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Gilhar O, Ben-Navi LR, Olender T, Aharoni A, Friedman J, Kolodkin-Gal I. Multigenerational inheritance drives symbiotic interactions of the bacterium Bacillus subtilis with its plant host. Microbiol Res 2024; 286:127814. [PMID: 38954993 DOI: 10.1016/j.micres.2024.127814] [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: 04/13/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Bacillus subtilis is a beneficial bacterium that supports plant growth and protects plants from bacterial, fungal, and viral infections. Using a simplified system of B. subtilis and Arabidopsis thaliana interactions, we studied the fitness and transcriptome of bacteria detached from the root over generations of growth in LB medium. We found that bacteria previously associated with the root or exposed to its secretions had greater stress tolerance and were more competitive in root colonization than bacteria not previously exposed to the root. Furthermore, our transcriptome results provide evidence that plant secretions induce a microbial stress response and fundamentally alter signaling by the cyclic nucleotide c-di-AMP, a signature maintained by their descendants. The changes in cellular physiology due to exposure to plant exudates were multigenerational, as they allowed not only the bacterial cells that colonized a new plant but also their descendants to have an advance over naive competitors of the same species, while the overall plasticity of gene expression and rapid adaptation were maintained. These changes were hereditary but not permanent. Our work demonstrates a bacterial memory manifested by multigenerational reversible adaptation to plant hosts in the form of activation of the stressosome, which confers an advantage to symbiotic bacteria during competition.
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Affiliation(s)
- Omri Gilhar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel; Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
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2
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Povolotsky TL, Levy Barazany H, Shacham Y, Kolodkin-Gal I. Bacterial epigenetics and its implication for agriculture, probiotics development, and biotechnology design. Biotechnol Adv 2024; 75:108414. [PMID: 39019123 DOI: 10.1016/j.biotechadv.2024.108414] [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: 05/04/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
In their natural habitats, organisms encounter numerous external stimuli and must be able to sense and adapt to those stimuli to survive. Unlike mutations, epigenetic changes do not alter the underlying DNA sequence. Instead, they create modifications that promote or silence gene expression. Bacillus subtilis has long been a model organism in studying genetics and development. It is beneficial for numerous biotechnological applications where it is included as a probiotic, in fermentation, or in bio-concrete design. This bacterium has also emerged recently as a model organism for studying bacterial epigenetic adaptation. In this review, we examine the evolving knowledge of epigenetic regulation (restriction-modification systems (RM), orphan methyltransferases, and chromosome condensation) in B. subtilis and related bacteria, and utilize it as a case study to test their potential roles and future applications in genetic engineering and microbial biotechnology. Finally, we suggest how the implementation of these fundamental findings promotes the design of synthetic epigenetic memory circuits and their future applications in agriculture, medicine, and biotechnology.
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Affiliation(s)
- Tatyana L Povolotsky
- Institute for Chemistry and Biochemistry, Physical and Theoretical Chemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Hilit Levy Barazany
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Yosi Shacham
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel.
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3
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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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Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA. Extensive cellular multi-tasking within Bacillus subtilis biofilms. mSystems 2023; 8:e0089122. [PMID: 37527273 PMCID: PMC10469600 DOI: 10.1128/msystems.00891-22] [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: 09/13/2022] [Accepted: 03/08/2023] [Indexed: 08/03/2023] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms. IMPORTANCE Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
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Affiliation(s)
- Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eric S. Beaudoin
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hunter S. Talley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Song W, Ryu J, Jung J, Yu Y, Choi S, Kweon J. Dispersive biofilm from membrane bioreactor strains: effects of diffusible signal factor addition and characterization by dispersion index. Front Microbiol 2023; 14:1211761. [PMID: 37560518 PMCID: PMC10409479 DOI: 10.3389/fmicb.2023.1211761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
INTRODUCTION Biofilm occurs ubiquitously in water system. Excessive biofilm formation deteriorates severely system performance in several water and wastewater treatment processes. Quorum sensing systems were controlled in this study with a signal compound cis-2-Decenoic acid (CDA) to regulate various functions of microbial communities, including motility, enzyme production, and extracellular polymeric substance (EPS) production in biofilm. METHODS The addition of CDA to six strains extracted from membrane bioreactor sludge and the Pseudomonas aeruginosa PAO1 strain was examined for modulating biofilm development by regulating DSF expression. RESULTS AND DISCUSSION As the CDA doses increased, optical density of the biofilm dispersion assay increased, and the decrease in EPS of the biofilm was obvious on membrane surfaces. The three-dimensional visual images and quantitative analyses of biofilm formation with CDA proved thinner, less massive, and more dispersive than those without; to evaluate its dispersive intensity, a dispersion index was proposed. This could compare the dispersive effects of CDA dosing to other biofilms or efficiencies of biofouling control practices such as backwashing or new cleaning methods.
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Affiliation(s)
- Wonjung Song
- The Academy of Applied Science and Technology, Konkuk University, Seoul, Republic of Korea
| | - Junhee Ryu
- Department of Civil and Environmental Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jaehyun Jung
- HANSU Technical Service Ltd, Sungnam-si, Gyeonggi-do, Republic of Korea
| | - Youngjae Yu
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, AZ, United States
| | - Suyoung Choi
- The Academy of Applied Science and Technology, Konkuk University, Seoul, Republic of Korea
| | - Jihyang Kweon
- Department of Environmental Engineering Konkuk University, Seoul, Republic of Korea
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Feng F, Sun X, Jiang W, Ma L, Wang Y, Sheng H, Li Y, Yu X. Stenotrophomonas pavanii DJL-M3 inoculated biochar stabilizes the rhizosphere soil homeostasis of carbendazim-stressed rice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121723. [PMID: 37105458 DOI: 10.1016/j.envpol.2023.121723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Plant-microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3-biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice.
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Affiliation(s)
- Fayun Feng
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xing Sun
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wenqi Jiang
- School of Environment, Nanjing University, Nanjing, 210014, China
| | - Liya Ma
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ya Wang
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Honjie Sheng
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yong Li
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xiangyang Yu
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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7
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Lyu D, Backer R, Berrué F, Martinez-Farina C, Hui JPM, Smith DL. Plant Growth-Promoting Rhizobacteria (PGPR) with Microbial Growth Broth Improve Biomass and Secondary Metabolite Accumulation of Cannabis sativa L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7268-7277. [PMID: 37130078 DOI: 10.1021/acs.jafc.2c06961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are a sustainable crop production input; some show positive effects under laboratory conditions but poorly colonize host field-grown plants. Inoculating with PGPR in microbial growth medium (e.g., King's B) could overcome this. We evaluated cannabis plant (cv. CBD Kush) growth promotion by inoculating three PGPR (Bacillus sp., Mucilaginibacter sp., and Pseudomonas sp.) in King's B at vegetative and flower stages. At the vegetative stage, Mucilaginibacter sp. inoculation increased flower dry weight (24%), total CBD (11.1%), and THC (11.6%); Pseudomonas sp. increased stem (28%) dry matter, total CBD (7.2%), and THC (5.9%); and Bacillus sp. increased total THC by 4.8%. Inoculation with Mucilaginibacter sp. and Pseudomonas sp. at the flowering stage led to 23 and 18% increases in total terpene accumulation, respectively. Overall, vegetative inoculation with PGPR enhanced cannabis yield attributes and chemical profiles. Further research into PGPR inoculation onto cannabis and the subsequent level of colonization could provide key insights regarding PGPR-host interactions.
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Affiliation(s)
- Dongmei Lyu
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
| | - Rachel Backer
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
| | - Fabrice Berrué
- National Research Council Canada, Halifax B3H 3Z1, Nova Scotia, Canada
| | | | - Joseph P M Hui
- National Research Council Canada, Halifax B3H 3Z1, Nova Scotia, Canada
| | - Donald Lawrence Smith
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue H9X3V9, Quebec, Canada
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Korangi Alleluya V, Argüelles Arias A, Ribeiro B, De Coninck B, Helmus C, Delaplace P, Ongena M. Bacillus lipopeptide-mediated biocontrol of peanut stem rot caused by Athelia rolfsii. FRONTIERS IN PLANT SCIENCE 2023; 14:1069971. [PMID: 36890892 PMCID: PMC9986434 DOI: 10.3389/fpls.2023.1069971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Peanut (Arachis hypogaea L.) is a widespread oilseed crop of high agricultural importance in tropical and subtropical areas. It plays a major role in the food supply in the Democratic Republic of Congo (DRC). However, one major constraint in the production of this plant is the stem rot (white mold or southern blight) disease caused by Athelia rolfsii which is so far controlled mainly using chemicals. Considering the harmful effect of chemical pesticides, the implementation of eco-friendly alternatives such as biological control is required for disease management in a more sustainable agriculture in the DRC as in the other developing countries concerned. Bacillus velezensis is among the rhizobacteria best described for its plant protective effect notably due to the production of a wide range of bioactive secondary metabolites. In this work, we wanted to evaluate the potential of B. velezensis strain GA1 at reducing A. rolfsii infection and to unravel the molecular basis of the protective effect. RESULTS AND DISCUSSION Upon growth under the nutritional conditions dictated by peanut root exudation, the bacterium efficiently produces the three types of lipopeptides surfactin, iturin and fengycin known for their antagonistic activities against a wide range of fungal phytopathogens. By testing a range of GA1 mutants specifically repressed in the production of those metabolites, we point out an important role for iturin and another unidentified compound in the antagonistic activity against the pathogen. Biocontrol experiments performed in greenhouse further revealed the efficacy of B. velezensis to reduce peanut disease caused by A. rolfsii both via direct antagonism against the fungus and by stimulating systemic resistance in the host plant. As treatment with pure surfactin yielded a similar level of protection, we postulate that this lipopeptide acts as main elicitor of peanut resistance against A. rolfsii infection.
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Affiliation(s)
- Virginie Korangi Alleluya
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Chemical and Agricultural Industries, Faculty of Agricultural Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Bianca Ribeiro
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Barbara De Coninck
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Catherine Helmus
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Pierre Delaplace
- Plant biology Unit, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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Miao S, Liang J, Xu Y, Yu G, Shao M. Bacillaene, sharp objects consist in the arsenal of antibiotics produced by Bacillus. J Cell Physiol 2023. [PMID: 36790954 DOI: 10.1002/jcp.30974] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
Bacillus species act as plant growth-promoting rhizobacteria (PGPR) that can produce a large number of bioactive metabolites. Bacillaene, a linear polyketide/nonribosomal peptide produced by Bacillus strains, is synthesized by the trans-acyltransferase polyketide synthetase. The complexity of the chemical structure, particularity of biosynthesis, potent bioactivity, and the important role of competition make Bacillus an ideal antibiotic weapon to resist other microbes and maintain the optimal rhizosphere environment. This review provides an updated view of the structural features, biological activity, biosynthetic regulators of biosynthetic pathways, and the important competitive role of bacillaene during Bacillus survival.
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Affiliation(s)
- Shuang Miao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Jianhao Liang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Yuan Xu
- College of Pharmaceutical Engineering, XinYang College Of Agriculture And Forestry, Xinyang, P.R. China
| | - Guohui Yu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
| | - Mingwei Shao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, P.R. China
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10
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Andrić S, Rigolet A, Argüelles Arias A, Steels S, Hoff G, Balleux G, Ongena L, Höfte M, Meyer T, Ongena M. Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor. THE ISME JOURNAL 2023; 17:263-275. [PMID: 36357782 PMCID: PMC9860033 DOI: 10.1038/s41396-022-01337-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022]
Abstract
Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.
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Affiliation(s)
- Sofija Andrić
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Augustin Rigolet
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sébastien Steels
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Grégory Hoff
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.5477.10000000120346234Present Address: Ecology and Biodiversity, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Guillaume Balleux
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Loïc Ongena
- grid.4861.b0000 0001 0805 7253Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Monica Höfte
- grid.5342.00000 0001 2069 7798Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thibault Meyer
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.7849.20000 0001 2150 7757Present Address: UMR Ecologie Microbienne, F-69622, University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Marc Ongena
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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11
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Shao M, Chen Y, Gong Q, Miao S, Li C, Sun Y, Qin D, Guo X, Yan X, Cheng P, Yu G. Biocontrol endophytes Bacillus subtilis R31 influence the quality, transcriptome and metabolome of sweet corn. PeerJ 2023; 11:e14967. [PMID: 36883062 PMCID: PMC9985898 DOI: 10.7717/peerj.14967] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
During colonization of soil and plants, biocontrol bacteria can effectively regulate the physiological metabolism of plants and induce disease resistance. To illustrate the influence of Bacillus subtilis R31 on the quality, transcriptome and metabolome of sweet corn, field studies were conducted at a corn experimental base in Zhuhai City. The results show that, after application of B. subtilis R31, sweet corn was more fruitful, with a 18.3 cm ear length, 5.0 cm ear diameter, 0.4 bald head, 403.9 g fresh weight of single bud, 272.0 g net weight of single ear, and 16.5 kernels sweetness. Combined transcriptomic and metabolomic analyses indicate that differentially expressed genes related to plant-pathogen interactions, MAPK signaling pathway-plant, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched. Moreover, the 110 upregulated DAMs were mainly involved in the flavonoid biosynthesis and flavone and flavonol biosynthesis pathways. Our study provides a foundation for investigating the molecular mechanisms by which biocontrol bacteria enhance crop nutrition and taste through biological means or genetic engineering at the molecular level.
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Affiliation(s)
- Mingwei Shao
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Yanhong Chen
- Zhuhai Modern Agriculture Development Center, Zhuhai, China
| | - Qingyou Gong
- Zhuhai Modern Agriculture Development Center, Zhuhai, China
| | - Shuang Miao
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Chunji Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Yunhao Sun
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Di Qin
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Xiaojian Guo
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Xun Yan
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Ping Cheng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
| | - Guohui Yu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China.,Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guanghzou, China.,Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangdong, China
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12
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Highmore CJ, Melaugh G, Morris RJ, Parker J, Direito SOL, Romero M, Soukarieh F, Robertson SN, Bamford NC. Translational challenges and opportunities in biofilm science: a BRIEF for the future. NPJ Biofilms Microbiomes 2022; 8:68. [PMID: 36038607 PMCID: PMC9424220 DOI: 10.1038/s41522-022-00327-7] [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: 07/23/2021] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Biofilms are increasingly recognised as a critical global issue in a multitude of industries impacting health, food and water security, marine sector, and industrial processes resulting in estimated economic cost of $5 trillion USD annually. A major barrier to the translation of biofilm science is the gap between industrial practices and academic research across the biofilms field. Therefore, there is an urgent need for biofilm research to notice and react to industrially relevant issues to achieve transferable outputs. Regulatory frameworks necessarily bridge gaps between different players, but require a clear, science-driven non-biased underpinning to successfully translate research. Here we introduce a 2-dimensional framework, termed the Biofilm Research-Industrial Engagement Framework (BRIEF) for classifying existing biofilm technologies according to their level of scientific insight, including the understanding of the underlying biofilm system, and their industrial utility accounting for current industrial practices. We evidence the BRIEF with three case studies of biofilm science across healthcare, food & agriculture, and wastewater sectors highlighting the multifaceted issues around the effective translation of biofilm research. Based on these studies, we introduce some advisory guidelines to enhance the translational impact of future research.
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Affiliation(s)
- C J Highmore
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - G Melaugh
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK.,School of Engineering, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - R J Morris
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - J Parker
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - S O L Direito
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - M Romero
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
| | - F Soukarieh
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
| | - S N Robertson
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK. .,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK.
| | - N C Bamford
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK. .,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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13
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Liu L, Ji Z, Zhao K, Zhao Y, Zhang Y, Huang S. Validation of housekeeping genes as internal controls for gene expression studies on biofilm formation in Bacillus velezensis. Appl Microbiol Biotechnol 2022; 106:2079-2089. [PMID: 35171340 DOI: 10.1007/s00253-022-11831-3] [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: 09/09/2021] [Revised: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 11/02/2022]
Abstract
Bacillus velezensis is an important bacterium widely applied in agriculture and industry, and biofilms play critical roles in its environmental tolerance. The appropriate choice of reference genes is essential for key gene expression studies. Multiple internal control genes were selected and validated from the 21 housekeeping genes of B. velezensis by expression stability evaluation during biofilm formation and were used to study the expression of key genes involved in the process. The results showed that pyk, gyrA, recA, and gyrB were stably expressed, and the expression of pyk was the most stable during biofilm formation. A pair of two genes, pyk and gyrA, provided high-quality data when used as internal controls, and the combination of three genes, pyk, gyrA, and recA, was even better. The expression levels of pyk, gyrA, and recA approximated those of five key genes, abrB, epsD, kinC, sinR, and tasA, in biofilm formation, meeting the requirements of ideal internal control genes. The expression patterns of 5 key genes were studied with 16S, pyk, the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA, as internal controls during the biofilm formation process. The results proved that pyk was a suitable internal control, as were the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA. This study provided genes and gene combinations which were validated as suitable internal controls for gene expression studies, especially those on the mechanism of biofilm formation in B. velezensis or even other Bacillus spp. KEY POINTS: • Reference genes is necessary for gene expression study in biofilm formation of Bacillus velezensis • Pyk and 2 gene combinations were selected and validated from 21 common used genes • Expression of key genes in biofilm formation was normalized with the selected internal controls.
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Affiliation(s)
- Lianmeng Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China.
| | - Zhiming Ji
- College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Kehan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Yuan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Yilin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China
| | - Shiwen Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, 311400, Hangzhou, China. .,College of Agriculture, Guangxi University, 530003, Nanning, China.
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14
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Maan H, Gilhar O, Porat Z, Kolodkin-Gal I. Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production. Front Cell Infect Microbiol 2021; 11:722778. [PMID: 34557426 PMCID: PMC8454505 DOI: 10.3389/fcimb.2021.722778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/01/2022] Open
Abstract
Beneficial and probiotic bacteria play an important role in conferring immunity of their hosts to a wide range of bacterial, viral, and fungal diseases. Bacillus subtilis is a Gram-positive bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great importance for the elimination of pathogens and establishing beneficial host-associated communities. In this work, we used B. subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and imaging flow cytometry (IFC) analysis supported the notion that Arabidopsis thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin, plipastatin, and the polyketide bacillaene. IFC was more robust in quantifying the inducing effects of A. thaliana, considering the overall heterogeneity of the population. Our results highlight IFC as a useful tool to study the effect of association with a plant host on bacterial gene expression. Furthermore, the common regulation of multiple biosynthetic clusters for antibiotic production by the plant can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omri Gilhar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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15
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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16
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Feng F, Zhan H, Wan Q, Wang Y, Li Y, Ge J, Sun X, Zhu H, Yu X. Rice recruits Sphingomonas strain HJY-rfp via root exudate regulation to increase chlorpyrifos tolerance and boost residual catabolism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5673-5686. [PMID: 33987653 DOI: 10.1093/jxb/erab210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Inoculation with pollution-degrading endophytes boosts the catabolism of residual contaminants and promotes the pollution adaptation of host plants. We investigated the interaction pattern between Sphingomonas strain HJY-rfp, a chlorpyrifos-degrading endophytic bacterium, and rice (Oryza sativa) under pesticide stress using hydroponic cultivation. We observed a notable trend of endophytic root colonization in rice plants treated with 10 mg l-1 chlorpyrifos solution, and after 24 h the migration of HJY-rfp enhanced the chlorpyrifos degradation rate in leaves and stems by 53.36% and 40.81%, respectively. Critically, the rice root exudate profile (organic acids and amino acids) changed under chlorpyrifos stress, and variations in the contents of several components affected the chemotactic behaviour of HJY-rfp. HJY-rfp colonization dramatically activated defensive enzymes, which enabled efficient scavenging of reactive oxygen species, and led to 9.8%, 22.5%, and 41.9% increases in shoot length, fresh weight, and accumulation of total chlorophyll, respectively, in rice suffering from oxidative damage by chlorpyrifos. Endophytic colonization caused up-regulation of detoxification genes that have shown a significant positive correlation with chlorpyrifos degradation in vivo. Collectively, our results demonstrate that agrochemical stress causes plants to actively recruit specific symbiotic microbes to detoxify contaminants and survive better under pollution conditions.
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Affiliation(s)
- Fayun Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing, China
| | - Honglin Zhan
- Department of Biotechnology, Qingdao University of Science &Technology, Qingdao, China
| | - Qun Wan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ya Wang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yong Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jing Ge
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xing Sun
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hong Zhu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing, China
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17
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Molina-Santiago C, Vela-Corcía D, Petras D, Díaz-Martínez L, Pérez-Lorente AI, Sopeña-Torres S, Pearson J, Caraballo-Rodríguez AM, Dorrestein PC, de Vicente A, Romero D. Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence. Cell Rep 2021; 36:109449. [PMID: 34320359 PMCID: PMC8333196 DOI: 10.1016/j.celrep.2021.109449] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/18/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA of P. chlororaphis and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance of B. amyloliquefaciens to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked by a decrease of Bacillus cell membrane permeability, among other pleiotropic responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial adaptive dynamics that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication. Bacillus and Pseudomonas interaction ranges from antagonism to co-existence Bacillaene from Bacillus is a bacteriostatic that targets FusA of Pseudomonas GlpK mutations in Bacillus confer unspecific antimicrobial resistance
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - David Vela-Corcía
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Daniel Petras
- University of California San Diego, Scripps Institution of Oceanography, La Jolla, CA, USA; University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, USA
| | - Luis Díaz-Martínez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Alicia Isabel Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Sara Sopeña-Torres
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - John Pearson
- Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, Málaga, Spain
| | | | - Pieter C Dorrestein
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, USA
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora," Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain.
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18
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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19
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Hou Q, Keren-Paz A, Korenblum E, Oved R, Malitsky S, Kolodkin-Gal I. Weaponizing volatiles to inhibit competitor biofilms from a distance. NPJ Biofilms Microbiomes 2021; 7:2. [PMID: 33402677 PMCID: PMC7785731 DOI: 10.1038/s41522-020-00174-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
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Affiliation(s)
- Qihui Hou
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- grid.13992.300000 0004 0604 7563Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- grid.13992.300000 0004 0604 7563Metabolic Profiling Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Hernandez-Valdes JA, Zhou L, de Vries MP, Kuipers OP. Impact of spatial proximity on territoriality among human skin bacteria. NPJ Biofilms Microbiomes 2020; 6:30. [PMID: 32764612 PMCID: PMC7413532 DOI: 10.1038/s41522-020-00140-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
Bacteria display social behavior and establish cooperative or competitive interactions in the niches they occupy. The human skin is a densely populated environment where many bacterial species live. Thus, bacterial inhabitants are expected to find a balance in these interactions, which eventually defines their spatial distribution and the composition of our skin microbiota. Unraveling the physiological basis of the interactions between bacterial species in organized environments requires reductionist analyses using functionally relevant species. Here, we study the interaction between two members of our skin microbiota, Bacillus subtilis and Staphylococcus epidermidis. We show that B. subtilis actively responds to the presence of S. epidermidis in its proximity by two strategies: antimicrobial production and development of a subpopulation with migratory response. The initial response of B. subtilis is production of chlorotetain, which degrades the S. epidermidis at the colony level. Next, a subpopulation of B. subtilis motile cells emerges. Remarkably this subpopulation slides towards the remaining S. epidermidis colony and engulfs it. A slow response back from S. epidermidis cells give origin to resistant cells that prevent both attacks from B. subtilis. We hypothesized that this niche conquering and back-down response from B. subtilis and S. epidermidis, respectively, which resembles other conflicts in nature as the ones observed in animals, may play a role in defining the presence of certain bacterial species in the specific microenvironments that these bacteria occupy on our skin.
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Affiliation(s)
- Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Biomedical Engineering Antonius Deusinglaan 1, University Medical Center Groningen, Groningen University, 9713 AW, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Steinberg N, Keren-Paz A, Hou Q, Doron S, Yanuka-Golub K, Olender T, Hadar R, Rosenberg G, Jain R, Cámara-Almirón J, Romero D, van Teeffelen S, Kolodkin-Gal I. The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms. Sci Signal 2020; 13:13/632/eaaw8905. [PMID: 32430292 DOI: 10.1126/scisignal.aaw8905] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In nature, bacteria form biofilms-differentiated multicellular communities attached to surfaces. Within these generally sessile biofilms, a subset of cells continues to express motility genes. We found that this subpopulation enabled Bacillus subtilis biofilms to expand on high-friction surfaces. The extracellular matrix (ECM) protein TasA was required for the expression of flagellar genes. In addition to its structural role as an adhesive fiber for cell attachment, TasA acted as a developmental signal stimulating a subset of biofilm cells to revert to a motile phenotype. Transcriptomic analysis revealed that TasA stimulated the expression of a specific subset of genes whose products promote motility and repress ECM production. Spontaneous suppressor mutations that restored motility in the absence of TasA revealed that activation of the biofilm-motility switch by the two-component system CssR/CssS antagonized the TasA-mediated reversion to motility in biofilm cells. Our results suggest that although mostly sessile, biofilms retain a degree of motility by actively maintaining a motile subpopulation.
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Affiliation(s)
- Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Department of Microbiology, Institute Pasteur, Paris, France
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Yanuka-Golub
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Hadar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rakeshkumar Jain
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jesus Cámara-Almirón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | | | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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Karygianni L, Ren Z, Koo H, Thurnheer T. Biofilm Matrixome: Extracellular Components in Structured Microbial Communities. Trends Microbiol 2020; 28:668-681. [PMID: 32663461 DOI: 10.1016/j.tim.2020.03.016] [Citation(s) in RCA: 540] [Impact Index Per Article: 135.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/16/2020] [Accepted: 03/25/2020] [Indexed: 02/04/2023]
Abstract
Biofilms consist of microbial communities embedded in a 3D extracellular matrix. The matrix is composed of a complex array of extracellular polymeric substances (EPS) that contribute to the unique attributes of biofilm lifestyle and virulence. This ensemble of chemically and functionally diverse biomolecules is termed the 'matrixome'. The composition and mechanisms of EPS matrix formation, and its role in biofilm biology, function, and microenvironment are being revealed. This perspective article highlights recent advances about the multifaceted role of the 'matrixome' in the development, physical-chemical properties, and virulence of biofilms. We emphasize that targeting biofilm-specific conditions such as the matrixome could lead to precise and effective antibiofilm approaches. We also discuss the limited knowledge in the context of polymicrobial biofilms, and the need for more in-depth analyses of the EPS matrix in mixed communities that are associated with many human infectious diseases.
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Affiliation(s)
- L Karygianni
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine University of Zurich, Zurich, Switzerland
| | - Z Ren
- Department of Orthodontics, Divisions of Pediatric Dentistry and Community of Oral Health, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - H Koo
- Department of Orthodontics, Divisions of Pediatric Dentistry and Community of Oral Health, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA; Center for Innovation and Precision Dentistry, University of Pennsylvania School of Dental Medicine, School of Engineering and Applied Sciences, Philadelphia, PA, USA
| | - T Thurnheer
- Clinic of Conservative and Preventive Dentistry, Center of Dental Medicine University of Zurich, Zurich, Switzerland.
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