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Liu Q, Dong D, Jin Y, Wang Q, Zhao F, Wu L, Wang J, Ren H. Quorum sensing bacteria improve microbial networks stability and complexity in wastewater treatment plants. Environ Int 2024; 187:108659. [PMID: 38678933 DOI: 10.1016/j.envint.2024.108659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 05/01/2024]
Abstract
Quorum-sensing bacteria (QSB) are crucial factors for microbial communication, yet their ecological role in wastewater treatment plants (WWTPs) remains unclear. Here, we developed a method to identify QSB by comparing 16S rRNA gene sequences. QSB in 388 activated sludge samples collected from 130 WWTPs across China primarily were identified as rare taxa and conditionally rare taxa. A co-occurrence network shared by all sludge communities revealed that QSB exhibited higher average clustering coefficient (0.46) than non-QSB (0.15). Individual sludge networks demonstrated that quorum sensing microbiomes were positively correlated with network robustness and network complexity, including average clustering coefficient and link density. We confirmed that QSB keystones and QSB nodes have a positive impact on network complexity by influencing network modularity through a structural equation model. Meanwhile, QSB communities directly contributed to maintaining network robustness (r = 0.29, P < 0.05). Hence, QSB play an important role in promoting network complexity and stability. Furthermore, QSB communities were positively associated with the functional composition of activated sludge communities (r = 0.33, P < 0.01), especially the denitrification capacity (r = 0.45, P < 0.001). Overall, we elucidated the ecological significance of QSB and provided support for QS-based regulation of activated sludge microbial communities.
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Affiliation(s)
- Qiuju Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Deyuan Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Ying Jin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Qian Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Fuzheng Zhao
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Linwei Wu
- College of Urban and Environmental Sciences, Peking University, Peking 100871, China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
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Greipel E, Nagy K, Csákvári E, Dér L, Galajda P, Kutasi J. Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods. Microb Ecol 2024; 87:52. [PMID: 38498218 PMCID: PMC10948495 DOI: 10.1007/s00248-024-02366-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.
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Affiliation(s)
- Erika Greipel
- Albitech Biotechnological Ltd, Berlini Út 47-49, 1045, Budapest, Hungary
- Department of Plant Anatomy, ELTE Eötvös Loránd University, Pázmány Péter Stny 1/C, H-1117, Budapest, Hungary
| | - Krisztina Nagy
- Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Temesvári Krt. 62, 6726, Szeged, Hungary.
| | - Eszter Csákvári
- Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Temesvári Krt. 62, 6726, Szeged, Hungary
- Division for Biotechnology, Bay Zoltán Nonprofit Ltd. for Applied Research, Derkovits Fasor 2, 6726, Szeged, Hungary
| | - László Dér
- Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Peter Galajda
- Institute of Biophysics, HUN-REN Biological Research Centre, Szeged, Temesvári Krt. 62, 6726, Szeged, Hungary
| | - József Kutasi
- Albitech Biotechnological Ltd, Berlini Út 47-49, 1045, Budapest, Hungary
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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Kim AN, Lee KY, Han CY, Choi SG. Effect of different vacuum levels for beef brisket during cold storage: A microbiological and physicochemical analysis. Food Microbiol 2023; 114:104287. [PMID: 37290866 DOI: 10.1016/j.fm.2023.104287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 06/10/2023]
Abstract
Effect of packaging at different vacuum levels such as 7.2 Pa (99.99% vacuum), 30 kPa (70.39%), 70 kPa (30.91%), and 101.33 kPa (0%, atmospheric condition) using a specially designed airtight container on physicochemical and microbial properties of beef brisket cuts during cold storage was investigated. Dramatic pH increase was found only in air atmospheric packaging. Higher vacuum level yielded higher water holding capacity and lower volatile basic nitrogen (VBN), 2-thiobarbituric acid (TBA), and growth rate of aerobic bacteria and coliforms, whereas the fatty acid composition showed no difference among various vacuum levels. The highest vacuum level (7.2 Pa) yielded no increases in VBN, TBA, and coliform and the least increase in aerobe counts. For bacterial communities, higher vacuum levels yielded higher proportions of Leuconostoc, Carnobacterium, and lactobacilli belonging to the phylum Firmicutes and lower proportions of Pseudomonas belonging to the phylum Proteobacteria. Predictive curves for bacterial communities showed that just a little oxygen significantly affects the bacterial dominance based on different oxygen dependence of individual bacteria and their logarithmic changes by vacuum level.
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Affiliation(s)
- Ah-Na Kim
- Research Group of Safety Distribution, Korea Food Research Institute, Wanju-gun, 55365, Republic of Korea.
| | - Kyo-Yeon Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Chae-Yeon Han
- Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Sung-Gil Choi
- Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Food Science and Technology (Institute of Agriculture and Life Sciences), Gyeongsang National University, Jinju, 52828, Republic of Korea.
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Jeong Y, Irudayaraj J. Hierarchical encapsulation of bacteria in functional hydrogel beads for inter- and intra- species communication. Acta Biomater 2023; 158:203-215. [PMID: 36632875 DOI: 10.1016/j.actbio.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023]
Abstract
To sequester prokaryotic cells in a biofilm-like niche, the creation of a pertinent and reliable microenvironment that reflects the heterogeneous nature of biological systems is vital for sustenance. Design of a microenvironment that is conducive for growth and survival of organisms, should account for factors such as mass transport, porosity, stability, elasticity, size, functionality, and biochemical characteristics of the organisms in the confined architecture. In this work we present an artificial long-term confinement model fabricated by natural alginate hydrogels that are structurally stable and can host organisms for over 10 days in physiologically relevant conditions. A unique feature of the confinement platform is the development of stratified habitats wherein bacterial cells can be entrapped in the core as well as in the shell layers, wherein the thickness and the number of shell layers are tunable at fabrication. We show that the hydrogel microenvironment in the beads can host complex subpopulations of organisms similar to that in a biofilm. Dynamic interaction of bacterial colonies encapsulated in different beads or within the core and stratified layers of single beads was demonstrated to show intra- species communication. Inter- species communication between probiotic bacteria and human colorectal carcinoma cells was also demonstrated to highlight a possible bidirectional communication between the organisms in the beads and the environment. STATEMENT OF SIGNIFICANCE: Bacteria confinement in a natural soft hydrogel structure has always been a challenge due to the collapse of hydrogel architectures. Alternative methods have been attempted to encapsulate microorganisms by employing various processes to avoid/minimize rupturing of hydrogel structures. However, most of the past approaches have been unfavorable in balancing cell proliferation and functionality upon confinement. Our study addresses the fundamental gap in knowledge necessary to create favorable and complex 3D biofilm mimics utilizing natural hydrogel for microbial colonization for long-term studies. Our approach represents a cornerstone in the development of 3D functional architectures not only to advance studies in microbial communication, host-microbe interaction but also to address basic and fundamental questions in biology.
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Affiliation(s)
- Yoon Jeong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA
| | - Joseph Irudayaraj
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle R. Woese Institute for Genomic Biology, Beckman Institute, Holonyak Micro and Nanotechnology Laboratory, Urbana, IL, USA; Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA.
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Domzalski A, Perez SD, Yoo B, Velasquez A, Vigo V, Pasolli HA, Oldham AL, Henderson DP, Kawamura A. Uncovering potential interspecies signaling factors in plant-derived mixed microbial culture. Bioorg Med Chem 2021; 42:116254. [PMID: 34119697 PMCID: PMC8273658 DOI: 10.1016/j.bmc.2021.116254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/05/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023]
Abstract
Microbes use signaling factors for intraspecies and interspecies communications. While many intraspecies signaling factors have been found and characterized, discovery of factors for interspecies communication is lagging behind. To facilitate the discovery of such factors, we explored the potential of a mixed microbial culture (MMC) derived from wheatgrass, in which heterogeneity of this microbial community might elicit signaling factors for interspecies communication. The stability of Wheatgrass MMC in terms of community structure and metabolic output was first characterized by 16S ribosomal RNA amplicon sequencing and liquid chromatography/mass spectrometry (LC/MS), respectively. In addition, detailed MS analyses led to the identification of 12-hydroxystearic acid (12-HSA) as one of the major metabolites produced by Wheatgrass MMC. Stereochemical analysis revealed that Wheatgrass MMC produces mostly the (R)-isomer, although a small amount of the (S)-isomer was also observed. Furthermore, 12-HSA was found to modulate planktonic growth and biofilm formation of various marine bacterial strains. The current study suggests that naturally derived MMCs could serve as a simple and reproducible platform to discover potential signaling factors for interspecies communication. In addition, the study indicates that hydroxylated long-chain fatty acids, such as 12-HSA, may constitute a new class of interspecies signaling factors.
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Affiliation(s)
- Alison Domzalski
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Susan D Perez
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Alexandria Velasquez
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Valeria Vigo
- Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
| | - Hilda Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Athenia L Oldham
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Douglas P Henderson
- Department of Biology, University of Texas of the Permian Basin, 4901 E. University Blvd, Odessa, TX, USA
| | - Akira Kawamura
- Biochemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Chemistry Ph.D. Program, The Graduate Center of CUNY, 365 5(th) Ave, New York, NY 10016, USA; Department of Chemistry, Hunter College of CUNY, 695 Park Ave, New York, NY 10065, USA
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Pokojna H, Livingstone D, Wall D, Burchmore R. Animated Guide to Represent a Novel Means of Gut-Brain Axis Communication. Adv Exp Med Biol 2020; 1262:39-57. [PMID: 32613579 DOI: 10.1007/978-3-030-43961-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Novel scientific concepts must be made understandable to allow their further development, highlighting the need for better communication of abstract ideas that these discoveries are built upon. This project focused on visually communicating the discovery of microbiome-derived molecules that play a major role in microbiome-gut-brain axis communication through multimedia learning.A 4-min animated video that was segmented and used a combination of 2D and 3D models was created. It communicated the important information about the process of discovering the molecules in mouse models, their production by bacteria and their potential implications for human health. The animation was then provided to a scientific audience, alongside a short-answer survey and a Likert scale, to assess how visual aspects accompanied with narration compare to learning and comprehension of the same content if it is read.The findings are based on the total of 15 participants, 9 of which were exposed to the information via animation (Group A) and 6 who were given information in a form of written narrative (Group B). It was found that Group A scored average M = 15 (out of 25) on the post assessment compared to Group B with an average of M = 7. Higher scores correlated with higher rating on questions about perceived understanding through animated media. Additionally, the animation scored higher on helpfulness in learning abstract ideas, especially having to do with structure and spatial navigation. This indicates that scientific abstract concepts that are likely comprehended are needed in order to make definite conclusions.
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Padder SA, Prasad R, Shah AH. Quorum sensing: A less known mode of communication among fungi. Microbiol Res 2018; 210:51-58. [PMID: 29625658 DOI: 10.1016/j.micres.2018.03.007] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/21/2018] [Accepted: 03/17/2018] [Indexed: 02/08/2023]
Abstract
Quorum sensing (QS), a density-dependent signaling mechanism of microbial cells, involves an exchange and sense of low molecular weight signaling compounds called autoinducers. With the increase in population density, the autoinducers accumulate in the extracellular environment and once their concentration reaches a threshold, many genes are either expressed or repressed. This cell density-dependent signaling mechanism enables single cells to behave as multicellular organisms and regulates different microbial behaviors like morphogenesis, pathogenesis, competence, biofilm formation, bioluminescence, etc guided by environmental cues. Initially, QS was regarded to be a specialized system of certain bacteria. The discovery of filamentation control in pathogenic polymorphic fungus Candida albicans by farnesol revealed the phenomenon of QS in fungi as well. Pathogenic microorganisms primarily regulate the expression of virulence genes using QS systems. The indirect role of QS in the emergence of multiple drug resistance (MDR) in microbial pathogens necessitates the finding of alternative antimicrobial therapies that target QS and inhibit the same. A related phenomenon of quorum sensing inhibition (QSI) performed by small inhibitor molecules called quorum sensing inhibitors (QSIs) has an ability for efficient reduction of gene expression regulated by quorum sensing. In the present review, recent advancements in the study of different fungal quorum sensing molecules (QSMs) and quorum sensing inhibitors (QSIs) of fungal origin along with their mechanism of action and/or role/s are discussed.
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Affiliation(s)
- Sajad Ahmad Padder
- Department of Bioresources, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India
| | - Rajendra Prasad
- Amity Institute of Integrative Sciences and Health and Amity Institute of Biotechnology, Amity University Haryana, Amity Education Valley, Gurgaon 122413, HR, India
| | - Abdul Haseeb Shah
- Department of Bioresources, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India.
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Abstract
A growing body of research is highlighting the impacts root-associated microbial communities can have on plant health and development. These impacts can include changes in yield quantity and quality, timing of key developmental stages and tolerance of biotic and abiotic stresses. With such a range of effects it is clear that understanding the factors that contribute to a plant-beneficial root microbiome may prove advantageous. Increasing demands for food by a growing human population increases the importance and urgency of understanding how microbiomes may be exploited to increase crop yields and reduce losses caused by disease. In addition, climate change effects may require novel approaches to overcoming abiotic stresses such as drought and salinity as well as new emerging diseases. This review discusses current knowledge on the formation and maintenance of root-associated microbial communities and plant-microbe interactions with a particular emphasis on the effect of microbe-microbe interactions on the shape of microbial communities at the root surface. Further, we discuss the potential for root microbiome modification to benefit agriculture and food production.
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Affiliation(s)
- Andrew Lareen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Frances Burton
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK.
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Abstract
Bacterial sets are complex dynamic systems, which interact with each other and through the interaction, bacteria coexist, collaborate, compete and share information in a coordinated manner. A way of bacterial communication is quorum sensing. Through this mechanism the bacteria can recognize its concentration in a given environment and they can decide the time at which the expression of a particular set of genes should be started for developing a specific and simultaneous response. The result of these interconnections raises properties that cannot be explained from a single isolated bacterial cell.
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