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Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN, Xie J, Jarmusch SA, Wibowo M, Kjeldgaard B, Surabhi S, Xu X, Jautzus T, Phippen CBW, Tyc O, Arentshorst M, Wang Y, Garbeva P, Larsen TO, Ram AFJ, van den Hondel CAM, Maróti G, Kovács ÁT. Enhanced surface colonisation and competition during bacterial adaptation to a fungus. Nat Commun 2024; 15:4486. [PMID: 38802389 PMCID: PMC11130161 DOI: 10.1038/s41467-024-48812-1] [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: 06/05/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.
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Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Felix Blei
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
| | - Jan W Schwitalla
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jiyu Xie
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Scott A Jarmusch
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Surabhi Surabhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Xinming Xu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Christopher B W Phippen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Olaf Tyc
- Netherlands Institute of Ecology, Wageningen, The Netherlands
- Department of Internal Medicine I, Goethe University Hospital, Frankfurt, Germany
| | - Mark Arentshorst
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Thomas Ostenfeld Larsen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Arthur F J Ram
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark.
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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Cao CY, Hou ZJ, Ding MZ, Gao GR, Qiao B, Wei SY, Cheng JS. Integrated Biofilm Modification and Transcriptional Analysis for Improving Fengycin Production in Bacillus amyloliquefaciens. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10266-8. [PMID: 38652228 DOI: 10.1007/s12602-024-10266-8] [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] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Although fengycin exhibits broad-spectrum antifungal properties, its application is hindered due to its low biosynthesis level and the co-existence of iturin A and surfactin in Bacillus amyloliquefaciens HM618, a probiotic strain. In this study, transcriptome analysis and gene editing were used to explore the potential mechanisms regulating fengycin production in B. amyloliquefaciens. The fengycin level of B. amyloliquefacien HM-3 (∆itu-ΔsrfAA) was 88.41 mg/L after simultaneously inhibiting the biosyntheses of iturin A and surfactin. The knockout of gene eps associated with biofilm formation significantly increased the fengycin level of the strain HM618, whereas the fengycin level decreased 32.05% after knocking out sinI, a regulator of biofilm formation. Transcriptome analysis revealed that the differentially expressed genes, involved in pathways of amino acid and fatty acid syntheses, were significantly down-regulated in the recombinant strains, which is likely associated with a decrease of fengycin production. The knockout of gene comQXPA and subsequent transcriptome analysis revealed that the ComQXPA quorum sensing system played a positive regulatory role in fengycin production. Through targeted genetic modifications and fermentation optimization, the fengycin production of the engineered strain HM-12 (∆itu-ΔsrfAA-ΔyvbJ) in a 5-L fermenter reached 1.172 g/L, a 12.26-fold increase compared to the fengycin level in the strain HM-3 (∆itu-ΔsrfAA) in the Erlenmeyer flask. Taken together, these results reveal the underlying metabolic mechanisms associated with fengycin synthesis and provide a potential strategy for improving fengycin production in B. amyloliquefaciens.
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Affiliation(s)
- Chun-Yang Cao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Zheng-Jie Hou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Ming-Zhu Ding
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Geng-Rong Gao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Si-Yu Wei
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China.
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Tianjin, 300350, People's Republic of China.
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3
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Wang J, Ping Y, Liu W, He X, Du C. Improvement of lipopeptide production in Bacillus subtilis HNDF2-3 by overexpression of the sfp and comA genes. Prep Biochem Biotechnol 2024; 54:184-192. [PMID: 37158496 DOI: 10.1080/10826068.2023.2209890] [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: 05/10/2023]
Abstract
Bacillus subtilis HNDF2-3 can produce a variety of lipopeptide antibiotics with lower production. To improve its lipopeptide production, three genetically engineered strains were constructed. The results of real-time PCR showed that the highest transcriptional levels of the sfp gene in F2-3sfp, F2-3comA and F2-3sfp-comA were 29.01, 6.65 and 17.50 times of the original strain, respectively, while the highest transcriptional levels of the comA gene in F2-3comA and F2-3sfp-comA were 10.44 and 4.13 times of the original strain, respectively. The results of ELISA showed that the malonyl-CoA transacylase activity of F2-3comA was the highest, reaching 18.53 IU/L at 24 h, the data was 32.74% higher than that of the original strain. The highest total lipopeptide production of F2-3sfp, F2-3comA and F2-3sfp-comA induced by IPTG at optimal concentration were 33.51, 46.05 and 38.96% higher than that of the original strain, respectively. The results of HPLC showed that iturin A production of F2-3sfp-comA was the highest, which was 63.16% higher than that of the original strain. This study laid the foundation for further construction of genetically engineered strains with high lipopeptide production.
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Affiliation(s)
- Jiawen Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Yuan Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wei Liu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xin He
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, China
| | - Chunmei Du
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, China
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, China
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Danevčič T, Spacapan M, Dragoš A, Kovács ÁT, Mandic-Mulec I. DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis. Microbiol Spectr 2023; 11:e0090823. [PMID: 37676037 PMCID: PMC10581247 DOI: 10.1128/spectrum.00908-23] [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: 03/01/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.
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Affiliation(s)
- Tjaša Danevčič
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Mihael Spacapan
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Ákos T. Kovács
- Department of Biotechnology and Biomedicine, Bacterial Interactions and Evolution Group, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ines Mandic-Mulec
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
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5
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Liu Y, Štefanič P, Miao Y, Xue Y, Xun W, Zhang N, Shen Q, Zhang R, Xu Z, Mandic-Mulec I. Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study. AMB Express 2022; 12:133. [DOI: 10.1186/s13568-022-01477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractBacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For B. amyloliquefaciens, B. pumilus, and B. megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that the gyrA gene may have broad application prospects in the study of Bacillus ecology.
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Šimunović K, Sahin O, Erega A, Štefanič P, Zhang Q, Mandic Mulec I, Smole Možina S, Klančnik A. Bacillus subtilis PS-216 Spores Supplemented in Broiler Chicken Drinking Water Reduce Campylobacter jejuni Colonization and Increases Weight Gain. Front Microbiol 2022; 13:910616. [PMID: 35875550 PMCID: PMC9304915 DOI: 10.3389/fmicb.2022.910616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is the leading cause of bacterial gastroenteritis, or campylobacteriosis, in humans worldwide, and poultry serves as a major source of infection. To reduce the risk associated with C. jejuni transmission via poultry meat, effective interventions during poultry production are needed, and the use of probiotics is a promising approach. In this study, 15 Bacillus subtilis strains were initially screened for their anti-Campylobacter activities. B. subtilis PS-216 strain demonstrated the best anti-Campylobacter activity against 15 C. jejuni isolates when examined using in vitro co-cultures. To evaluate the suitability of B. subtilis PS-216 for probiotic use, its susceptibility to eight clinically important antimicrobials and simulated gastric conditions was investigated. B. subtilis PS-216 was sensitive to all of the tested antibiotics. Although vegetative cells were sensitive to gastric conditions, B. subtilis PS-216 spores were highly resistant. We further evaluated the use of a B. subtilis PS-216 spore preparation (2.5 × 106 CFU/mL water) to prevent and/or reduce C. jejuni colonization in broiler chickens in vivo. Compared to the untreated group, significantly lower Campylobacter counts were detected in caeca of broilers continuously treated with B. subtilis PS-216 spores in their drinking water. Furthermore, broilers continuously treated with B. subtilis PS-216 spores showed improved weight gain, compared to the control group. Together, these results demonstrate the potential of B. subtilis PS-216 for use in poultry to reduce C. jejuni colonization and improve weight gain.
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Affiliation(s)
- Katarina Šimunović
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Orhan Sahin
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Andi Erega
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Polonca Štefanič
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Qijing Zhang
- Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Ines Mandic Mulec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Anja Klančnik,
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7
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Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
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8
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Refactoring transcription factors for metabolic engineering. Biotechnol Adv 2022; 57:107935. [PMID: 35271945 DOI: 10.1016/j.biotechadv.2022.107935] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 12/19/2022]
Abstract
Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic regulation systems composed of transcription factors have been widely used in metabolic engineering and synthetic biology. This review introduced the categories, action principles, prediction strategies, and related databases of transcription factors. Then, the application of global transcription machinery engineering technology and the transcription factor-based biosensors and quorum sensing systems are overviewed. In addition, strategies for optimizing the transcriptional regulatory tools' performance by refactoring transcription factors are summarized. Finally, the current limitations and prospects of constructing various regulatory tools based on transcription factors are discussed. This review will provide theoretical guidance for the rational design and construction of transcription factor-based metabolic regulation systems.
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9
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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: 155] [Impact Index Per Article: 51.7] [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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10
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Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis. Nat Commun 2021; 12:3457. [PMID: 34103505 PMCID: PMC8187645 DOI: 10.1038/s41467-021-23685-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.
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11
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Zeng Y, Liu H, Zhu T, Han S, Li S. Preparation of Nanomaterial Wettable Powder Formulations of Antagonistic Bacteria from Phellodendron chinense and the Biological Control of Brown Leaf Spot Disease. THE PLANT PATHOLOGY JOURNAL 2021; 37:215-231. [PMID: 34111912 PMCID: PMC8200580 DOI: 10.5423/ppj.oa.02.2021.0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Brown leaf spot disease caused by Nigrospora guilinensis on Phellodendron chinense occurs in a large area in Dayi County, Chengdu City, Sichuan Province, China each year. This outbreak has severely reduced the production of Chinese medicinal plants P. chinense and caused substantial economic losses. The bacterial isolate JKB05 was isolated from the healthy leaves of P. chinense, exhibited antagonistic effects against N. guilinensis and was identified as Bacillus megaterium. The following fermentation medium and conditions improved the inhibitory effect of B. megaterium JKB05 on N. guilinensis: 2% glucose, 0.1% soybean powder, 0.1% KCl, and 0.05% MgSO4; initial concentration 6 × 106 cfu/ml, and a 42-h optimal fermentation time. A composite of 0.1% nano-SiO2 JKB05 improved the thermal stability, acid-base stability and ultraviolet resistance by 16%, 12%, and 38.9%, respectively, and nano-SiO2 was added to the fermentation process. The best formula for the wettable powder was 35% kaolin, 4% polyethylene glycol, 8% Tween, and 2% humic acid. The following quality test results for the wettable powder were obtained: wetting time 87.0 s, suspension rate 80.33%, frequency of microbial contamination 0.08%, pH 7.2, fineness 95.8%, drying loss 1.47%, and storage stability ≥83.5%. A pot experiment revealed that the ability of JKB05 to prevent fungal infections on P. chinense increased considerably and achieved levels of control as high as 94%. The use of nanomaterials significantly improved the ability of biocontrol bacteria to control this disease.
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Affiliation(s)
- Yanling Zeng
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Han Liu
- Ganzi Institute of Forestry Research, Kangding 626001, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
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12
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Albarracín Orio AG, Petras D, Tobares RA, Aksenov AA, Wang M, Juncosa F, Sayago P, Moyano AJ, Dorrestein PC, Smania AM. Fungal-bacterial interaction selects for quorum sensing mutants with increased production of natural antifungal compounds. Commun Biol 2020; 3:670. [PMID: 33184402 PMCID: PMC7661731 DOI: 10.1038/s42003-020-01342-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/07/2020] [Indexed: 01/05/2023] Open
Abstract
Soil microorganisms coexist and interact showing antagonistic or mutualistic behaviors. Here, we show that an environmental strain of Bacillus subtilis undergoes heritable phenotypic variation upon interaction with the soil fungal pathogen Setophoma terrestris (ST). Metabolomics analysis revealed differential profiles in B. subtilis before (pre-ST) and after (post-ST) interacting with the fungus, which paradoxically involved the absence of lipopeptides surfactin and plipastatin and yet acquisition of antifungal activity in post-ST variants. The profile of volatile compounds showed that 2-heptanone and 2-octanone were the most discriminating metabolites present at higher concentrations in post-ST during the interaction process. Both ketones showed strong antifungal activity, which was lost with the addition of exogenous surfactin. Whole-genome analyses indicate that mutations in ComQPXA quorum-sensing system, constituted the genetic bases of post-ST conversion, which rewired B. subtilis metabolism towards the depletion of surfactins and the production of antifungal compounds during its antagonistic interaction with S. terrestris.
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Affiliation(s)
- Andrea G Albarracín Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina.
- Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina.
- CONICET. Universidad Nacional de Córdoba. Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Romina A Tobares
- Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET. Universidad Nacional de Córdoba. Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Florencia Juncosa
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Pamela Sayago
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Alejandro J Moyano
- Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET. Universidad Nacional de Córdoba. Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Andrea M Smania
- Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina.
- CONICET. Universidad Nacional de Córdoba. Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina.
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13
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Balderas-Ruíz KA, Bustos P, Santamaria RI, González V, Cristiano-Fajardo SA, Barrera-Ortíz S, Mezo-Villalobos M, Aranda-Ocampo S, Guevara-García ÁA, Galindo E, Serrano-Carreón L. Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. AMB Express 2020; 10:163. [PMID: 32894363 PMCID: PMC7477031 DOI: 10.1186/s13568-020-01101-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/30/2020] [Indexed: 01/05/2023] Open
Abstract
Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains. ![]()
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14
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Špacapan M, Danevčič T, Štefanic P, Porter M, Stanley-Wall NR, Mandic-Mulec I. The ComX Quorum Sensing Peptide of Bacillus subtilis Affects Biofilm Formation Negatively and Sporulation Positively. Microorganisms 2020; 8:E1131. [PMID: 32727033 PMCID: PMC7463575 DOI: 10.3390/microorganisms8081131] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023] Open
Abstract
Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of Bacillus subtilis as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells. We confirm that ComX positively affects the transcriptional activity of the PepsA promoter, which controls the synthesis of the major matrix polysaccharide. In contrast, ComX negatively controls the PtapA promoter, which drives the production of TasA, a fibrous matrix protein. Overall, the biomass of the mutant biofilm lacking ComX accumulates more monosaccharide and protein content than the wild type. We conclude that this QS phenotype might be due to extended investment into growth rather than spore development. Consistent with this, the ComX deficient mutant shows a delayed activation of the pre-spore specific promoter, PspoIIQ, and a delayed, more synchronous commitment to sporulation. We conclude that ComX mediated early commitment to sporulation of the wild type slows down biofilm formation and modulates the coexistence of multiple biological states during the early stages of biofilm development.
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Affiliation(s)
- Mihael Špacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Polonca Štefanic
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
| | - Michael Porter
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; (M.P.); (N.R.S.-W.)
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia; (M.Š.); (T.D.); (P.Š.)
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15
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Polonca S. Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates. MICROBIAL ECOLOGY 2020; 79:853-864. [PMID: 31707464 DOI: 10.1007/s00248-019-01455-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.
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Affiliation(s)
- Stefanic Polonca
- Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia.
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16
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Thérien M, Kiesewalter HT, Auria E, Charron-Lamoureux V, Wibowo M, Maróti G, Kovács ÁT, Beauregard PB. Surfactin production is not essential for pellicle and root-associated biofilm development of Bacillus subtilis. Biofilm 2020; 2:100021. [PMID: 33447807 PMCID: PMC7798449 DOI: 10.1016/j.bioflm.2020.100021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Secondary metabolites have an important impact on the biocontrol potential of soil-derived microbes. In addition, various microbe-produced chemicals have been suggested to impact the development and phenotypic differentiation of bacteria, including biofilms. The non-ribosomal synthesized lipopeptide of Bacillus subtilis, surfactin, has been described to impact the plant promoting capacity of the bacterium. Here, we investigated the impact of surfactin production on biofilm formation of B. subtilis using the laboratory model systems; pellicle formation at the air-medium interface and architecturally complex colony development, in addition to plant root-associated biofilms. We found that the production of surfactin by B. subtilis is not essential for pellicle biofilm formation neither in the well-studied strain, NCIB 3610, nor in the newly isolated environmental strains, but lack of surfactin reduces colony expansion. Further, plant root colonization was comparable both in the presence or absence of surfactin synthesis. Our results suggest that surfactin-related biocontrol and plant promotion in B. subtilis strains are independent of biofilm formation.
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Affiliation(s)
- Maude Thérien
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Emile Auria
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada.,Biology Department, Ecole Normale Supérieure Paris-Saclay, Paris-Saclay University, Cachan, France
| | - Vincent Charron-Lamoureux
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
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17
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Comparative Genome Assessment of the Two Novel Poly-γ-Glutamic Acid Producing Bacillus Strains. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Silva KPT, Boedicker JQ. A neural network model predicts community-level signaling states in a diverse microbial community. PLoS Comput Biol 2019; 15:e1007166. [PMID: 31233492 PMCID: PMC6611639 DOI: 10.1371/journal.pcbi.1007166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/05/2019] [Accepted: 06/06/2019] [Indexed: 11/19/2022] Open
Abstract
Signal crosstalk within biological communication networks is common, and such crosstalk can have unexpected consequences for decision making in heterogeneous communities of cells. Here we examined crosstalk within a bacterial community composed of five strains of Bacillus subtilis, with each strain producing a variant of the quorum sensing peptide ComX. In isolation, each strain produced one variant of the ComX signal to induce expression of genes associated with bacterial competence. When strains were combined, a mixture of ComX variants was produced resulting in variable levels of gene expression. To examine gene regulation in mixed communities, we implemented a neural network model. Experimental quantification of asymmetric crosstalk between pairs of strains parametrized the model, enabling the accurate prediction of activity within the full five-strain network. Unlike the single strain system in which quorum sensing activated upon exceeding a threshold concentration of the signal, crosstalk within the five-strain community resulted in multiple community-level quorum sensing states, each with a unique combination of quorum sensing activation among the five strains. Quorum sensing activity of the strains within the community was influenced by the combination and ratio of strains as well as community dynamics. The community-level signaling state was altered through an external signal perturbation, and the output state depended on the timing of the perturbation. Given the ubiquity of signal crosstalk in diverse microbial communities, the application of such neural network models will increase accuracy of predicting activity within microbial consortia and enable new strategies for control and design of bacterial signaling networks. Bacteria can communicate with each other using chemical signals to activate genetic expression in a process known as quorum sensing. Quorum sensing in bacteria is known to regulate a number collective behaviors in bacteria such as biofilm formation, antibiotic production and production of virulence factors which leads to bacterial infections. In a community, different species of bacteria can crosstalk using these signals, such that they regulate each other’s quorum sensing activation. Crosstalk can be either excitatory or inhibitory towards quorum sensing activation. Generally, in a bacterial community, it is not straightforward to understand how cells utilize mixtures of quorum sensing signals to regulate quorum sensing activation. To address this issue, we used a neural network approach in which we were able to predict patterns of quorum sensing activation in a diverse community of Bacillus subtilis cells producing five different signals and we observed that quorum sensing activation depended on signal concentration, species ratio and time sensitive external perturbations. Our findings can be useful in systematically controlling quorum sensing and potentially devising better strategies to fight bacterial infections.
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Affiliation(s)
- Kalinga Pavan T. Silva
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
| | - James Q. Boedicker
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, United States of America
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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19
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Kalamara M, Spacapan M, Mandic‐Mulec I, Stanley‐Wall NR. Social behaviours by Bacillus subtilis: quorum sensing, kin discrimination and beyond. Mol Microbiol 2018; 110:863-878. [PMID: 30218468 PMCID: PMC6334282 DOI: 10.1111/mmi.14127] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 12/14/2022]
Abstract
Here, we review the multiple mechanisms that the Gram‐positive bacterium Bacillus subtilis uses to allow it to communicate between cells and establish community structures. The modes of action that are used are highly varied and include routes that sense pheromone levels during quorum sensing and control gene regulation, the intimate coupling of cells via nanotubes to share cytoplasmic contents, and long‐range electrical signalling to couple metabolic processes both within and between biofilms. We explore the ability of B. subtilis to detect ‘kin’ (and ‘cheater cells’) by looking at the mechanisms used to potentially ensure beneficial sharing (or limit exploitation) of extracellular ‘public goods’. Finally, reflecting on the array of methods that a single bacterium has at its disposal to ensure maximal benefit for its progeny, we highlight that a large future challenge will be integrating how these systems interact in mixed‐species communities.
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Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD15EHUK
| | - Mihael Spacapan
- Department of Food Science and Technology, Biotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | - Ines Mandic‐Mulec
- Department of Food Science and Technology, Biotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | - Nicola R. Stanley‐Wall
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD15EHUK
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20
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Santos RM, Kandasamy S, Rigobelo EC. Sugarcane growth and nutrition levels are differentially affected by the application of PGPR and cane waste. Microbiologyopen 2018; 7:e00617. [PMID: 29653035 PMCID: PMC6291826 DOI: 10.1002/mbo3.617] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 11/16/2022] Open
Abstract
Mineral and organic fertilization can be optimized by using rhizobacteria which increases dry matter, yield, and nutrients in the soil and plant, among the other biological inputs. However, the discovery of single microbes or a consortium that can benefit plants has been a challenge. In this context, this study aimed to evaluate the effects of Bacillus subtilis and Bacillus pumilus combined with mineral fertilization and sugar and alcohol industry by‐products in presprouted and the initial growth phase of sugar cane seedlings. The study was carried out in two phases. Phase 1 included presprouted seedlings with T1 = untreated control, T2 = B. subtilis, T3 = B. pumilus, and T4 = B. subtilis + B. pumilus treatments. Phase 2 included the same treatments with four types of fertilization: F1 = mineral fertilization, F2 = mineral fertilization + vinasse, F3 = mineral fertilization + filter cake, and F4 = mineral fertilization + filter cake compost. Of the phase 1 treatments, T2 (B. subtilis) was the best promoter of root growth and the total dry matter compared to the control with an increase of 23.0% compared to the control. In phase 2, B. pumilus application, increased the total dry matter by 13%, the number of tillers by 37%, and the diameter of the tillers by 48% when combined with mineral fertilization. The combined application of B. subtilis and B. pumilus increased the phosphorus content by 13% in soil treated with mineral fertilization and filter cake compost. The results of the this study strongly suggest that the use of B. subtilis and B. pumilus together with these by‐products can improve soil fertility parameters and decrease adverse effects associated with vinasse fertilization, in addition to providing shoot and root growth and providing collective synergy for a high yield of sugarcane production with environmental benefits.
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Affiliation(s)
- Roberta M Santos
- Agricultural and Livestock Microbiology Post - Graduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Saveetha Kandasamy
- A&L Biologicals, Agroecological Research Services Centre, London, ON, Canada
| | - Everlon Cid Rigobelo
- Agricultural and Livestock Microbiology Post - Graduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
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21
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Spacapan M, Danevčič T, Mandic-Mulec I. ComX-Induced Exoproteases Degrade ComX in Bacillus subtilis PS-216. Front Microbiol 2018; 9:105. [PMID: 29449835 PMCID: PMC5799266 DOI: 10.3389/fmicb.2018.00105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Gram-positive bacteria use peptides as auto-inducing (AI) signals to regulate the production of extracellular enzymes (e.g., proteases). ComX is an AI peptide, mostly known for its role in the regulation of bacterial competence and surfactant production in Bacillus subtilis. These two traits are regulated accordingly to the bacterial population size, thus classifying ComX as a quorum sensing signal. ComX also indirectly regulates exoprotease production through the intermediate transcriptional regulator DegQ. We here use this peptide-based AI system (the ComQXPA system) as a model to address exoprotease regulation by ComX in biofilms. We also investigate the potential of ComX regulated proteases to degrade the ComX AI peptide. Results indicate that ComX indeed induces the expression of aprE, the gene for the major serine protease subtilisin, and stimulates overall exoprotease production in biofilms of B. subtilis PS-216 and several other B. subtilis soil isolates. We also provide evidence that these exoproteases can degrade ComX. The ComX biological activity decay is reduced in the spent media of floating biofilms with low proteolytic activity found in the comP and degQ mutants. ComX biological activity decay can be restored by the addition of subtilisin to such media. In contrast, inhibition of metalloproteases by EDTA reduces ComX biological activity decay. This suggests that both serine and metalloproteases, which are induced by ComX, are ultimately capable of degrading this signaling peptide. This work brings novel information on regulation of exoproteases in B. subtilis floating biofilms and reveals that these proteolytic enzymes degrade the AI signaling peptide ComX, which is also a major determinant of their expression in biofilms.
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Affiliation(s)
- Mihael Spacapan
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Danevčič
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Chair of Microbiology, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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22
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Pitzschke A. Molecular dynamics in germinating, endophyte-colonized quinoa seeds. PLANT AND SOIL 2018; 422:135-154. [PMID: 29416180 PMCID: PMC5798591 DOI: 10.1007/s11104-017-3184-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/17/2017] [Indexed: 06/08/2023]
Abstract
AIMS The pseudo-cereal quinoa has an outstanding nutritional value. Seed germination is unusually fast, and plant tolerance to salt stress exceptionally high. Seemingly all seeds harbor bacterial endophytes. This work examines mitogen-activated protein kinase (MAPK) activities during early development. It evaluates possible contribution of endophytes to rapid germination and plant robustness. METHODS MAPK activities were monitored in water- and NaCl-imbibed seeds over a 4-h-period using an immunoblot-based approach. Cellulolytic and pectinolytic abilities of bacteria were assessed biochemically, and cellular movement, biofilm, elicitor and antimicrobial compound synthesis genes sequenced. GyrA-based, cultivation-independent studies provided first insight into endophyte diversity. RESULTS Quinoa seeds and seedlings exhibit remarkably complex and dynamic MAPK activity profiles. Depending on seed origin, variances exist in MAPK patterns and probably also in endophyte assemblages. Mucilage-degrading activities enable endophytes to colonize seed surfaces of a non-host species, chia, without apparent adverse effects. CONCLUSIONS Owing to their motility, cell wall-loosening and elicitor-generating abilities, quinoa endophytes have the potential to drive cell expansion, move across cell walls, generate damage-associated molecular patterns and activate MAPKs in their host. Bacteria may thus facilitate rapid germination and confer a primed state directly upon seed rehydration. Transfer into non-native crops appears both desirable and feasible.
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Affiliation(s)
- Andrea Pitzschke
- Division of Plant Physiology, Department of Cell Biology, University of Salzburg, Hellbrunner Strasse 34, A-5020 Salzburg, Austria
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23
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Abstract
Kin discrimination systems are found in numerous communal contexts like multicellularity and are theorized to prevent exploitation of cooperative behaviors. The kin discrimination system in Bacillus subtilis differs from most other such systems because it excludes nonkin cells rather than including kin cells. Because nonkin are the target of the system, B. subtilis can potentially distinguish degrees of nonkin relatedness, not just kin versus nonkin. We examined this by testing a large strain collection of diverse Bacillus species against B. subtilis in different multicellular contexts. The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin. Species in the less-related pumilus clade started to display varied phenotypes but were mostly still discriminated against, while cereus clade members and beyond were no longer subject to kin discrimination. Seeking a reason why other species are perceived as antagonistic nonkin, we tested the ability of B. subtilis to steal communally produced surfactant from these species. We found that the species treated as nonkin were the only ones that made a surfactant that B. subtilis could utilize and that nonkin antagonism prevented such stealing when the two strains were mixed. The nonkin exclusion kin discrimination method thus allows effective protection of the cooperative behaviors prevalent in multicellularity while still permitting interactions with more distant species that are not a threat. Multicellular systems like bacterial biofilms and swarms rely on cooperative behaviors that could be undermined by exploitative invaders. Discriminating kin from nonkin is one way to help guard against such exploitation but has thus far been examined only intraspecifically, so the phylogenetic range of this important trait is unknown. We tested whether Bacillus subtilis treats other species as nonkin by testing a single strain against a diverse collection of Bacillus isolates. We found that the species in the same clade were treated as nonkin, which then lessened in more distant relatives. Further experiments showed that these nonkin species produced a cooperative good that could be stolen by B. subtilis and that treating each other as nonkin largely prevented this exploitation. These results impact our understanding of interspecies interactions, as bacterial populations can interact only after they have diverged enough to no longer be a threat to their cooperative existences.
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Gallegos-Monterrosa R, Mhatre E, Kovács ÁT. Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium. MICROBIOLOGY-SGM 2016; 162:1922-1932. [PMID: 27655338 DOI: 10.1099/mic.0.000371] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacillus subtilis is an intensively studied Gram-positive bacterium that has become one of the models for biofilm development. B. subtilis 168 is a well-known domesticated strain that has been suggested to be deficient in robust biofilm formation. Moreover, the diversity of available B. subtilis laboratory strains and their derivatives have made it difficult to compare independent studies related to biofilm formation. Here, we analysed numerous 168 stocks from multiple laboratories for their ability to develop biofilms in different set-ups and media. We report a wide variation among the biofilm-forming capabilities of diverse stocks of B. subtilis 168, both in architecturally complex colonies and liquid-air interface pellicles, as well as during plant root colonization. Some 168 variants are indeed unable to develop robust biofilm structures, while others do so as efficiently as the non-domesticated NCIB 3610 strain. In all cases studied, the addition of glucose to the medium dramatically improved biofilm development of the laboratory strains. Furthermore, the expression of biofilm matrix component operons, epsA-O and tapA-sipW-tasA, was monitored during colony biofilm formation. We found a lack of direct correlation between the expression of these genes and the complexity of wrinkles in colony biofilms. However, the presence of a single mutation in the exopolysaccharide-related gene epsC correlates with the ability of the stocks tested to form architecturally complex colonies and pellicles, and to colonize plant roots.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Magno-Pérez-Bryan MC, Martínez-García PM, Hierrezuelo J, Rodríguez-Palenzuela P, Arrebola E, Ramos C, de Vicente A, Pérez-García A, Romero D. Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1102-1116. [PMID: 26035127 DOI: 10.1094/mpmi-02-15-0023-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Bacillus amyloliquefaciens CECT 8237 and CECT 8238, formerly known as Bacillus subtilis UMAF6639 and UMAF6614, respectively, contribute to plant health by facing microbial pathogens or inducing the plant's defense mechanisms. We sequenced their genomes and developed a set of ad hoc scripts that allowed us to search for the features implicated in their beneficial interaction with plants. We define a core set of genes that should ideally be found in any beneficial Bacillus strain, including the production of secondary metabolites, volatile compounds, metabolic plasticity, cell-to-cell communication systems, and biofilm formation. We experimentally prove that some of these genetic elements are active, such as i) the production of known secondary metabolites or ii) acetoin and 2-3-butanediol, compounds that stimulate plant growth and host defense responses. A comparison with other Bacillus genomes permits us to find differences in the cell-to-cell communication system and biofilm formation and to hypothesize variations in their persistence and resistance ability in diverse environmental conditions. In addition, the major protection provided by CECT 8237 and CECT 8238, which is different from other Bacillus strains against bacterial and fungal melon diseases, permits us to propose a correlation with their singular genetic background and determine the need to search for additional blind biocontrol-related features.
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Affiliation(s)
- M C Magno-Pérez-Bryan
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - P M Martínez-García
- 2 Centro de Biotecnología y Genómica de Plantas UPM-INIA (CBGP), Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- 3 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Universidad de Málaga
| | - J Hierrezuelo
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - P Rodríguez-Palenzuela
- 2 Centro de Biotecnología y Genómica de Plantas UPM-INIA (CBGP), Parque Científico y Tecnológico de la Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - E Arrebola
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - C Ramos
- 3 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Universidad de Málaga
| | - A de Vicente
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - A Pérez-García
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - D Romero
- 1 Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
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