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Ding X, Zheng Z, Zhao G, Wang L, Wang H, Wang P. Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis. Appl Microbiol Biotechnol 2024; 108:75. [PMID: 38194140 DOI: 10.1007/s00253-023-12877-7] [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: 06/19/2023] [Revised: 10/10/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024]
Abstract
Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.
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Affiliation(s)
- Xiumin Ding
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, China
- University of Science and Technology of China, Hefei, China
| | - Zhiming Zheng
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
| | - Genhai Zhao
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Li Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Han Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Peng Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.
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2
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Akabuogu E, Zhang L, Krašovec R, Roberts IS, Waigh TA. Electrical Impedance Spectroscopy with Bacterial Biofilms: Neuronal-like Behavior. NANO LETTERS 2024; 24:2234-2241. [PMID: 38320294 PMCID: PMC10885197 DOI: 10.1021/acs.nanolett.3c04446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/08/2024]
Abstract
Negative capacitance at low frequencies for spiking neurons was first demonstrated in 1941 (K. S. Cole) by using extracellular electrodes. The phenomenon subsequently was explained by using the Hodgkin-Huxley model and is due to the activity of voltage-gated potassium ion channels. We show that Escherichia coli (E. coli) biofilms exhibit significant stable negative capacitances at low frequencies when they experience a small DC bias voltage in electrical impedance spectroscopy experiments. Using a frequency domain Hodgkin-Huxley model, we characterize the conditions for the emergence of this feature and demonstrate that the negative capacitance exists only in biofilms containing living cells. Furthermore, we establish the importance of the voltage-gated potassium ion channel, Kch, using knock-down mutants. The experiments provide further evidence for voltage-gated ion channels in E. coli and a new, low-cost method to probe biofilm electrophysiology, e.g., to understand the efficacy of antibiotics. We expect that the majority of bacterial biofilms will demonstrate negative capacitances.
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Affiliation(s)
- Emmanuel
U. Akabuogu
- Division
of Infection, Lydia Becker Institute of Immunology and Inflammation,
School of Biological Sciences, University
of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Lin Zhang
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Rok Krašovec
- Division
of Evolution, Infection and Genomics, School of Biological Sciences,
Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United
Kingdom
| | - Ian S. Roberts
- Division
of Infection, Lydia Becker Institute of Immunology and Inflammation,
School of Biological Sciences, University
of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Thomas A. Waigh
- Biological
Physics, Department of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Photon
Science Institute, Alan
Turing Building, Oxford Road, Manchester, M13 9PY, United
Kingdom
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3
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Sun H, Si F, Zhao X, Li F, Qi G. The cellular redox state in Bacillus amyloliquefaciens WH1 affects biofilm formation indirectly in a surfactant direct manner. J Basic Microbiol 2023. [PMID: 37189223 DOI: 10.1002/jobm.202300064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
Surfactin is a signal to trigger biofilm formation against harsh environments. Generally, harsh environments can result in change of the cellular redox state to induce biofilm formation, but we know little about whether the cellular redox state influences biofilm formation via surfactin. Here, the reductant glucose could reduce surfactin and enhance biofilm formation by a surfactin-indirect way. The oxidant H2 O2 led to a decrease of surfactin accompanying with weakened biofilm formation. Spx and PerR were both necessary for surfactin production and biofilm formation. H2 O2 improved surfactin production but inhibited biofilm formation by a surfactin-indirect manner in Δspx, while it reduced surfactin production without obvious influence on biofilm formation in ΔperR. The ability against H2 O2 stress was enhanced in Δspx, but weakened in ΔperR. Thereby, PerR was favorable for resisting oxidative stress, while Spx played a negative role in this action. Knockout and compensation of rex also supported that the cells could form biofilm by a surfactin-indirect way. Collectively, surfactin is not a unique signal to trigger biofilm formation, and the cellular redox state can influence biofilm formation by a surfactin-direct or -indirect way in Bacillus amyloliquefaciens WH1.
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Affiliation(s)
- Huiwan Sun
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengmei Si
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Li
- 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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Abstract
By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates the division frequency of Bacillus subtilis without affecting its growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than do those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media as well as in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but this occurred only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 4.0 mM, with little or no detectable change being observed in labile, intracellular Mg2+, based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with the increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed an enhanced expression of a large number of SigB-regulated genes and the activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple the growth rate from the division frequency and identify transcriptional changes that suggest that cell division is accompanied by the general stress response and an enhanced demand to sequester and/or increase the uptake of iron, Mn2+, and Zn2+. IMPORTANCE The signals that cells use to trigger cell division are unknown. Although division is often considered intrinsic to the cell cycle, microorganisms can continue to grow and repeat rounds of DNA replication without dividing, indicating that cycles of division can be skipped. Here, we show that by manipulating a single nutrient, namely, Mg2+, cell division can be uncoupled from the growth rate. This finding can be applied to investigate the nature of the cell division signal(s).
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Hennes M, Bender N, Cronenberg T, Welker A, Maier B. Collective polarization dynamics in bacterial colonies signify the occurrence of distinct subpopulations. PLoS Biol 2023; 21:e3001960. [PMID: 36652440 PMCID: PMC9847958 DOI: 10.1371/journal.pbio.3001960] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023] Open
Abstract
Membrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single-cell level. However, little is known about spatiotemporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a transition from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behavior transitions to collective dynamics: A hyperpolarized shell forms at the center, travels radially outward, and halts several micrometers from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarization. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics increases. These findings highlight that the polarization pattern can signify the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance.
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Affiliation(s)
- Marc Hennes
- Institute for Biological Physics, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- * E-mail: (MH); (BM)
| | - Niklas Bender
- Institute for Biological Physics, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Tom Cronenberg
- Institute for Biological Physics, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Anton Welker
- Institute for Biological Physics, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Berenike Maier
- Institute for Biological Physics, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- * E-mail: (MH); (BM)
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Karnwal A, Shrivastava S, Al-Tawaha ARMS, Kumar G, Singh R, Kumar A, Mohan A, Malik T. Microbial Biosurfactant as an Alternate to Chemical Surfactants for Application in Cosmetics Industries in Personal and Skin Care Products: A Critical Review. BIOMED RESEARCH INTERNATIONAL 2023; 2023:2375223. [PMID: 37090190 PMCID: PMC10118887 DOI: 10.1155/2023/2375223] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023]
Abstract
Cosmetics and personal care items are used worldwide and administered straight to the skin. The hazardous nature of the chemical surfactant utilized in the production of cosmetics has caused alarm on a global scale. Therefore, bacterial biosurfactants (BS) are becoming increasingly popular in industrial product production as a biocompatible, low-toxic alternative surfactant. Chemical surfactants can induce allergic responses and skin irritations; thus, they should be replaced with less harmful substances for skin health. The cosmetic industry seeks novel biological alternatives to replace chemical compounds and improve product qualities. Most of these chemicals have a biological origin and can be obtained from plant, bacterial, fungal, and algal sources. Various biological molecules have intriguing capabilities, such as biosurfactants, vitamins, antioxidants, pigments, enzymes, and peptides. These are safe, biodegradable, and environmentally friendly than chemical options. Plant-based biosurfactants, such as saponins, offer numerous advantages over synthetic surfactants, i.e., biodegradable, nontoxic, and environmentally friendly nature. Saponins are a promising source of natural biosurfactants for various industrial and academic applications. However, microbial glycolipids and lipopeptides have been used in biotechnology and cosmetics due to their multifunctional character, including detergency, emulsifying, foaming, and skin moisturizing capabilities. In addition, some of them have the potential to be used as antibacterial agents. In this review, we like to enlighten the application of microbial biosurfactants for replacing chemical surfactants in existing cosmetic and personal skincare pharmaceutical formulations due to their antibacterial, skin surface moisturizing, and low toxicity characteristics.
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Affiliation(s)
- Arun Karnwal
- Department of Microbiology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Shrivastava
- Department of Plant Pathology, School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | | | - Gaurav Kumar
- Department of Microbiology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rattandeep Singh
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anupam Kumar
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Anand Mohan
- Department of Biotechnology, School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, Ethiopia
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7
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Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rebecca N Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sophie Jean Walton
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Katherine S Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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8
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Arjes HA, Gui H, Porter R, Atolia E, Peters JM, Gross C, Kearns DB, Huang KC. Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis. mBio 2022; 13:e0138822. [PMID: 36069446 PMCID: PMC9600695 DOI: 10.1128/mbio.01388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/05/2022] [Indexed: 02/05/2023] Open
Abstract
Many bacterial species typically live in complex three-dimensional biofilms, yet much remains unknown about differences in essential processes between nonbiofilm and biofilm lifestyles. Here, we created a CRISPR interference (CRISPRi) library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain NCIB 3610 and investigated growth, biofilm colony wrinkling, and sporulation phenotypes of the knockdown library. First, we showed that gene essentiality is largely conserved between liquid and surface growth and between two media. Second, we quantified biofilm colony wrinkling using a custom image analysis algorithm and found that fatty acid synthesis and DNA gyrase knockdown strains exhibited increased wrinkling independent of biofilm matrix gene expression. Third, we designed a high-throughput screen to quantify sporulation efficiency after essential gene knockdown; we found that partial knockdowns of essential genes remained competent for sporulation in a sporulation-inducing medium, but knockdown of essential genes involved in fatty acid synthesis exhibited reduced sporulation efficiency in LB, a medium with generally lower levels of sporulation. We conclude that a subset of essential genes are particularly important for biofilm structure and sporulation/germination and suggest a previously unappreciated and multifaceted role for fatty acid synthesis in bacterial lifestyles and developmental processes. IMPORTANCE For many bacteria, life typically involves growth in dense, three-dimensional communities called biofilms that contain cells with differentiated roles held together by extracellular matrix. To examine how essential gene function varies between vegetative growth and the developmental states of biofilm formation and sporulation, we created and screened a comprehensive library of strains using CRISPRi to knockdown expression of each essential gene in the biofilm-capable Bacillus subtilis strain 3610. High-throughput assays and computational algorithms identified a subset of essential genes involved in biofilm wrinkling and sporulation and indicated that fatty acid synthesis plays important and multifaceted roles in bacterial development.
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Affiliation(s)
- Heidi A. Arjes
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Rachel Porter
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Esha Atolia
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Carol Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Ja'afaru MI, Abbas T, Ajunwa OM, Olaifa K. Characterization and statistical optimization of biosurfactant production using Bacillus subtilis isolated from automotive oil-contaminated soil in Yola, Nigeria. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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10
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Gudiña EJ, Teixeira JA. Bacillus licheniformis: The unexplored alternative for the anaerobic production of lipopeptide biosurfactants? Biotechnol Adv 2022; 60:108013. [PMID: 35752271 DOI: 10.1016/j.biotechadv.2022.108013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/27/2022] [Accepted: 06/19/2022] [Indexed: 11/02/2022]
Abstract
Microbial biosurfactants have attracted the attention of researchers and companies for the last decades, as they are considered promising candidates to replace chemical surfactants in numerous applications. Although in the last years, considerable advances were performed regarding strain engineering and the use of low-cost substrates in order to reduce their production costs, one of the main bottlenecks is their production at industrial scale. Conventional aerobic biosurfactant production processes result in excessive foaming, due to the use of high agitation and aeration rates necessary to increase dissolved oxygen concentration to allow microbial growth and biosurfactant production. Different approaches have been studied to overcome this problem, although with limited success. A not widely explored alternative is the development of foam-free processes through the anaerobic growth of biosurfactant-producing microorganisms. Surfactin, produced by Bacillus subtilis, is the most widely studied lipopeptide biosurfactant, and the most powerful biosurfactant known so far. Bacillus licheniformis strains produce lichenysin, a lipopeptide biosurfactant which structure is similar to surfactin. However, despite its extraordinary surface-active properties and potential applications, lichenysin has been scarcely studied. According to previous studies, B. licheniformis is better adapted to anaerobic growth than B. subtilis, and could be a good alternative for the anaerobic production of lipopeptide biosurfactants. In this review, the potential and limitations of surfactin and lichenysin production under anaerobic conditions will be analyzed, and the possibility of implementing foam-free processes for lichenysin production, in order to expand the market and applications of biosurfactants in different fields, will be discussed.
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Affiliation(s)
- Eduardo J Gudiña
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - José A Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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11
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A mini-review: mechanism of antimicrobial action and application of surfactin. World J Microbiol Biotechnol 2022; 38:143. [PMID: 35718798 DOI: 10.1007/s11274-022-03323-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/26/2022] [Indexed: 10/18/2022]
Abstract
Surfactin, an antibacterial lipopeptide produced by different strains of Bacillus subtilis, is a powerful biosurfactant. It also has multiple biological activities including antiviral, anti-mycoplasma and antiprotozoal activities, in addition to the broad-spectrum antimicrobial activities against Gram-positive bacteria, Gram-negative bacteria and fungi. Surfactin may be one of the promising alternatives to antibiotics. Surfactin's chemical structure and physicochemical properties are briefly discussed in this mini-review. Surfactin's antibacterial mechanism is mainly outlined as follows: (1) attacking pathogenic bacteria's cell membrane, causing cell membrane disintegration or osmotic pressure imbalance; (2) inhibiting pathogenic bacteria's protein synthesis, preventing cell reproduction; (3) inhibiting pathogenic bacteria's enzyme activity, affecting normal cell metabolism. This provides basis for the further research and application of surfactin. Finally, the application of surfactin in food and its prospect are summarized in brief.
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12
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Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
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13
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Cesar S, Willis L, Huang KC. Bacterial respiration during stationary phase induces intracellular damage that leads to delayed regrowth. iScience 2022; 25:103765. [PMID: 35243217 PMCID: PMC8858994 DOI: 10.1016/j.isci.2022.103765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Corresponding author
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14
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Nitric oxide stimulates type IV MSHA pilus retraction in Vibrio cholerae via activation of the phosphodiesterase CdpA. Proc Natl Acad Sci U S A 2022; 119:2108349119. [PMID: 35135874 PMCID: PMC8851539 DOI: 10.1073/pnas.2108349119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 01/30/2023] Open
Abstract
All organisms sense and respond to their environments. One way bacteria interact with their surroundings is by dynamically extending and retracting filamentous appendages from their surface called pili. While pili are critical for many functions, such as attachment, motility, and DNA uptake, the factors that regulate their dynamic activity are poorly understood. Here, we describe how an environmental signal induces a signaling pathway to promote the retraction of mannose-sensitive hemagglutinin pili in Vibrio cholerae. The retraction of these pili promotes the detachment of V. cholerae from a surface and may provide a means by which V. cholerae can respond to changes in its environment. Bacteria use surface appendages called type IV pili to perform diverse activities including DNA uptake, twitching motility, and attachment to surfaces. The dynamic extension and retraction of pili are often required for these activities, but the stimuli that regulate these dynamics remain poorly characterized. To address this question, we study the bacterial pathogen Vibrio cholerae, which uses mannose-sensitive hemagglutinin (MSHA) pili to attach to surfaces in aquatic environments as the first step in biofilm formation. Here, we use a combination of genetic and cell biological approaches to describe a regulatory pathway that allows V. cholerae to rapidly abort biofilm formation. Specifically, we show that V. cholerae cells retract MSHA pili and detach from a surface in a diffusion-limited, enclosed environment. This response is dependent on the phosphodiesterase CdpA, which decreases intracellular levels of cyclic-di-GMP to induce MSHA pilus retraction. CdpA contains a putative nitric oxide (NO)–sensing NosP domain, and we demonstrate that NO is necessary and sufficient to stimulate CdpA-dependent detachment. Thus, we hypothesize that the endogenous production of NO (or an NO-like molecule) in V. cholerae stimulates the retraction of MSHA pili. These results extend our understanding of how environmental cues can be integrated into the complex regulatory pathways that control pilus dynamic activity and attachment in bacterial species.
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15
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Liu H, Yuan W, Zhou P, Liang G, Gao C, Guo L, Hu G, Song W, Wu J, Chen X, Liu L. Engineering membrane asymmetry to increase medium-chain fatty acid tolerance in Saccharomyces cerevisiae. Biotechnol Bioeng 2021; 119:277-286. [PMID: 34708879 DOI: 10.1002/bit.27973] [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: 07/06/2021] [Revised: 10/04/2021] [Accepted: 10/23/2021] [Indexed: 11/11/2022]
Abstract
Saccharomyces cerevisiae is an attractive chassis for the production of medium-chain fatty acids, but the toxic effect of these compounds often prevents further improvements in titer, yield, and productivity. To address this issue, Lem3 and Sfk1 were identified from adaptive laboratory evolution mutant strains as membrane asymmetry regulators. Co-overexpression of Lem3 and Sfk1 [Lem3(M)-Sfk1(H) strain] through promoter engineering remodeled the membrane phospholipid distribution, leading to an increased accumulation of phosphatidylethanolamine in the inner leaflet of the plasma membrane. As a result, membrane potential and integrity were increased by 131.5% and 29.2%, respectively; meanwhile, the final OD600 in the presence of hexanoic acid, octanoic acid, and decanoic acid was improved by 79.6%, 73.4%, and 57.7%, respectively. In summary, this study shows that membrane asymmetry engineering offers an efficient strategy to enhance medium-chain fatty acids tolerance in S. cerevisiae, thus generating a robust industrial strain for producing high-value biofuels.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Weijia Yuan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guangjie Liang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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16
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Shan MY, Meng FQ, Zhou LB, Lu FX, Bie XM, Zhao HZ, Lu ZX. Surfactin inhibits the growth of Propionibacterium acnes by destroying the cell wall and membrane. Lett Appl Microbiol 2021; 73:684-693. [PMID: 34607389 DOI: 10.1111/lam.13576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 01/08/2023]
Abstract
Propionibacterium acnes plays a major role in acne vulgaris. In the pre-experiment, the growth of P. acnes was inhibited effectively using surfactin; however, the antibacterial mechanism has not been described. Therefore, the aim of this study was to evaluate antibacterial activity and analyse the mechanism of surfactin against P. acnes. Minimum inhibitory concentration, time-killing kinetics and scanning electron microscopy were used to evaluate the activity of surfactin against P. acnes, which showed that 128 μg ml-1 effectively inhibited growth. Cell wall permeability was evaluated by detecting the extracellular alkaline phosphatase activity, which increased to 1·83- and 2·32-fold after incubating with 128 and 256 μg ml-1 of surfactin for 10 h, respectively. Propidium iodide fluorescence, leakage of nucleic acid, protein, K+ , and Ca2+ , membrane potential and the leakage of calcein from small unilamellar vesicles all increased after incubation with surfactin, indicating that its strong biological activities act mainly by altering membrane integrity. In a mouse model of acne, surfactin significantly reduced P. acnes-induced epidermal swelling and erythema. These results indicate that surfactin effectively inhibited the growth of P. acnes by destroying the cell wall and membrane, and is a potential candidate for acne treatment.
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Affiliation(s)
- M Y Shan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - F Q Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - L B Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - F X Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - X M Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - H Z Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Z X Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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17
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Kyrila G, Katsoulas A, Schoretsaniti V, Rigopoulos A, Rizou E, Doulgeridou S, Sarli V, Samanidou V, Touraki M. Bisphenol A removal and degradation pathways in microorganisms with probiotic properties. JOURNAL OF HAZARDOUS MATERIALS 2021; 413:125363. [PMID: 33592490 DOI: 10.1016/j.jhazmat.2021.125363] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Bisphenol-A (BPA) is a constituent of polycarbonate plastics and epoxy resins, widely applied on food packaging materials. As BPA exposure results in health hazards, its efficient removal is of crucial importance. In our study five potentially probiotic microorganisms, namely Lactococcus lactis, Bacillus subtilis, Lactobacillus plantarum, Enterococcus faecalis, and Saccharomyces cerevisiae, were tested for their toxicity tolerance to BPA and their BPA removal ability. Although BPA toxicity, evident on all microorganisms, presented a correlation to both BPA addition time and its concentration, all strains exhibited BPA-removal ability with increased removal rate between 0 and 24 h of incubation. BPA degradation resulted in the formation of two dimer products in cells while the compounds Hydroquinone (HQ), 4-Hydroxyacetophenone (HAP), 4-Hydroxybenzoic acid (HBA) and 4-Isopropenylphenol (PP) were identified in the culture medium. In the proposed BPA degradation pathways BPA adducts formation appears as a common pattern, while BPA decomposition as well as the formation, and the levels of its end products present differences among microorganisms. The BPA degradation ability of the tested beneficial microorganisms demonstrates their potential application in the bioremediation of BPA contaminated foods and feeds and provides a means to suppress the adverse effects of BPA on human and animal health.
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Affiliation(s)
- Gloria Kyrila
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonis Katsoulas
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Vasiliki Schoretsaniti
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Angelos Rigopoulos
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleftheria Rizou
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Savvoula Doulgeridou
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Vasiliki Sarli
- Organic Chemistry Laboratory, Department of Organic Chemistry and Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Victoria Samanidou
- Laboratory of Analytical Chemistry, Department of Physical, Analytical and Environmental Chemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki (A.U.TH.), 54124 Thessaloniki, Greece
| | - Maria Touraki
- Laboratory of General Biology, Division of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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18
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Hoffmann M, Braig A, Fernandez Cano Luna DS, Rief K, Becker P, Treinen C, Klausmann P, Morabbi Heravi K, Henkel M, Lilge L, Hausmann R. Evaluation of an oxygen-dependent self-inducible surfactin synthesis in B. subtilis by substitution of native promoter P srfA by anaerobically active P narG and P nasD. AMB Express 2021; 11:57. [PMID: 33876328 PMCID: PMC8055807 DOI: 10.1186/s13568-021-01218-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 01/09/2023] Open
Abstract
A novel approach targeting self-inducible surfactin synthesis under oxygen-limited conditions is presented. Because both the nitrate (NarGHI) and nitrite (NasDE) reductase are highly expressed during anaerobic growth of B. subtilis, the native promoter PsrfA of the surfactin operon in strain B. subtilis JABs24 was replaced by promoters PnarG and PnasD to induce surfactin synthesis anaerobically. Shake flask cultivations with varying oxygen availabilities indicated no significant differences in native PsrfA expression. As hypothesized, activity of PnarG and PnasD increased with lower oxygen levels and surfactin was not produced by PsrfA::PnarG as well as PsrfA::PnasD mutant strains under conditions with highest oxygen availability. PnarG showed expressions similar to PsrfA at lowest oxygen availability, while maximum value of PnasD was more than 5.5-fold higher. Although the promoter exchange PsrfA::PnarG resulted in a decreased surfactin titer at lowest oxygen availability, the strain carrying PsrfA::PnasD reached a 1.4-fold increased surfactin concentration with 696 mg/L and revealed an exceptional high overall YP/X of 1.007 g/g. This value also surpassed the YP/X of the reference strain JABs24 at highest and moderate oxygen availability. Bioreactor cultivations illustrated that significant cell lysis occurred when the process of "anaerobization" was performed too fast. However, processes with a constantly low agitation and aeration rate showed promising potential for process improvement, especially by employing the strain carrying PsrfA::PnasD promoter exchange. Additionally, replacement of other native promoters by nitrite reductase promoter PnasD represents a promising tool for anaerobic-inducible bioprocesses in Bacillus.
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Affiliation(s)
- Mareen Hoffmann
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Alina Braig
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Diana Stephanie Fernandez Cano Luna
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Katharina Rief
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Philipp Becker
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Chantal Treinen
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Peter Klausmann
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Kambiz Morabbi Heravi
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Marius Henkel
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
| | - Lars Lilge
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany.
| | - Rudolf Hausmann
- Institute of Food Science and Biotechnology (150), Department of Bioprocess Engineering (150k), University of Hohenheim, Fruwirthstr. 12, 70599, Stuttgart, Germany
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19
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Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi. mSystems 2021; 6:6/1/e00770-20. [PMID: 33622852 PMCID: PMC8573961 DOI: 10.1128/msystems.00770-20] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacillus subtilis produces a wide range of secondary metabolites providing diverse plant growth-promoting and biocontrol abilities. These secondary metabolites include nonribosomal peptides with strong antimicrobial properties, causing either cell lysis, pore formation in fungal membranes, inhibition of certain enzymes, or bacterial protein synthesis. However, the natural products of B. subtilis are mostly studied either in laboratory strains or in individual isolates, and therefore, a comparative overview of secondary metabolites from various environmental B. subtilis strains is missing. In this study, we isolated 23 B. subtilis strains from 11 sampling sites, compared the fungal inhibition profiles of wild types and their nonribosomal peptide mutants, followed the production of targeted lipopeptides, and determined the complete genomes of 13 soil isolates. We discovered that nonribosomal peptide production varied among B. subtilis strains coisolated from the same soil samples. In vitro antagonism assays revealed that biocontrol properties depend on the targeted plant pathogenic fungus and the tested B. subtilis isolate. While plipastatin alone is sufficient to inhibit Fusarium spp., a combination of plipastatin and surfactin is required to hinder growth of Botrytis cinerea Detailed genomic analysis revealed that altered nonribosomal peptide production profiles in specific isolates are due to missing core genes, nonsense mutation, or potentially altered gene regulation. Our study combines microbiological antagonism assays with chemical nonribosomal peptide detection and biosynthetic gene cluster predictions in diverse B. subtilis soil isolates to provide a broader overview of the secondary metabolite chemodiversity of B. subtilis IMPORTANCE Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity. To facilitate the prediction of the biocontrol potential of new Bacillus subtilis isolates, we have explored the in vitro antifungal inhibitory profiles of recent B. subtilis isolates, combined with analytical natural product chemistry, mutational analysis, and detailed genome analysis of biosynthetic gene clusters. Such a comparative analysis helped to explain why selected B. subtilis isolates lack the production of certain secondary metabolites.
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20
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Arjes HA, Willis L, Gui H, Xiao Y, Peters J, Gross C, Huang KC. Three-dimensional biofilm colony growth supports a mutualism involving matrix and nutrient sharing. eLife 2021; 10:e64145. [PMID: 33594973 PMCID: PMC7925131 DOI: 10.7554/elife.64145] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Yangbo Xiao
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Jason Peters
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-MadisonMadisonUnited States
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Carol Gross
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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21
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Hederstedt L. Molecular Biology of Bacillus subtilis Cytochromes anno 2020. BIOCHEMISTRY (MOSCOW) 2021; 86:8-21. [DOI: 10.1134/s0006297921010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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22
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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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23
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Kiesewalter HT, Lozano-Andrade CN, Strube ML, Kovács ÁT. Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities. Beilstein J Org Chem 2020; 16:2983-2998. [PMID: 33335606 PMCID: PMC7722629 DOI: 10.3762/bjoc.16.248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Secondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular, nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition, or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established soil-derived semisynthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, the NRP-deficient strain sfp, or single-NRP mutants incapable of producing surfactin, plipastatin, or bacillaene. Through 16S amplicon sequencing, it was revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundance of the two genera Lysinibacillus and Viridibacillus was reduced. Interestingly, this effect was diminished in communities supplemented with the NRP-deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicated the sensitivity of this strain towards the biosurfactant surfactin. Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semisynthetic bacterial communities and helps to understand their ecological role.
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Affiliation(s)
- Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael L Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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24
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Atolia E, Cesar S, Arjes HA, Rajendram M, Shi H, Knapp BD, Khare S, Aranda-Díaz A, Lenski RE, Huang KC. Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth. mBio 2020; 11:e01378-20. [PMID: 33082255 PMCID: PMC7587430 DOI: 10.1128/mbio.01378-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/10/2020] [Indexed: 11/20/2022] Open
Abstract
Bacterial growth under nutrient-rich and starvation conditions is intrinsically tied to the environmental history and physiological state of the population. While high-throughput technologies have enabled rapid analyses of mutant libraries, technical and biological challenges complicate data collection and interpretation. Here, we present a framework for the execution and analysis of growth measurements with improved accuracy over that of standard approaches. Using this framework, we demonstrate key biological insights that emerge from consideration of culturing conditions and history. We determined that quantification of the background absorbance in each well of a multiwell plate is critical for accurate measurements of maximal growth rate. Using mathematical modeling, we demonstrated that maximal growth rate is dependent on initial cell density, which distorts comparisons across strains with variable lag properties. We established a multiple-passage protocol that alleviates the substantial effects of glycerol on growth in carbon-poor media, and we tracked growth rate-mediated fitness increases observed during a long-term evolution of Escherichia coli in low glucose concentrations. Finally, we showed that growth of Bacillus subtilis in the presence of glycerol induces a long lag in the next passage due to inhibition of a large fraction of the population. Transposon mutagenesis linked this phenotype to the incorporation of glycerol into lipoteichoic acids, revealing a new role for these envelope components in resuming growth after starvation. Together, our investigations underscore the complex physiology of bacteria during bulk passaging and the importance of robust strategies to understand and quantify growth.IMPORTANCE How starved bacteria adapt and multiply under replete nutrient conditions is intimately linked to their history of previous growth, their physiological state, and the surrounding environment. While automated equipment has enabled high-throughput growth measurements, data interpretation and knowledge gaps regarding the determinants of growth kinetics complicate comparisons between strains. Here, we present a framework for growth measurements that improves accuracy and attenuates the effects of growth history. We determined that background absorbance quantification and multiple passaging cycles allow for accurate growth rate measurements even in carbon-poor media, which we used to reveal growth-rate increases during long-term laboratory evolution of Escherichia coli Using mathematical modeling, we showed that maximum growth rate depends on initial cell density. Finally, we demonstrated that growth of Bacillus subtilis with glycerol inhibits the future growth of most of the population, due to lipoteichoic acid synthesis. These studies highlight the challenges of accurate quantification of bacterial growth behaviors.
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Affiliation(s)
- Esha Atolia
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Benjamin D Knapp
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
| | - Somya Khare
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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25
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Abstract
Oxygen is essential for many organisms who have therefore evolved mechanisms to enable survival during hypoxia. A new study describes how a well-known bacterial surfactant, called surfactin, facilitates bacterial viability when oxygen becomes limiting by reducing oxygen consumption.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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