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Seručnik M, Dogsa I, Zadravec LJ, Mandic-Mulec I, Žnidaršič-Plazl P. Development of a Microbioreactor for Bacillus subtilis Biofilm Cultivation. MICROMACHINES 2024; 15:1037. [PMID: 39203688 PMCID: PMC11356062 DOI: 10.3390/mi15081037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024]
Abstract
To improve our understanding of Bacillus subtilis growth and biofilm formation under different environmental conditions, two versions of a microfluidic reactor with two channels separated by a polydimethylsiloxane (PDMS) membrane were developed. The gas phase was introduced into the channel above the membrane, and oxygen transfer from the gas phase through the membrane was assessed by measuring the dissolved oxygen concentration in the liquid phase using a miniaturized optical sensor and oxygen-sensitive nanoparticles. B. subtilis biofilm formation was monitored in the growth channels of the microbioreactors, which were designed in two shapes: one with circular extensions and one without. The volumes of these microbioreactors were (17 ± 4) μL for the reactors without extensions and (28 ± 4) μL for those with extensions. The effect of microbioreactor geometry and aeration on B. subtilis biofilm growth was evaluated by digital image analysis. In both microbioreactor geometries, stable B. subtilis biofilm formation was achieved after 72 h of incubation at a growth medium flow rate of 1 μL/min. The amount of oxygen significantly influenced biofilm formation. When the culture was cultivated with a continuous air supply, biofilm surface coverage and biomass concentration were higher than in cultivations without aeration or with a 100% oxygen supply. The channel geometry with circular extensions did not lead to a higher total biomass in the microbioreactor compared to the geometry without extensions.
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Affiliation(s)
- Mojca Seručnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; (M.S.); (L.J.Z.)
| | - Iztok Dogsa
- Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia; (I.D.); (I.M.-M.)
| | - Lan Julij Zadravec
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; (M.S.); (L.J.Z.)
| | - Ines Mandic-Mulec
- Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia; (I.D.); (I.M.-M.)
- Chair of Micro Process Engineering and Technology—COMPETE, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Polona Žnidaršič-Plazl
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia; (M.S.); (L.J.Z.)
- Chair of Micro Process Engineering and Technology—COMPETE, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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Hu Y, Yang X, Tai B, Wang G, Zhang X, Yin Y, Xing F. Bacillus amyloliquefaciens A-1 inhibiting fungal spoilage in agricultural products is improved by metabolic engineering of enhancing surfactin yield. Food Res Int 2024; 175:113752. [PMID: 38129052 DOI: 10.1016/j.foodres.2023.113752] [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: 07/25/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Fungi and subsequent mycotoxins contamination in agricultural products have caused enormous losses and great harm to human and animal health. Biological control has attracted the attention of researchers due to its advantages, including mild conditions, low cost, high efficiency and low nutrient loss. In this study, a newly isolated strain Bacillus amyloliquefaciens A-1 (A-1), was screened for its ability to inhibit the growth and Aflatoxin B1 (AFB1) production of Aspergillus flavus NRRL 3357. Electron microscopy results revealed that mycelium and conidia of A. flavus were destroyed by A-1, affecting hyphae, cell walls, cell membranes and organelles. RNA-seq analysis indicated disturbance in gene expression profiles of A. flavus, including amino acid degradation and starch and sucrose metabolism pathways. Importantly, the biosynthesis of AFB1 was significantly inhibited by the down-regulation of key regulatory genes, aflR and aflS, and the simultaneous down-regulation of most structural genes. Genome analysis predicted six secondary metabolites biosynthetic gene clusters. Then, four surfactin synthesized by cluster C were identified as the main active substance of A-1 using HPLC-Q-TOF-MS. The addition of alanine, threonine, Fe2+ increased surfactin production. Notably, the overexpression of comX also improved surfactin production. The vivo test results indicated that A-1 could significantly inhibit the decay of pear by Aspergillus westerdijkiae, and the mildew of maize and peanuts. Especially, the overexpression of comX in A-1 could enhance the inhibitory activity. In conclusion, the inhibition mechanism of A-1 was revealed, and comX was found can improve the production of surfactin and subsequent activities, which provides the scientific basis for the development of biocontrol agents to reduce spoilage in agricultural products.
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Affiliation(s)
- Yafan Hu
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xu Yang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Bowen Tai
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Gang Wang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Xinlong Zhang
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Yixuan Yin
- Shandong Xinfurui Agricultural Science and Technology Co., Ltd. Liaocheng 252000, PR China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs / Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Xia L, Wen J. Available strategies for improving the biosynthesis of surfactin: a review. Crit Rev Biotechnol 2023; 43:1111-1128. [PMID: 36001039 DOI: 10.1080/07388551.2022.2095252] [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: 01/04/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022]
Abstract
Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.
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Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of 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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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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Qi X, Liu W, He X, Du C. A review on surfactin: molecular regulation of biosynthesis. Arch Microbiol 2023; 205:313. [PMID: 37603063 DOI: 10.1007/s00203-023-03652-3] [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: 06/13/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Surfactin has many biological activities, such as inhibiting plant diseases, resisting bacteria, fungi, viruses, tumors, mycoplasma, anti-adhesion, etc. It has great application potential in agricultural biological control, clinical medical treatment, environmental treatment and other fields. However, the low yield has been the bottleneck of its popularization and application. It is very important to understand the synthesis route and control strategy of surfactin to improve its yield and purity. In this paper, based on the biosynthetic pathway and regulatory factors of surfactin, its biosynthesis regulation strategy was comprehensively summarized, involving enhancement of endogenous and exogenous precursor supply, modification of the synthesis pathway of lipid chain and peptide chain, improvement of secretion and efflux, and manipulation some global regulatory factors, such as Spo0A, AbrB, ComQXP, phrCSF, etc. to directly or indirectly stimulate surfactin synthesis. And the current production and separation and purification process of surfactin are briefly described. This review also provides a scientific reference for promoting surfactin production and its applications in various fields.
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Affiliation(s)
- Xiaohua Qi
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region and Key Laboratory of Microbiology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Wei Liu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region and Key Laboratory of Microbiology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Xin He
- Hebei University of Environmental Engineering, Hebei Key Laboratory of Agroecological Safety, Qinhuangdao, 066102, China
| | - Chunmei Du
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education and Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region and Key Laboratory of Microbiology, College of Heilongjiang Province and School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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7
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Echlin M, Aguilar B, Shmulevich I. Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. ENTROPY (BASEL, SWITZERLAND) 2023; 25:319. [PMID: 36832685 PMCID: PMC9955575 DOI: 10.3390/e25020319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/29/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Communication between cells enables the coordination that drives structural and functional complexity in biological systems. Both single and multicellular organisms have evolved diverse communication systems for a range of purposes, including synchronization of behavior, division of labor, and spatial organization. Synthetic systems are also increasingly being engineered to utilize cell-cell communication. While research has elucidated the form and function of cell-cell communication in many biological systems, our knowledge is still limited by the confounding effects of other biological phenomena at play and the bias of the evolutionary background. In this work, our goal is to push forward the context-free understanding of what impact cell-cell communication can have on cellular and population behavior to more fully understand the extent to which cell-cell communication systems can be utilized, modified, and engineered. We use an in silico model of 3D multiscale cellular populations, with dynamic intracellular networks interacting via diffusible signals. We focus on two key communication parameters: the effective interaction distance at which cells are able to interact and the receptor activation threshold. We found that cell-cell communication can be divided into six different forms along the parameter axes, three asocial and three social. We also show that cellular behavior, tissue composition, and tissue diversity are all highly sensitive to both the general form and specific parameters of communication even when the cellular network has not been biased towards that behavior.
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Affiliation(s)
- Moriah Echlin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Boris Aguilar
- Institute for Systems Biology, Seattle, WA 98109, USA
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The Antibacterial Type VII Secretion System of Bacillus subtilis: Structure and Interactions of the Pseudokinase YukC/EssB. mBio 2022; 13:e0013422. [PMID: 36154281 PMCID: PMC9600267 DOI: 10.1128/mbio.00134-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Type VIIb secretion systems (T7SSb) were recently proposed to mediate different aspects of Firmicutes physiology, including bacterial pathogenicity and competition. However, their architecture and mechanism of action remain largely obscure. Here, we present a detailed analysis of the T7SSb-mediated bacterial competition in Bacillus subtilis, using the effector YxiD as a model for the LXG secreted toxins. By systematically investigating protein-protein interactions, we reveal that the membrane subunit YukC contacts all T7SSb components, including the WXG100 substrate YukE and the LXG effector YxiD. YukC’s crystal structure shows unique features, suggesting an intrinsic flexibility that is required for T7SSb antibacterial activity. Overall, our results shed light on the role and molecular organization of the T7SSb and demonstrate the potential of B. subtilis as a model system for extensive structure-function studies of these secretion machineries.
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Wang S, Wang R, Zhao X, Ma G, Liu N, Zheng Y, Tan J, Qi G. Systemically engineering Bacillus amyloliquefaciens for increasing its antifungal activity and green antifungal lipopeptides production. Front Bioeng Biotechnol 2022; 10:961535. [PMID: 36159666 PMCID: PMC9490133 DOI: 10.3389/fbioe.2022.961535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/17/2022] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of antifungal lipopeptides iturin and fengycin has attracted broad interest; however, there is a bottleneck in its low yield in wild strains. Because the key metabolic mechanisms in the lipopeptides synthesis pathway remain unclear, genetic engineering approaches are all ending up with a single or a few gene modifications. The aim of this study is to develop a systematic engineering approach to improve the antifungal activity and biosynthesis of iturin and fengycin in Bacillus amyloliquefaciens. First, blocking the carbon overflow metabolic pathway to increase precursor supply of the branched-chain amino acids by knockout of bdh, disrupting sporulation to extend the stage for producing antifungal lipopeptides by deletion of kinA, blocking of siderophore synthesis to enhance the availability of amino acids and fatty acids by deletion of dhbF, and increasing Spo0A∼P by deletion of rapA, could improve the antifungal activity by 24%, 10%, 13% and 18%, respectively. Second, the double knockout strain ΔbdhΔkinA, triple knockout strain ΔbdhΔkinAΔdhbF and quadruple knockout strain ΔkinAΔbdhΔdhbFΔrapA could improve the antifungal activity by 38%, 44% and 53%, respectively. Finally, overexpression of sfp in ΔkinAΔbdhΔdhbFΔrapA further increased the antifungal activity by 65%. After purifying iturin and fengycin as standards for quantitative analysis of lipopeptides, we found the iturin titer was 17.0 mg/L in the final engineered strain, which was 3.2-fold of the original strain. After fermentation optimization, the titer of iturin and fengycin reached 31.1 mg/L and 175.3 mg/L in flask, and 123.5 mg/L and 1200.8 mg/L in bioreactor. Compared to the original strain, the iturin and fengycin titer in bioreactor increased by 22.8-fold and 15.9-fold in the final engineered strain, respectively. This study may pave the way for the commercial production of green antifungal lipopeptides, and is also favorable for understanding the regulatory and biosynthetic mechanism of iturin and fengycin.
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Affiliation(s)
- Susheng Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Wang
- Enshi Tobacco Technology Center, Enshi City, Hubei, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gaoqiang Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Na Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuqing Zheng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Tan
- Enshi Tobacco Technology Center, Enshi City, Hubei, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- *Correspondence: Gaofu Qi,
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Abdul Hamid NW, Nadarajah K. Microbe Related Chemical Signalling and Its Application in Agriculture. Int J Mol Sci 2022; 23:ijms23168998. [PMID: 36012261 PMCID: PMC9409198 DOI: 10.3390/ijms23168998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.
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Jakab Á, Kovács F, Balla N, Tóth Z, Ragyák Á, Sajtos Z, Csillag K, Nagy-Köteles C, Nemes D, Bácskay I, Pócsi I, Majoros L, Kovács ÁT, Kovács R. Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans. Biomed Pharmacother 2022; 152:113220. [PMID: 35671583 DOI: 10.1016/j.biopha.2022.113220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022] Open
Abstract
Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production was increased following 2 h of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, ethanol and fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy.
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Affiliation(s)
- Ágnes Jakab
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary; Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Noémi Balla
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Tóth
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Ágota Ragyák
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary; Department of Inorganic and Analytical Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Debrecen, Hungary
| | - Zsófi Sajtos
- Department of Inorganic and Analytical Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Debrecen, Hungary
| | - Kinga Csillag
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Csaba Nagy-Köteles
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Dániel Nemes
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Ildikó Bácskay
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Majoros
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary.
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12
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Mitra S, Dhar R, Sen R. Designer bacterial cell factories for improved production of commercially valuable non-ribosomal peptides. Biotechnol Adv 2022; 60:108023. [PMID: 35872292 DOI: 10.1016/j.biotechadv.2022.108023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Non-ribosomal peptides have gained significant attention as secondary metabolites of high commercial importance. This group houses a diverse range of bioactive compounds, ranging from biosurfactants to antimicrobial and cytotoxic agents. However, low yield of synthesis by bacteria and excessive losses during purification hinders the industrial-scale production of non-ribosomal peptides, and subsequently limits their widespread applicability. While isolation of efficient producer strains and optimization of bioprocesses have been extensively used to enhance yield, further improvement can be made by optimization of the microbial strain using the tools and techniques of metabolic engineering, synthetic biology, systems biology, and adaptive laboratory evolution. These techniques, which directly target the genome of producer strains, aim to redirect carbon and nitrogen fluxes of the metabolic network towards the desired product, bypass the feedback inhibition and repression mechanisms that limit the maximum productivity of the strain, and even extend the substrate range of the cell for synthesis of the target product. The present review takes a comprehensive look into the biosynthesis of bacterial NRPs, how the same is regulated by the cell, and dives deep into the strategies that have been undertaken for enhancing the yield of NRPs, while also providing a perspective on other potential strategies that can allow for further yield improvement. Furthermore, this review provides the reader with a holistic perspective on the design of cellular factories of NRP production, starting from general techniques performed in the laboratory to the computational techniques that help a biochemical engineer model and subsequently strategize the architectural plan.
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Affiliation(s)
- Sayak Mitra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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13
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Qin Y, Angelini LL, Chai Y. Bacillus subtilis Cell Differentiation, Biofilm Formation and Environmental Prevalence. Microorganisms 2022; 10:microorganisms10061108. [PMID: 35744626 PMCID: PMC9227780 DOI: 10.3390/microorganisms10061108] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling, spore-forming Gram-positive bacterium capable of cell differentiation. For decades, B. subtilis has been used as a model organism to study development of specialized cell types. In this minireview, we discuss cell differentiation in B. subtilis, covering both past research and recent progresses, and the role of cell differentiation in biofilm formation and prevalence of this bacterium in the environment. We review B. subtilis as a classic model for studies of endospore formation, and highlight more recent investigations on cell fate determination and generation of multiple cell types during biofilm formation. We present mechanistic details of how cell fate determination and mutually exclusive cell differentiation are regulated during biofilm formation.
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Affiliation(s)
- Yuxuan Qin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Q.); (Y.C.)
| | | | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA 02115, USA;
- Correspondence: (Y.Q.); (Y.C.)
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14
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Nephali L, Steenkamp P, Burgess K, Huyser J, Brand M, van der Hooft JJJ, Tugizimana F. Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Bacillus Strains. FRONTIERS IN PLANT SCIENCE 2022; 13:920963. [PMID: 35755693 PMCID: PMC9218640 DOI: 10.3389/fpls.2022.920963] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/18/2022] [Indexed: 05/17/2023]
Abstract
Beneficial soil microbes like plant growth-promoting rhizobacteria (PGPR) significantly contribute to plant growth and development through various mechanisms activated by plant-PGPR interactions. However, a complete understanding of the biochemistry of the PGPR and microbial intraspecific interactions within the consortia is still enigmatic. Such complexities constrain the design and use of PGPR formulations for sustainable agriculture. Therefore, we report the application of mass spectrometry (MS)-based untargeted metabolomics and molecular networking (MN) to interrogate and profile the intracellular chemical space of PGPR Bacillus strains: B. laterosporus, B. amyloliquefaciens, B. licheniformis 1001, and B. licheniformis M017 and their consortium. The results revealed differential and diverse chemistries in the four Bacillus strains when grown separately, and also differing from when grown as a consortium. MolNetEnhancer networks revealed 11 differential molecular families that are comprised of lipids and lipid-like molecules, benzenoids, nucleotide-like molecules, and organic acids and derivatives. Consortium and B. amyloliquefaciens metabolite profiles were characterized by the high abundance of surfactins, whereas B. licheniformis strains were characterized by the unique presence of lichenysins. Thus, this work, applying metabolome mining tools, maps the microbial chemical space of isolates and their consortium, thus providing valuable insights into molecular information of microbial systems. Such fundamental knowledge is essential for the innovative design and use of PGPR-based biostimulants.
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Affiliation(s)
- Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Karl Burgess
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Margaretha Brand
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Justin J. J. van der Hooft
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
- *Correspondence: Justin J. J. van der Hooft,
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
- Fidele Tugizimana,
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15
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Abstract
Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.
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16
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Umar A, Zafar A, Wali H, Siddique MP, Qazi MA, Naeem AH, Malik ZA, Ahmed S. Low-cost production and application of lipopeptide for bioremediation and plant growth by Bacillus subtilis SNW3. AMB Express 2021; 11:165. [PMID: 34894306 PMCID: PMC8665955 DOI: 10.1186/s13568-021-01327-0] [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: 09/22/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
At present time, every nation is absolutely concern about increasing agricultural production and bioremediation of petroleum-contaminated soil. Hence, with this intention in the current study potent natural surfactants characterized as lipopeptides were evaluated for low-cost production by Bacillus subtilis SNW3, previously isolated from the Fimkessar oil field, Chakwal Pakistan. The significant results were obtained by using substrates in combination (white beans powder (6% w/v) + waste frying oil (1.5% w/v) and (0.1% w/v) urea) with lipopeptides yield of about 1.17 g/L contributing 99% reduction in cost required for medium preparation. To the best of our knowledge, no single report is presently describing lipopeptide production by Bacillus subtilis using white beans powder as a culture medium. Additionally, produced lipopeptides display great physicochemical properties of surface tension reduction value (SFT = 28.8 mN/m), significant oil displacement activity (ODA = 4.9 cm), excessive emulsification ability (E24 = 69.8%), and attains critical micelle concentration (CMC) value at 0.58 mg/mL. Furthermore, biosurfactants produced exhibit excellent stability over an extensive range of pH (1-11), salinity (1-8%), temperature (20-121°C), and even after autoclaving. Subsequently, produced lipopeptides are proved suitable for bioremediation of crude oil (86%) and as potent plant growth-promoting agent that significantly (P < 0.05) increase seed germination and plant growth promotion of chili pepper, lettuce, tomato, and pea maximum at a concentration of (0.7 g/100 mL), showed as a potential agent for agriculture and bioremediation processes by lowering economic and environmental stress.
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17
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Maan H, Povolotsky TL, Porat Z, Itkin M, Malitsky S, Kolodkin-Gal I. Imaging flow cytometry reveals a dual role for exopolysaccharides in biofilms: To promote self-adhesion while repelling non-self-community members. Comput Struct Biotechnol J 2021; 20:15-25. [PMID: 34976308 PMCID: PMC8666610 DOI: 10.1016/j.csbj.2021.11.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
In nature, bacteria frequently reside in differentiated communities or biofilms. These multicellular communities are held together by self-produced polymers that allow the community members to adhere to the surface as well as to neighbor bacteria. Here, we report that exopolysaccharides prevent Bacillus subtilis from co-aggregating with a distantly related bacterium Bacillus mycoides, while maintaining their role in promoting self-adhesion and co-adhesion with phylogenetically related bacterium, Bacillus atrophaeus. The defensive role of the exopolysaccharides is due to the specific regulation of bacillaene. Single cell analysis of biofilm and free-living bacterial cells using imaging flow cytometry confirmed a specific role for the exopolysaccharides in microbial competition repelling B. mycoides. Unlike exopolysaccharides, the matrix protein TasA induced bacillaene but inhibited the expression of the biosynthetic clusters for surfactin, and therefore its overall effect on microbial competition during floating biofilm formation was neutral. Thus, the exopolysaccharides provide a dual fitness advantage for biofilm-forming cells, as it acts to promote co-aggregation of related species, as well as, a secreted cue for chemical interference with non-compatible partners. These results experimentally demonstrate a general assembly principle of complex communities and provides an appealing explanation for how closely related species are favored during community assembly. Furthermore, the differential regulation of surfactin and bacillaene by the extracellular matrix may explain the spatio-temporal gradients of antibiotic production within biofilms.
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Affiliation(s)
- Harsh Maan
- 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
| | - Maxim Itkin
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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18
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Rahman FB, Sarkar B, Moni R, Rahman MS. Molecular genetics of surfactin and its effects on different sub-populations of Bacillus subtilis. ACTA ACUST UNITED AC 2021; 32:e00686. [PMID: 34786355 PMCID: PMC8578018 DOI: 10.1016/j.btre.2021.e00686] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/28/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022]
Abstract
Insight into the role of surfactin on B. subtilis cell differentiation. Insight into the molecular genetics of surfactin and its production. Graphical presentation of surfactin mediated signaling cascades via quorum sensing.
Surfactin is a biosurfactant produced by Bacillus subtilis. The srfA operon, Sfp gene, and two quorum sensing systems are required for its production. The master regulator spo0A also plays an indispensable role in proper surfactin synthesis. Upon production, surfactin itself acts as a signaling molecule and triggers the activation of Spo0A gene which in turn regulates cell differentiation. Interestingly, surfactin producing cells are immune to the action of surfactin but trigger other cells to differentiate into non-motile cells, matrix producing cells, cannibals, and spores. In case of competent cell differentiation, comS, which resides within the srfA operon, is co-expressed along with surfactin and plays a vital role in competent cell differentiation in response to quorum sensing signal. Surfactin inhibits the motility of certain cell subpopulations, although it helps the non-motile cells to swarm. Thus, surfactin plays significant roles in the differentiation of different subpopulations of specialized cell types of B. subtilis.
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Affiliation(s)
- Faisal Bin Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
- Wazed Miah Science Research Center (WMSRC), Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Ripa Moni
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mohammad Shahedur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
- Wazed Miah Science Research Center (WMSRC), Jahangirnagar University, Savar, Dhaka, Bangladesh
- Corresponding author.
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19
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Surfactin Stimulated by Pectin Molecular Patterns and Root Exudates Acts as a Key Driver of the Bacillus-Plant Mutualistic Interaction. mBio 2021; 12:e0177421. [PMID: 34724831 PMCID: PMC8561381 DOI: 10.1128/mbio.01774-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bacillus velezensis is considered as a model species belonging to the so-called Bacillus subtilis complex that evolved typically to dwell in the soil rhizosphere niche and establish an intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved a polymer-sensing system to perceive their host and that, in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favored upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility, and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues coproduced in planta and forms mainly variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. IMPORTANCE Within the plant-associated microbiome, some bacterial species are of particular interest due to the disease protective effect they provide via direct pathogen suppression and/or stimulation of host immunity. While these biocontrol mechanisms are quite well characterized, we still poorly understand the molecular basis of the cross talk these beneficial bacteria initiate with their host. Here, we show that the model species Bacillus velezensis stimulates the production of the surfactin lipopeptide upon sensing pectin as a cell surface molecular pattern and upon feeding on root exudates. Surfactin favors bacterial rhizosphere fitness on one hand and primes the plant immune system on the other hand. Our data therefore illustrate how both partners use this multifunctional compound as a unique shared good to sustain a mutualistic interaction.
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20
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Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
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Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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21
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Luo C, Liu J, Bilal M, Liu X, Wang X, Dong F, Liu Y, Zang S, Yin X, Yang X, Zhu T, Zhang S, Zhang W, Li B. Extracellular lipopeptide bacillomycin L regulates serial expression of genes for modulating multicellular behavior in Bacillus velezensis Bs916. Appl Microbiol Biotechnol 2021; 105:6853-6870. [PMID: 34477941 DOI: 10.1007/s00253-021-11524-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
In wild strains of Bacillus, a handful of extracellular natural products act as signals that can regulate multicellular behavior, but relatively little is known about molecular mechanisms' detail. We proposed a previously unreported molecular mechanism for triggering multicellularity in B. velezensis Bs916 by an endogenous cyclic lipopeptide, bacillomycin L. The genome-wide effect on gene expression was caused by the disruption of bacillomycin L gene cluster, and 100 µg/mL bacillomycin L was revealed by quantitative transcriptomics. A total of 878 differentially expressed genes among Bs916, Δbl, and Δbl + 100BL were identified and grouped into 9 functional categories. The transcription levels of 40 candidate genes were further evaluated by RT-qPCR analysis. The expression of eight candidate genes regulated by bacillomycin L in a dose-dependent manner was revealed by LacZ fusion experiment. Although the addition of bacillomycin L could not completely restore the expression levels of the differentially regulated genes in △bl, our results strongly suggest that bacillomycin L acts as a tuning signal of swarming motility and complex biofilm formation by indirectly regulating the expression levels of some two-component systems (TCSs) connector genes, particularly including several Raps that potentially regulate the phosphorylation levels of three major regulators ComA, DegU, and Spo0A.Key points• Proposed model for bacillomycin L regulation in B. velezensis Bs916.• Bacillomycin L can act as an extracellular signal to regulate the phosphorylation levels of three major regulators, ComA, DegU, and Spo0A and control the multicellular processes of vegetative growth, competent, motility, matrix production, sporulation, and autolysis.
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Affiliation(s)
- Chuping Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Jiachen Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Muhammad Bilal
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xuehui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaohua Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Fei Dong
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Yuan Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China.,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shanshan Zang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiulian Yin
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xueting Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tao Zhu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Shuangyu Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Weifeng Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Bin Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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22
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van Gestel J, Wagner A. Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation. PLoS Biol 2021; 19:e3001250. [PMID: 33983920 PMCID: PMC8148357 DOI: 10.1371/journal.pbio.3001250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/25/2021] [Accepted: 04/28/2021] [Indexed: 12/20/2022] Open
Abstract
The repeated evolution of multicellularity led to a wide diversity of organisms, many of which are sessile, including land plants, many fungi, and colonial animals. Sessile organisms adhere to a surface for most of their lives, where they grow and compete for space. Despite the prevalence of surface-associated multicellularity, little is known about its evolutionary origin. Here, we introduce a novel theoretical approach, based on spatial lineage tracking of cells, to study this origin. We show that multicellularity can rapidly evolve from two widespread cellular properties: cell adhesion and the regulatory control of adhesion. By evolving adhesion, cells attach to a surface, where they spontaneously give rise to primitive cell collectives that differ in size, life span, and mode of propagation. Selection in favor of large collectives increases the fraction of adhesive cells until a surface becomes fully occupied. Through kin recognition, collectives then evolve a central-peripheral polarity in cell adhesion that supports a division of labor between cells and profoundly impacts growth. Despite this spatial organization, nascent collectives remain cryptic, lack well-defined boundaries, and would require experimental lineage tracking technologies for their identification. Our results suggest that cryptic multicellularity could readily evolve and originate well before multicellular individuals become morphologically evident.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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23
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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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Théatre A, Cano-Prieto C, Bartolini M, Laurin Y, Deleu M, Niehren J, Fida T, Gerbinet S, Alanjary M, Medema MH, Léonard A, Lins L, Arabolaza A, Gramajo H, Gross H, Jacques P. The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range. Front Bioeng Biotechnol 2021; 9:623701. [PMID: 33738277 PMCID: PMC7960918 DOI: 10.3389/fbioe.2021.623701] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Surfactin is a lipoheptapeptide produced by several Bacillus species and identified for the first time in 1969. At first, the biosynthesis of this remarkable biosurfactant was described in this review. The peptide moiety of the surfactin is synthesized using huge multienzymatic proteins called NonRibosomal Peptide Synthetases. This mechanism is responsible for the peptide biodiversity of the members of the surfactin family. In addition, on the fatty acid side, fifteen different isoforms (from C12 to C17) can be incorporated so increasing the number of the surfactin-like biomolecules. The review also highlights the last development in metabolic modeling and engineering and in synthetic biology to direct surfactin biosynthesis but also to generate novel derivatives. This large set of different biomolecules leads to a broad spectrum of physico-chemical properties and biological activities. The last parts of the review summarized the numerous studies related to the production processes optimization as well as the approaches developed to increase the surfactin productivity of Bacillus cells taking into account the different steps of its biosynthesis from gene transcription to surfactin degradation in the culture medium.
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Affiliation(s)
- Ariane Théatre
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, Gembloux, Belgium
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Marco Bartolini
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Yoann Laurin
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium.,Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, France
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Joachim Niehren
- Inria Lille, and BioComputing Team of CRISTAL Lab (CNRS UMR 9189), Lille, France
| | - Tarik Fida
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Saïcha Gerbinet
- Chemical Engineering, Products, Environment, and Processes, University of Liège, Liège, Belgium
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Angélique Léonard
- Chemical Engineering, Products, Environment, and Processes, University of Liège, Liège, Belgium
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Ana Arabolaza
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Philippe Jacques
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Joint Research Unit BioEcoAgro, UMRt 1158, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, Gembloux, Belgium
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25
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Peptide signaling without feedback in signal production operates as a true quorum sensing communication system in Bacillus subtilis. Commun Biol 2021; 4:58. [PMID: 33420264 PMCID: PMC7794433 DOI: 10.1038/s42003-020-01553-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial quorum sensing (QS) is based on signal molecules (SM), which increase in concentration with cell density. At critical SM concentration, a variety of adaptive genes sharply change their expression from basic level to maximum level. In general, this sharp transition, a hallmark of true QS, requires an SM dependent positive feedback loop, where SM enhances its own production. Some communication systems, like the peptide SM-based ComQXPA communication system of Bacillus subtilis, do not have this feedback loop and we do not understand how and if the sharp transition in gene expression is achieved. Based on experiments and mathematical modeling, we observed that the SM peptide ComX encodes the information about cell density, specific cell growth rate, and even oxygen concentration, which ensure power-law increase in SM production. This enables together with the cooperative response to SM (ComX) a sharp transition in gene expression level and this without the SM dependent feedback loop. Due to its ultra-sensitive nature, the ComQXPA can operate at SM concentrations that are 100-1000 times lower than typically found in other QS systems, thereby substantially reducing the total metabolic cost of otherwise expensive ComX peptide.
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26
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Kuchina A, Brettner LM, Paleologu L, Roco CM, Rosenberg AB, Carignano A, Kibler R, Hirano M, DePaolo RW, Seelig G. Microbial single-cell RNA sequencing by split-pool barcoding. Science 2020; 371:science.aba5257. [PMID: 33335020 DOI: 10.1126/science.aba5257] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/08/2020] [Indexed: 12/16/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.
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Affiliation(s)
- Anna Kuchina
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Leandra M Brettner
- Department of Bioengineering, University of Washington, Seattle, WA, USA.,Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Luana Paleologu
- Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Biology, University of Washington, Seattle, WA, USA
| | - Charles M Roco
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Alexander B Rosenberg
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Alberto Carignano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Ryan Kibler
- Biological Physics, Structure, and Design, University of Washington, Seattle, WA, USA
| | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - R William DePaolo
- Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Gastroenterology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA. .,Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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28
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Fazle Rabbee M, Baek KH. Antimicrobial Activities of Lipopeptides and Polyketides of Bacillus velezensis for Agricultural Applications. Molecules 2020; 25:molecules25214973. [PMID: 33121115 PMCID: PMC7662345 DOI: 10.3390/molecules25214973] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of penicillin, bacteria are known to be major sources of secondary metabolites that can function as drugs or pesticides. Scientists worldwide attempted to isolate novel compounds from microorganisms; however, only less than 1% of all existing microorganisms have been successfully identified or characterized till now. Despite the limitations and gaps in knowledge, in recent years, many Bacillus velezensis isolates were identified to harbor a large number of biosynthetic gene clusters encoding gene products for the production of secondary metabolites. These chemically diverse bioactive metabolites could serve as a repository for novel drug discovery. More specifically, current projects on whole-genome sequencing of B. velezensis identified a large number of biosynthetic gene clusters that encode enzymes for the synthesis of numerous antimicrobial compounds, including lipopeptides and polyketides; nevertheless, their biological applications are yet to be identified or established. In this review, we discuss the recent research on synthesis of bioactive compounds by B. velezensis and related Bacillus species, their chemical structures, bioactive gene clusters of interest, as well as their biological applications for effective plant disease management.
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29
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Negative Interplay between Biofilm Formation and Competence in the Environmental Strains of Bacillus subtilis. mSystems 2020; 5:5/5/e00539-20. [PMID: 32873610 PMCID: PMC7470987 DOI: 10.1128/msystems.00539-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilisin situ during biofilm formation, we reveal that robust biofilm formation often greatly reduces the frequency of competent cells within the biofilm. We then characterize a cross-pathway regulation that allows cells in these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm. Environmental strains of the soil bacterium Bacillus subtilis have valuable applications in agriculture, industry, and biotechnology; however, environmental strains are genetically less accessible. This reduced accessibility is in sharp contrast to laboratory strains, which are well known for their natural competence, and a limitation in their applications. In this study, we observed that robust biofilm formation by environmental strains of B. subtilis greatly reduced the frequency of competent cells in the biofilm. By using model strain 3610, we revealed a cross-pathway regulation that allows biofilm matrix producers and competence-developing cells to undergo mutually exclusive cell differentiation. We further demonstrated that the competence activator ComK represses the key biofilm regulatory gene sinI by directly binding to the sinI promoter, thus blocking competent cells from simultaneously becoming matrix producers. In parallel, the biofilm activator SlrR represses competence through three distinct mechanisms involving both genetic regulation and cell morphological changes. Finally, we discuss the potential implications of limiting competence in a bacterial biofilm. IMPORTANCE The soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilisin situ during biofilm formation, we reveal that robust biofilm formation often greatly reduces the frequency of competent cells within the biofilm. We then characterize a cross-pathway regulation that allows cells in these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm.
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30
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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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31
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Chen B, Wen J, Zhao X, Ding J, Qi G. Surfactin: A Quorum-Sensing Signal Molecule to Relieve CCR in Bacillus amyloliquefaciens. Front Microbiol 2020; 11:631. [PMID: 32425896 PMCID: PMC7203447 DOI: 10.3389/fmicb.2020.00631] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
Bacillus utilize preferred sugars such as glucose over other carbon sources due to carbon catabolite repression (CCR). Surfactin is a small signal molecule to regulate the quorum-sensing (QS) response such as biofilm formation and sporulation in B. subtilis. Here, the srfA operon for synthesis of surfactin was mutated for disrupting the production of surfactin in B. amyloliquefaciens. The srfA-mutant strain showed a defective biofilm and sporulation but could be restored by addition with surfactin, indicating that surfactin is a QS signal molecule in B. amyloliquefaciens. Unexpectedly, mutation of srfA also led to the cells' death although nutrients were still enough to support the bacterial growth during this period. Analysis of transcriptomes found that the srfA-mutant strain could not relieve CCR to use non-preferred carbon sources after glucose exhaustion due to deficiency of surfactin. This was further verified by the fact that addition with glucose could dramatically restore the growth, and addition with surfactin could improve the enzymes' activity (e.g., glucanase and α-amylase) to use non-preferred carbon sources in the srfA-mutant strain. After glucose exhaustion, the cells produce surfactin to relieve CCR for utilizing non-preferred sugars. As a signal molecule to regulate QS, surfactin also directly or indirectly relieves the CcpA-mediated CCR to utilize non-preferred carbon sources countering nutrient limitation (e.g., glucose deprivation) in the environment. In conclusion, our findings provide the first evidence that the QS signal molecule of surfactin is also involved in relieving the CcpA-mediated CCR in B. amyloliquefaciens.
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Affiliation(s)
- Bing Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiahong Wen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia Ding
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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32
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Dual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane. Nat Commun 2020; 11:1859. [PMID: 32313019 PMCID: PMC7171179 DOI: 10.1038/s41467-020-15758-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria can form biofilms that consist of multicellular communities embedded in an extracellular matrix (ECM). In Bacillus subtilis, the main protein component of the ECM is the functional amyloid TasA. Here, we study further the roles played by TasA in B. subtilis physiology and biofilm formation on plant leaves and in vitro. We show that ΔtasA cells exhibit a range of cytological symptoms indicative of excessive cellular stress leading to increased cell death. TasA associates to the detergent-resistant fraction of the cell membrane, and the distribution of the flotillin-like protein FloT is altered in ΔtasA cells. We propose that, in addition to a structural function during ECM assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics as cells enter stationary phase. The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.
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33
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Saurav K, Borbone N, Burgsdorf I, Teta R, Caso A, Bar-Shalom R, Esposito G, Britstein M, Steindler L, Costantino V. Identification of Quorum Sensing Activators and Inhibitors in The Marine Sponge Sarcotragus spinosulus. Mar Drugs 2020; 18:md18020127. [PMID: 32093216 PMCID: PMC7074164 DOI: 10.3390/md18020127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 12/27/2022] Open
Abstract
Marine sponges, a well-documented prolific source of natural products, harbor highly diverse microbial communities. Their extracts were previously shown to contain quorum sensing (QS) signal molecules of the N-acyl homoserine lactone (AHL) type, known to orchestrate bacterial gene regulation. Some bacteria and eukaryotic organisms are known to produce molecules that can interfere with QS signaling, thus affecting microbial genetic regulation and function. In the present study, we established the production of both QS signal molecules as well as QS inhibitory (QSI) molecules in the sponge species Sarcotragus spinosulus. A total of eighteen saturated acyl chain AHLs were identified along with six unsaturated acyl chain AHLs. Bioassay-guided purification led to the isolation of two brominated metabolites with QSI activity. The structures of these compounds were elucidated by comparative spectral analysis of 1HNMR and HR-MS data and were identified as 3-bromo-4-methoxyphenethylamine (1) and 5,6-dibromo-N,N-dimethyltryptamine (2). The QSI activity of compounds 1 and 2 was evaluated using reporter gene assays for long- and short-chain AHL signals (Escherichia coli pSB1075 and E. coli pSB401, respectively). QSI activity was further confirmed by measuring dose-dependent inhibition of proteolytic activity and pyocyanin production in Pseudomonas aeruginosa PAO1. The obtained results show the coexistence of QS and QSI in S. spinosulus, a complex signal network that may mediate the orchestrated function of the microbiome within the sponge holobiont.
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Affiliation(s)
- Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel 31905, Haifa, Israel; (K.S.); (I.B.); (R.B.-S.); (M.B.); (L.S.)
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovickýmlýn, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - Nicola Borbone
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel 31905, Haifa, Israel; (K.S.); (I.B.); (R.B.-S.); (M.B.); (L.S.)
| | - Roberta Teta
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
| | - Alessia Caso
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel 31905, Haifa, Israel; (K.S.); (I.B.); (R.B.-S.); (M.B.); (L.S.)
| | - Germana Esposito
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
| | - Maya Britstein
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel 31905, Haifa, Israel; (K.S.); (I.B.); (R.B.-S.); (M.B.); (L.S.)
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel 31905, Haifa, Israel; (K.S.); (I.B.); (R.B.-S.); (M.B.); (L.S.)
| | - Valeria Costantino
- The Blue Chemistry Lab, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy; (N.B.); (R.T.); (A.C.); (G.E.)
- Correspondence: ; Tel.: +39-081-678-504
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Pessotti RDC, Hansen BL, Zacharia VM, Polyakov D, Traxler MF. High Spatial Resolution Imaging Mass Spectrometry Reveals Chemical Heterogeneity Across Bacterial Microcolonies. Anal Chem 2019; 91:14818-14823. [PMID: 31694373 DOI: 10.1021/acs.analchem.9b03909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbes interact with the world around them at the chemical level. However, directly examining the chemical exchange between microbes and microbes and their environment, at ecological scales, i.e., the scale of a single bacterial cell or small groups of cells, remains a key challenge. Here we address this obstacle by presenting a methodology that enables matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) of bacterial microcolonies. By combining optimized sample preparation with subatmospheric pressure MALDI, we demonstrate that chemical output from groups of as few as ∼50 cells can be visualized with MALDI-IMS. Application of this methodology to Bacillus subtilis and Streptomyces coelicolor revealed heterogeneity in chemical output across microcolonies and asymmetrical metabolite production when cells grew within physiological gradients produced by Medicago sativa roots. Taken together, these results indicate that MALDI-IMS can readily visualize metabolites made by very small assemblages of bacterial cells and that even these small groups of cells can differentially produce metabolites in response to local chemical gradients.
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Affiliation(s)
- Rita de Cassia Pessotti
- University of California, Berkeley , 111 Koshland Hall , Berkeley , California 94720 , United States
| | - Bridget L Hansen
- University of California, Berkeley , 111 Koshland Hall , Berkeley , California 94720 , United States
| | - Vineetha M Zacharia
- University of California, Berkeley , 111 Koshland Hall , Berkeley , California 94720 , United States
| | - Daniel Polyakov
- University of California, Berkeley , 111 Koshland Hall , Berkeley , California 94720 , United States
| | - Matthew F Traxler
- University of California, Berkeley , 111 Koshland Hall , Berkeley , California 94720 , United States
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35
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Heterogeneity in Bacterial Specialized Metabolism. J Mol Biol 2019; 431:4589-4598. [DOI: 10.1016/j.jmb.2019.04.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/17/2022]
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Weiss CA, Hoberg JA, Liu K, Tu BP, Winkler WC. Single-Cell Microscopy Reveals That Levels of Cyclic di-GMP Vary among Bacillus subtilis Subpopulations. J Bacteriol 2019; 201:e00247-19. [PMID: 31138629 PMCID: PMC6657594 DOI: 10.1128/jb.00247-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022] Open
Abstract
The synthesis of signaling molecules is one strategy bacteria employ to sense alterations in their environment and rapidly adjust to those changes. In Gram-negative bacteria, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulates the transition from a unicellular motile state to a multicellular sessile state. However, c-di-GMP signaling has been less intensively studied in Gram-positive organisms. To that end, we constructed a fluorescent yfp reporter based on a c-di-GMP-responsive riboswitch to visualize the relative abundance of c-di-GMP for single cells of the Gram-positive model organism Bacillus subtilis Coupled with cell-type-specific fluorescent reporters, this riboswitch reporter revealed that c-di-GMP levels are markedly different among B. subtilis cellular subpopulations. For example, cells that have made the decision to become matrix producers maintain higher intracellular c-di-GMP concentrations than motile cells. Similarly, we find that c-di-GMP levels differ between sporulating and competent cell types. These results suggest that biochemical measurements of c-di-GMP abundance are likely to be inaccurate for a bulk ensemble of B. subtilis cells, as such measurements will average c-di-GMP levels across the population. Moreover, the significant variation in c-di-GMP levels between cell types hints that c-di-GMP might play an important role during B. subtilis biofilm formation. This study therefore emphasizes the importance of using single-cell approaches for analyzing metabolic trends within ensemble bacterial populations.IMPORTANCE Many bacteria have been shown to differentiate into genetically identical yet morphologically distinct cell types. Such population heterogeneity is especially prevalent among biofilms, where multicellular communities are primed for unexpected environmental conditions and can efficiently distribute metabolic responsibilities. Bacillus subtilis is a model system for studying population heterogeneity; however, a role for c-di-GMP in these processes has not been thoroughly investigated. Herein, we introduce a fluorescent reporter, based on a c-di-GMP-responsive riboswitch, to visualize the relative abundance of c-di-GMP for single B. subtilis cells. Our analysis shows that c-di-GMP levels are conspicuously different among B. subtilis cellular subtypes, suggesting a role for c-di-GMP during biofilm formation. These data highlight the utility of riboswitches as tools for imaging metabolic changes within individual bacterial cells. Analyses such as these offer new insight into c-di-GMP-regulated phenotypes, especially given that other biofilms also consist of multicellular communities.
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Affiliation(s)
- Cordelia A Weiss
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Jakob A Hoberg
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Kuanqing Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wade C Winkler
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
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Ganin H, Kemper N, Meir S, Rogachev I, Ely S, Massalha H, Mandaby A, Shanzer A, Keren-Paz A, Meijler MM, Malitsky S, Aharoni A, Kolodkin-Gal I. Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1013-1025. [PMID: 30811315 DOI: 10.1094/mpmi-12-18-0327-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.
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Affiliation(s)
- Hadas Ganin
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalie Kemper
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sagit Meir
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Rogachev
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Shir Ely
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hassan Massalha
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Aviad Mandaby
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Alona Keren-Paz
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael M Meijler
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Asaph Aharoni
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Kolodkin-Gal
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Biofilm Formation and Synthesis of Antimicrobial Compounds by the Biocontrol Agent Bacillus velezensis QST713 in an Agaricus bisporus Compost Micromodel. Appl Environ Microbiol 2019; 85:AEM.00327-19. [PMID: 30979839 DOI: 10.1128/aem.00327-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus velezensis QST713 is widely used as a biological control agent for crop protection and disease suppression. This strain is used industrially in France for the protection of Agaricus bisporus against Trichoderma aggressivum f. europaeum, which causes green mold disease. The efficacy of this biocontrol process was evaluated in a previous study, yet the mode of its action has not been explored under production conditions. In order to decipher the underlying biocontrol mechanisms for effective biofilm formation by strain QST713 in the compost and for the involvement of antimicrobial compounds, we developed a simplified micromodel for the culture of A. bisporus during its early culture cycle. By using this micromodel system, we studied the transcriptional response of strain QST713 in the presence or absence of A. bisporus and/or T. aggressivum in axenic industrial compost. We report the overexpression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to their expression during growth in broth compost extract either in the exponential growth phase (the epsC, blsA, and tapA genes) or in the stationary growth phase (the tapA gene), while a gene encoding a flagellar protein (hag) was underexpressed. We also report the overexpression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.IMPORTANCE Biocontrol agents are increasingly used to replace chemical pesticides to prevent crop diseases. In the button mushroom field in France, the use of Bacillus velezensis QST713 as a biocontrol agent against the green mold Trichoderma aggressivum has been shown to be efficient. However, the biocontrol mechanisms effective in the Agaricus bisporus/Trichoderma aggressivum/Bacillus velezensis QST713 pathosystem are still unknown. Our paper focuses on the exploration of the bioprotection mechanisms of the biocontrol agent Bacillus velezensis QST713 during culture of the button mushroom (Agaricus bisporus) in a micromodel culture system to study the specific response of strain QST713 in the presence of T. aggressivum and/or A. bisporus.
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Wang C, Cao Y, Wang Y, Sun L, Song H. Enhancing surfactin production by using systematic CRISPRi repression to screen amino acid biosynthesis genes in Bacillus subtilis. Microb Cell Fact 2019; 18:90. [PMID: 31122258 PMCID: PMC6533722 DOI: 10.1186/s12934-019-1139-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/17/2019] [Indexed: 11/12/2022] Open
Abstract
Background Surfactin is a cyclic lipopeptide that is of great industrial use owing to its extraordinary surfactant power and antimicrobial, antiviral, and antitumor activities. Surfactin is synthesized by a condensation reaction in microbes, which uses fatty acids and four kinds of amino acids (l-glutamate, l-aspartate, l-leucine and l-valine) as precursors. Surfactin biosynthesis could be improved by increasing the supply of fatty acids; however, the effect of the regulation of amino acid metabolism on surfactin production was not yet clear. Results In this study, we aimed to improve surfactin production in B. subtilis by repressing the genes on the branch metabolic pathways of amino acid biosynthesis using CRISPRi technology. First, 20 genes were inhibited individually, resulting in 2.5- to 627-fold decreases in transcriptional level as determined by RT-qPCR. Among the 20 recombinant strains, 16 strains obtained higher surfactin titres than that produced by the parent BS168NU-Sd strain (the surfactin production of BS168NU-Sd with only dCas9 but no sgRNA expression was 0.17 g/L). In particular, the strains in which the yrpC, racE or murC genes were inhibited individually produced 0.54, 0.41, or 0.42 g/L surfactin, respectively. All three genes are related to the metabolism of l-glutamate, whose acylation is the first step in the surfactin condensation reaction. Furthermore, these three genes were repressed in combination, and the strain with co-inhibition of yrpC and racE produced 0.75 g/L surfactin, which was 4.69-fold higher than that of the parent strain. In addition, the inhibition of bkdAA and bkdAB, which are related to the metabolism of l-leucine and l-valine, not only improved surfactin production but also increased the proportion of the C14 isoform. Conclusions This study, to the best of our knowledge for the first time, systematically probed the regulatory effect of increasing the supply of amino acids on surfactin production. It provided an effective strategy and a new perspective for systematic studies on surfactin and other amino acid-derived chemicals. Electronic supplementary material The online version of this article (10.1186/s12934-019-1139-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congya Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Yongping Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Liming Sun
- Petrochemical Research Institute, PetroChina Company Limited, Beijing, 102206, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China.
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40
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Bettenworth V, Steinfeld B, Duin H, Petersen K, Streit WR, Bischofs I, Becker A. Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems. J Mol Biol 2019; 431:4530-4546. [PMID: 31051177 DOI: 10.1016/j.jmb.2019.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Quorum sensing is usually thought of as a collective behavior in which all members of a population partake. However, over the last decade, several reports of phenotypic heterogeneity in quorum sensing-related gene expression have been put forward, thus challenging this view. In the respective systems, cells of isogenic populations did not contribute equally to autoinducer production or target gene activation, and in some cases, the fraction of contributing cells was modulated by environmental factors. Here, we look into potential origins of these incidences and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity. We furthermore discuss potential functions heterogeneity in bacterial quorum sensing systems could serve: as a preparation for environmental fluctuations (bet hedging), as a more cost-effective way of producing public goods (division of labor), as a loophole for genotypic cooperators when faced with non-contributing mutants (cheat protection), or simply as a means to fine-tune the output of the population as a whole (output modulation). We illustrate certain aspects of these recent developments with the model organisms Sinorhizobium meliloti, Sinorhizobium fredii and Bacillus subtilis, which possess quorum sensing systems of different complexity, but all show phenotypic heterogeneity therein.
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Affiliation(s)
- Vera Bettenworth
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - Benedikt Steinfeld
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Hilke Duin
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Katrin Petersen
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Ilka Bischofs
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
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Ostrov I, Sela N, Belausov E, Steinberg D, Shemesh M. Adaptation of Bacillus species to dairy associated environment facilitates their biofilm forming ability. Food Microbiol 2019; 82:316-324. [PMID: 31027789 DOI: 10.1016/j.fm.2019.02.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/17/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Biofilm-forming Bacillus species are often involved in contamination of dairy products and therefore present a major microbiological challenge in the field of food quality and safety. In this study, we sequenced and analyzed the genomes of milk- and non-milk-derived Bacillus strains, and evaluated their biofilm-formation potential in milk. Unlike non-dairy Bacillus isolates, the dairy-associated Bacillus strains were characterized by formation of robust submerged and air-liquid interface biofilm (pellicle) during growth in milk. Moreover, genome comparison analysis revealed notable differences in putative biofilm-associated determinants between the dairy and non-dairy Bacillus isolates, which correlated with biofilm phenotype. These results suggest that biofilm formation by Bacillus species might represent a presumable adaptation strategy to the dairy environment.
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Affiliation(s)
- Ievgeniia Ostrov
- Department of Food Sciences, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO) the Volcani Center, Rishon LeZion, Israel; Biofilm Research Laboratory, Hebrew University - Hadassah, Jerusalem, Israel.
| | - Noa Sela
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Rishon LeZion, Israel.
| | - Eduard Belausov
- Department of Ornamental Plants and Agricultural Biotechnology, ARO, The Volcani Center, Rishon LeZion, Israel.
| | - Doron Steinberg
- Biofilm Research Laboratory, Hebrew University - Hadassah, Jerusalem, Israel.
| | - Moshe Shemesh
- Department of Food Sciences, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO) the Volcani Center, Rishon LeZion, Israel.
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Hu F, Liu Y, Li S. Rational strain improvement for surfactin production: enhancing the yield and generating novel structures. Microb Cell Fact 2019; 18:42. [PMID: 30819187 PMCID: PMC6394072 DOI: 10.1186/s12934-019-1089-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/18/2019] [Indexed: 01/10/2023] Open
Abstract
Surfactin, one of the most powerful microbial surfactants, is a lipopeptide-type biosurfactant which combines interesting physicochemical properties and biological activities. However, the high cost caused by its low productivity largely limits the commercial application of surfactin. Hence, many engineered bacterium have also been used to enhance surfactin biosynthesis. This review briefly summarizes the mechanism of surfactin biosynthesis, highlighting the synthesis pathway of N-terminally attached fatty acids, and outlines the main genetic engineering strategies for improving the yield and generating novel structures of surfactin, including promoter engineering, enhancing efflux systems, modifying the transcriptional regulatory genes of surfactin synthase (srfA), genomics and transcriptomics analysis, non ribosomal peptide synthetase (NRPS) domain and combinatorial biosynthesis. Finally, we discuss the future prospects of the research on surfactin.
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Affiliation(s)
- Fangxiang Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing, Jiangsu, China
| | - Yuyue Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing, Jiangsu, China
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu South Road, Nanjing, Jiangsu, China.
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Posada LF, Álvarez J, Romero-Tabarez M, de-Bashan L, Villegas-Escobar V. Enhanced molecular visualization of root colonization and growth promotion by Bacillus subtilis EA-CB0575 in different growth systems. Microbiol Res 2018; 217:69-80. [DOI: 10.1016/j.micres.2018.08.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 11/26/2022]
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44
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Wu Q, Zhi Y, Xu Y. Systematically engineering the biosynthesis of a green biosurfactant surfactin by Bacillus subtilis 168. Metab Eng 2018; 52:87-97. [PMID: 30453038 DOI: 10.1016/j.ymben.2018.11.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022]
Abstract
The biosynthesis of surfactin has attracted broad interest; however, there is a bottleneck in its low yield in wild strains and the ability to engineer Bacillus producers. Because the key metabolic mechanisms in the surfactin synthesis pathway remain unclear, genetic engineering approaches are all ending up with a single or a few gene modifications. The aim of this study is to develop a systematic engineering approach to improve the biosynthesis of surfactin. First, we restored surfactin biosynthetic activity by integrating a complete sfp gene into the nonproducing Bacillus subtilis 168 strain and obtained a surfactin titer of 0.4 g/l. Second, we reduced competition by deleting biofilm formation-related genes and nonribosomal peptide synthetases/polyketide synthase pathways (3.8% of the total genome), which increased the surfactin titer by 3.3-fold. Third, we improved cellular tolerance to surfactin by overexpressing potential self-resistance-associated proteins, which further increased the surfactin titer by 8.5-fold. Fourth, we increased the supply of precursor branched-chain fatty acids by engineering the branched-chain fatty acid biosynthesis pathway, resulting in an increase of the surfactin titer to 8.5 g/l (a 20.3-fold increase). Finally, due to the preference of the glycolytic pathway for cell growth, we diverted precursor acetyl-CoA away from cell growth to surfactin biosynthesis by enhancing the transcription of srfA. The final surfactin titer increased to 12.8 g/l, with a yield of 65.0 mmol/mol sucrose (42% of the theoretical yield) in the metabolically engineered strain. To the best of our knowledge, this is the highest titer and yield that has been reported. This study may pave the way for the commercial production of green surfactin. More broadly, our work presents another successful example of the modularization of metabolic pathways for improving titer and yield in biotechnological production.
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Affiliation(s)
- Qun Wu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223800, China
| | - Yan Zhi
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT. Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 2018; 93:4604779. [PMID: 29126191 DOI: 10.1093/femsec/fix155] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Nivedha Lakshmanan
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Balázs Horváth
- Seqomics Biotechnology Ltd, Vállalkozók útja 7, Mórahalom 6782, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
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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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47
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Richter A, Hölscher T, Pausch P, Sehrt T, Brockhaus F, Bange G, Kovács ÁT. Hampered motility promotes the evolution of wrinkly phenotype in Bacillus subtilis. BMC Evol Biol 2018; 18:155. [PMID: 30326845 PMCID: PMC6192195 DOI: 10.1186/s12862-018-1266-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/26/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Selection for a certain trait in microbes depends on the genetic background of the strain and the selection pressure of the environmental conditions acting on the cells. In contrast to the sessile state in the biofilm, various bacterial cells employ flagellum-dependent motility under planktonic conditions suggesting that the two phenotypes are mutually exclusive. However, flagellum dependent motility facilitates the prompt establishment of floating biofilms on the air-medium interface, called pellicles. Previously, pellicles of B. subtilis were shown to be preferably established by motile cells, causing a reduced fitness of non-motile derivatives in the presence of the wild type strain. RESULTS Here, we show that lack of active flagella promotes the evolution of matrix overproducers that can be distinguished by the characteristic wrinkled colony morphotype. The wrinkly phenotype is associated with amino acid substitutions in the master repressor of biofilm-related genes, SinR. By analyzing one of the mutations, we show that it alters the tetramerization and DNA binding properties of SinR, allowing an increased expression of the operon responsible for exopolysaccharide production. Finally, we demonstrate that the wrinkly phenotype is advantageous when cells lack flagella, but not in the wild type background. CONCLUSIONS Our experiments suggest that loss of function phenotypes could expose rapid evolutionary adaptation in bacterial biofilms that is otherwise not evident in the wild type strains.
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Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 221, 2800, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Tim Sehrt
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Franziska Brockhaus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 221, 2800, Kongens Lyngby, Denmark. .,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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A single mutation in rapP induces cheating to prevent cheating in Bacillus subtilis by minimizing public good production. Commun Biol 2018; 1:133. [PMID: 30272012 PMCID: PMC6123732 DOI: 10.1038/s42003-018-0136-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
Cooperation is beneficial to group behaviors like multicellularity, but is vulnerable to exploitation by cheaters. Here we analyze mechanisms that protect against exploitation of extracellular surfactin in swarms of Bacillus subtilis. Unexpectedly, the reference strain NCIB 3610 displays inherent resistance to surfactin-non-producing cheaters, while a different wild isolate is susceptible. We trace this interstrain difference down to a single amino acid change in the plasmid-borne regulator RapP, which is necessary and sufficient for cheater mitigation. This allele, prevalent in many Bacillus species, optimizes transcription of the surfactin operon to the minimum needed for full cooperation. When combined with a strain lacking rapP, NCIB 3610 acts as a cheater itself—except it does not harm the population at high proportions since it still produces enough surfactin. This strategy of minimal production is thus a doubly advantageous mechanism to limit exploitation of public goods, and is readily evolved from existing regulatory networks. Lyons and Kolter describe a single-point mutation in the plasmid-borne gene rapP of Bacillus subtilis that optimizes surfactin transcription to express the minimum required for cooperation. The decrease in the production of this public good significantly prevented the exploitation of cooperative traits by cheaters.
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Hassanov T, Karunker I, Steinberg N, Erez A, Kolodkin-Gal I. Novel antibiofilm chemotherapies target nitrogen from glutamate and glutamine. Sci Rep 2018; 8:7097. [PMID: 29740028 PMCID: PMC5940852 DOI: 10.1038/s41598-018-25401-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/19/2018] [Indexed: 01/06/2023] Open
Abstract
Bacteria in nature often reside in differentiated communities termed biofilms, which are an active interphase between uni-cellular and multicellular life states for bacteria. Here we demonstrate that the development of B. subtilis biofilms is dependent on the use of glutamine or glutamate as a nitrogen source. We show a differential metabolic requirement within the biofilm; while glutamine is necessary for the dividing cells at the edges, the inner cell mass utilizes lactic acid. Our results indicate that biofilm cells preserve a short-term memory of glutamate metabolism. Finally, we establish that drugs that target glutamine and glutamate utilization restrict biofilm development. Overall, our work reveals a spatial regulation of nitrogen and carbon metabolism within the biofilm, which contributes to the fitness of bacterial complex communities. This acquired metabolic division of labor within biofilm can serve as a target for novel anti-biofilm chemotherapies
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Affiliation(s)
- Tal Hassanov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Karunker
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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50
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Bacterial Surface Spreading Is More Efficient on Nematically Aligned Polysaccharide Substrates. J Bacteriol 2018; 200:JB.00610-17. [PMID: 29311278 DOI: 10.1128/jb.00610-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023] Open
Abstract
Biofilm-forming bacteria typically deposit layers of polysaccharides on the surfaces they inhabit; hence, polysaccharides are their immediate environment on such surfaces. Previously, we showed that many biofilm-forming bacteria preferentially spread in the direction of aligned and densely packed polysaccharide fibers in compressed substrates, a behavior we referred to as polymertropism. This arrangement of polysaccharide fibers is likely to be similar to that found in the "slime" trails deposited by many biofilm-forming bacteria and would explain previous observations that bacteria tend to follow these trails of polysaccharides. Here, we show that groups of cells or flares spread more rapidly on substrates containing aligned and densely packed polysaccharide fibers. Flares also persist longer, tend to hold their trajectories parallel to the long axes of polysaccharide fibers longer, and ultimately show an increase in displacement away from their origin. On the basis of these findings and others, we propose a model for polymertropism. Namely, we suggest that the packing of the aligned polymers increases the efficiency of surface spreading in the direction of the polymer's long axes; therefore, bacteria tend to spread more rapidly in this direction. Additional work suggests that bacteria can leverage polymertropism, and presumably more efficient surface spreading, for a survival advantage. In particular, when two bacterial species were placed in close proximity and in competition with each other, the ability of one species to move rapidly and directly away from the other by utilizing the aligned polymers of compressed agar substrates led to a clear survival benefit.IMPORTANCE The directed movement of bacteria on compressed substrates was first described in the 1940s and referred to as elasticotaxis (R. Y. Stanier, J Bacteriol 44:405-412, 1942). More recently, this behavior was referred to as polymertropism, as it seems to be a response to the nematic alignment and tight packing of polymers in the substrate (D. J. Lemon, X. Yang, P. Srivastava, Y. Y. Luk, A. G. Garza, Sci Rep 7:7643, 2017, https://doi.org/10.1038/s41598-017-07486-0). The data presented here suggest that bacteria are more efficient at surface spreading when the polymers in the substrate are arranged in this manner. These data also suggest that bacteria can leverage polymertropism, and presumably more efficient surface spreading, for a survival advantage. Namely, one bacterial species was able to use its strong polymertropism response to escape from and survive competition with another species that normally outcompetes it.
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