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He Q, Tan B, Li M, Su J, Lin B, Wu NP, Shen HN, Chen JJ, Zhang Q. Deciphering the influence of salinity stress on the biological aniline degradation system: Pollutants degradation performance and microbial response. ENVIRONMENTAL RESEARCH 2024; 255:119162. [PMID: 38762003 DOI: 10.1016/j.envres.2024.119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/14/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results presented the salinity except for 5% imposed negligible effects on aniline degradation performance. Nitrification had prominent resistance to salinity (0%-1.5%) while were significantly restrained when salinity increased. The total nitrogen (TN) removal efficiency of Z4 (1.5%) was 20.5% higher than Z1 (0%) during the stable operation phase. Moreover, high throughput sequencing analysis showed that halophilic bacterium, such as Halomonas, Rhodococcus, remained greater survival advantages in high salinity system. The substantial enrichment of Flavobacterium, Dokdonella, Paracoccus observed in Z4 ensured its excellent nitrogen removal performance. The close cooperation among dominant functional bacteria was strengthened when salt content was below 1.5% while exceeding 1.5% led to the collapse of metabolic capacity through integrating the toxicity of aniline and high osmotic pressure.
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Affiliation(s)
- Qi He
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Bin Tan
- CCCC Second Highway Consultants Co., Ltd., Wuhan, 430056, PR China
| | - Meng Li
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Hainan, 572024, PR China
| | - Junhao Su
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Bing Lin
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Nan-Ping Wu
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Hao-Nan Shen
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Jia-Jing Chen
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Hainan, 572024, PR China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan, 430070, PR China.
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2
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Dolan SK, Duong AT, Whiteley M. Convergent evolution in toxin detection and resistance provides evidence for conserved bacterial-fungal interactions. Proc Natl Acad Sci U S A 2024; 121:e2304382121. [PMID: 39088389 DOI: 10.1073/pnas.2304382121] [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: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 08/03/2024] Open
Abstract
Microbes rarely exist in isolation and instead form complex polymicrobial communities. As a result, microbes have developed intricate offensive and defensive strategies that enhance their fitness in these complex communities. Thus, identifying and understanding the molecular mechanisms controlling polymicrobial interactions is critical for understanding the function of microbial communities. In this study, we show that the gram-negative opportunistic human pathogen Pseudomonas aeruginosa, which frequently causes infection alongside a plethora of other microbes including fungi, encodes a genetic network which can detect and defend against gliotoxin, a potent, disulfide-containing antimicrobial produced by the ubiquitous filamentous fungus Aspergillus fumigatus. We show that gliotoxin exposure disrupts P. aeruginosa zinc homeostasis, leading to transcriptional activation of a gene encoding a previously uncharacterized dithiol oxidase (herein named as DnoP), which detoxifies gliotoxin and structurally related toxins. Despite sharing little homology to the A. fumigatus gliotoxin resistance protein (GliT), the enzymatic mechanism of DnoP from P. aeruginosa appears to be identical that used by A. fumigatus. Thus, DnoP and its transcriptional induction by low zinc represent a rare example of both convergent evolution of toxin defense and environmental cue sensing across kingdoms. Collectively, these data provide compelling evidence that P. aeruginosa has evolved to survive exposure to an A. fumigatus disulfide-containing toxin in the natural environment.
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Affiliation(s)
- Stephen K Dolan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30310
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA 30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30310
| | - Ashley T Duong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30310
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30310
- Emory-Children's Cystic Fibrosis Center, Atlanta, GA 30310
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30310
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3
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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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4
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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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5
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Gupta G, Labrie S, Filteau M. Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening. Microorganisms 2024; 12:1396. [PMID: 39065164 PMCID: PMC11279232 DOI: 10.3390/microorganisms12071396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve Labrie
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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6
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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7
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Dorfan Y, Nahami A, Morris Y, Shohat B, Kolodkin-Gal I. The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties. Microorganisms 2024; 12:1226. [PMID: 38930607 PMCID: PMC11205451 DOI: 10.3390/microorganisms12061226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.
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Affiliation(s)
- Yuval Dorfan
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Avichay Nahami
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
| | - Yael Morris
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Benny Shohat
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Ilana Kolodkin-Gal
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
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8
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Kennedy NW, Comstock LE. Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare. Cell Host Microbe 2024; 32:794-803. [PMID: 38870897 PMCID: PMC11216714 DOI: 10.1016/j.chom.2024.05.006] [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: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.
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Affiliation(s)
- Nolan W Kennedy
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
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9
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Yang L, Jia S, Sun S, Wang L, Zhao B, Zhang M, Yin Y, Yang M, Fulano AM, Shen X, Pan J, Wang Y. A pyocin-like T6SS effector mediates bacterial competition in Yersinia pseudotuberculosis. Microbiol Spectr 2024; 12:e0427823. [PMID: 38712967 PMCID: PMC11237486 DOI: 10.1128/spectrum.04278-23] [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: 12/22/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Within the realm of Gram-negative bacteria, bacteriocins are secreted almost everywhere, and the most representative are colicin and pyocin, which are secreted by Escherichia coli and Pseudomonas aeruginosa, respectively. Signal peptides at the amino terminus of bacteriocins or ABC transporters can secrete bacteriocins, which then enter bacteria through cell membrane receptors and exert toxicity. In general, the bactericidal spectrum is usually narrow, killing only the kin or closely related species. Our previous research indicates that YPK_0952 is an effector of the third Type VI secretion system (T6SS-3) in Yersinia pseudotuberculosis. Next, we sought to determine its identity and characterize its toxicity. We found that YPK_0952 (a pyocin-like effector) can achieve intra-species and inter-species competitive advantages through both contact-dependent and contact-independent mechanisms mediated by the T6SS-3 while enhancing the intestinal colonization capacity of Y. pseudotuberculosis. We further identified YPK_0952 as a DNase dependent on Mg2+, Ni2+, Mn2+, and Co2+ bivalent metal ions, and the homologous immune protein YPK_0953 can inhibit its activity. In summary, YPK_0952 exerts toxicity by degrading nucleic acids from competing cells, and YPK_0953 prevents self-attack in Y. pseudotuberculosis.IMPORTANCEBacteriocins secreted by Gram-negative bacteria generally enter cells through specific interactions on the cell surface, resulting in a narrow bactericidal spectrum. First, we identified a new pyocin-like effector protein, YPK_0952, in the third Type VI secretion system (T6SS-3) of Yersinia pseudotuberculosis. YPK_0952 is secreted by T6SS-3 and can exert DNase activity through contact-dependent and contact-independent entry into nearby cells of the same and other species (e.g., Escherichia coli) to help Y. pseudotuberculosis to exert a competitive advantage and promote intestinal colonization. This discovery lays the foundation for an in-depth study of the different effector protein types within the T6SS and their complexity in competing interactions. At the same time, this study provides a new development for the toolbox of toxin/immune pairs for studying Gram-negative bacteriocin translocation.
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Affiliation(s)
- Leilei Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuangkai Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Sihuai Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Bobo Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengsi Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanling Yin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Mingming Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Alex M. Fulano
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Sciences, Tarim University, Alar, Xinjiang, China
| | - Junfeng Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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10
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Díaz-Cruz GA, Bignell DRD. Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2. Sci Rep 2024; 14:10414. [PMID: 38710735 DOI: 10.1038/s41598-024-60630-5] [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: 11/02/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
- Phytopathology Department, Plant Protection Research Center (CIPROC), Agronomy School, Universidad de Costa Rica, San Jose, Costa Rica
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
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11
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Chodkowski JL, Shade A. Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 2024; 9:e0006424. [PMID: 38470039 PMCID: PMC11019792 DOI: 10.1128/msystems.00064-24] [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: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure. IMPORTANCE Free-living microbial populations often persist and engage in environments that offer few or inconsistently available resources. Thus, it is important to investigate microbial interactions in this common and ecologically relevant condition of non-growth. This work investigates the consequences of resource limitation for community metabolic output and for population interactions in simple synthetic bacterial communities. Despite non-growth, we observed active, exometabolite-mediated competition among the bacterial populations. Many of these interactions and produced exometabolites were dependent on the community composition but we also observed that one dominant competitor consistently produced interfering exometabolites regardless. These results are important for predicting and understanding microbial interactions in resource-limited environments.
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Affiliation(s)
- John L. Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne, France
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12
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Hoskisson PA, Barona-Gómez F, Rozen DE. Phenotypic heterogeneity in Streptomyces colonies. Curr Opin Microbiol 2024; 78:102448. [PMID: 38447313 DOI: 10.1016/j.mib.2024.102448] [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: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | | | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, The Netherlands.
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13
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Goult JD, Van DCL, Taylor YV, Inns PG, Kaminska R, Vesely M, Kleanthous C, Paci E. Structural constraints of pyocin S2 import through the ferripyoverdine receptor FpvAI. PNAS NEXUS 2024; 3:pgae124. [PMID: 38577260 PMCID: PMC10994204 DOI: 10.1093/pnasnexus/pgae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
TonB-dependent transporters (TBDTs) mediate energized transport of essential nutrients into gram-negative bacteria. TBDTs are increasingly being exploited for the delivery of antibiotics to drug-resistant bacteria. While much is known about ground state complexes of TBDTs, few details have emerged about the transport process itself. In this study, we exploit bacteriocin parasitization of a TBDT to probe the mechanics of transport. Previous work has shown that the N-terminal domain of Pseudomonas aeruginosa-specific bacteriocin pyocin S2 (PyoS2NTD) is imported through the pyoverdine receptor FpvAI. PyoS2NTD transport follows the opening of a proton-motive force-dependent pore through FpvAI and the delivery of its own TonB box that engages TonB. We use molecular models and simulations to formulate a complete translocation pathway for PyoS2NTD that we validate using protein engineering and cytotoxicity measurements. We show that following partial removal of the FpvAI plug domain which occludes the channel, the pyocin's N-terminus enters the channel by electrostatic steering and ratchets to the periplasm. Application of force, mimicking that exerted by TonB, leads to unraveling of PyoS2NTD as it squeezes through the channel. Remarkably, while some parts of PyoS2NTD must unfold, complete unfolding is not required for transport, a result we confirmed by disulfide bond engineering. Moreover, the section of the FpvAI plug that remains embedded in the channel appears to serve as a buttress against which PyoS2NTD is pushed to destabilize the domain. Our study reveals the limits of structural deformation that accompanies import through a TBDT and the role the TBDT itself plays in accommodating transport.
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Affiliation(s)
- Jonathan D Goult
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Daniel C L Van
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Yasmin V Taylor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Patrick G Inns
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Martin Vesely
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia, Università di Bologna, Bologna 40127, Italy
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14
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Nuñez Santiago I, Machushynets NV, Mladic M, van Bergeijk DA, Elsayed SS, Hankemeier T, van Wezel GP. nanoRAPIDS as an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at the nanoscale. Commun Chem 2024; 7:71. [PMID: 38561415 PMCID: PMC10984978 DOI: 10.1038/s42004-024-01153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Microbial natural products form the basis of most of the antibiotics used in the clinic. The vast majority has not yet been discovered, among others because the hidden chemical space is obscured by previously identified (and typically abundant) antibiotics in culture extracts. Efficient dereplication is therefore key to the discovery of our future medicines. Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 μL crude extract is fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their bioactivity. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.
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Affiliation(s)
- Isabel Nuñez Santiago
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Marija Mladic
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- DSM-Firmenich, Delft, The Netherlands
| | - Doris A van Bergeijk
- Department of Microbiology, KU Leuven, Immunology and Transplantation (Laboratory of Molecular Bacteriology), Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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15
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Kastrat E, Cheng HP. Escherichia coli has an undiscovered ability to inhibit the growth of both Gram-negative and Gram-positive bacteria. Sci Rep 2024; 14:7420. [PMID: 38548840 PMCID: PMC10978900 DOI: 10.1038/s41598-024-57996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
The ability for bacteria to form boundaries between neighboring colonies as the result of intra-species inhibition has been described for a limited number of species. Here, we report that intra-species inhibition is more common than previously recognized. We demonstrated that swimming colonies of four Escherichia coli strains and six other bacteria form inhibitory zones between colonies, which is not caused by nutrient depletion. This phenomenon was similarly observed with non-flagellated bacteria. We developed a square-streaking pattern assay which revealed that Escherichia coli BW25113 inhibits the growth of other E. coli, and surprisingly, other Gram-positive and negative bacteria, including multi-drug resistant clinical isolates. Altogether, our findings demonstrate intra-species inhibition is common and might be used by E. coli to inhibit other bacteria. Our findings raise the possibility for a common mechanism shared across bacteria for intra-species inhibition. This can be further explored for a potential new class of antibiotics.
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Affiliation(s)
- Ertan Kastrat
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA
- The Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Hai-Ping Cheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA.
- The Graduate Center, City University of New York, New York, NY, 10016, USA.
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16
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Lories B, Belpaire TER, Smeets B, Steenackers HP. Competition quenching strategies reduce antibiotic tolerance in polymicrobial biofilms. NPJ Biofilms Microbiomes 2024; 10:23. [PMID: 38503782 PMCID: PMC10951329 DOI: 10.1038/s41522-024-00489-6] [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: 10/20/2022] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Bacteria typically live in dense communities where they are surrounded by other species and compete for a limited amount of resources. These competitive interactions can induce defensive responses that also protect against antimicrobials, potentially complicating the antimicrobial treatment of pathogens residing in polymicrobial consortia. Therefore, we evaluate the potential of alternative antivirulence strategies that quench this response to competition. We test three competition quenching approaches: (i) interference with the attack mechanism of surrounding competitors, (ii) inhibition of the stress response systems that detect competition, and (iii) reduction of the overall level of competition in the community by lowering the population density. We show that either strategy can prevent the induction of antimicrobial tolerance of Salmonella Typhimurium in response to competitors. Competition quenching strategies can thus reduce tolerance of pathogens residing in polymicrobial communities and could contribute to the improved eradication of these pathogens via traditional methods.
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Affiliation(s)
- Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
| | - Tom E R Belpaire
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium
- Division of Mechatronics, Biostatistics, and Sensors (MeBioS), Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Bart Smeets
- Division of Mechatronics, Biostatistics, and Sensors (MeBioS), Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium.
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17
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Van Goethem MW, Marasco R, Hong P, Daffonchio D. The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms. Microb Biotechnol 2024; 17:e14430. [PMID: 38465465 PMCID: PMC10926060 DOI: 10.1111/1751-7915.14430] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
In the relentless battle for human health, the proliferation of antibiotic-resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening 'antibiotic discovery void'. With nearly 80% of our current antibiotics originating from natural or semi-synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so-called 'microbial oases of interactions'. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever-evolving microbial 'arms race' is constantly in place. Such a continuous cycle of adaptation and counter-adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a 'missing piece of the puzzle' in our fight against antibiotic resistance.
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Affiliation(s)
- Marc W. Van Goethem
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Pei‐Ying Hong
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Water Desalination and Reuse CenterBiological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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18
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Arbulu S, Kjos M. Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins. MICROBIAL ECOLOGY 2024; 87:41. [PMID: 38351266 PMCID: PMC10864542 DOI: 10.1007/s00248-024-02357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.
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Affiliation(s)
- Sara Arbulu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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19
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Qiao Y, Huang Q, Guo H, Qi M, Zhang H, Xu Q, Shen Q, Ling N. Nutrient status changes bacterial interactions in a synthetic community. Appl Environ Microbiol 2024; 90:e0156623. [PMID: 38126758 PMCID: PMC10807438 DOI: 10.1128/aem.01566-23] [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: 09/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.
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Affiliation(s)
- Yizhu Qiao
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qiwei Huang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Meijie Qi
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - He Zhang
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qicheng Xu
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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20
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Wang C, Kuzyakov Y. Mechanisms and implications of bacterial-fungal competition for soil resources. THE ISME JOURNAL 2024; 18:wrae073. [PMID: 38691428 PMCID: PMC11104273 DOI: 10.1093/ismejo/wrae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.
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Affiliation(s)
- Chaoqun Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Biogeochemistry of Agroecosystems, University of Göttingen, Göttingen 37077, Germany
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yakov Kuzyakov
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen 37077, Germany
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21
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Song L, Xu L, Wu T, Shi Z, Kareem HA, Wang Z, Dai Q, Guo C, Pan J, Yang M, Wei X, Wang Y, Wei G, Shen X. Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition. THE ISME JOURNAL 2024; 18:wrad028. [PMID: 38365238 PMCID: PMC10833071 DOI: 10.1093/ismejo/wrad028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 02/18/2024]
Abstract
The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.
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Affiliation(s)
- Li Song
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Xu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenkun Shi
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hafiz Abdul Kareem
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuo Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingyun Dai
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenghao Guo
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junfeng Pan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomeng Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihui Shen
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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22
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Hansen ML, Dénes Z, Jarmusch SA, Wibowo M, Lozano-Andrade CN, Kovács ÁT, Strube ML, Andersen AJC, Jelsbak L. Resistance towards and biotransformation of a Pseudomonas-produced secondary metabolite during community invasion. THE ISME JOURNAL 2024; 18:wrae105. [PMID: 38874164 PMCID: PMC11203913 DOI: 10.1093/ismejo/wrae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains less clear. Here, we use a four-species synthetic community (SynCom) in which individual members are sensitive towards key P. protegens antimicrobial metabolites (DAPG, pyoluteorin, and orfamide A) to determine how antibiotic production contributes to P. protegens community invasion and to identify community traits that counteract the antimicrobial effects. We show that P. protegens readily invades and alters the SynCom composition over time, and that P. protegens establishment requires production of DAPG and pyoluteorin. An orfamide A-deficient mutant of P. protegens invades the community as efficiently as wildtype, and both cause similar perturbations to community composition. Here, we identify the microbial interactions underlying the absence of an orfamide A mediated impact on the otherwise antibiotic-sensitive SynCom member, and show that the cyclic lipopeptide is inactivated and degraded by the combined action of Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.
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Affiliation(s)
- Morten L Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Zsófia Dénes
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Mikael L Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Aaron J C Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
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23
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Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
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Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
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24
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Li Y, Chen Z, Wagg C, Castellano MJ, Zhang N, Ding W. Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism. GLOBAL CHANGE BIOLOGY 2024; 30:e17101. [PMID: 38273560 DOI: 10.1111/gcb.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.
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Affiliation(s)
- Ye Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Cameron Wagg
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
| | | | - Nan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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25
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Sadhukhan S, Jacques MA, Potnis N. Influence of Co-occurring Weakly Pathogenic Bacterial Species on Bacterial Spot Disease Dynamics on Tomato. PLANT DISEASE 2024; 108:190-199. [PMID: 37537791 DOI: 10.1094/pdis-05-23-0837-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Mixed infections caused by multiple pathogenic and weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of coinfection on disease dynamics on tomato using the bacterial spot pathogen Xanthomonas perforans (Xp), the co-occurring weakly pathogenic strain of X. arboricola (Xa), and the co-occurring potential weak pathogenic strain of Pseudomonas capsici (Pc). Time-series coinfection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in coinfection by three species compared with infection by Xp alone. However, coinfection by dual species, Xp and Pc, or Xa resulted in lower disease severity compared with Xp alone. Thus, coinfection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in coinfection. However, Xp population dynamics were dependent on the coinfecting partner. While resource competition might be a possible explanation for lower Xp population in dual coinfection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in the presence of three-species interaction compared with Xp and Xa coinfection, suggesting potential modulation of cooperative interactions among Xp and Xa in three-species coinfection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted the importance of coinfection dynamics in studying plant disease outbreaks.
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Affiliation(s)
- Shreya Sadhukhan
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | | | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
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26
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Booth SC, Smith WPJ, Foster KR. The evolution of short- and long-range weapons for bacterial competition. Nat Ecol Evol 2023; 7:2080-2091. [PMID: 38036633 PMCID: PMC10697841 DOI: 10.1038/s41559-023-02234-2] [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: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
Bacteria possess a diverse range of mechanisms for inhibiting competitors, including bacteriocins, tailocins, type VI secretion systems and contact-dependent inhibition (CDI). Why bacteria have evolved such a wide array of weapon systems remains a mystery. Here we develop an agent-based model to compare short-range weapons that require cell-cell contact, with long-range weapons that rely on diffusion. Our model predicts that contact weapons are useful when an attacking strain is outnumbered, facilitating invasion and establishment. By contrast, ranged weapons tend to be effective only when attackers are abundant. We test our predictions with the opportunistic pathogen Pseudomonas aeruginosa, which naturally carries multiple weapons, including CDI and diffusing tailocins. As predicted, short-range CDI can function at low and high frequencies, while long-range tailocins require high frequency and cell density to function effectively. Head-to-head competition experiments with the two weapon types further support our predictions: a tailocin attacker defeats CDI only when it is numerically dominant, but then we find it can be devastating. Finally, we show that the two weapons work well together when one strain employs both. We conclude that short- and long-range weapons serve different functions and allow bacteria to fight both as individuals and as a group.
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Affiliation(s)
- Sean C Booth
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - William P J Smith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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27
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Crow J, Geng H, Schultz D. Short-term evolution of antibiotic responses in highly dynamic environments favors loss of regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569327. [PMID: 38076825 PMCID: PMC10705423 DOI: 10.1101/2023.11.29.569327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Microbes inhabit natural environments that are remarkably dynamic, with sudden environmental shifts that require immediate action by the cell. To cope with changing environments, microbes are equipped with regulated response mechanisms that are only activated when needed. However, when exposed to extreme environments such as clinical antibiotic treatments, complete loss of regulation is frequently observed. Although recent studies suggest that the initial evolution of microbes in new environments tends to favor mutations in regulatory pathways, it is not clear how this evolution is affected by how quickly conditions change (i.e. dynamics), or which mechanisms are commonly used to implement new regulation. Here, we perform experimental evolution on continuous cultures of E. coli carrying the tetracycline resistance tet operon to identify specific types of mutations that adapt drug responses to different dynamical regimens of drug administration. When cultures are evolved under gradually increasing tetracycline concentrations, we observe no mutations in the tet operon, but a predominance of fine-tuning mutations increasing the affinity of alternative efflux pump AcrB to tetracycline. When cultures are instead periodically exposed to large drug doses, all populations developed transposon insertions in repressor TetR, resulting in loss of regulation of efflux pump TetA. We use a mathematical model of the dynamics of antibiotic responses to show that sudden exposure to large drug concentrations can overwhelm regulated responses, which cannot induce resistance fast enough, resulting in fitness advantage for constitutive expression of resistance. These results help explain the loss of regulation of antibiotic resistance by opportunistic pathogens evolving in clinical environments. Our experiment supports the notion that initial evolution in new ecological niches proceeds largely through regulatory mutations and suggests that transposon insertions are a main mechanism driving this process.
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Affiliation(s)
- John Crow
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
| | - Hao Geng
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
| | - Daniel Schultz
- Department of Microbiology & Immunology, Dartmouth – Geisel School of Medicine, Hanover, NH, USA
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28
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Garg S, Sharma N, Bharmjeet, Das A. Unraveling the intricate relationship: Influence of microbiome on the host immune system in carcinogenesis. Cancer Rep (Hoboken) 2023; 6:e1892. [PMID: 37706437 PMCID: PMC10644337 DOI: 10.1002/cnr2.1892] [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: 03/25/2023] [Revised: 07/05/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Cancer is an outcome of various disrupted or dysregulated metabolic processes like apoptosis, growth, and self-cell transformation. Human anatomy harbors trillions of microbes, and these microbes actively influence all kinds of human metabolic activities, including the human immune response. The immune system which inherently acts as a sentinel against microbes, curiously tolerates and even maintains a distinct normal microflora in our body. This emphasizes the evolutionarily significant role of microbiota in shaping our adaptive immune system and even potentiating its function in chronic ailments like cancers. Microbes interact with the host immune cells and play a part in cancer progression or regression by modulating immune cells, producing immunosuppressants, virulence factors, and genotoxins. RECENT FINDINGS An expanding plethora of studies suggest and support the evidence of microbiome impacting cancer etiology. Several studies also indicate that the microbiome can supplement various cancer therapies, increasing their efficacy. The present review discusses the relationship between bacterial and viral microbiota with cancer, discussing different carcinogenic mechanisms influenced by prokaryotes with special emphasis on their immunomodulatory axis. It also elucidates the potential of the microbiome in transforming the efficacy of immunotherapeutic treatments. CONCLUSION This review offers a thorough overview of the complex interaction between the human immune system and the microbiome and its impact on the development of cancer. The microbiome affects the immune responses as well as progression of tumor transformation, hence microbiome-based therapies can vastly improve the effectiveness of cancer immunotherapies. Individual variations of the microbiome and its dynamic variability in every individual impacts the immune modulation and cancer progression. Therefore, further research is required to understand these underlying processes in detail, so as to design better microbiome-immune system axis in the treatment of cancer.
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Affiliation(s)
- Saksham Garg
- Department of BiotechnologyDelhi Technological UniversityDelhiIndia
| | - Nikita Sharma
- Department of BiotechnologyDelhi Technological UniversityDelhiIndia
| | - Bharmjeet
- Department of BiotechnologyDelhi Technological UniversityDelhiIndia
| | - Asmita Das
- Department of BiotechnologyDelhi Technological UniversityDelhiIndia
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29
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Pavia MJ, Finn D, Macedo-Tafur F, Tello-Espinoza R, Penaccio C, Bouskill N, Cadillo-Quiroz H. Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients. Environ Microbiol 2023; 25:2388-2403. [PMID: 37501535 DOI: 10.1111/1462-2920.16469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.
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Affiliation(s)
- Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Damien Finn
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Franco Macedo-Tafur
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Rodil Tello-Espinoza
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
- School of Forestry, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Christa Penaccio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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30
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De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS. Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. EBioMedicine 2023; 97:104822. [PMID: 37806286 PMCID: PMC10579285 DOI: 10.1016/j.ebiom.2023.104822] [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: 04/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei. METHODS We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics. FINDINGS Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent. INTERPRETATION Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings. FUNDING Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.
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Affiliation(s)
- P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Rebecca J Bennett
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Patryk Ngondo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Lorine Debande
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Brian Ho
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Benoît S Marteyn
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom; Department of Genetics, University of Cambridge, Downing Place, Cambridge, UK.
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Svet L, Parijs I, Isphording S, Lories B, Marchal K, Steenackers HP. Competitive interactions facilitate resistance development against antimicrobials. Appl Environ Microbiol 2023; 89:e0115523. [PMID: 37819078 PMCID: PMC10617502 DOI: 10.1128/aem.01155-23] [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: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 10/13/2023] Open
Abstract
While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.
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Affiliation(s)
- Luka Svet
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Simon Isphording
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Data Integration and Biological Networks, UGent, Technologiepark 15, Gent, Belgium
| | - Hans P. Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), Leuven, Belgium
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Chen Y, Zhang J, Zhu X, Wang Y, Chen J, Sui B, Teng HH. Unraveling the complexities of Cd-aniline composite pollution: Insights from standalone and joint toxicity assessments in a bacterial community. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 265:115509. [PMID: 37742573 DOI: 10.1016/j.ecoenv.2023.115509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Cadmium (Cd) and aniline frequently co-occur in industrial settings but have rarely been addressed as composite toxicants in terms of the overall toxicity despite extensive knowledge of the environmental impact of each individual pollutant. In this study, we attempt to assess the relation of individual and combined toxic effects of Cd and aniline using a bacterial consortium cultured from soils as a model system. Results showed that the consortial bacteria exhibited drastically stronger tolerance to stand-alone Cd and aniline in comparison to literature data acquired from single species studies. When occurring simultaneously, the joint toxicity displayed a concentration-dependent behavior that wasn't anticipated based on individual chemical tests. Specifically, additive effects manifested with Cd and aniline at their IC10s, but changed to synergistic when the concentrations increased to IC20, and finally transitioned into antagonistic at IC30s and beyond. In addition, co-occurring aniline appeared to have retarded the cellular accumulation of Cd while increasing the enzymatic activities of superoxide dismutase and catalase relative to that in Cd-alone treatments. Finally, the bacterial community experienced distinct compositional changes under solo and combined toxicities with several genera exhibiting inconsistent behavior between treatments of single and composite toxicants. Findings from this study highlight the complexity of bacterial response to composite pollutions and point to the need for more comprehensive references in risk and toxicology assessment at multi-chemical contamination sites.
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Affiliation(s)
- Yuxuan Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China.
| | - Xiangyu Zhu
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Yuebo Wang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Jiubin Chen
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China
| | - Biao Sui
- College of Resources and Environment, Jilin Agricultural University, Changchun 130118, China
| | - H Henry Teng
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin 30072, China.
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Zhang S, Su J, Liu S, Ren Y, Cao S. Regulating mechanism of denitrifier Comamonas sp. YSF15 in response to carbon deficiency: Based on carbon/nitrogen functions and bioaggregation. ENVIRONMENTAL RESEARCH 2023; 235:116661. [PMID: 37451570 DOI: 10.1016/j.envres.2023.116661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
There is an urgent demand to investigate mechanisms for the improvement of denitrification in carbon-deficient environment, which will effectively reduce the eutrophication in water bodies polluted by nitrate. In this study, denitrifying bacterium Comamonas sp. YSF15 was used to explore the differences in different carbon source concentrations, with the complete genome, metabolomics, and other detecting methods. Results showed that strain YSF15 was able to achieve efficient denitrification, with complete pathways for denitrification and central carbon metabolism. The carbon deficiency prompted the bacteria to use extracellular amino acid-like metabolites initially, to alleviate inhibition and maintain bioactivity, which also facilitated glycogen storage. The biogenic inhibitors (tautomycin, navitoclax, and glufosinate) at extremely low level potentially favored the competitiveness and intraspecific utilization of extracellular polysaccharides (PS). Optimal solutions for bioaggregation in carbon-deficient condition are achieved by regulating the hydrophobicity, and hydrogen bond in extracellular metabolites. The strategy contributes to the maintenance of bioactivity and adaptation to carbon deficiency. Overall, this study provides a new perspective on understanding the denitrification strategies in carbon-deficient environment, and helps to improve the nitrate removal in low-carbon wastewater treatment.
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Affiliation(s)
- Shuai Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Shuyu Liu
- School of Environment and Chemistry Engineering, Shanghai University, Shanghai, 200444, China.
| | - Yi Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Shumiao Cao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
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Gkerekou MA, Kaparakou EH, Tarantilis PA, Skandamis PN. Studying the metabolic factors that may impact the growth of co-cultured Listeria monocytogenes strains at low temperature. Food Res Int 2023; 171:113056. [PMID: 37330855 DOI: 10.1016/j.foodres.2023.113056] [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: 02/05/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
The simultaneous presence of more than one strains of Listeria monocytogenes in the same food product may affect the growth capacity of each strain. The present study evaluated the metabolites composition that may potentially influence the growth of individual L. monocytogenes strains in a dual strain composite. Based on previous studies, L. monocytogenes strains, C5 (4b) and 6179 (1/2a) were selected due to the remarkable interaction, which was observed during their co-culture. The selected strains were inoculated (2.0 - 3.0 log CFU/mL) in Tryptic Soy Broth with 0.6% Yeast Extract (TSB-YE) in single and two-strain cultures (1:1 strain ratio). Bacterial growth was assessed during storage at 7 °C, under aerobic conditions (AC). Their resistance to different antibiotics enabled the selective enumeration of each strain in the co-culture. After reaching stationary phase, single and dual cultures were centrifuged and filtered. The cell-free spent medium (CFSM) was either characterized by Fourier transform infrared (FTIR-ATR) spectrometry or re-inoculated, after the addition of concentrated TSB-YE (for nutrient replenishment), with single and two-strain cultures for the evaluation of growth under the influence of metabolites produced from the same singly and co-cultured strains in the different combinations of strains and CFSM origin (7 °C/AC) (n = 2x3). By the end of storage, singly-cultured C5 and 6179 had reached 9.1 log CFU/mL, while in dual culture, 6179 was affected by the presence of C5 attaining only 6.4 ± 0.8 log CFU/mL. FTIR-ATR spectra of CFSM produced by singly-cultured 6179 and the co-culture were almost identical. Characteristic peaks in FTIR-ATR spectrum of CFSM of singly-cultured C5 at 1741, 1645 and 1223 cm-1 represent functional groups which were not present in the CFSM of the co-culture. These molecules may be located intracellularly or mounted on bacterial cell surface and removed from the supernatant during cell filtration of the co-culture. Both singly- and co-cultured 6179 managed to grow similarly regardless of CFSM origin. Contrarily, both singly- and co-cultured C5 managed to outgrow 6179 in CFSM which contained high concentration of C5 metabolites, while in CFSM produced by singly-cultured 6179, C5 did not grow, suggesting that the produced metabolites of strain 6179 appears to be harmful to strain C5. However, during co-culture, C5 may produce molecules that counteract the inhibitory effect of 6179. The findings shed more light on the mechanism behind the inter-strain interactions of L. monocytogenes indicating that both contact of cells and extracellular metabolites may influence the behavior of the different co-existing strains.
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Affiliation(s)
- Maria A Gkerekou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece
| | - Eleftheria H Kaparakou
- Laboratory of General Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece
| | - Petros A Tarantilis
- Laboratory of General Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece
| | - Panagiotis N Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Greece.
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Li X, Xu H, Li Y, Liao S, Liu Y. Exploring Diverse Bioactive Secondary Metabolites from Marine Microorganisms Using Co-Culture Strategy. Molecules 2023; 28:6371. [PMID: 37687200 PMCID: PMC10489945 DOI: 10.3390/molecules28176371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The isolation and identification of an increasing number of secondary metabolites featuring unique skeletons and possessing diverse bioactivities sourced from marine microorganisms have garnered the interest of numerous natural product chemists. There has been a growing emphasis on how to cultivate microorganisms to enhance the chemical diversity of metabolites and avoid the rediscovery of known ones. Given the significance of secondary metabolites as a means of communication among microorganisms, microbial co-culture has been introduced. By mimicking the growth patterns of microbial communities in their natural habitats, the co-culture strategy is anticipated to stimulate biosynthetic gene clusters that remain dormant under traditional laboratory culture conditions, thereby inducing the production of novel secondary metabolites. Different from previous reviews mainly focusing on fermentation conditions or metabolite diversities from marine-derived co-paired strains, this review covers the marine-derived co-culture microorganisms from 2012 to 2022, and turns to a particular discussion highlighting the selection of co-paired strains for marine-derived microorganisms, especially the fermentation methods for their co-cultural apparatus, and the screening approaches for the convenient and rapid detection of novel metabolites, as these are important in the co-culture. Finally, the structural and bioactivity diversities of molecules are also discussed. The challenges and prospects of co-culture are discussed on behave of the views of the authors.
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Affiliation(s)
- Xiaolin Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayan Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuyue Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengrong Liao
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Liu
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
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36
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Li X, Chen D, Carrión VJ, Revillini D, Yin S, Dong Y, Zhang T, Wang X, Delgado-Baquerizo M. Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections. Nat Commun 2023; 14:5090. [PMID: 37607924 PMCID: PMC10444831 DOI: 10.1038/s41467-023-40810-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.
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Affiliation(s)
- Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dele Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
| | - Daniel Revillini
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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Zoheir AE, Sobol MS, Meisch L, Ordoñez-Rueda D, Kaster AK, Niemeyer CM, Rabe KS. A three-colour stress biosensor reveals multimodal response in single cells and spatiotemporal dynamics of biofilms. NPJ Biofilms Microbiomes 2023; 9:57. [PMID: 37604827 PMCID: PMC10442448 DOI: 10.1038/s41522-023-00424-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
The plethora of stress factors that can damage microbial cells has evolved sophisticated stress response mechanisms. While existing bioreporters can monitor individual responses, sensors for detecting multimodal stress responses in living microorganisms are still lacking. Orthogonally detectable red, green, and blue fluorescent proteins combined in a single plasmid, dubbed RGB-S reporter, enable simultaneous, independent, and real-time analysis of the transcriptional response of Escherichia coli using three promoters which report physiological stress (PosmY for RpoS), genotoxicity (PsulA for SOS), and cytotoxicity (PgrpE for RpoH). The bioreporter is compatible with standard analysis and Fluorescent Activated Cell Sorting (FACS) combined with subsequent transcriptome analysis. Various stressors, including the biotechnologically relevant 2-propanol, activate one, two, or all three stress responses, which can significantly impact non-stress-related metabolic pathways. Implemented in microfluidic cultivation with confocal fluorescence microscopy imaging, the RGB-S reporter enabled spatiotemporal analysis of live biofilms revealing stratified subpopulations of bacteria with heterogeneous stress responses.
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Affiliation(s)
- Ahmed E Zoheir
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Department of Genetics and Cytology, National Research Centre (NRC), Cairo, Egypt
| | - Morgan S Sobol
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Laura Meisch
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility, Heidelberg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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Lu Y, Fu Y, Chen L, Cui J, Huang M, Fu Y, Liu H. Combined effect of simulated microgravity and low-dose ionizing radiation on structure and antibiotic resistance of a synthetic community model of bacteria isolated from spacecraft assembly room. LIFE SCIENCES IN SPACE RESEARCH 2023; 38:29-38. [PMID: 37481305 DOI: 10.1016/j.lssr.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/25/2023] [Indexed: 07/24/2023]
Abstract
Understanding the structural and antibiotic resistance changes of microbial communities in space environments is critical for identifying potential pathogens that may pose health risks to astronauts and for preventing and controlling microbial contamination. The research to date on microbes under simulated space factors has primarily been carried out on single bacterial species under the individual effects of microgravity or low-dose radiation. However, microgravity (MG) and low-dose ionizing radiation (LDIR) coexist in the actual spacecraft environment, and microorganisms coexist as communities in the spacecraft environment. Thus, the microbial response to the real changes present during space habitation has not been adequately explored. To address this knowledge gap, we compared the dynamics of community composition and antibiotic resistance of synthetic bacterial communities under simulated microgravit, low-dose ionizing radiation, and the conditions combined, as it occurs in spacecraft. To ensure representative bacteria were selected, we co-cultured of 12 bacterial strains isolated from spacecraft cleanrooms. We found that the weakened competition between communities increased the possibility of species coexistence, community diversity, and homogeneity. The number of Bacilli increased significantly, while different species under the combined conditions showed various changes in abundance compared to those under the individual conditions. The resistance of the synthetic community to penicillins increased significantly under low doses of ionizing radiation but did not change significantly under simulated microgravity or the combined conditions. The results of functional predictions revealed that antibiotic biosynthesis and resistance increased dramatically in the community under space environmental stress, which confirmed the results of the drug sensitivity assays. Our results show that combined space environmental factors exert different effects on the microbial community structure and antibiotic resistance, which provides new insights into our understanding of the mechanisms of evolution of microorganisms in spacecraft, and is relevant to effective microbial pollution prevention and control strategies.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Yifan Fu
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; 4+4 M D. Program, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Letian Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Jingjing Cui
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China
| | - Min Huang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China.
| | - Hong Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 37 Xueyuan Road, Haidian District, Beijing 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing 100083, China
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Nagpal S, Mande SS. Environmental insults and compensative responses: when microbiome meets cancer. Discov Oncol 2023; 14:130. [PMID: 37453005 DOI: 10.1007/s12672-023-00745-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.
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Affiliation(s)
- Sunil Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, 411013, India.
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Sharmila S Mande
- TCS Research, Tata Consultancy Services Ltd, Pune, 411013, India.
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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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Forsyth JH, Barron NL, Scott L, Watson BNJ, Chisnall MAW, Meaden S, van Houte S, Raymond B. Decolonizing drug-resistant E. coli with phage and probiotics: breaking the frequency-dependent dominance of residents. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001352. [PMID: 37418300 PMCID: PMC10433417 DOI: 10.1099/mic.0.001352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Widespread antibiotic resistance in commensal bacteria creates a persistent challenge for human health. Resident drug-resistant microbes can prevent clinical interventions, colonize wounds post-surgery, pass resistance traits to pathogens or move to more harmful niches following routine interventions such as catheterization. Accelerating the removal of resistant bacteria or actively decolonizing particular lineages from hosts could therefore have a number of long-term benefits. However, removing resident bacteria via competition with probiotics, for example, poses a number of ecological challenges. Resident microbes are likely to have physiological and numerical advantages and competition based on bacteriocins or other secreted antagonists is expected to give advantages to the dominant partner, via positive frequency dependence. Since a narrow range of Escherichia coli genotypes (primarily those belonging to the clonal group ST131) cause a significant proportion of multidrug-resistant infections, this group presents a promising target for decolonization with bacteriophage, as narrow-host-range viral predation could lead to selective removal of particular genotypes. In this study we tested how a combination of an ST131-specific phage and competition from the well-known probiotic E. coli Nissle strain could displace E. coli ST131 under aerobic and anaerobic growth conditions in vitro. We showed that the addition of phage was able to break the frequency-dependent advantage of a numerically dominant ST131 isolate. Moreover, the addition of competing E. coli Nissle could improve the ability of phage to suppress ST131 by two orders of magnitude. Low-cost phage resistance evolved readily in these experiments and was not inhibited by the presence of a probiotic competitor. Nevertheless, combinations of phage and probiotic produced stable long-term suppression of ST131 over multiple transfers and under both aerobic and anaerobic growth conditions. Combinations of phage and probiotic therefore have real potential for accelerating the removal of drug-resistant commensal targets.
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Affiliation(s)
- Jessica H. Forsyth
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
- Present address: Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Natalie L. Barron
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Lucy Scott
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | | | | | - Sean Meaden
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
- Present address: Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Stineke van Houte
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
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42
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Anne F, Gwenaëlle G, Isabelle S, Pierre F. Improved engineering of Pseudomonas aeruginosa to study the adaptation of pyoverdine production under intra- or inter- specific bacterial competition. J Microbiol Methods 2023; 210:106753. [PMID: 37271375 DOI: 10.1016/j.mimet.2023.106753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/27/2023] [Accepted: 05/28/2023] [Indexed: 06/06/2023]
Abstract
Pseudomonas aeruginosa (PA) is a common cause of chronic infections, particularly feared by cystic fibrosis patients. PA colonizes the lung where it adapts to the local environment, and/or to treatments by drugs. This genotypic and phenotypic adaptation, in turns, influences its interaction with its environment, like bacteria from the microbiota. As an example, to access iron, PA produces and secretes two siderophores, pyoverdine and pyochelin that are iron chelators scavenging iron from the environment and bringing it back into the bacterial cells. Siderophores production depends on the level of iron starvation, on the presence of other bacteria, etc. this latter component being less well investigated. Even if studies on bacterial interactions, and their evolution, have been increasing since several years, we are still facing a lack of tools, for example, to specifically follow the growth of PA isolates in such competitive environments. We thus improved a cloning method to gain time in the cloning steps, to lower the polar effects, and to accurately follow the interactions of any PA isolate with other bacteria. For that, a fluorescent reporter gene was inserted between two genes, the glutamine-fructose-6-phosphate transaminase (glmS) and PA5548. This reporter was efficiently produced either from an inducible or a house-keeping promoter, and its expression did not lead to polar effects. We used this strain to study intra and inter-specific bacterial competitions for iron between different lung pathogens. We thus grew wild-type PA together either with an isogenic PA ΔpvdS variant, that does not produce the most efficient siderophore pyoverdine, or with Klebsiella pneumoniae or Acinetobacter baumanii, two other lung pathogens. We finally monitored the effect of the loss of pvdS on the competition between PA and the other bacterial species. These studies enabled us to differentiate intra from inter specific competitions, both arising in the lung environment, and pinpoint the importance of the bacterial specie for the adaptation of pyoverdine production.
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Affiliation(s)
- Forster Anne
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Graulier Gwenaëlle
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Schalk Isabelle
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France
| | - Fechter Pierre
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France; CNRS, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg, France.
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43
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Jha S, Anand S. Development and Control of Biofilms: Novel Strategies Using Natural Antimicrobials. MEMBRANES 2023; 13:579. [PMID: 37367783 DOI: 10.3390/membranes13060579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
Separation membranes have a wide application in the food industry, for instance, in the clarification/fractionation of milk, the concentration/separation of selected components, and wastewater treatment. They provide a large area for bacteria to attach and colonize. When a product comes into contact with a membrane, it initiates bacterial attachment/colonization and eventually forms biofilms. Several cleaning and sanitation protocols are currently utilized in the industry; however, the heavy fouling of the membrane over a prolonged duration affects the overall cleaning efficiency. In view of this, alternative approaches are being developed. Therefore, the objective of this review is to describe the novel strategies for controlling membrane biofilms such as enzyme-based cleaner, naturally produced antimicrobials of microbial origin, and preventing biofilm development using quorum interruption. Additionally, it aims to report the constitutive microflora of the membrane and the development of the predominance of resistant strains over prolonged usage. The emergence of predominance could be associated with several factors, of which, the release of antimicrobial peptides by selective strains is a prominent factor. Therefore, naturally produced antimicrobials of microbial origin could thus provide a promising approach to control biofilms. Such an intervention strategy could be implemented by developing a bio-sanitizer exhibiting antimicrobial activity against resistant biofilms.
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Affiliation(s)
- Sheetal Jha
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - Sanjeev Anand
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA
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44
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Aguilar-Salinas B, Olmedo-Álvarez G. A three-species synthetic community model whose rapid response to antagonism allows the study of higher-order dynamics and emergent properties in minutes. Front Microbiol 2023; 14:1057883. [PMID: 37333661 PMCID: PMC10272403 DOI: 10.3389/fmicb.2023.1057883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/02/2023] [Indexed: 06/20/2023] Open
Abstract
Microbial communities can be considered complex adaptive systems. Understanding how these systems arise from different components and how the dynamics of microbial interactions allow for species coexistence are fundamental questions in ecology. To address these questions, we built a three-species synthetic community, called BARS (Bacillota A + S + R). Each species in this community exhibits one of three ecological roles: Antagonistic, Sensitive, or Resistant, assigned in the context of a sediment community. We show that the BARS community reproduces features of complex communities and exhibits higher-order interaction (HOI) dynamics. In paired interactions, the majority of the S species (Sutcliffiella horikoshii 20a) population dies within 5 min when paired with the A species (Bacillus pumilus 145). However, an emergent property appears upon adding the third interactor, as antagonism of species A over S is not observed in the presence of the R species (Bacillus cereus 111). For the paired interaction, within the first 5 min, the surviving population of the S species acquires tolerance to species A, and species A ceases antagonism. This qualitative change reflects endogenous dynamics leading to the expression for tolerance to an antagonistic substance. The stability reached in the triple interaction exhibits a nonlinear response, highly sensitive to the density of the R species. In summary, our HOI model allows the study of the assembly dynamics of a three-species community and evaluating the immediate outcome within a 30 min frame. The BARS has features of a complex system where the paired interactions do not predict the community dynamics. The model is amenable to mechanistic dissection and to modeling how the parts integrate to achieve collective properties.
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45
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Coleman S, Unterhauser K, Rezaul K, Ledala N, Lesmes S, Caimano MJ, Zhou Y, Jackson E, Gratalo D, Driscoll MD, Matson AP. High-resolution microbiome analysis reveals exclusionary Klebsiella species competition in preterm infants at risk for necrotizing enterocolitis. Sci Rep 2023; 13:7893. [PMID: 37193703 DOI: 10.1038/s41598-023-34735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023] Open
Abstract
Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~ 2500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiella species colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichia in NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecalis was co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiella strains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.
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Affiliation(s)
- Spencer Coleman
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Stephanie Lesmes
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa J Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA
- Department of Medicine, UConn Health, Farmington, CT, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Adam P Matson
- Department of Pediatrics, UConn Health, Farmington, CT, USA.
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.
- Department of Immunology, UConn Health, Farmington, CT, USA.
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46
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Kuhn T, Junier P, Bshary R, Terrettaz C, Gonzalez D, Richter XYL. Nutrients and flow shape the cyclic dominance games between Escherichia coli strains. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210503. [PMID: 36934746 PMCID: PMC10024984 DOI: 10.1098/rstb.2021.0503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Abstract
Evolutionary game theory has provided various models to explain the coexistence of competing strategies, one of which is the rock-paper-scissors (RPS) game. A system of three Escherichia coli strains-a toxin-producer, a resistant and a sensitive-has become a classic experimental model for studying RPS games. Previous experimental and theoretical studies, however, often ignored the influence of ecological factors such as nutrients and toxin dynamics on the evolutionary game dynamics. In this work, we combine experiments and modelling to study how these factors affect competition dynamics. Using three-dimensional printed mini-bioreactors, we tracked the frequency of the three strains in different culturing media and under different flow regimes. Although our experimental system fulfilled the requirements of cyclic dominance, we did not observe clear cycles or long-term coexistence between strains. We found that both nutrients and flow rates strongly impacted population dynamics. In our simulations, we explicitly modelled the release, removal and diffusion of toxin. We showed that the amount of toxin that is retained in the system is a simple indicator that can predict competition outcomes across broad parameter space. Moreover, our simulation results suggest that high rates of toxin diffusion might have prevented cyclic patterns from emerging in our experimental system. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.
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Affiliation(s)
- Thierry Kuhn
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Redouan Bshary
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Céline Terrettaz
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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48
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Gao Z, Yi S, Xue M, Zhu K, Yang R, Wang T, Sun H, Zhu L. Microbial biotransformation mechanisms of PFPiAs in soil unveiled by metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130896. [PMID: 36764254 DOI: 10.1016/j.jhazmat.2023.130896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/15/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
As alternatives of long-chain PFASs (Poly- and perfluoroalkyl substances), perfluoroalkyl phosphinic acids (PFPiAs) are increasingly observed in the environment, but their environmental behaviors have not been well understood. Here, the microbial biotransformation of C6/C6 and C8/C8 PFPiA in two soils (Soil N and Y) was investigated. After 252 d and 330 d of incubation with PFPiAs in Soil N and Y respectively, the levels of PFPiAs decreased distinctly, accompanied by the increasing perfluorohexaphosphonic acid (PFHxPA) or perfluorooctanophosphonic acid (PFOPA) formation, magnifying PFPiAs were susceptible to C-P cleavage, which was also confirmed by the density functional theory calculations. The half-lives of the PFPiAs were longer than one year, while generally shorter in Soil N than in Soil Y and that of C6/C6 was shorter than C8/C8 PFPiA (392 d and 746 d in Soil N, and 603 and 1155 d in Soil Y, respectively). Metagenomic sequencing analysis revealed that Proteobacteria as the primary host of the potential functional genes related to CP bond cleavage might be the crucial phyla contributing to the biotransformation of PFPiAs. Meanwhile, the more intensive interactions between the microbes in Soil N consistently contribute to its greater capacity for transforming PFPiAs.
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Affiliation(s)
- Zhuo Gao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Shujun Yi
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Mengzhu Xue
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Kecheng Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Rongyan Yang
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; Key Laboratory of Plant Nutrition and The Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, PR China
| | - Hongwen Sun
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China; College of Environmental Science and Engineering, Nankai University, Tianjin 300071, PR China.
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [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: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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50
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Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing. mBio 2023; 14:e0358422. [PMID: 36877031 PMCID: PMC10128055 DOI: 10.1128/mbio.03584-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.
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