1
|
Povolotsky TL, Levy Barazany H, Shacham Y, Kolodkin-Gal I. Bacterial epigenetics and its implication for agriculture, probiotics development, and biotechnology design. Biotechnol Adv 2024; 75:108414. [PMID: 39019123 DOI: 10.1016/j.biotechadv.2024.108414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
In their natural habitats, organisms encounter numerous external stimuli and must be able to sense and adapt to those stimuli to survive. Unlike mutations, epigenetic changes do not alter the underlying DNA sequence. Instead, they create modifications that promote or silence gene expression. Bacillus subtilis has long been a model organism in studying genetics and development. It is beneficial for numerous biotechnological applications where it is included as a probiotic, in fermentation, or in bio-concrete design. This bacterium has also emerged recently as a model organism for studying bacterial epigenetic adaptation. In this review, we examine the evolving knowledge of epigenetic regulation (restriction-modification systems (RM), orphan methyltransferases, and chromosome condensation) in B. subtilis and related bacteria, and utilize it as a case study to test their potential roles and future applications in genetic engineering and microbial biotechnology. Finally, we suggest how the implementation of these fundamental findings promotes the design of synthetic epigenetic memory circuits and their future applications in agriculture, medicine, and biotechnology.
Collapse
Affiliation(s)
- Tatyana L Povolotsky
- Institute for Chemistry and Biochemistry, Physical and Theoretical Chemistry, Freie Universität Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Hilit Levy Barazany
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Yosi Shacham
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel
| | - Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Hauniversita 8, Herzeliya, Israel.
| |
Collapse
|
2
|
Wang L, Hu J, Li K, Zhao Y, Zhu M. Advancements in gene editing technologies for probiotic-enabled disease therapy. iScience 2024; 27:110791. [PMID: 39286511 PMCID: PMC11403445 DOI: 10.1016/j.isci.2024.110791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Probiotics typically refer to microorganisms that have been identified for their health benefits, and they are added to foods or supplements to promote the health of the host. A growing number of probiotic strains have been identified lately and developed into valuable regulatory pharmaceuticals for nutritional and medical applications. Gene editing technologies play a crucial role in addressing the need for safe and therapeutic probiotics in disease treatment. These technologies offer valuable assistance in comprehending the underlying mechanisms of probiotic bioactivity and in the development of advanced probiotics. This review aims to offer a comprehensive overview of gene editing technologies applied in the engineering of both traditional and next-generation probiotics. It further explores the potential for on-demand production of customized products derived from enhanced probiotics, with a particular emphasis on the future of gene editing in the development of live biotherapeutics.
Collapse
Affiliation(s)
- Lixuan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Motao Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
Moroz N, Colvin B, Jayasinghe S, Gleason C, Tanaka K. Phytocytokine StPep1-Secreting Bacteria Suppress Potato Powdery Scab Disease. PHYTOPATHOLOGY 2024; 114:2055-2063. [PMID: 38970808 DOI: 10.1094/phyto-01-24-0019-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Powdery scab is an important potato disease caused by the soilborne pathogen Spongospora subterranea f. sp. subterranea. Currently, reliable chemical control and resistant cultivars for powdery scab are unavailable. As an alternative control strategy, we propose a novel approach involving the effective delivery of a phytocytokine to plant roots by the rhizobacterium Bacillus subtilis. The modified strain is designed to secrete the plant elicitor peptide StPep1. In our experiments employing a hairy root system, we observed a significant reduction in powdery scab pathogen infection when we directly applied the StPep1 peptide. Furthermore, our pot assay, which involved pretreating potato roots with StPep1-secreting B. subtilis, demonstrated a substantial decrease in disease symptoms, including reduced root galling and fewer tuber lesions. These findings underscore the potential of engineered bacteria as a promising strategy for safeguarding plants against powdery scab.
Collapse
Affiliation(s)
- Natalia Moroz
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Benjamin Colvin
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Samodya Jayasinghe
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| |
Collapse
|
4
|
Leistikow KR, May DS, Suh WS, Vargas Asensio G, Schaenzer AJ, Currie CR, Hristova KR. Bacillus subtilis-derived peptides disrupt quorum sensing and biofilm assembly in multidrug-resistant Staphylococcus aureus. mSystems 2024; 9:e0071224. [PMID: 38990088 PMCID: PMC11334493 DOI: 10.1128/msystems.00712-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/15/2024] [Indexed: 07/12/2024] Open
Abstract
Multidrug-resistant Staphylococcus aureus is one of the most clinically important pathogens in the world, with infections leading to high rates of morbidity and mortality in both humans and animals. The ability of S. aureus to form biofilms protects cells from antibiotics and promotes the transfer of antibiotic resistance genes; therefore, new strategies aimed at inhibiting biofilm growth are urgently needed. Probiotic species, including Bacillus subtilis, are gaining interest as potential therapies against S. aureus for their ability to reduce S. aureus colonization and virulence. Here, we search for strains and microbially derived compounds with strong antibiofilm activity against multidrug-resistant S. aureus by isolating and screening Bacillus strains from a variety of agricultural environments. From a total of 1,123 environmental isolates, we identify a single strain B. subtilis 6D1, with a potent ability to inhibit biofilm growth, disassemble mature biofilm, and improve antibiotic sensitivity of S. aureus biofilms through an Agr quorum sensing interference mechanism. Biochemical and molecular networking analysis of an active organic fraction revealed multiple surfactin isoforms, and an uncharacterized peptide was driving this antibiofilm activity. Compared with commercial high-performance liquid chromatography grade surfactin obtained from B. subtilis, we show these B. subtilis 6D1 peptides are significantly better at inhibiting biofilm formation in all four S. aureus Agr backgrounds and preventing S. aureus-induced cytotoxicity when applied to HT29 human intestinal cells. Our study illustrates the potential of exploring microbial strain diversity to discover novel antibiofilm agents that may help combat multidrug-resistant S. aureus infections and enhance antibiotic efficacy in clinical and veterinary settings. IMPORTANCE The formation of biofilms by multidrug-resistant bacterial pathogens, such as Staphylococcus aureus, increases these microorganisms' virulence and decreases the efficacy of common antibiotic regimens. Probiotics possess a variety of strain-specific strategies to reduce biofilm formation in competing organisms; however, the mechanisms and compounds responsible for these phenomena often go uncharacterized. In this study, we identified a mixture of small probiotic-derived peptides capable of Agr quorum sensing interference as one of the mechanisms driving antibiofilm activity against S. aureus. This collection of peptides also improved antibiotic killing and protected human gut epithelial cells from S. aureus-induced toxicity by stimulating an adaptive cytokine response. We conclude that purposeful strain screening and selection efforts can be used to identify unique probiotic strains that possess specially desired mechanisms of action. This information can be used to further improve our understanding of the ways in which probiotic and probiotic-derived compounds can be applied to prevent bacterial infections or improve bacterial sensitivity to antibiotics in clinical and agricultural settings.
Collapse
Affiliation(s)
- Kyle R. Leistikow
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Daniel S. May
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, Washington College, Chestertown, Maryland, USA
| | - Won Se Suh
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | | | - Adam J. Schaenzer
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | | |
Collapse
|
5
|
Abraha HB, Ramesha RM, Ferdiansyah MK, Son H, Kim G, Park B, Jeong DY, Kim KP. Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution. Curr Microbiol 2024; 81:305. [PMID: 39133322 DOI: 10.1007/s00284-024-03819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.
Collapse
Affiliation(s)
- Haftom Baraki Abraha
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | | | | | - Hyeonro Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Gayeong Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Beomseok Park
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Do-Youn Jeong
- Microbial Institute for Fermentation Industry, Sunchang, 56048, South Korea
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
| |
Collapse
|
6
|
Marton Menendez A, Nesbitt DJ. Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches. Biophys J 2024:S0006-3495(24)00516-2. [PMID: 39091026 DOI: 10.1016/j.bpj.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
T. maritima and B. subtilis are bacteria that inhabit significantly different thermal environments, ∼80 vs. ∼40°C, yet employ similar lysine riboswitches to aid in the transcriptional regulation of the genes involved in the synthesis and transport of amino acids. Despite notable differences in G-C basepair frequency and primary sequence, the aptamer moieties of each riboswitch have striking similarities in tertiary structure, with several conserved motifs and long-range interactions. To explore genetic adaptation in extreme thermal environments, we compare the kinetic and thermodynamic behaviors in T. maritima and B. subtilis lysine riboswitches via single-molecule fluorescence resonance energy transfer analysis. Kinetic studies reveal that riboswitch folding rates increase with lysine concentration while the unfolding rates are independent of lysine. This indicates that both riboswitches bind lysine through an induced-fit ("bind-then-fold") mechanism, with lysine binding necessarily preceding conformational changes. Temperature-dependent van't Hoff studies reveal qualitative similarities in the thermodynamic landscapes for both riboswitches in which progression from the open, lysine-unbound state to both transition states (‡) and closed, lysine-bound conformations is enthalpically favored yet entropically penalized, with comparisons of enthalpic and entropic contributions extrapolated to a common [K+] = 100 mM in quantitative agreement. Finally, temperature-dependent Eyring analysis reveals the TMA and BSU riboswitches to have remarkably similar folding/unfolding rate constants when extrapolated to their respective (40 and 80°C) environmental temperatures. Such behavior suggests a shared strategy for ligand binding and aptamer conformational change in the two riboswitches, based on thermodynamic adaptations in number of G-C basepairs and/or modifications in tertiary structure that stabilize the ligand-unbound conformation to achieve biocompetence under both hyperthermophilic and mesothermophilic conditions.
Collapse
Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado; Department of Chemistry, University of Colorado Boulder, Boulder, Colorado.
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado; Department of Chemistry, University of Colorado Boulder, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
| |
Collapse
|
7
|
Aguilar Suárez R, Kohlstedt M, Öktem A, Neef J, Wu Y, Ikeda K, Yoshida KI, Altenbuchner J, Wittmann C, van Dijl JM. Metabolic Profile of the Genome-Reduced Bacillus subtilis Strain IIG-Bs-27-39: An Attractive Chassis for Recombinant Protein Production. ACS Synth Biol 2024; 13:2199-2214. [PMID: 38981062 PMCID: PMC11264325 DOI: 10.1021/acssynbio.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is extensively used in the industry for the secretory production of proteins with commercial value. To further improve its performance, this microbe has been the subject of extensive genome engineering efforts, especially the removal of large genomic regions that are dispensable or even counterproductive. Here, we present the genome-reduced B. subtilis strain IIG-Bs-27-39, which was obtained through systematic deletion of mobile genetic elements, as well as genes for extracellular proteases, sporulation, flagella formation, and antibiotic production. Different from previously characterized genome-reduced B. subtilis strains, the IIG-Bs-27-39 strain was still able to grow on minimal media. We used this feature to benchmark strain IIG-Bs-27-39 against its parental strain 168 with respect to heterologous protein production and metabolic parameters during bioreactor cultivation. The IIG-Bs-27-39 strain presented superior secretion of difficult-to-produce staphylococcal antigens, as well as higher specific growth rates and biomass yields. At the metabolic level, changes in byproduct formation and internal amino acid pools were observed, whereas energetic parameters such as the ATP yield, ATP/ADP levels, and adenylate energy charge were comparable between the two strains. Intriguingly, we observed a significant increase in the total cellular NADPH level during all tested conditions and increases in the NAD+ and NADP(H) pools during protein production. This indicates that the IIG-Bs-27-39 strain has more energy available for anabolic processes and protein production, thereby providing a link between strain physiology and production performance. On this basis, we conclude that the genome-reduced strain IIG-Bs-27-39 represents an attractive chassis for future biotechnological applications.
Collapse
Affiliation(s)
- Rocío Aguilar Suárez
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Michael Kohlstedt
- Institute
for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Ayşegül Öktem
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Jolanda Neef
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| | - Yuzheng Wu
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Kaiya Ikeda
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Ken-Ichi Yoshida
- Department
of Science, Technology and Innovation, Kobe
University, 657-8501 Kobe, Japan
| | - Josef Altenbuchner
- Institute
for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christoph Wittmann
- Institute
for Systems Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University Medical
Center Groningen-University of Groningen, 9700RB Groningen, The Netherlands
| |
Collapse
|
8
|
Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
Collapse
Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| |
Collapse
|
9
|
Abdelhalim A, Mazrou YSA, Shahin N, El-Kot GA, Elzaawely AA, Maswada HF, Makhlouf AH, Nehela Y. Enhancing the Storage Longevity of Apples: The Potential of Bacillus subtilis and Streptomyces endus as Preventative Bioagents against Post-Harvest Gray Mold Disease, Caused by Botrytis cinerea. PLANTS (BASEL, SWITZERLAND) 2024; 13:1844. [PMID: 38999685 PMCID: PMC11243874 DOI: 10.3390/plants13131844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Gray mold, caused by Botrytis cinerea Pers. Fr., is one of the most vital plant diseases, causing extensive pre- and post-harvest losses in apple fruits. In the current study, we isolated and identified two potential endophytic bioagents, Bacillus subtilis and Streptomyces endus. Both bioagents exhibited a potent fungistatic effect against B. cinerea under both in vitro and in planta conditions. Moreover, two experiments were carried out; (i) the first experiment was conducted at room temperature after artificial inoculation with B. cinerea to monitor the progression of the infection and the corresponding biochemical responses of the apples. Our in vivo findings showed that the treated B. cinerea-infected apple fruits with the cell-free bacterial filtrate of B. subtilis and S. endus (dipping or wrapping) significantly reduced the rotten area of the treated apple at room temperature. Additionally, B. subtilis and S. endus enhanced the enzymatic (POX and PPO) and non-enzymatic (phenolics and flavonoids) antioxidant defense machinery in treated apples. (ii) The second experiment focused on the preventive effects of both bioagents over a 90-day storage period at 1 °C of healthy apples (no artificial inoculation). The application of both bacterial filtrates prolonged the storage period, reduced the relative weight loss, and maintained high-quality parameters including titratable acidity, firmness, and total soluble solids of apple fruits under cold storage at 1 °C. The Kaplan-Meier analysis of rotten apples over 90 days during cold storage showed that the treated apples lasted longer than the non-treated apples. Moreover, the lifespan of apple fruits dipped in the culture filtrate of B. subtilis, or a fungicide, was increased, with no significant differences, compared with the non-treated apples. The current results showed the possibility of using both bioagents as a safe and eco-friendly alternative to chemical fungicides to control gray mold disease in apples.
Collapse
Affiliation(s)
- Aya Abdelhalim
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Yasser S A Mazrou
- Business Administration Department, Community College, King Khalid University, Abha 62521, Saudi Arabia
| | - Nabila Shahin
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Gabr A El-Kot
- Department of Agricultural Botany, Faculty of Agriculture, Kafr Elsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Abdelnaser A Elzaawely
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Hanafey F Maswada
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| | - Abeer H Makhlouf
- Department of Agricultural Botany, Faculty of Agriculture, Minufiya University, Shibin El-Kom 6131567, Egypt
| | - Yasser Nehela
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt
| |
Collapse
|
10
|
Zhang G, Feng S, Qin M, Sun J, Liu Y, Luo C, Lin M, Xu S, Liao M, Fan H, Liang Z. Influence of PepF peptidase and sporulation on microcin J25 production in Bacillus subtilis. Microbiol Spectr 2024; 12:e0374823. [PMID: 38780256 PMCID: PMC11218540 DOI: 10.1128/spectrum.03748-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
The lasso peptide microcin J25 (MccJ25) possesses strong antibacterial properties and is considered a potential effective component of bacterial disease treatment drugs and safe food preservatives. Although MccJ25 can be heterologously expressed in Bacillus subtilis as we have previously reported, its regulation and accumulation are yet to be understood. Here, we investigated the expression level and stability of MccJ25 in B. subtilis strains with disruption in peptidase genes pepA, pepF, and pepT. Oligoendopeptidase F (PepF) was found to be involved in reduction of the production of MccJ25 by degradation of its precursor peptide. In the pepF mutant, the MccJ25 reached a concentration of 1.68 µM after a cultivation time exceeding 60 hours, while the wild-type strain exhibited a concentration of only 0.14 µM. Moreover, the production of MccJ25 in B. subtilis downregulated the genes associated with sporulation, and this may contribute to its accumulation. Finally, this study provides a strategy to improve the stability and production of MccJ25 in B. subtilis. IMPORTANCE MccJ25 displays significant antibacterial activity, a well-defined mode of action, exceptional safety, and remarkable stability. Hence, it presents itself as a compelling candidate for an optimal antibacterial or anti-endotoxin medication. The successful establishment of exogenous production of MccJ25 in Bacillus subtilis provides a strategy for reducing its production cost and diversifying its utilization. In this study, we have provided evidence indicating that both peptidase PepF and sporulation are significant factors that limit the expression of MccJ25 in B. subtilis. The ΔpepF and ΔsigF mutants of B. subtilis express MccJ25 with higher production yield and enhanced stability. To sum up, this study developed several better engineered strains of B. subtilis, which greatly reduced the consumption of MccJ25 during the nutrient depletion stage of the host strain, improved its production, and elucidated factors that may be involved in reducing MccJ25 accumulation in B. subtilis.
Collapse
Affiliation(s)
- Guangwen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Juan Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yutong Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Changqi Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Min Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Siqi Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Huiying Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Zhaoping Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| |
Collapse
|
11
|
Si H, Wang R, Zhao Y, Hao H, Zhao C, Xing S, Yu H, Liang X, Lu J, Chen X, Wang B. Large-scale soil application of hydrochar: Reducing its polycyclic aromatic hydrocarbon content and toxicity by heating. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134467. [PMID: 38691930 DOI: 10.1016/j.jhazmat.2024.134467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
The beneficial roles of hydrochar in carbon sequestration and soil improvement are widely accepted. Despite few available reports regarding polycyclic aromatic hydrocarbons (PAHs) generated during preparation, their potential negative impacts on ecosystems remain a concern. A heating treatment method was employed in this study for rapidly removing PAHs and reducing the toxicity of corn stover-based hydrochar (CHC). The result showed total PAHs content (∑PAH) decreased and then sharply increased within the temperature range from 150 °C to 400 °C. The ∑PAH and related toxicity in CHC decreased by more than 80% under 200 °C heating temperature, compared with those in the untreated sample, representing the lowest microbial toxicity. Benzo(a)pyrene produced a significant influence on the ecological toxicity of the hydrochar among the 16 types of PAHs. The impact of thermal treatment on the composition, content, and toxicity of PAHs was significantly influenced by the adsorption, migration, and desorption of PAHs within hydrochar pores, as well as the disintegration and aggregation of large molecular polymers. The combination of hydrochar with carbonized waste heat and exhaust gas collection could be a promising method to efficiently and affordably reduce hydrochar ecological toxicity.
Collapse
Affiliation(s)
- Hongyu Si
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Rui Wang
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Yuqing Zhao
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Han Hao
- Jinan Xinhang Experimental Foreign Language School, Jinan 250014, China
| | - Changkai Zhao
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Sen Xing
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Hewei Yu
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Xiaohui Liang
- School of Life Sciences, Qilu Normal University, Jinan 250200, China
| | - JiKai Lu
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Xiuxiu Chen
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China.
| | - Bing Wang
- Shandong Provincial Key Laboratory of Biomass Gasification Technology, Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China; School of Environment and Resources, Taiyuan University of Science and Technology, 66 Wa-liu Road, Taiyuan 030024, Shanxi, China.
| |
Collapse
|
12
|
Wang T, Shi Y, Zheng M, Zheng J. Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group. Microorganisms 2024; 12:986. [PMID: 38792815 PMCID: PMC11124052 DOI: 10.3390/microorganisms12050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.
Collapse
Affiliation(s)
- Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiling Shi
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhuo Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
13
|
Zhao L, Zhang S, Xiao R, Zhang C, Lyu Z, Zhang F. Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches. MICROBIAL ECOLOGY 2024; 87:67. [PMID: 38703220 PMCID: PMC11069485 DOI: 10.1007/s00248-024-02383-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.
Collapse
Affiliation(s)
- Likun Zhao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China
- The Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, 071002, People's Republic of China
| | - Shanfeng Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Ruoyi Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Chao Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Zhitang Lyu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China.
- The Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, 071002, People's Republic of China.
| | - Feng Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, People's Republic of China.
- The Key Laboratory of Zoological Systematics and Application of Hebei Province, Baoding, 071002, People's Republic of China.
| |
Collapse
|
14
|
Kim HS, Noh MH, White EM, Kandefer MV, Wright AF, Datta D, Lim HG, Smiggs E, Locklin JJ, Rahman MA, Feist AM, Pokorski JK. Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. Nat Commun 2024; 15:3338. [PMID: 38688899 PMCID: PMC11061138 DOI: 10.1038/s41467-024-47132-8] [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: 09/11/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
The field of hybrid engineered living materials seeks to pair living organisms with synthetic materials to generate biocomposite materials with augmented function since living systems can provide highly-programmable and complex behavior. Engineered living materials have typically been fabricated using techniques in benign aqueous environments, limiting their application. In this work, biocomposite fabrication is demonstrated in which spores from polymer-degrading bacteria are incorporated into a thermoplastic polyurethane using high-temperature melt extrusion. Bacteria are engineered using adaptive laboratory evolution to improve their heat tolerance to ensure nearly complete cell survivability during manufacturing at 135 °C. Furthermore, the overall tensile properties of spore-filled thermoplastic polyurethanes are substantially improved, resulting in a significant improvement in toughness. The biocomposites facilitate disintegration in compost in the absence of a microbe-rich environment. Finally, embedded spores demonstrate a rationally programmed function, expressing green fluorescent protein. This research provides a scalable method to fabricate advanced biocomposite materials in industrially-compatible processes.
Collapse
Affiliation(s)
- Han Sol Kim
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Myung Hyun Noh
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30 Jongga-ro, Ulsan, 44429, Republic of Korea
| | - Evan M White
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | | | - Austin F Wright
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Debika Datta
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Ethan Smiggs
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jason J Locklin
- New Materials Institute, University of Georgia, Athens, GA, 30602, USA
| | - Md Arifur Rahman
- Thermoplastic Polyurethane Research, BASF Corporation, 1609 Biddle Ave., Wyandotte, MI, 48192, USA.
| | - Adam M Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs, Lyngby, Denmark.
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
- Institute for Materials Discovery and Design, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| |
Collapse
|
15
|
Hansel J, Saville AC, Ristaino JB. Evaluation of a Formulation of Bacillus subtilis for Control of Phytophthora Blight of Bell Pepper. PLANT DISEASE 2024; 108:1014-1024. [PMID: 38085974 DOI: 10.1094/pdis-04-23-0807-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Phytophthora blight, caused by Phytophthora capsici, is one of the most economically significant diseases of bell pepper in the United States. Over the past several decades, isolates of P. capsici exhibiting resistance to mefenoxam and other fungicides have been reported. Fungicide resistance coupled with an increased market for organically grown crops has led to interest in biological control as a disease management option. In this work, an isolate of Bacillus subtilis (AFS032321) was evaluated for control of Phytophthora blight of bell pepper in the greenhouse and field. A 28% active ingredient wettable powder formulation of the strain was applied as a soil drench at transplanting prior to inoculation. Treatment with this formulation of B. subtilis significantly reduced the area under the disease progress curve (AUDPC) by up to 52% compared to untreated control plants in greenhouse tests. Comparisons between applying the biocontrol weekly after seeding for 5 weeks versus a single application at transplanting (5 weeks) indicated no significant benefits of additional applications. The formulation of B. subtilis reduced disease caused by a mefenoxam-resistant isolate of P. capsici, while mefenoxam failed. The biocontrol efficacy of formulated strains was not affected in different soil types or potting media. However, disease was more severe in sandy soils. In field experiments that were conducted with a mefenoxam-sensitive isolate, disease incidence and severity of Phytophthora blight were significantly reduced at all rates of B. subtilis in 2019 except the 16.8 kg ha-1 rate. In both years, mefenoxam was more effective than B. subtilis in controlling disease in the field. B. subtilis did not affect the spatial dynamics of pathogen spread within rows. While the precise mechanism(s) of action is unclear, in vitro dual-culture tests suggest direct antagonism, as B. subtilis significantly inhibited colony growth of P. capsici. AgBiome has recently released a new formulation of the AFS032321 strain named Theia, with higher active ingredients for commercial applications and biocontrol of P. capsici.
Collapse
Affiliation(s)
- Jeana Hansel
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC 27695
| | - Amanda C Saville
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC 27695
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC 27695
- Emerging Plant Disease and Global Food Security Cluster, NC State University, Raleigh, NC 27695
| |
Collapse
|
16
|
Ashajyothi M, Mahadevakumar S, Venkatesh YN, Sarma PVSRN, Danteswari C, Balamurugan A, Prakash G, Khandelwal V, Tarasatyavathi C, Podile AR, Mysore KS, Chandranayaka S. Comprehensive genomic analysis of Bacillus subtilis and Bacillus paralicheniformis associated with the pearl millet panicle reveals their antimicrobial potential against important plant pathogens. BMC PLANT BIOLOGY 2024; 24:197. [PMID: 38500040 PMCID: PMC10946124 DOI: 10.1186/s12870-024-04881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Plant microbiome confers versatile functional roles to enhance survival fitness as well as productivity. In the present study two pearl millet panicle microbiome member species Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36 found to have beneficial traits including plant growth promotion and broad-spectrum antifungal activity towards taxonomically diverse plant pathogens. Understanding the genomes will assist in devising a bioformulation for crop protection while exploiting their beneficial functional roles. RESULTS Two potential firmicute species were isolated from pearl millet panicles. Morphological, biochemical, and molecular characterization revealed their identities as Bacillus subtilis PBs 12 and Bacillus paralicheniformis PBl 36. The seed priming assays revealed the ability of both species to enhance plant growth promotion and seedling vigour index. Invitro assays with PBs 12 and PBl 36 showed the antibiosis effect against taxonomically diverse plant pathogens (Magnaporthe grisea; Sclerotium rolfsii; Fusarium solani; Alternaria alternata; Ganoderma sp.) of crops and multipurpose tree species. The whole genome sequence analysis was performed to unveil the genetic potential of these bacteria for plant protection. The complete genomes of PBs 12 and PBl 36 consist of a single circular chromosome with a size of 4.02 and 4.33 Mb and 4,171 and 4,606 genes, with a G + C content of 43.68 and 45.83%, respectively. Comparative Average Nucleotide Identity (ANI) analysis revealed a close similarity of PBs 12 and PBl 36 with other beneficial strains of B. subtilis and B. paralicheniformis and found distant from B. altitudinis, B. amyloliquefaciens, and B. thuringiensis. Functional annotation revealed a majority of pathway classes of PBs 12 (30) and PBl 36 (29) involved in the biosynthesis of secondary metabolites, polyketides, and non-ribosomal peptides, followed by xenobiotic biodegradation and metabolism (21). Furthermore, 14 genomic regions of PBs 12 and 15 of PBl 36 associated with the synthesis of RiPP (Ribosomally synthesized and post-translationally modified peptides), terpenes, cyclic dipeptides (CDPs), type III polyketide synthases (T3PKSs), sactipeptides, lanthipeptides, siderophores, NRPS (Non-Ribosomal Peptide Synthetase), NRP-metallophone, etc. It was discovered that these areas contain between 25,458 and 33,000 secondary metabolite-coding MiBiG clusters which code for a wide range of products, such as antibiotics. The PCR-based screening for the presence of antimicrobial peptide (cyclic lipopeptide) genes in PBs 12 and 36 confirmed their broad-spectrum antifungal potential with the presence of spoVG, bacA, and srfAA AMP genes, which encode antimicrobial compounds such as subtilin, bacylisin, and surfactin. CONCLUSION The combined in vitro studies and genome analysis highlighted the antifungal potential of pearl millet panicle-associated Bacillus subtilis PBs12 and Bacillus paralicheniformis PBl36. The genetic ability to synthesize several antimicrobial compounds indicated the industrial value of PBs 12 and PBl 36, which shed light on further studies to establish their action as a biostimulant for crop protection.
Collapse
Affiliation(s)
- Mushineni Ashajyothi
- Plant Protection Lab, ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, 284003, India
| | - Shivannegowda Mahadevakumar
- Botanical Survey of India, Andaman and Nicobar Regional Centre, Haddo, Port Blair, Andaman and Nicobar Islands, 744102, India
| | - Y N Venkatesh
- Plant Protection Lab, ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, 284003, India
| | - Pullabhotla V S R N Sarma
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Chalasani Danteswari
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | | | - Ganesan Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vikas Khandelwal
- All India Coordinated Research Project On Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342304, India
| | - C Tarasatyavathi
- All India Coordinated Research Project On Pearl Millet, Agriculture University, Jodhpur, Rajasthan, 342304, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Kirankumar S Mysore
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - Siddaiah Chandranayaka
- Department of Studies in Biotechnology, University of Mysore, Mysore, Karnataka, 570 006, India.
| |
Collapse
|
17
|
Ochi T, Oh K, Konishi H. Pylephlebitis Caused by Bacillus subtilis and Fusobacterium nucleatum. Intern Med 2024; 63:799-802. [PMID: 37438133 PMCID: PMC11009003 DOI: 10.2169/internalmedicine.2150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/05/2023] [Indexed: 07/14/2023] Open
Abstract
A 90-year-old man presented with a 3-day history of general malaise. He was febrile (39.3°C) but the initial evaluation did not reveal the cause of the fever. After admission, Bacillus subtilis and Fusobacterium nucleatum were grown from multiple sets of blood cultures. In addition, contrast-enhanced computed tomography revealed thrombi in the portal vein and superior mesenteric vein; he was diagnosed with pylephlebitis. After receiving antimicrobial treatment and anticoagulation, the patient was cured. Pylephlebitis is a rare condition and may be the cause of unknown fevers. This is the first reported case of pylephlebitis caused by Bacillus subtilis.
Collapse
Affiliation(s)
- Tatsuya Ochi
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
- Department of Emergency and Critical Care Medicine, Hyogo Emergency Medical Center, Japan
| | - Koji Oh
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
| | - Hiroki Konishi
- Department of General Internal Medicine, Kobe City Medical Center West Hospital, Japan
| |
Collapse
|
18
|
Hao Z, Ding X, Wang J. Effects of gut bacteria and their metabolites on gut health of animals. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:223-252. [PMID: 38763528 DOI: 10.1016/bs.aambs.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The intestine tract is a vital site for the body to acquire nutrients, serving as the largest immune organ. Intestinal health is crucial for maintaining a normal physiological state. Abundant microorganisms reside in the intestine, colonized in a symbiotic manner. These microorganisms can generate various metabolites that influence host physiological activities. Microbial metabolites serve as signaling molecules or metabolic substrates in the intestine, and some intestinal microorganisms act as probiotics and promote intestinal health. Researches on host, probiotics, microbial metabolites and their interactions are ongoing. This study reviews the effects of gut bacteria and their metabolites on intestinal health to provide useful references for animal husbandry.
Collapse
Affiliation(s)
- Zhuang Hao
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China
| | - Xuedong Ding
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China
| | - Jing Wang
- College of Animal Science and Technology, Nanjing Agricultural University, National Center for International Research on Animal Gut Nutrition, Nanjing, Jiangsu, P.R. China.
| |
Collapse
|
19
|
Naveed M, Wen S, Chan MWH, Wang F, Aslam S, Yin X, Xu B, Ullah A. Expression of BSN314 lysozyme genes in Escherichia coli BL21: a study to demonstrate microbicidal and disintegarting potential of the cloned lysozyme. Braz J Microbiol 2024; 55:215-233. [PMID: 38146050 PMCID: PMC10920529 DOI: 10.1007/s42770-023-01219-4] [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: 09/09/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
This study is an extension of our previous studies in which the lysozyme was isolated and purified from Bacillus subtilis BSN314 (Naveed et al., 2022; Naveed et al., 2023). In this study, the lysozyme genes were cloned into the E. coli BL21. For the expression of lysozyme in E. coli BL21, two target genes, Lyz-1 and Lyz-2, were ligated into the modified vector pET28a to generate pET28a-Lyz1 and pET28a-Lyz2, respectively. To increase the production rate of the enzyme, 0.5-mM concentration of IPTG was added to the culture media and incubated at 37 °C and 220 rpm for 24 h. Lyz1 was identified as N-acetylmuramoyl-L-alanine amidase and Lyz2 as D-alanyl-D-alanine carboxypeptidase. They were purified by multi-step methodology (ammonium sulfate, precipitation, dialysis, and ultrafiltration), and antimicrobial activity was determined. For Lyz1, the lowest MIC/MBC (0.25 μg/mL; with highest ZOI = 22 mm) were recorded against Micrococcus luteus, whereas the highest MIC/MBC with lowest ZOI were measured against Salmonella typhimurium (2.50 μg /mL; with ZOI = 10 mm). As compared with Aspergillus oryzae (MIC/MFC; 3.00 μg/mL), a higher concentration of lysozyme was required to control the growth of Saccharomyces cerevisiae (MIC/MFC; 50 μg/mL). Atomic force microscopy (AFM) was used to analyze the disintegrating effect of Lyz1 on the cells of selected Gram-positive bacteria, Gram-negative bacteria, and yeast. The AFM results showed that, as compared to Gram-negative bacteria, a lower concentration of lysozyme (Lyz1) was required to disintegrate the cell of Gram-positive bacteria.
Collapse
Affiliation(s)
- Muhammad Naveed
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Sai Wen
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Malik Wajid Hussain Chan
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China.
| | - Fenghuan Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China.
| | - Sadar Aslam
- Department of Zoology, University of Baltistan, Skardu, Pakistan
| | - Xian Yin
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Baocai Xu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Asad Ullah
- Food and Marine Resources Research Center, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, 75280, Pakistan
| |
Collapse
|
20
|
Mohamadzadeh M, Ghiasi M, Aghamollaei H. Optimization of plasmid electrotransformation into Bacillus subtilis using an antibacterial peptide. Arch Microbiol 2024; 206:116. [PMID: 38388903 DOI: 10.1007/s00203-024-03847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 02/24/2024]
Abstract
Bacillus subtilis can potentially serve as an efficient expression host for biotechnology due to its ability to secrete extracellular proteins and enzymes directly into the culture medium. One of the important challenges in the biotechnology industry is to optimize the transformation conditions of B. subtilis bacteria. This study aims to provide a new method to optimize the transformation conditions and improve the transformation efficiency of B. subtilis WB600. To increase the transformation efficiency in B. subtilis, two methods of adding CM11 antibacterial peptides to the bacterial medium along with electroporation and optimizing the variables including the growth medium composition, time to adding CM11 peptide, electroporation voltage, recovery medium, and cell recovery time are used. The results of this study showed that the addition of antimicrobial peptides (AMPs) with a concentration of 2 μg/ml increases the transformation efficiency by 4 times compared to the absence of AMP in the bacterial medium. Additionally, the findings from our study indicated that the most optimal rate of transformation for B. subtilis was observed at a voltage of 7.5 kV/cm, with a recovery period of 12 h. With the optimized method, the transformation efficiency came up to 1.69 × 104 CFU/µg DNA. This improvement in transformation efficiency will be attributed to the research of expression of exogenous genes in B. subtilis, gene library construction for transformation of wild-type B. subtilis strains.
Collapse
Affiliation(s)
| | - Mohsen Ghiasi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hossein Aghamollaei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
21
|
So YJ, Park OJ, Kwon Y, Im J, Lee D, Yun SH, Cho K, Yun CH, Han SH. Bacillus subtilis Induces Human Beta Defensin-2 Through its Lipoproteins in Human Intestinal Epithelial Cells. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10224-4. [PMID: 38376819 DOI: 10.1007/s12602-024-10224-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 02/21/2024]
Abstract
Human intestinal epithelial cells (IECs) play an important role in maintaining gut homeostasis by producing antimicrobial peptides (AMPs). Bacillus subtilis, a commensal bacterium, is considered a probiotic. Although its protective effects on intestinal health are widely reported, the key component of B. subtilis responsible for its beneficial effects remains elusive. In this study, we tried to identify the key molecules responsible for B. subtilis-induced AMPs and their molecular mechanisms in a human IEC line, Caco-2. B. subtilis increased human beta defensin (HBD)-2 mRNA expression in a dose- and time-dependent manner. Among the B. subtilis microbe-associated molecular patterns, lipoprotein (LPP) substantially increased the mRNA expression and protein production of HBD-2, whereas lipoteichoic acid and peptidoglycan did not show such effects. Those results were confirmed in primary human IECs. In addition, both LPP recognition and HBD-2 secretion mainly took place on the apical side of fully differentiated and polarized Caco-2 cells through Toll-like receptor 2-mediated JNK/p38 MAP kinase/AP-1 and NF-κB pathways. HBD-2 efficiently inhibited the growth of the intestinal pathogens Staphylococcus aureus and Bacillus cereus. Furthermore, LPPs pre-incubated with lipase or proteinase K decreased LPP-induced HBD-2 expression, suggesting that the lipid and protein moieties of LPP are crucial for HBD-2 expression. Q Exactive Plus mass spectrometry identified 35 B. subtilis LPP candidates within the LPP preparation, and most of them were ABC transporters. Taken together, these results suggest that B. subtilis promotes HBD-2 secretion in human IECs mainly with its LPPs, which might enhance the protection from intestinal pathogens.
Collapse
Affiliation(s)
- Yoon Ju So
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ok-Jin Park
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yeongkag Kwon
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jintaek Im
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongwook Lee
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Ho Yun
- Center for Research Equipment, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Kun Cho
- Center for Research Equipment, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
22
|
Medeiros L, Dall'Agno L, Riet J, Nornberg B, Azevedo R, Cardoso A, da Silva JLS, de Sousa OV, Rosas VT, Tesser MB, Pedrosa VF, Romano LA, Wasielesky W, Marins LF. A native strain of Bacillus subtilis increases lipid accumulation and modulates expression of genes related to digestion and amino acid metabolism in Litopenaeus vannamei. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110924. [PMID: 37995828 DOI: 10.1016/j.cbpb.2023.110924] [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: 09/18/2023] [Revised: 10/28/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
In the field of shrimp aquaculture, the utilization of probiotics represents a promising avenue, due to the well-documented benefits conferred by these microorganisms. In the current study, a Bacillus subtilis strain, referred to as strain E, was isolated from the gastrointestinal tract of the shrimp Litopenaeus vannamei and subsequently identified via molecular methods and phylogeny. The probiotic potential of strain E was characterized, and its application as a feed shrimp additive was evaluated in a 45-day experiment. Several parameters were assessed, including zootechnical performance, muscle tissue proximate composition, hepatopancreas lipid concentration, and the expression of genes associated with digestion, amino acid metabolism, and antioxidant defense mechanisms in various shrimp tissues. Although no significant impact on zootechnical performance was observed, supplementation with strain E led to an increase in lipid concentration within both muscle and hepatopancreas tissues. Furthermore, a marked decrease in the expression of genes linked to digestion and amino acid metabolism was noted. These findings suggest that the addition of the B. subtilis strain E to shrimp feed may enhance nutrient absorption and modulate the expression of genes related to digestion and amino acid metabolism.
Collapse
Affiliation(s)
- Luiza Medeiros
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil. https://twitter.com/Luf07709017
| | - Laura Dall'Agno
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Jade Riet
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Bruna Nornberg
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Raíza Azevedo
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Arthur Cardoso
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | | | - Oscarina Viana de Sousa
- Environmental and Fish Microbiology Laboratory, Marine Sciences Institute, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Marcelo Borges Tesser
- Laboratory of Nutrition of Aquatic Organisms, Institute of Oceanography, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Virgínia F Pedrosa
- Laboratory of Immunology and Pathology of Aquatic Organisms, Institute of Oceanography, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Luis A Romano
- Laboratory of Immunology and Pathology of Aquatic Organisms, Institute of Oceanography, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Wilson Wasielesky
- Laboratory of Shrimp Culture, Institute of Oceanography, Federal University of Rio Grande, Rio Grande, RS, Brazil
| | - Luis F Marins
- LEGENE - Research Group in Genetic Engineering and Biotechnology, Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, RS, Brazil.
| |
Collapse
|
23
|
Bontà V, Battelli M, Rama E, Casanova M, Pasotti L, Galassi G, Colombini S, Calvio C. An In Vitro Study on the Role of Cellulases and Xylanases of Bacillus subtilis in Dairy Cattle Nutrition. Microorganisms 2024; 12:300. [PMID: 38399704 PMCID: PMC10891753 DOI: 10.3390/microorganisms12020300] [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: 01/16/2024] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The administration of Bacilli to dairy cows exerts beneficial effects on dry matter intake, lactation performance, and milk composition, but the rationale behind their efficacy is still poorly understood. In this work, we sought to establish whether cellulases and xylanases, among the enzymes secreted by B. subtilis, are involved in the positive effect exerted by Bacilli on ruminal performance. We took advantage of two isogenic B. subtilis strains, only differing in the secretion levels of those two enzymes. A multi-factorial study was conducted in which eight feed ingredients were treated in vitro, using ruminal fluid from cannulated cows, with cultures of the two strains conveniently grown in a growth medium based on inexpensive waste. Feed degradability and gas production were assessed. Fiber degradability was 10% higher (p < 0.001) in feeds treated with the enzyme-overexpressing strain than in the untreated control, while the non-overexpressing strain provided a 5% increase. The benefit of the fibrolytic enzymes was maximal for maize silage, the most recalcitrant feed. Gas production also correlated with the amount of enzymes applied (p < 0.05). Our results revealed that B. subtilis cellulases and xylanases effectively contribute to improving forage quality, justifying the use of Bacilli as direct-fed microbials to increase animal productivity.
Collapse
Affiliation(s)
- Valeria Bontà
- Laboratories of Genetics and Microbiology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Marco Battelli
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (M.B.); (G.G.); (S.C.)
| | - Erlinda Rama
- Laboratories of Genetics and Microbiology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Michela Casanova
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100 Pavia, Italy (L.P.)
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100 Pavia, Italy (L.P.)
| | - Gianluca Galassi
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (M.B.); (G.G.); (S.C.)
| | - Stefania Colombini
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (M.B.); (G.G.); (S.C.)
| | - Cinzia Calvio
- Laboratories of Genetics and Microbiology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| |
Collapse
|
24
|
Ulker Turan C, Derviscemaloglu M, Guvenilir Y. Herbal active ingredient-loaded poly(ω-pentadecalactone-co-δ-valerolactone)/gelatin nanofibrous membranes. Eur J Pharm Biopharm 2024; 194:62-73. [PMID: 38042509 DOI: 10.1016/j.ejpb.2023.11.021] [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: 08/23/2023] [Revised: 11/21/2023] [Accepted: 11/25/2023] [Indexed: 12/04/2023]
Abstract
Recently, there has been an accelerating interest in novel biocompatible wound dressings made of nano-sized materials, especially nanofibers. Electrospun nanofibers provide high surface area and mimic the extracellular matrix which enhances biocompatibility. Besides, nanofibrous structures have high active ingredient loading capacity as a result of their high surface-to-volume ratio and porosity. In the present study, curcumin-loaded poly(ω-pentadecalactone-co-δ-valerolactone)/gelatin (PDL-VL/Gel) nanofibrous membranes were fabricated to be used for healing skin wounds. Poly(ω-pentadecalactone-co-δ-valerolactone) copolymer has been enzymatically synthesized in previous studies, thus it improves the originality of the membrane. It was aimed to obtain a synergetic effect and increase the novelty of the work by blending synthetic and natural polymers. Moreover, it was preferred to provide antibacterial activity by the incorporation of a herbal ingredient (curcumin) as a natural alternative to commercial antibiotics. Varied amounts of curcumin (5-25 %, w:v) were electrospun together with PDL-VL/Gel (equal volume ratio) polymer blend (fiber diameters ranged between 554 and 1074 nm) and several characterizations (morphological and molecular structure, wettability characteristics, and thermal behavior) were applied to examine the curcumin incorporation. Afterwards, in vitro curcumin release studies were carried out and mathematical modeling was applied to release data to clarify the transport mechanism. Curcumin release profiles comprised of an initial burst release in the first hour followed by a sustained release through 24 h. Based on the antibacterial activity test results, 15 % curcumin loading ratio was found to be sufficient for the treatment of skin wounds infected by Gram-negative (E. coli) and Gram-positive (S. aureus and B. subtilis) bacteria. Additionally, nanofibrous membranes did not lead to cytotoxicity, and curcumin content further enhanced the viability of fibroblasts. Thus, the presented antibacterial nanofibrous membrane is suggested to be applied for the treatment of wound infections and accelerating the healing process.
Collapse
Affiliation(s)
- Cansu Ulker Turan
- Gebze Technical University, Department of Bioengineering, Kocaeli 41400, Turkey.
| | - Mete Derviscemaloglu
- Istanbul Technical University, Department of Molecular Biology and Genetics, Istanbul 34369, Turkey
| | - Yuksel Guvenilir
- Istanbul Technical University, Department of Chemical Engineering, Istanbul 34369, Turkey
| |
Collapse
|
25
|
Valencia-Marin MF, Chávez-Avila S, Guzmán-Guzmán P, Orozco-Mosqueda MDC, de Los Santos-Villalobos S, Glick BR, Santoyo G. Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health. Biotechnol Adv 2024; 70:108303. [PMID: 38128850 DOI: 10.1016/j.biotechadv.2023.108303] [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: 08/16/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.
Collapse
Affiliation(s)
- María F Valencia-Marin
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Salvador Chávez-Avila
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Paulina Guzmán-Guzmán
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México en Celaya, 38010 Celaya, Gto, Mexico
| | | | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico.
| |
Collapse
|
26
|
Dergham Y, Le Coq D, Bridier A, Sanchez-Vizuete P, Jbara H, Deschamps J, Hamze K, Yoshida KI, Noirot-Gros MF, Briandet R. Bacillus subtilis NDmed, a model strain for biofilm genetic studies. Biofilm 2023; 6:100152. [PMID: 37694162 PMCID: PMC10485040 DOI: 10.1016/j.bioflm.2023.100152] [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: 03/27/2023] [Revised: 06/20/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.
Collapse
Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hadi Jbara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| |
Collapse
|
27
|
Walgraeve J, Ferrero-Bordera B, Maaß S, Becher D, Schwerdtfeger R, van Dijl JM, Seefried M. Diamide-based screening method for the isolation of improved oxidative stress tolerance phenotypes in Bacillus mutant libraries. Microbiol Spectr 2023; 11:e0160823. [PMID: 37819171 PMCID: PMC10714788 DOI: 10.1128/spectrum.01608-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE During their life cycle, bacteria are exposed to a range of different stresses that need to be managed appropriately in order to ensure their growth and viability. This applies not only to bacteria in their natural habitats but also to bacteria employed in biotechnological production processes. Oxidative stress is one of these stresses that may originate either from bacterial metabolism or external factors. In biotechnological settings, it is of critical importance that production strains are resistant to oxidative stresses. Accordingly, this also applies to the major industrial cell factory Bacillus subtilis. In the present study, we, therefore, developed a screen for B. subtilis strains with enhanced oxidative stress tolerance. The results show that our approach is feasible and time-, space-, and resource-efficient. We, therefore, anticipate that it will enhance the development of more robust industrial production strains with improved robustness under conditions of oxidative stress.
Collapse
Affiliation(s)
| | | | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | | | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | |
Collapse
|
28
|
BiBi A, Bibi S, Al-Ghouti MA, Abu-Dieyeh MH. Isolation and evaluation of Qatari soil rhizobacteria for antagonistic potential against phytopathogens and growth promotion in tomato plants. Sci Rep 2023; 13:22050. [PMID: 38086854 PMCID: PMC10716397 DOI: 10.1038/s41598-023-49304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
Plant growth promoting rhizobacteria are a diverse group of microorganisms that enhance the growth of plants under various conditions. In this study, 55 isolates of endogenous rhizobacteria were collected from the rhizosphere of Avicennia marina, Suaeda vermiculata, Salsola soda, Anabasis setifera, Salicornia europaea, Arthrocnemum macrostachyum, Limonium axillare, Tetraena qatarensis, Aeluropus lagopoides, and Prosopis juliflora. The isolates were evaluated in-vitro for their antagonist potential against Fusarium oxysporum and Botrytis cinerea using the dual culture technique, where the maximum growth inhibition reached 49% and 57%, respectively. In-vivo evaluation was accomplished to determine the growth-promoting potential of the rhizobacteria under greenhouse conditions where the strain ANABR3 (Bacillus subtilis) showed the strongest growth-promoting effects. Further in-vivo testing regarding the effectiveness of rhizobacteria in the presence of the phytopathogen was also completed using the Hoagland medium. LEMR3 and SALIR5 (both identified as two strains of B. subtilis) supported the tomato seedlings to overcome the disease and significantly (p ≤ 0.05) increased above and belowground biomass compared to the control. Additionally, several characterizing tests were carried out on the selected strains, these strains were found to possess numerous features that promote plant growth directly and indirectly such as the production of IAA, HCN, hydrolytic enzymes, ACC deaminase, NH3, and some rhizobacteria were capable of phosphate solubilization. In conclusion, this study showed that local rhizobacterial isolates collected from arid lands possess valuable traits, making them promising bio-control agents and bio-fertilizers for agricultural purposes.
Collapse
Affiliation(s)
- Amina BiBi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Shazia Bibi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Mohammad A Al-Ghouti
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Scieances, Qatar University, P.O. Box: 2713, Doha, Qatar
| | - Mohammed H Abu-Dieyeh
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box: 2713, Doha, Qatar.
| |
Collapse
|
29
|
Vasiliauskienė D, Lukša J, Servienė E, Urbonavičius J. Changes in the Bacterial Communities of Biocomposites with Different Flame Retardants. Life (Basel) 2023; 13:2306. [PMID: 38137906 PMCID: PMC10744946 DOI: 10.3390/life13122306] [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: 11/13/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In today's world, the use of environmentally friendly materials is strongly encouraged. These materials derive from primary raw materials of plant origin, like fibrous hemp, flax, and bamboo, or recycled materials, such as textiles or residual paper, making them suitable for the growth of microorganisms. Here, we investigate changes in bacterial communities in biocomposites made of hemp shives, corn starch, and either expandable graphite or a Flovan compound as flame retardants. Using Next Generation Sequencing (NGS), we found that after 12 months of incubation at 22 °C with a relative humidity of 65%, Proteobacteria accounted for >99.7% of the microbiome in composites with either flame retardant. By contrast, in the absence of flame retardants, the abundance of Proteobacteria decreased to 32.1%, while Bacteroidetes (36.6%), Actinobacteria (8.4%), and Saccharobacteria (TM7, 14.51%) appeared. Using the increasing concentrations of either expandable graphite or a Flovan compound in an LB medium, we were able to achieve up to a 5-log reduction in the viability of Bacillus subtilis, Pseudomonas aeruginosa, representatives of the Bacillus and Pseudomonas genera, the abundance of which varied in the biocomposites tested. Our results demonstrate that flame retardants act on both Gram-positive and Gram-negative bacteria and suggest that their antimicrobial activities also have to be tested when producing new compounds.
Collapse
Affiliation(s)
| | | | | | - Jaunius Urbonavičius
- Department of Chemistry and Bioengineering, Faculty of Fundamental Sciences, Vilnius Gediminas Technical University (VILNIUS TECH), Saulėtekio al. 11, 10223 Vilnius, Lithuania; (D.V.); (J.L.); (E.S.)
| |
Collapse
|
30
|
Su X, Fang T, Fang L, Wang D, Jiang X, Liu C, Zhang H, Guo R, Wang J. Effects of short-term exposure to simulated microgravity on the physiology of Bacillus subtilis and multiomic analysis. Can J Microbiol 2023; 69:464-478. [PMID: 37463516 DOI: 10.1139/cjm-2023-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
In our study, Bacillus subtilis was disposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14 days, while the control group was disposed to the same bioreactors in a normal gravity (NG) environment for 14 days. The B. subtilis strain exposed to the SMG (labeled BSS) showed an enhanced growth ability, increased biofilm formation ability, increased sensitivity to ampicillin sulbactam and cefotaxime, and some metabolic alterations compared with the B. subtilis strain under NG conditions (labeled BSN) and the original strain of B. subtilis (labeled BSO). The differentially expressed proteins (DEPs) associated with an increased growth rate, such as DNA strand exchange activity, oxidoreductase activity, proton-transporting ATP synthase complex, and biosynthetic process, were significantly upregulated in BSS. The enhanced biofilm formation ability may be related with the DEPs of spore germination and protein processing in BSS, and differentially expressed genes involved in protein localization and peptide secretion were also significantly enriched. The results revealed that SMG may increase the level of related functional proteins by upregulating or downregulating affiliated genes to change physiological characteristics and modulate growth ability, biofilm formation ability (epsB, epsC, epsN), antibiotic sensitivity (penP) and metabolism. Our experiment may gives new ideas for the study of space microbiology.
Collapse
Affiliation(s)
- Xiaolei Su
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Tingzheng Fang
- Sixth Department of Health Care, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Lin Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Dapeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Xuege Jiang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Changting Liu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Honglei Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Rui Guo
- Department of Otorhinolaryngology Head and Neck Surgery, Air Force Medical Center, PLA, Beijing, China
| | - Junfeng Wang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center and National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
31
|
Solís-Sandí I, Cordero-Fuentes S, Pereira-Reyes R, Vega-Baudrit JR, Batista-Menezes D, Montes de Oca-Vásquez G. Optimization of the biosynthesis of silver nanoparticles using bacterial extracts and their antimicrobial potential. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 40:e00816. [PMID: 38020726 PMCID: PMC10643114 DOI: 10.1016/j.btre.2023.e00816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
In the present study, silver nanoparticles (AgNPs) were biosynthesized using the supernatant and the intracellular extract of Cupriavidus necator, Bacillus megaterium, and Bacillus subtilis. The characterization of the AgNPs was carried out using UV-Vis spectroscopy, FTIR, DLS and TEM. Resazurin microtiter-plate assay was used to determine the antimicrobial action of AgNPs against Escherichia coli. UV-Visible spectra showed peaks between 414 and 460 nm. TEM analysis revealed that the synthesized AgNPs showed mostly spherical shapes. DLS results determined sizes from 20.8 to 118.4 nm. The highest antimicrobial activity was obtained with the AgNPs synthesized with supernatant rather than those using the intracellular extract. Therefore, it was determined that the bacterial species, temperature, pH, and type of extract (supernatant or intracellular) influence the biosynthesis. This synthesis thus offers a simple, environmentally friendly, and low-cost method for the production of AgNPs, which can be used as antibacterial agents.
Collapse
Affiliation(s)
- Iván Solís-Sandí
- School of Biology, Tecnológico de Costa Rica, Campus Central, 159-7050 Cartago, Costa Rica
| | - Sara Cordero-Fuentes
- School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Reinaldo Pereira-Reyes
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica
| | - José Roberto Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica
- Laboratory of Polymer Science and Technology, School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Diego Batista-Menezes
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica
| | - Gabriela Montes de Oca-Vásquez
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica
- Center for Sustainable Development Studies, Universidad Técnica Nacional, 1902-4050, Alajuela, Costa Rica
| |
Collapse
|
32
|
Loney RE, Delesalle VA, Chaudry BE, Czerpak M, Guffey AA, Goubet-McCall L, McCarty M, Strine MS, Tanke NT, Vill AC, Krukonis GP. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023; 15:2267. [PMID: 38005943 PMCID: PMC10674732 DOI: 10.3390/v15112267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.
Collapse
Affiliation(s)
- Rachel E. Loney
- University Program in Genetics and Genomics, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Véronique A. Delesalle
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | | | - Megan Czerpak
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Alexandra A. Guffey
- Janssen Scientific Affairs, LLC. 200 Tournament Dr., Horsham, PA 19044, USA;
| | - Leo Goubet-McCall
- Department of Biology, The Pennsylvania State University, 201 Huck Life Sciences Building, University Park, PA 16802, USA;
| | - Michael McCarty
- Department of Biology, Gettysburg College, 300 N Washington St., Gettysburg, PA 17325, USA; (M.C.); (M.M.)
| | - Madison S. Strine
- Department of Immunobiology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA;
| | - Natalie T. Tanke
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Albert C. Vill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA;
| | - Greg P. Krukonis
- Department of Biology, Angelo State University, Cavness Science Building 101, ASU Station #10890, San Angelo, TX 76909, USA;
| |
Collapse
|
33
|
Aina ST, Kyomuhimbo HD, Du Plessis B, Mjimba V, Haneklaus N, Brink HG. Cytotoxic-Ag-Modified Eggshell Membrane Nanocomposites as Bactericides in Concrete Mortar. Int J Mol Sci 2023; 24:15463. [PMID: 37895142 PMCID: PMC10607369 DOI: 10.3390/ijms242015463] [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: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Against the backdrop of escalating infrastructure budgets worldwide, a notable portion-up to 45%-is allocated to maintenance endeavors rather than innovative infrastructure development. A substantial fraction of this maintenance commitment involves combatting concrete degradation due to microbial attacks. In response, this study endeavors to propose a remedial strategy employing nano metals and repurposed materials within cement mortar. The methodology entails the adsorption onto eggshell membranes (ESM) of silver nitrate (ESM/AgNO3) or silver nanoparticles (ESM/AgNPs) yielding silver-eggshell membrane composites. Subsequently, the resulting silver-eggshell membrane composites were introduced in different proportions to replace cement, resulting in the formulation of ten distinct mortar compositions. A thorough analysis encompassing a range of techniques, such as spectrophotometry, scanning electron microscopy, thermogravimetric analysis, X-ray fluorescence analysis, X-ray diffraction (XRD), and MTT assay, was performed on these composite blends. Additionally, evaluations of both compressive and tensile strengths were carried out. The mortar blends 3, 5, and 6, characterized by 2% ESM/AgNO3, 1% ESM/AgNPs, and 2% ESM/AgNPs cement replacement, respectively, exhibited remarkable antimicrobial efficacy, manifesting in substantial reduction in microbial cell viability (up to 50%) of typical waste activated sludge. Concurrently, a marginal reduction of approximately 10% in compressive strength was noted, juxtaposed with an insignificant change in tensile strength. This investigation sheds light on a promising avenue for addressing concrete deterioration while navigating the balance between material performance and structural integrity.
Collapse
Affiliation(s)
- Samuel Tomi Aina
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa; (S.T.A.); (H.D.K.); (B.D.P.)
| | - Hilda Dinah Kyomuhimbo
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa; (S.T.A.); (H.D.K.); (B.D.P.)
| | - Barend Du Plessis
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa; (S.T.A.); (H.D.K.); (B.D.P.)
| | - Vuyo Mjimba
- Human Sciences Research Council, 134 Pretorius Street, Pretoria 0083, South Africa;
| | - Nils Haneklaus
- Td Lab Sustainable Mineral Resources, University for Continuing Education Krems, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria;
| | - Hendrik Gideon Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa; (S.T.A.); (H.D.K.); (B.D.P.)
| |
Collapse
|
34
|
Lei LY, Xiong ZX, Li JL, Yang DZ, Li L, Chen L, Zhong QF, Yin FY, Li RX, Cheng ZQ, Xiao SQ. Biological control of Magnaporthe oryzae using natively isolated Bacillus subtilis G5 from Oryza officinalis roots. Front Microbiol 2023; 14:1264000. [PMID: 37876784 PMCID: PMC10591090 DOI: 10.3389/fmicb.2023.1264000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production causing significant crop losses and impacting grain quality. The annual loss of rice production due to this disease ranges from 10% to 30%. The use of biologically controlled strains, instead of chemical pesticides, to control plant diseases has become a research hotspot. In this study, an antagonistic endophytic bacterial strain was isolated from the roots of Oryza officinalis using the traditional isolation and culture methods. A phylogenetic tree based on 16S RNA and whole-genome sequencing identified isolate G5 as a strain of Bacillus subtilis. This isolate displayed strong antagonistic effects against different physiological strains of M. oryzae. After co-culture in LB medium for 7 days, the inhibition rates of the mycelial growth of four strains of M. oryzae, ZB15, WH97, Guy11, and T-39800E were 98.07 ± 0.0034%, 98.59 ± 0.0051%, 99.16 ± 0.0012%, and 98.69 ± 0.0065%, respectively. Isolate G5 significantly inhibited the formation of conidia of M. oryzae, with an inhibition rate of 97% at an OD600 of 2. Isolate G5 was able to provide 66.81% protection against rice blast under potted conditions. Whole-genome sequencing revealed that the genome size of isolate G5 was 4,065,878 bp, including 4,182 coding genes. Using the anti-SMASH software, 14 secondary metabolite synthesis gene clusters were predicted to encode antifungal substances, such as fengycin, surfactin, and bacilysin. The G5 isolate also contained genes related to plant growth promotion. These findings provide a theoretical basis for expounding the biocontrol mechanisms of this strain and suggest further development of biogenic agents that could effectively inhibit rice blast pathogen growth and reduce crop damage, while being environmentally friendly, conducive to ecological development, and a sustainable alternative to chemical pesticides. This study also enriches the relevant research on endophytes of wild rice, which proves that wild rice is a valuable microbial resource bank.
Collapse
Affiliation(s)
- Ling-Yun Lei
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zi-Xuan Xiong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Jin-Lu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - De-Zheng Yang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Liu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiao-Fang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fu-You Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Rong-Xin Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- School of Agriculture, Yunnan University, Kunming, China
| | - Zai-Quan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Su-Qin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| |
Collapse
|
35
|
Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
Collapse
Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
36
|
Dai M, Yan N, Brusseau ML. Potential impact of bacteria on the transport of PFAS in porous media. WATER RESEARCH 2023; 243:120350. [PMID: 37499541 PMCID: PMC10530518 DOI: 10.1016/j.watres.2023.120350] [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: 03/25/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
The transport and fate of per- and poly-fluoroalkyl substances (PFAS) in soil and groundwater is a topic of critical concern. A number of factors and processes may influence the transport and fate of PFAS in porous media. One factor that has received minimal attention to date is the impact of bacteria on the retention and transport of PFAS, which is the focus of this current study. The first part of this work comprised a critical review of prior studies to delineate observed PFAS-bacteria interactions and to summarize the mechanisms of PFAS sorption and retention by bacteria. Retention of PFAS by bacteria can occur through sorption onto cell surfaces and/or by incorporation into the cell interior. Factors such as the molecular structure of PFAS, solution chemistry, and bacterial species can affect the magnitude of PFAS sorption. The influence of bacteria on the retention and transport of PFAS was investigated in the second part of the study with a series of batch and miscible-displacement experiments. Batch experiments were conducted using Gram-negative Pseudomonas aeruginosa and Gram-positive Bacillus subtilis to quantify the sorption of perfluorooctane sulfonic acid (PFOS). The results indicated that both bacteria showed strong adsorption of PFOS, with no significant difference in adsorption capacity. Miscible-displacement experiments were then conducted to examine the retention and transport of PFOS in both untreated sand and sand inoculated with Pseudomonas aeruginosa or Bacillus subtilis for 1 and 3 days. The transport of PFOS exhibited greater retardation for the experiments with inoculated sand. Furthermore, the enhanced sorption was greater for the 3-day inoculation compared to the 1-day, indicating that biomass is an important factor affecting PFOS transport. A mathematical model representing transport with nonlinear and rate-limited sorption successfully simulated the observed PFOS transport. This study highlights the need for future studies to evaluate the effect of bacteria on the transport of PFAS in soil and groundwater.
Collapse
Affiliation(s)
- Mengfan Dai
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao 266100, China
| | - Ni Yan
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao 266100, China.
| | - Mark L Brusseau
- Environmental Science Department, University of Arizona, Tucson, AZ 85721, United States; Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ 85721, United States.
| |
Collapse
|
37
|
Zelaya-Molina LX, Guerra-Camacho JE, Ortiz-Alvarez JM, Vigueras-Cortés JM, Villa-Tanaca L, Hernández-Rodríguez C. Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings. Arch Microbiol 2023; 205:318. [PMID: 37615783 DOI: 10.1007/s00203-023-03650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/25/2023]
Abstract
Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.
Collapse
Affiliation(s)
- Lily X Zelaya-Molina
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N. Col. Sto. Tomás, C.P. 11340, Ciudad de México, México
- Centro Nacional de Recursos Genéticos-INIFAP, Boulevard de La Biodiversidad 400, Rancho Las Cruces, C.P. 47600, Tepatitlán de Morelos, Jalisco, México
| | - Jairo E Guerra-Camacho
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N. Col. Sto. Tomás, C.P. 11340, Ciudad de México, México
| | - Jossue M Ortiz-Alvarez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N. Col. Sto. Tomás, C.P. 11340, Ciudad de México, México
- Programa "Investigadoras E Investigadores Por México". Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, C.P. 03940, Ciudad de México, México
| | - Juan M Vigueras-Cortés
- Laboratorio de Prototipos de Agua, Centro Interdisciplinario de Investigación Para El Desarrollo Integral Regional, IPN CIIDIR Durango, Sigma 119, Fracc. 20 de Noviembre II, C.P. 34220, Durango, Durango, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N. Col. Sto. Tomás, C.P. 11340, Ciudad de México, México
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala S/N. Col. Sto. Tomás, C.P. 11340, Ciudad de México, México.
| |
Collapse
|
38
|
Rosazza T, Eigentler L, Earl C, Davidson FA, Stanley‐Wall NR. Bacillus subtilis extracellular protease production incurs a context-dependent cost. Mol Microbiol 2023; 120:105-121. [PMID: 37380434 PMCID: PMC10952608 DOI: 10.1111/mmi.15110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.
Collapse
Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
- Mathematics, School of Science and EngineeringUniversity of DundeeDundeeUK
- Present address:
Evolutionary Biology DepartmentUniversität BielefeldKonsequenz 45Bielefeld33615Germany
| | - Chris Earl
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
| | | | | |
Collapse
|
39
|
Liu Y, Lee PKH, Nah T. Emerging investigator series: aqueous photooxidation of live bacteria with hydroxyl radicals under cloud-like conditions: insights into the production and transformation of biological and organic matter originating from bioaerosols. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:1150-1168. [PMID: 37376782 DOI: 10.1039/d3em00090g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Live bacteria in clouds are exposed to free radicals such as the hydroxyl radical (˙OH), which is the main driver of many photochemical processes. While the ˙OH photooxidation of organic matter in clouds has been widely studied, equivalent investigations on the ˙OH photooxidation of bioaerosols are limited. Little is known about the daytime encounters between ˙OH and live bacteria in clouds. Here we investigated the aqueous ˙OH photooxidation of four bacterial strains, B. subtilis, P. putida, E. hormaechei B0910, and E. hormaechei pf0910, in microcosms composed of artificial cloud water that mimicked the chemical composition of cloud water in Hong Kong. The survival rates for the four bacterial strains decreased to zero within 6 hours during exposure to 1 × 10-16 M of ˙OH under artificial sunlight. Bacterial cell damage and lysis released biological and organic compounds, which were subsequently oxidized by ˙OH. The molecular weights of some of these biological and organic compounds were >50 kDa. The O/C, H/C, and N/C ratios increased at the initial onset of photooxidation. As the photooxidation progressed, there were few changes in the H/C and N/C, whereas the O/C continued to increase for hours after all the bacterial cells had died. The increase in the O/C was due to functionalization and fragmentation reactions, which increased the O content and decreased the C content, respectively. In particular, fragmentation reactions played key roles in transforming biological and organic compounds. Fragmentation reactions cleaved the C-C bonds of carbon backbones of higher molecular weight proteinaceous-like matter to form a variety of lower molecular weight compounds, including HULIS of molecular weight <3 kDa and highly oxygenated organic compounds of molecular weight <1.2 kDa. Overall, our results provided new insights at the process level into how daytime reactive interactions between live bacteria and ˙OH in clouds contribute to the formation and transformation of organic matter.
Collapse
Affiliation(s)
- Yushuo Liu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- City University of Hong Kong Shenzhen Research Institute, Nanshan District, Shenzhen, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Theodora Nah
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- City University of Hong Kong Shenzhen Research Institute, Nanshan District, Shenzhen, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
40
|
Aina ST, Kyomuhimbo HD, Ramjee S, Du Plessis B, Mjimba V, Maged A, Haneklaus N, Brink HG. Synthesis and Assessment of Antimicrobial Composites of Ag Nanoparticles or AgNO 3 and Egg Shell Membranes. Molecules 2023; 28:4654. [PMID: 37375207 DOI: 10.3390/molecules28124654] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Engineering research has been expanded by the advent of material fusion, which has led to the development of composites that are more reliable and cost-effective. This investigation aims to utilise this concept to promote a circular economy by maximizing the adsorption of silver nanoparticles and silver nitrate onto recycled chicken eggshell membranes, resulting in optimized antimicrobial silver/eggshell membrane composites. The pH, time, concentration, and adsorption temperatures were optimized. It was confirmed that these composites were excellent candidates for use in antimicrobial applications. The silver nanoparticles were produced through chemical synthesis using sodium borohydride as a reducing agent and through adsorption/surface reduction of silver nitrate on eggshell membranes. The composites were thoroughly characterized by various techniques, including spectrophotometry, atomic absorption spectrometry, scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy, as well as agar well diffusion and MTT assay. The results indicate that silver/eggshell membrane composites with excellent antimicrobial properties were produced using both silver nanoparticles and silver nitrate at a pH of 6, 25 °C, and after 48 h of agitation. These materials exhibited remarkable antimicrobial activity against Pseudomonas aeruginosa and Bacillus subtilis, resulting in 27.77% and 15.34% cell death, respectively.
Collapse
Affiliation(s)
- Samuel Tomi Aina
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa
| | | | - Shatish Ramjee
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa
| | - Barend Du Plessis
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa
| | - Vuyo Mjimba
- Human Sciences Research Council, Pretoria 0083, South Africa
| | - Ali Maged
- Geology Department, Faculty of Science, Suez University, El-Salam City P.O. Box 43518, Egypt
| | - Nils Haneklaus
- Td Lab Sustainable Mineral Resources, University for Continuing Education Krems, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria
| | - Hendrik Gideon Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0002, South Africa
| |
Collapse
|
41
|
Luo Y, Chavez-Rico VS, Sechi V, Bezemer TM, Buisman CJN, Ter Heijne A. Effect of organic amendments obtained from different pretreatment technologies on soil microbial community. ENVIRONMENTAL RESEARCH 2023:116346. [PMID: 37295594 DOI: 10.1016/j.envres.2023.116346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
The application of organic amendments (OAs) obtained from biological treatment technologies is a common agricultural practice to increase soil functionality and fertility. OAs and their respective pretreatment processes have been extensively studied. However, comparing the properties of OAs obtained from different pretreatment processes remains challenging. In most cases, the organic residues used to produce OAs exhibit intrinsic variability and differ in origin and composition. In addition, few studies have focused on comparing OAs from different pretreatment processes in the soil microbiome, and the extent to which OAs affect the soil microbial community remains unclear. This limits the design and implementation of effective pretreatments aimed at reusing organic residues and facilitating sustainable agricultural practices. In this study, we used the same model residues to produce OAs to enable meaningful comparisons among compost, digestate, and ferment. These three OAs contained different microbial communities. Compost had higher bacterial but lower fungal alpha diversity than ferment and digestate. Compost-associated microbes were more prevalent in the soil than ferment- and digestate-associated microbes. More than 80% of the bacterial ASVs and fungal OTUs from the compost were detected 3 months after incorporation into the soil. However, the addition of compost had less influence on the resulting soil microbial biomass and community composition than the addition of ferment or digestate. Specific native soil microbes, members from Chloroflexi, Acidobacteria, and Mortierellomycota, were absent after ferment and digestate application. The addition of OAs increased the soil pH, particularly in the compost-amended soil, whereas the addition of digestate enhanced the concentrations of dissolved organic carbon (DOC) and available nutrients (such as ammonium and potassium). These physicochemical variables were key factors that influenced soil microbial communities. This study furthers our understanding of the effective recycling of organic resources for the development of sustainable soils.
Collapse
Affiliation(s)
- Yujia Luo
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands.
| | - Vania Scarlet Chavez-Rico
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - Valentina Sechi
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - T Martijn Bezemer
- Institute of Biology, Aboveground Belowground Interactions Group, Leiden University, P.O. Box 9505, 2300, RA, Leiden, the Netherlands; Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Droevendaalsesteeg 10, 6708, PB, Wageningen, the Netherlands
| | - Cees J N Buisman
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911, MA, Leeuwarden, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Department of Agrotechnology and Food Sciences, Wageningen University, P.O. Box 17, 6700, AA, Wageningen, the Netherlands
| |
Collapse
|
42
|
Kalamara M, Abbott J, Sukhodub T, MacPhee C, Stanley-Wall NR. The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001344. [PMID: 37289492 PMCID: PMC7614699 DOI: 10.1099/mic.0.001344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.
Collapse
Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - James Abbott
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Cait MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| |
Collapse
|
43
|
Deng A, Wang T, Wang J, Li L, Wang X, Liu L, Wen T. Adaptive mechanisms of Bacillus to near space extreme environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 886:163952. [PMID: 37164076 DOI: 10.1016/j.scitotenv.2023.163952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0-10-6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.
Collapse
Affiliation(s)
- Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tiantian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueliang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid medical school, University of Chinese Academy of Sciences, Beijing 100049, China; China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
44
|
Filluelo O, Ferrando J, Picart P. Metabolic engineering of Bacillus subtilis toward the efficient and stable production of C 30-carotenoids. AMB Express 2023; 13:38. [PMID: 37119332 PMCID: PMC10148934 DOI: 10.1186/s13568-023-01542-x] [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: 02/05/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023] Open
Abstract
Commercial carotenoid production is dominated by chemical synthesis and plant extraction, both of which are unsustainable and can be detrimental to the environment. A promising alternative for the mass production of carotenoids from both an ecological and commercial perspective is microbial synthesis. To date, C30 carotenoid production in Bacillus subtilis has been achieved using plasmid systems for the overexpression of biosynthetic enzymes. In the present study, we employed a clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) system to develop an efficient, safe, and stable C30 carotenoid-producing B. subtilis strain, devoid of plasmids and antibiotic selection markers. To this end, the expression levels of crtM (dehydrosqualene synthase) and crtN (dehydrosqualene desaturase) genes from Staphylococcus aureus were upregulated by the insertion of three gene copies into the chromosome of B. subtilis. Subsequently, the supply of the C30 carotenoid precursor farnesyl diphosphate (FPP), which is the substrate for CrtMN enzymes, was enhanced by expressing chromosomally integrated Bacillus megaterium-derived farnesyl diphosphate synthase (FPPS), a key enzyme in the FPP pathway, and abolishing the expression of farnesyl diphosphate phosphatase (YisP), an enzyme responsible for the undesired conversion of FPP to farnesol. The consecutive combination of these features resulted in a stepwise increased production of C30 carotenoids. For the first time, a B. subtilis strain that can endogenously produce C30 carotenoids has been constructed, which we anticipate will serve as a chassis for further metabolic engineering and fermentation optimization aimed at developing a commercial scale bioproduction process.
Collapse
Affiliation(s)
- Oriana Filluelo
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Jordi Ferrando
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Pere Picart
- Faculty of Pharmacy and Food Science Technology, Department of Biology, Healthcare and the Environment, Microbiology Section, University of Barcelona, Avinguda Joan XXIII, 27-31, Barcelona, 08028, Spain.
| |
Collapse
|
45
|
Zhang G, Lin M, Qin M, Xie Q, Liang M, Jiang J, Dai H, Xu S, Feng S, Liao M. Establishing Heterologous Production of Microcins J25 and Y in Bacillus subtilis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5600-5613. [PMID: 36995900 DOI: 10.1021/acs.jafc.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Microcin J25 (MccJ25) and microcin Y (MccY) are lasso peptides and considered potential alternatives to antibiotics and harmful preservatives. The combination of these two microcins can provide a wide antimicrobial spectrum against food-borne Salmonella. Currently, MccJ25 and MccY are produced using Escherichia coli expression systems; however, the entire production process is accompanied by negative effects from endotoxins. In this study, we identified Bacillus subtilis as a suitable host for MccJ25 and MccY production. High-level production of microcins was achieved by promoter optimization, host strain selection, and recombinant expression. The engineered strains produced maximum yields of 2.827 μM MccJ25 and 1.481 μM MccY. This is the first study to demonstrate the expression of MccJ25 and MccY in B. subtilis, and it offers a few engineered strains that are without antibiotic resistance markers, inducer-free, sporulation-deficient, and free of the negative effects of endotoxins for antibacterial therapy and food preservation.
Collapse
Affiliation(s)
- Guangwen Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Min Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Miaomiao Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qianmei Xie
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Mingzhi Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Jinfei Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Huilin Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Siqi Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, P. R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, P. R. China
- Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Guangzhou 510642, P. R. China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou 510642, P. R. China
| |
Collapse
|
46
|
Wang Y, Xu Y, Cao G, Zhou X, Wang Q, Fu A, Zhan X. Bacillus subtilis DSM29784 attenuates Clostridium perfringens-induced intestinal damage of broilers by modulating intestinal microbiota and the metabolome. Front Microbiol 2023; 14:1138903. [PMID: 37007491 PMCID: PMC10060821 DOI: 10.3389/fmicb.2023.1138903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Necrotic enteritis (NE), especially subclinical NE (SNE), without clinical symptoms, in chicks has become one of the most threatening problems to the poultry industry. Therefore, increasing attention has been focused on the research and application of effective probiotic strains as an alternative to antibiotics to prevent SNE in broilers. In the present study, we evaluated the effects of Bacillus subtilis DSM29784 (BS) on the prevention of subclinical necrotic enteritis (SNE) in broilers. A total of 480 1-day-old broiler chickens were randomly assigned to four dietary treatments, each with six replicates pens of twenty birds for 63 d. The negative (Ctr group) and positive (SNE group) groups were only fed a basal diet, while the two treatment groups received basal diets supplemented with BS (1 × 109 colony-forming units BS/kg) (BS group) and 10mg/kg enramycin (ER group), respectively. On days 15, birds except those in the Ctr group were challenged with 20-fold dose coccidiosis vaccine, and then with 1 ml of C. perfringens (2 × 108) at days 18 to 21 for SNE induction. BS, similar to ER, effectively attenuated CP-induced poor growth performance. Moreover, BS pretreatment increased villi height, claudin-1 expression, maltase activity, and immunoglobulin abundance, while decreasing lesional scores, as well as mucosal IFN-γ and TNF-α concentrations. In addition, BS pretreatment increased the relative abundance of beneficial bacteria and decreased that of pathogenic species; many lipid metabolites were enriched in the cecum of treated chickens. These results suggest that BS potentially provides active ingredients that may serve as an antibiotic substitute, effectively preventing SNE-induced growth decline by enhancing intestinal health in broilers.
Collapse
Affiliation(s)
- Yuanyuan Wang
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
| | - Yibin Xu
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
| | | | - Xihong Zhou
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qian Wang
- Yancheng Biological Engineering Higher Vocational Technology School, Yancheng, China
| | - Aikun Fu
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
- *Correspondence: Xiuan Zhan, ; Aikun Fu,
| | - Xiuan Zhan
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
- *Correspondence: Xiuan Zhan, ; Aikun Fu,
| |
Collapse
|
47
|
Perera LJ, Cockell CS. Dispersion of Bacteria by Low-Pressure Boiling: Life Detection in Enceladus' Plume Material. ASTROBIOLOGY 2023; 23:269-279. [PMID: 36689196 DOI: 10.1089/ast.2022.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The plume of Enceladus is thought to originate from the dispersion of a liquid source beneath the icy crust. Cryovolcanic activity on Enceladus may present a direct way of accessing material originating from the potentially habitable subsurface ocean. One way to test the hypothesis of whether life is present within the ocean of Enceladus would be to investigate the plume material for the presence of microbial life. In this study, we investigated the entrainment of Bacillus subtilis within Enceladus-like fluids under boiling conditions caused by exposure of the fluids to low pressure. We show that boiling, associated with exposure of a fluid to low pressure, works as a mechanism for dispersing bacteria in Enceladus plume-like environments. Exposure of Enceladus-type fluids (0.01-0.1 molal Na2CO3 and 0.05-0.2 molal NaCl) to low pressure (5 mbar) results in the dispersion of bacteria in droplets that evaporate to produce particles of salt. We find that, for particles with radius (r) ≤ 10 μm, the number of dispersed particles containing cells was between 7.7% and 10.9%. However, for larger particles 10 < r ≤ 50 μm, 64.4% and 56.4% contained cells for lower and upper end-member solutions, respectively. Our results suggest that the gravity-induced size sorting of plume particles will result in plume deposits closer to the vent source containing a larger volume of biological material than within the plume. If life is present in the ocean of Enceladus, we would expect that it would be effectively entrained and deposited on the surface; therefore, it would be accessible with a surface-lander-based instrument.
Collapse
Affiliation(s)
- L J Perera
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, UK
| | - C S Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
48
|
Yu C, Chen H, zhu L, Song Y, Jiang Q, Zhang Y, Ali Q, Gu Q, Gao X, Borriss R, Dong S, Wu H. Profiling of Antimicrobial Metabolites Synthesized by the Endophytic and Genetically Amenable Biocontrol Strain Bacillus velezensis DMW1. Microbiol Spectr 2023; 11:e0003823. [PMID: 36809029 PMCID: PMC10100683 DOI: 10.1128/spectrum.00038-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
The genus Bacillus is one of the most important genera for the biological control of plant diseases that are caused by various phytopathogens. The endophytic Bacillus strain DMW1 was isolated from the inner tissues of potato tubers and exhibited strong biocontrol activity. Based on its whole-genome sequence, DMW1 belongs to the Bacillus velezensis species, and it is similar to the model strain B. velezensis FZB42. 12 secondary metabolite biosynthetic gene clusters (BGCs), including two unknown function BGCs, were detected in the DMW1 genome. The strain was shown to be genetically amenable, and seven secondary metabolites acting antagonistically against plant pathogens were identified by a combined genetic and chemical approach. Strain DMW1 did significantly improve the growth of tomato and soybean seedlings, and it was able to control the Phytophthora sojae and Ralstonia solanacearum that were present in the plant seedlings. Due to these properties, the endophytic strain DMW1 appears to be a promising candidate for comparative investigations performed together with the Gram-positive model rhizobacterium FZB42, which is only able to colonize the rhizoplane. IMPORTANCE Phytopathogens are responsible for the wide spread of plant diseases as well as for great losses of crop yields. At present, the strategies used to control plant disease, including the development of resistant cultivars and chemical control, may become ineffective due to the adaptive evolution of pathogens. Therefore, the use of beneficial microorganisms to deal with plant diseases attracts great attention. In the present study, a new strain DMW1, belonging to the species B. velezensis, was discovered with outstanding biocontrol properties. It showed plant growth promotion and disease control abilities that are comparable with those of B. velezensis FZB42 under greenhouse conditions. According to a genomic analysis and a bioactive metabolites analysis, genes that are responsible for promoting plant growth were detected, and metabolites with different antagonistic activities were identified. Our data provide a basis for DMW1 to be further developed and applied as a biopesticide, which is similar to the closely related model strain FZB42.
Collapse
Affiliation(s)
- Chenjie Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Han Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Linli zhu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Yan Song
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Qifan Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Yaming Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Rainer Borriss
- Humboldt University Berlin, Institut für Biologie, Berlin, Germany
| | - Suomeng Dong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| |
Collapse
|
49
|
Ferrando J, Filluelo O, Zeigler DR, Picart P. Barriers to simultaneous multilocus integration in Bacillus subtilis tumble down: development of a straightforward screening method for the colorimetric detection of one-step multiple gene insertion using the CRISPR-Cas9 system. Microb Cell Fact 2023; 22:21. [PMID: 36721198 PMCID: PMC9890709 DOI: 10.1186/s12934-023-02032-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Despite recent advances in genetic engineering tools for effectively regulating and manipulating genes, efficient simultaneous multigene insertion methods have not been established in Bacillus subtilis. To date, multilocus integration systems in B. subtilis, which is one of the main industrial enzyme producers and a GRAS (generally regarded as safe) microbial host, rely on iterative rounds of plasmid construction for sequential insertions of genes into the B. subtilis chromosome, which is tedious and time consuming. RESULTS In this study, we present development and proof-of-concept of a novel CRISPR-Cas9-based genome-editing strategy for the colorimetric detection of one-step multiple gene insertion in B. subtilis. First, up to three copies of the crtMN operon from Staphylococcus aureus, encoding a yellow pigment, were incorporated at three ectopic sites within the B. subtilis chromosome, rendering engineered strains able to form yellow colonies. Second, a single CRISPR-Cas9-based plasmid carrying a highly specific single guide RNA (sgRNA) targeting crtMN operon and a changeable editing template was constructed to facilitate simultaneous insertion of multiple gene-copies through homology-directed repair (HDR). Upon transformation of engineered strains with engineered plasmids, strains harboring up to three gene copies integrated into the chromosome formed white colonies because of the removal of the crtMN operon, clearly distinguishable from yellow colonies harboring undesired genetic modifications. As a result, construction of a plasmid-less, marker-free, high-expression stable producer B. subtilis strain can be completed in only seven days, demonstrating the potential that the implementation of this technology may bring for biotechnology purposes. CONCLUSIONS The novel technology expands the genome-editing toolset for B. subtilis and means a substantial improvement over current methodology, offering new application possibilities that we envision should significantly boost the development of B. subtilis as a chassis in the field of synthetic biology.
Collapse
Affiliation(s)
- Jordi Ferrando
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | - Oriana Filluelo
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | | | - Pere Picart
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| |
Collapse
|
50
|
Huang J, Xu Y, Wang M, Yu S, Li Y, Tian H, Zhang C, Li H. Enterococcus faecium R-026 combined with Bacillus subtilis R-179 alleviate hypercholesterolemia and modulate the gut microbiota in C57BL/6 mice. FEMS Microbiol Lett 2023; 370:fnad118. [PMID: 37960899 DOI: 10.1093/femsle/fnad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
Probiotics have been demonstrated to lower total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) in individuals with mild hypercholesterolemia. Our previous study found that intervention with Bacillus subtilis R-179 and Enterococcus faecium R-026, well-known probiotics, improved obesity-associated dyslipidemia through ameliorating the gut microbiota, but similar studies on hypercholesterolemia have not been reported to date. Here, we investigated the therapeutic effect of live combined B. subtilis R-179 and E. faecium R-026 (LCBE) in a C57BL/6 mouse model of hypercholesterolemia. A total of 40 mice were administered with a high-cholesterol diet (containing 1.2% cholesterol) to establish a state of hypercholesterolemia for 4 weeks. Then, mice were divided into one model group (group M) and three treatment groups (n = 10 per group), which were administered with LCBE at 0.023 g/mouse/day (group L) or 0.230 g/mouse/day (group H), or atorvastatin 0.010 g/kg/day (group A), for 5 weeks while on a high-cholesterol diet. LCBE at high doses significantly alleviated the symptoms of group M and reduced serum TC, LDL-C, and lipopolysaccharide (LPS). LCBE improved liver steatosis and adipocyte enlargement caused by a high-cholesterol diet. In addition, the administration of LCBE regulated the change in gut microbiota and diversity (Shannon index). Compared with group M, the relative abundance of Actinobacteriota, Colidextribacter, and Dubosiella dramatically decreased in the treatment groups, which were positively correlated with serum TC and LPS. These findings indicated that the mechanism of action of LCBE in treating hypercholesterolemia may be modulation of the gut microbiota. In conclusion, LCBE ameliorated lipid accumulation, reduced inflammation, and alleviated the gut microbiota imbalance in hypercholesterolemic mice. These findings support the probiotic role of LCBE as a clinical candidate for the treatment of hypercholesterolemia.
Collapse
Affiliation(s)
- Jinli Huang
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
- Department of Pediatrics, Xijing Hospital, the Fourth Military Medical University, 710032, Xi'an, China
| | - Yafang Xu
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
| | - Minghao Wang
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
| | - Shu Yu
- Dalian Women and Children Medical Center (Group), 116033, Dalian, China
| | - Yixuan Li
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
| | - Haoxin Tian
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
| | - Caihua Zhang
- Department of Pathophysiology, Dalian Medical University, 116044, Dalia, China
| | - Huajun Li
- Department of Microecology, Dalian Medical University, 116044, Dalian, China
| |
Collapse
|