comparison and validation of the different growth models proposed, and only recently have data collected from nutrient-controlled chemostat cultures allowed us to compare different kinetic models on a statistical basis. The problems are mainly due to (i) the analytical difficulty in measuring substrates at growth-controlling concentrations and (ii) the fact that during a kinetic experiment, particularly in batch systems, microorganisms alter their kinetic properties because of adaptation to the changing environment. For example, for Escherichia coli growing with glucose, a physiological long-term adaptation results in a change in KS for glucose from some 5 mg liter-1 to ca. 30 microg liter-1. The data suggest that a dilemma exists, namely, that either "intrinsic" KS (under substrate-controlled conditions in chemostat culture) or micromax (under substrate-excess conditions in batch culture) can be measured but both cannot be determined at the same time. The above-described conventional growth kinetics derived from single-substrate-controlled laboratory experiments have invariably been used for describing both growth and substrate utilization in ecosystems. However, in nature, microbial cells are exposed to a wide spectrum of potential substrates, many of which they utilize simultaneously (in particular carbon sources). The kinetic data available to date for growth of pure cultures in carbon-controlled continuous culture with defined mixtures of two or more carbon sources (including pollutants) clearly demonstrate that simultaneous utilization results in lowered residual steady-state concentrations of all substrates. This should result in a competitive advantage of a cell capable of mixed-substrate growth because it can grow much faster at low substrate concentrations than one would expect from single-substrate kinetics. Additionally, the relevance of the kinetic principles obtained from defined culture systems with single, mixed, or multicomponent substrates to the kinetics of pollutant degradation as it occurs in the presence of alternative carbon sources in complex environmental systems is discussed. The presented overview indicates that many of the environmentally relevant apects in growth kinetics are still waiting to be discovered, established, and exploited.
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Affiliation(s)
- K Kovárová-Kovar
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), CH-8600 Dübendorf, Switzerland
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27
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Schmid A, Kollmer A, Witholt B. Effects of Biosurfactant and Emulsification on Two-Liquid Phase Pseudomonas oleovorans Cultures and Cell-Free Emulsions Containing n-Decane. Enzyme Microb Technol 1998. [DOI: 10.1016/s0141-0229(97)00238-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Gisi D, Willi L, Traber H, Leisinger T, Vuilleumier S. Effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane. Appl Environ Microbiol 1998; 64:1194-202. [PMID: 9546153 PMCID: PMC106129 DOI: 10.1128/aem.64.4.1194-1202.1998] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/1997] [Accepted: 01/14/1998] [Indexed: 02/07/2023] Open
Abstract
Methylobacterium sp. strain DM4 and Methylophilus sp. strain DM11 can grow with dichloromethane (DCM) as the sole source of carbon and energy by virtue of homologous glutathione-dependent DCM dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 S-1, respectively, and the Km values are 9 and 59 microM, respectively). These strains, as well as transconjugant bacteria expressing the DCM dehalogenase gene (dcmA) from DM11 or DM4 on a broad-host-range plasmid in the background of dcmA mutant DM4-2cr, were investigated by growing them under growth-limiting conditions and in the presence of an excess of DCM. The maximal growth rates and maximal levels of dehalogenase for chemostat-adapted bacteria were higher than the maximal growth rates and maximal levels of dehalogenase for batch-grown bacteria. The substrate saturation constant of strain DM4 was much lower than the Km of its associated dehalogenase, suggesting that this strain is adapted to scavenge low concentrations of DCM. Strains and transconjugants expressing the DCM dehalogenase from strain DM11, on the other hand, had higher growth rates than bacteria expressing the homologous dehalogenase from strain DM4. Competition experiments performed with pairs of DCM-degrading strains revealed that a strain expressing the dehalogenase from DM4 had a selective advantage in continuous culture under substrate-limiting conditions, while strains expressing the DM11 dehalogenase were superior in batch culture when there was an excess of substrate. Only DCM-degrading bacteria with a dcmA gene similar to that from strain DM4, however, were obtained in batch enrichment cultures prepared with activated sludge from sewage treatment plants.
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Affiliation(s)
- D Gisi
- Mikrobiologisches Institut, ETH Zürich, ETH-Zentrum, Switzerland
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29
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Rutgers M, Gooch DD, Breure AM, Van Andel JG. Assessment of inhibition kinetics of the growth of strain P5 on pentachlorophenol under steady-state conditions in a nutristat. Arch Microbiol 1996; 165:194-200. [PMID: 8599537 DOI: 10.1007/bf01692861] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A bacterium degrading pentachlorophenol (PCP) as the only source of carbon and energy was grown in a nutristat , i.e., a continuous culture with on-line measurement and control of the substrate concentration. We improved the PCP nutristat by incorporation of a personal computer with a proportional integral derivative (PID) algorithm for controlling the medium feed pump. The controlled value deviated from the average (set-point) value by 1% maximally. In the PCP nutristat (30 degrees C), the steady-state dilution rate, and hence, specific growth rate, showed a maximum value of 0.142 +/- 0.004 h-1 at set-point PCP concentrations between 37 and 168 microM. At PCP concentrations above 168 microM, the steady-state growth rate decreased because of inhibition. The growth yield coefficient was not seriously affected by the PCP concentration, suggesting that uncoupling was not the inhibitory mechanism. It was concluded that the PCP nutristat is very useful for establishing steady-state conditions that maintain growth-inhibitory PCP concentrations and high cell concentrations, conditions for which the chemostat is not suitable.
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Affiliation(s)
- M Rutgers
- Laboratory for Waste Materials and Emissions, National Institute of Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
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30
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The Ecological and Physiological Significance of the Growth of Heterotrophic Microorganisms with Mixtures of Substrates. ADVANCES IN MICROBIAL ECOLOGY 1995. [DOI: 10.1007/978-1-4684-7724-5_8] [Citation(s) in RCA: 159] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Senn H, Lendenmann U, Snozzi M, Hamer G, Egli T. The growth of Escherichia coli in glucose-limited chemostat cultures: a re-examination of the kinetics. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1201:424-36. [PMID: 7803473 DOI: 10.1016/0304-4165(94)90072-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The relationship between specific growth rate (mu) and steady-state glucose concentration was investigated for Escherichia coli ML30 in carbon-limited chemostat culture. This was made possible by the development of a method for measuring reducing sugars in culture media in the microgram.1-1-range. Cells initially cultivated in batch culture at high glucose concentrations required long-term adaptation to nutrient-limited growth conditions in the chemostat (between 100-200 volume changes at D = 0.6 h-1) until steady-state with respect to residual glucose concentration was reached; for adapted cells, however, new steady-state glucose concentrations were usually obtained within less than 10 volume changes. A statistical evaluation of different kinetic models showed that between 0.2 h-1 < D < 0.8 h-1 the three models proposed by Monod (1942), Shehata and Marr (1971), and Westerhoff et al. (1982) described the data equally well and the applicability of the different models is discussed. Depending on the model used, calculated glucose concentrations supporting half maximum growth rate (Ks) were in the range of 40-88 micrograms.1-1. The data strongly suggest that the large differences in Ks constants reported in the literature (ranging from 40 micrograms.1-1 up to 99 mg.1-1) are due to the use of E. coli cells adapted to different degrees to nutrient-limited growth conditions. This indicates that it is probably not possible to describe the kinetic properties of a bacterium with a single set of kinetic 'constants'.
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Affiliation(s)
- H Senn
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), Dübendorf
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Duarte LC, Nobre AP, Gírio FM, Amaral-Collaço MT. Determination of the kinetic parameters in continuous cultivation byDebaryomyces hansenii grown on D-xylose. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf02447728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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van den Wijngaard AJ, Wind RD, Janssen DB. Kinetics of Bacterial Growth on Chlorinated Aliphatic Compounds. Appl Environ Microbiol 1993; 59:2041-8. [PMID: 16348981 PMCID: PMC182233 DOI: 10.1128/aem.59.7.2041-2048.1993] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the pure bacterial cultures
Ancylobacter aquaticus
AD20 and AD25,
Xanthobacter autotrophicus
GJ10, and
Pseudomonas
sp. strain AD1, Monod kinetics was observed during growth in chemostat cultures on 1,2-dichloroethane (AD20, AD25, and GJ10), 2-chloroethanol (AD20 and GJ10), and 1,3-dichloro-2-propanol (AD1). Both the Michaelis-Menten constants (
K
m
) of the first catabolic (dehalogenating) enzyme and the Monod half-saturation constants (
K
s
) followed the order 2-chloroethanol, 1,3-dichloro-2-propanol, epichlorohydrin, and 1,2-dichloroethane. The
K
s
values of strains GJ10, AD20, and AD25 for 1,2-dichloroethane were 260, 222, and 24 μM, respectively. The low
K
s
value of strain AD25 was correlated with a higher haloalkane dehalogenase content of this bacterium. The growth rates of strains AD20 and GJ10 in continuous cultures on 1,2-dichloroethane were higher than the rates predicted from the kinetics of the haloalkane dehalogenase and the concentration of the enzyme in the cells. The results indicate that the efficiency of chlorinated compound removal is indeed influenced by the kinetic properties and cellular content of the first catabolic enzyme. The cell envelope did not seem to act as a barrier for permeation of 1,2-dichloroethane.
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Affiliation(s)
- A J van den Wijngaard
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Effect of oxygen on steady-state product distribution inBacillus polymyxa fermentations. Biotechnol Bioeng 1992; 40:413-26. [DOI: 10.1002/bit.260400311] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Gerritse J, Schut F, Gottschal JC. Modelling of mixed chemostat cultures of an aerobic bacterium, Comamonas testosteroni, and an anaerobic bacterium, Veillonella alcalescens: comparison with experimental data. Appl Environ Microbiol 1992; 58:1466-76. [PMID: 1622213 PMCID: PMC195627 DOI: 10.1128/aem.58.5.1466-1476.1992] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the consumption of substrates, with noncompetitive inhibition of V. alcalescens by O2. The growth characteristics of the aerobic and anaerobic organisms were determined experimentally with pure cultures of the individual species in (oxygen-limited) chemostats. Using these pure-culture data in the model of the mixed culture resulted in a good description of the actual mixed cultures of the two bacteria. In the actual mixed-culture experiments, coexistence of the two species occurred only when the cultures were oxygen limited. With increasing oxygen supply (the actual oxygen concentration in the culture remaining at less than 0.2 microM), the biomass of C. testosteroni increased, whereas that of V. alcalescens decreased. Apparently, C. testosteroni protected V. alcalescens from inhibition by oxygen by maintaining sufficiently low oxygen concentrations. The model calculations indicated that competition between the aerobic and the anaerobic bacterium for common substrates (L-lactate and oxygen) occurred and that the anaerobe was the better competitor. Analysis of the culture fluid indicated that C. testosteroni grew primarily at the expense of the fermentation products of V. alcalescens, i.e., propionate and acetate. The model further indicated that with different values of several growth parameters (e.g., substrate affinity and/or inhibition constants), the affinity of the aerobic organism for oxygen and the sensitivity of the anaerobic organism for oxygen were the most important properties determining the coexistence of these two physiologically different types of bacteria.
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Affiliation(s)
- J Gerritse
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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Kooijman SA, Muller EB, Stouthamer AH. Microbial growth dynamics on the basis of individual budgets. Antonie Van Leeuwenhoek 1991; 60:159-74. [PMID: 1807193 DOI: 10.1007/bf00430363] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The popular theories for microbial dynamics by Monod, Pirt and Droop are shown to be special cases of a model for individual budgets, in which growth and maintenance are on the expense of reserve materials. The dynamics of reserve materials is a first order process with a relaxation time proportional to cell length; maintenance is proportional to cell volume, and uptake, which depends hyperbolically on substrate density, is proportional to cell volume as well. Because of the latter, population dynamics depends on the behaviour of the individuals in a simple way, such that the cell volume distribution has no quantitative effect. When uptake is proportional to the surface area of the cell, which is realistic from a physical point of view, the relation between the individual level and the population one becomes more complicated and the cell size and shape distribution affects population dynamics. It is shown how the changing shape of rods modifies uptake and, consequently, growth. The concept of energy conductance, defined as the ratio of the maximum surface area specific uptake and the volume specific energy reserve has been introduced in the analysis of microbial dynamics. The first tentative results indicate that the value for E. coli is close to the mean value for a wide variety of animals. Properties of the model for cell suspension at constant substrate densities are analyzed and tested against a variety of experimental data from the literature on both the individual and the population level.
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Affiliation(s)
- S A Kooijman
- Biological Laboratory, Free University, Amsterdam, The Netherlands
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van Dam K, Jansen N. Quantification of control of microbial metabolism by substrates and enzymes. Antonie Van Leeuwenhoek 1991; 60:209-23. [PMID: 1807195 DOI: 10.1007/bf00430366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The control of substrates or enzymes on metabolic processes can be expressed in quantitative terms. Most of the experimental material found in the literature, however, has been obtained under non-standardized conditions, precluding definite conclusions concerning the magnitude of control. A number of representative examples is discussed and it is concluded that a quantitative analysis of the factors that control metabolism is essential for understanding the microbial behaviour.
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Affiliation(s)
- K van Dam
- E.C. Slater Institute for Biochemical Research, University of Amsterdam, The Netherlands
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Rutgers M, Balk PA, van Dam K. Effect of concentration of substrates and products on the growth of Klebsiella pneumoniae in chemostat cultures. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 977:142-9. [PMID: 2508755 DOI: 10.1016/s0005-2728(89)80064-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Non-equilibrium thermodynamics (NET) can be used to describe microbial growth. In this description, the concentrations of products contribute to the driving forces of the metabolic processes (anabolism and catabolism). Thus, in contrast to the model of bacterial growth of Monod (Recherches sur la Croissance les Cultures Bactériennes (1942) Herman et Cie, Paris), it is predicted that the growth rate of a bacterial chemostat culture is, in principle, dependent on the concentration of the catabolic product (for instance HCO3-) during catabolite limitation and on the concentration of the anabolic product (for instance biomass) during anabolite limitation. In order to test this prediction, Klebsiella pneumoniae was grown in aerobic citrate-limited, glucose-limited or ammonia-limited chemostat cultures. Ammonia-limited cultures were considered to be essentially anabolite-limited, whereas citrate limitation was used as a representative for catabolite limitation. In ammonia-limited or in glucose-limited cultures it was found that the growth rate was independent of the biomass concentration present. In the NET description this means that the 'back' reaction (i.e., in the direction from biomass to substrates) is saturated with respect to biomass. On the other hand, in citrate-limited cultures, the steady-state concentration of citrate increased with the concentration of the catabolic product HCO3-. At relatively low concentrations of HCO3-, 'thermodynamic back-pressure' of growth (i.e., increase in product concentration was compensated by an increase in substrate concentration so that the driving force for growth remained almost constant) was demonstrated as predicted by the NET model. At concentrations above 40 mM, a kinetic (allosteric) effect of HCO3- was detected. This was concluded from a reduced growth yield on citrate, and from a significant decrease in the maximal growth rate and the maximal oxygen consumption rate after relief of the citrate limitation.
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Affiliation(s)
- M Rutgers
- E.C. Slater Institute for Biochemical Research and Biotechnological Center, University of Amsterdam, The Netherlands
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Hoeven HS, Gottschal JC. Growth of mixed cultures ofActinomyces viscosusandStreptococcus mutansunder dual limitation of glucose and oxygen. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03381.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rutgers M, van der Gulden HM, van Dam K. Thermodynamic efficiency of bacterial growth calculated from growth yield of Pseudomonas oxalaticus OX1 in the chemostat. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 973:302-7. [PMID: 2492828 DOI: 10.1016/s0005-2728(89)80436-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to determine the thermodynamic efficiency of bacterial growth, Pseudomonas oxalaticus OX1 was grown in carbon-limited continuous cultures. 11 different carbon sources, ranging from oxalate (most oxidised component) to ethanol (most reduced component), were used as limiting substrate in these experiments. From the experimental yield values (expressed as C-mol dry weight produced per C-mol carbon substrate consumed) the thermodynamic efficiencies were calculated. On substrates more reduced than biomass (such as ethanol and glycerol) the thermodynamic efficiency of growth of P. oxalaticus was negative but it reached a maximum of 23 +/- 3% with substrates with a degree of reduction of 3 (citrate) and lower. The actual concentrations of the components involved were incorporated into the calculations but this affected the overall thermodynamic efficiency only to a small extent. This result strengthens the conclusion of Westerhoff et al. (Westerhoff, H.V., Hellingwerf, K.J. and Van Dam, K. (1983) Proc. Natl. Acad. Sci. 80, 305-309) that bacteria have been optimised towards a theoretical thermodynamic efficiency of 24%, corresponding with maximisation of growth rate at optimal efficiency, with highly oxidised substrates.
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Affiliation(s)
- M Rutgers
- Laboratory of Biochemistry and Biotechnology Centre, University of Amsterdam, The Netherlands
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