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Xu S, Liu Z, Ren P, Liu Y, Xiao F, Li W. BmfR, a novel GntR family regulator, regulates biofilm formation in marine-derived, Bacillus methylotrophicus B-9987. Microbiol Res 2024; 287:127859. [PMID: 39098095 DOI: 10.1016/j.micres.2024.127859] [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: 06/12/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Biofilms are common living states for microorganisms, allowing them to adapt to environmental changes. Numerous Bacillus strains can form complex biofilms that play crucial roles in biocontrol processes. However, our current understanding of the molecular mechanisms of biofilm formation in Bacillus is mainly based on studies of Bacillus subtilis. Knowledge regarding the biofilm formation of other Bacillus species remains limited. In this study, we identified a novel transcriptional regulator, BmfR, belonging to the GntR family, that regulates biofilm formation in marine-derived Bacillus methylotrophicus B-9987. We demonstrated that BmfR induces biofilm formation by activating the extracellular polysaccharide structural genes epsA-O and negatively regulating the matrix gene repressor, SinR; of note it positively affects the expression of the master regulator of sporulation, Spo0A. Furthermore, database mining for BmfR homologs has revealed their widespread distribution among many bacterial species, mainly Firmicutes and Proteobacteria. This study advances our understanding of the biofilm regulatory network of Bacillus strains, and provides a new target for exploiting and manipulating biofilm formation.
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Affiliation(s)
- Shanshan Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Pengfei Ren
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yang Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shannxi 712100, China.
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2
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Kasapovic A, Hischebeth G, Jaenisch M, Ali T, Gathen M, Babasiz M, Bojko J, Roos J, Smajic S. Sonication in Patients With Spinal Cord Stimulation: A New Approach for Infection Diagnostics. Neuromodulation 2024; 27:1076-1081. [PMID: 36997452 DOI: 10.1016/j.neurom.2023.02.079] [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: 11/04/2022] [Revised: 01/31/2023] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
INTRODUCTION Spinal cord stimulation (SCS) offers improvement in pain and function for several chronic pain conditions. There are concerns regarding bacterial colonization of the temporary lead extensions and subsequent infection risk in a two-session implantation procedure. Although there is no standardized evaluation of SCS lead contamination, this study evaluates the infection rate and microbial colonization of SCS lead extensions with sonication, a method that is established in implant-related infection diagnostics. MATERIALS AND METHODS This prospective observational study comprised 32 patients with a two-stage SCS implantation procedure. Microbial colonization of the lead extensions was assessed with sonication. The presence of organisms in the subcutaneous tissue was evaluated separately. Surgical-site infections were recorded. Patient demographics and risk factors including diabetes, tobacco use, obesity, trial length, and infection parameters in serum were recorded and analyzed. RESULTS The mean age of the patients was 55 years. On average, the trial length was 13 days. In seven cases (21.9%), a microbial lead colonization was found with sonication. In contrast, there was one positive culture (3.1%) from the subcutaneous tissue samples. The C-reactive protein and leukocyte count remained at the preoperative level. One early surgical-site infection (3.1%) occurred. No other late infections occurred six months after surgery. CONCLUSIONS There is a discrepancy between the presence of microbial colonization and the occurrence of clinically relevant infections. Although the rate of microbial colonization of the lead extensions is high (21.9%), the surgical-site infection rate remained low (3.1%). Therefore, we can conclude that the two-session procedure is a safe approach that is not associated with a higher incidence of infection. Although the sonication method cannot be used as the sole tool for detecting infections in patients with SCS, it can provide additional value in microbial diagnostics in combination with clinical and laboratory parameters and conventional microbiological methods.
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Affiliation(s)
- Adnan Kasapovic
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany.
| | - Gunnar Hischebeth
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Max Jaenisch
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Thaer Ali
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Martin Gathen
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Mari Babasiz
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Jessica Bojko
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Jonas Roos
- Department of Orthopedic and Trauma Surgery, University Hospital Bonn Venusberg Campus 1, Bonn, Germany
| | - Samir Smajic
- Department of Orthopedic, Trauma and Spine Surgery, St. Josef Hospital, Linnich, Germany
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Zhang X, Gao Y, Zhao C, Wang L, Wen S, Shi B, Zhu L, Wang J, Kim YM, Wang J. Rhizosphere bacteria G-H27 significantly promoted the degradation of chlorpyrifos and fosthiazate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:169838. [PMID: 38232838 DOI: 10.1016/j.scitotenv.2023.169838] [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: 11/03/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024]
Abstract
Microbial remediation of polluted environments is the most promising and significant research direction in the field of bioremediation. In this study, chlorpyrifos and fosthiazate were selected as representative organophosphorus pesticides, wheat was the tested plant, and fluorescently labeled degrading Bacillus cereus G-H27 were the film-forming bacteria. Exogenous strengthening technology was used to establish degrading bacterial biofilms on the root surface of wheat. The influence of root surface-degrading bacterial biofilms on the enrichment of chlorpyrifos and fosthiazate in wheat was comprehensively evaluated. First, the fluorescently-labeled degrading bacteria G-H27 was constructed, and its film-forming ability was investigated. Second, the growth- promoting characteristics and degradation ability of the bacteria G-H27 were investigated. Finally, the degradation effect of the root surface-degrading bacterial biofilm on chlorpyrifos and fosthiazate was determined. The above research provides an important material basis and method for the bioremediation of pesticide-contaminated soil.
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Affiliation(s)
- Xuzhi Zhang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Yuanfei Gao
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Changyu Zhao
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Lanjun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China.
| | - Shengfang Wen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Baihui Shi
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China
| | - Lusheng Zhu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China.
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
| | - Jinhua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an 271018, People's Republic of China.
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4
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Yunus J, Wan Dagang WRZ, Jamaluddin H, Jemon K, Mohamad SE, Jonet MA. Bacterial biofilm growth and perturbation by serine protease from Bacillus sp. Arch Microbiol 2024; 206:138. [PMID: 38436775 DOI: 10.1007/s00203-024-03857-0] [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: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 03/05/2024]
Abstract
In nature, bacteria are ubiquitous and can be categorized as beneficial or harmless to humans, but most bacteria have one thing in common which is their ability to produce biofilm. Biofilm is encased within an extracellular polymeric substance (EPS) which provides resistance against antimicrobial agents. Protease enzymes have the potential to degrade or promote the growth of bacterial biofilms. In this study, the effects of a recombinant intracellular serine protease from Bacillus sp. (SPB) on biofilms from Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa were analyzed. SPB was purified using HisTrap HP column and concentrated using Amicon 30 ultra-centrifugal filter. SPB was added with varying enzyme activity and assay incubation period after biofilms were formed in 96-well plates. SPB was observed to have contrasting effects on different bacterial biofilms, where biofilm degradations were observed for both 7-day-old A. baumannii (37.26%) and S. aureus (71.51%) biofilms. Meanwhile, SPB promoted growth of P. aeruginosa biofilm up to 176.32%. Compatibility between protein components in S. aureus biofilm with SPB as well as a simpler membrane structure morphology led to higher biofilm degradation for S. aureus compared to A. baumannii. However, SPB promoted growth of P. aeruginosa biofilm due likely to its degrading protein factors that are responsible for biofilm detachment and dispersion, thus resulting in more multi-layered biofilm formation. Commercial protease Savinase which was used as a comparison showed degradation for all three bacterial biofilms. The results obtained are unique and will expand our understanding on the effects that bacterial proteases have toward biofilms.
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Affiliation(s)
- Julia Yunus
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wan Rosmiza Zana Wan Dagang
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Khairunadwa Jemon
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology (EGT), Malaysia Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Mohd Anuar Jonet
- Structural And Applied Genomics Centre, Malaysia Genome and Vaccine Institute (MGVI), National Institute of Biotechnology Malaysia (NIBM), Jalan Bangi, 43000, Kajang, Selangor, Malaysia
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5
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Wang X, Hao G, Zhou M, Chen M, Ling H, Shang Y. Secondary metabolites of Bacillus subtilis L2 show antiviral activity against pseudorabies virus. Front Microbiol 2023; 14:1277782. [PMID: 37965547 PMCID: PMC10642297 DOI: 10.3389/fmicb.2023.1277782] [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: 08/15/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Bacillus subtilis (B. subtilis) is a commercially important probiotic known to produce secondary metabolites with antibacterial, antifungal and anti-inflammatory activities. However, the potential ability of B. subtilis to combat viruses, especially DNA viruses, has not been extensively investigated. In this study, we identified two distinct B. subtilis strains and examined the efficiency of their secondary metabolites against pseudorabies virus (PRV), a swine herpesvirus resulting in economic losses worldwide. We found that treatment with the secondary metabolites of B. subtilis L2, but not the metabolites of B. subtilis V11, significantly inhibited PRV replication in multiple cells. Notably, the antiviral activity of the metabolites of B. subtilis L2 was thermal stable, resistant to protease digestion. Moreover, these metabolites effectively impeded PRV binding, entry and replication. Importantly, oral administration of the metabolites of B. subtilis L2 protected mice from lethal PRV infection, rescuing weight loss and reducing the viral load in vivo. In summary, our results reveal that the metabolites of B. subtilis L2 exhibit anti-PRV activity both in vitro and in vivo, providing a potential candidate for novel antiviral drugs.
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Affiliation(s)
- Xiaoli Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Guijuan Hao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Meng Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Meng Chen
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | | | - Yingli Shang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
- Institute of Immunology, Shandong Agricultural University, Taian, China
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6
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Dobrzyński J, Jakubowska Z, Kulkova I, Kowalczyk P, Kramkowski K. Biocontrol of fungal phytopathogens by Bacillus pumilus. Front Microbiol 2023; 14:1194606. [PMID: 37560520 PMCID: PMC10407110 DOI: 10.3389/fmicb.2023.1194606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.
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Affiliation(s)
- Jakub Dobrzyński
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Zuzanna Jakubowska
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Iryna Kulkova
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jabłonna, Poland
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Białystok, Białystok, Poland
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7
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Zhao D, Wang J, Wang H, Zhu X, Han C, Liu A. The Transcription Regulator GntR/HutC Regulates Biofilm Formation, Motility and Stress Tolerance in Lysobacter capsici X2-3. Curr Microbiol 2023; 80:281. [PMID: 37439829 DOI: 10.1007/s00284-023-03390-1] [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: 11/02/2022] [Accepted: 06/28/2023] [Indexed: 07/14/2023]
Abstract
Lysobacter capsici X2-3, a plant growth-promoting rhizobacteria (PGPR), was isolated from wheat rhizosphere and has inhibitory effects against a wide range of pathogens. One important characteristic of L. capsici is its ability to produce diverse antibiotics and lytic enzymes. The GntR family of transcription factors is a common transcription factor superfamily in bacteria that has fundamental roles in bacterial metabolism regulation. However, the GntR family transcription factor in Lysobacter has not been identified. In this study, to obtain an understanding of the GntR/HutC gene function in L. capsici X2-3, a random Tn5-insertion mutant library of X2-3 was constructed to select genes showing pleiotropic effects on phenotype. We identified a Tn5 mutant with an insertion in LC4356 that showed reduced biofilm levels, and sequence analysis indicated that the inserted gene encodes a GntR/HutC family transcription regulator. Furthermore, the LC4356 mutant showed reduced extracellular polysaccharide (EPS) production, diminished twitching motility and decreased survival under UV radiation and high-temperature. The RT‒qPCR results indicated that the pentose phosphate pathway-related genes G6PDH, 6PGL and PGDH were upregulated in the LC4356 mutant. Thus, since L. capsici is an efficient biocontrol agent for crop protection, our findings provide fundamental insights into GntR/HutC and will be worthwhile to improve PGPR biocontrol efficacy.
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Affiliation(s)
- Dan Zhao
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Jing Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Hong Wang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoping Zhu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Chao Han
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
| | - Aixin Liu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
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8
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [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: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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9
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Shen G, Yang L, Lv X, Zhang Y, Hou X, Li M, Zhou M, Pan L, Chen A, Zhang Z. Antibiofilm Activity and Mechanism of Linalool against Food Spoilage Bacillus amyloliquefaciens. Int J Mol Sci 2023; 24:10980. [PMID: 37446158 DOI: 10.3390/ijms241310980] [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: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Pellicle biofilm-forming bacteria Bacillus amyloliquefaciens are the major spoilage microorganisms of soy products. Due to their inherent resistance to antibiotics and disinfectants, pellicle biofilms formed are difficult to eliminate and represent a threat to food safety. Here, we assessed linalool's ability to prevent the pellicle of two spoilage B. amyloliquefaciens strains. The minimum biofilm inhibitory concentration (MBIC) of linalool against B. amyloliquefaciens DY1a and DY1b was 4 μL/mL and 8 μL/mL, respectively. The MBIC of linalool had a considerable eradication rate of 77.15% and 83.21% on the biofilm of the two strains, respectively. Scanning electron microscopy observations revealed that less wrinkly and thinner pellicle biofilms formed on a medium supplemented with 1/2 MBIC and 1/4 MBIC linalool. Also, linalool inhibited cell motility and the production of extracellular polysaccharides and proteins of the biofilm matrix. Furthermore, linalool exposure reduced the cell surface hydrophobicity, zeta potential, and cell auto-aggregation of B. amyloliquefaciens. Molecular docking analysis demonstrated that linalool interacted strongly with quorum-sensing ComP receptor and biofilm matrix assembly TasA through intermolecular hydrogen bonds, hydrophobic contacts, and van der Waals forces interacting with site residues. Overall, our findings suggest that linalool may be employed as a potential antibiofilm agent to control food spoilage B. amyloliquefaciens.
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Affiliation(s)
- Guanghui Shen
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Lu Yang
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xinyu Lv
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yingfan Zhang
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiaoyan Hou
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Meiliang Li
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Man Zhou
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Le Pan
- Chemical Engineering College, Xinjiang Agricultural University, Urumqi 830052, China
| | - Anjun Chen
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhiqing Zhang
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
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10
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Carrasco Calzada F, Jairo Aguilera J, Moreno JE, Cuadros González J, Roca Biosca D, Prieto-Pérez L, Pérez-Tanoira R. Differences in Virulence Factors and Antimicrobial Susceptibility of Uropathogenic Enterococcus spp. Strains in a Rural Area of Uganda and a Spanish Secondary Hospital. Trop Med Infect Dis 2023; 8:tropicalmed8050282. [PMID: 37235330 DOI: 10.3390/tropicalmed8050282] [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: 04/11/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium have become two of the most important agents of nosocomial diseases due to their constantly growing resistance. Enterococcal infections are associated with biofilms, which are intrinsically sensitive to antimicrobials. The main goal of this study was to compare and relate their capacity to form biofilm and their antimicrobial sensitivity, as well as their virulence factors and their implicated genes, of strains isolated from patients with urinary tract infection (UTI) in a rural hospital in Uganda and a secondary hospital in Spain. A prospective study was conducted with 104 strains of E. faecalis and E. faecium isolated from patients with suspected UTI and who presented leukocyturia at the Saint Joseph Kitgum hospital (Uganda) and at the Hospital Universitario Principe de Asturias (Spain). All microorganisms were identified in Spain by MALDI-TOF mass spectrometry. Antimicrobial susceptibility studies were carried out using the Vitek® 2 system (Biomériux, France). The biofilm formation capacity was studied by photospectrometry. Phenotypic and genotypic virulence factors were studied in all cases by PCR or expression techniques. In Uganda, we found a higher incidence of E. faecium (65.3%, n = 32), contrary to the situation found in Spain where most of the bacteria found belonged to E. faecalis (92.7%, n = 51). All E. faecalis strains were found to have very low levels of resistance to ampicillin, imipenem, and nitrofurantoin. However, E. faecium exhibited more than 25% resistance to these antibiotics. Although the esp gene has been shown in the results obtained to be an important initial agent in biofilm formation, we have also demonstrated in this study the intervention of other genes when esp is not present, such as the ace1 gene. No statistically significant relationships were found between the presence of agg and gelE genes and increased biofilm formation. The significant difference between the incidence of E. faecalis and E. faecium and biofilm formation, between samples from Spain and Uganda, shows us very different profiles between countries.
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Affiliation(s)
- Félix Carrasco Calzada
- Clinical Microbiology Department, Hospital Universitario Príncipe de Asturias, 28805 Alcalá de Henares, Spain
- Health Sciences Department, Faculty of Med, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
| | - John Jairo Aguilera
- IIS-Fundación Jiménez Díaz, 28007 Madrid, Spain
- CIBERINFEC-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28222 Madrid, Spain
| | - Jaime Esteban Moreno
- IIS-Fundación Jiménez Díaz, 28007 Madrid, Spain
- CIBERINFEC-CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28222 Madrid, Spain
| | - Juan Cuadros González
- Clinical Microbiology Department, Hospital Universitario Príncipe de Asturias, 28805 Alcalá de Henares, Spain
- Health Sciences Department, Faculty of Med, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Máster Medicina Tropical y Salud Internacional, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David Roca Biosca
- Máster Medicina Tropical y Salud Internacional, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Fundación El Alto, 12500 Vinaroz, Spain
| | - Laura Prieto-Pérez
- IIS-Fundación Jiménez Díaz, 28007 Madrid, Spain
- Máster Medicina Tropical y Salud Internacional, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ramón Pérez-Tanoira
- Clinical Microbiology Department, Hospital Universitario Príncipe de Asturias, 28805 Alcalá de Henares, Spain
- Health Sciences Department, Faculty of Med, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Máster Medicina Tropical y Salud Internacional, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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11
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Shen Y, Yang H, Lin Z, Chu L, Pan X, Wang Y, Liu W, Jin P, Miao W. Screening of compound-formulated Bacillus and its effect on plant growth promotion. FRONTIERS IN PLANT SCIENCE 2023; 14:1174583. [PMID: 37235009 PMCID: PMC10208273 DOI: 10.3389/fpls.2023.1174583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/27/2023] [Indexed: 05/28/2023]
Abstract
Bacillus bacteria can produce abundant secondary metabolites that are useful for biocontrol, especially in maintaining plant root microecology, and for plant protection. In this study, we determine the indicators of six Bacillus strains for colonization, promotion of plant growth, antimicrobial activity, and other aspects, with the aim of obtaining a compound bacteriological agent to construct a beneficial Bacillus microbial community in plant roots. We found that there was no significant difference in the growth curves of the six Bacillus strains over 12 h. However, strain HN-2 was found to have the strongest swimming ability and the highest bacteriostatic effect of n-butanol extract on the blight-causing bacteria Xanthomonas oryzae pv. oryzicola. The hemolytic circle produced by the n-butanol extract of strain FZB42 was the largest (8.67 ± 0.13 mm) and had the greatest bacteriostatic effect on the fungal pathogen Colletotrichum gloeosporioides, with a bacteriostatic circle diameter of 21.74 ± 0.40 mm. Strains HN-2 and FZB42 can rapidly form biofilms. Time-of-flight mass spectrometry and hemolytic plate tests showed that strains HN-2 and FZB42 may have significantly different activities because of their ability to produce large quantities of lipopeptides (i.e., surfactin, iturin, and fengycin). Different growth-promoting experiments revealed that the strains FZB42, HN-2, HAB-2, and HAB-5 had better growth-promoting potential than the control, and therefore these four strains were compounded in an equal ratio and used to treat pepper seedlings through root irrigation. We found an increase in the stem thickness (13%), leaf dry weight (14%), leaf number (26%), and chlorophyll content (41%) of pepper seedlings treated with the composite-formulated bacterial solution compared to the optimal single-bacterial solution treatment. Furthermore, several of these indicators increased by an average of 30% in the composite solution-treated pepper seedlings compared with the control water treatment group. In conclusion, the composite solution obtained by compounding strains FZB42 (OD600 = 1.2), HN-2 (OD600 = 0.9), HAB-2 (OD600 = 0.9), and HAB-5 (OD600 = 1.2) in equal parts highlights the advantages of a single bacterial solution, which includes achieving good growth promotion and antagonistic effects against pathogenic bacteria. The promotion of this compound-formulated Bacillus can reduce the application of chemical pesticides and fertilizers; promote plant growth and development; avoid the imbalances of soil microbial communities and thus reduce the risk of plant disease; and provide an experimental basis for the production and application of various types of biological control preparations in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Pengfei Jin
- *Correspondence: Pengfei Jin, ; Weiguo Miao,
| | - Weiguo Miao
- *Correspondence: Pengfei Jin, ; Weiguo Miao,
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12
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Pérez-Lorente AI, Molina-Santiago C, de Vicente A, Romero D. Sporulation Activated via σ W Protects Bacillus from a Tse1 Peptidoglycan Hydrolase Type VI Secretion System Effector. Microbiol Spectr 2023; 11:e0504522. [PMID: 36916921 PMCID: PMC10100999 DOI: 10.1128/spectrum.05045-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Within bacterial communities, community members engage in interactions employing diverse offensive and defensive tools to reach coexistence. Extracellular-matrix production and sporulation are defensive mechanisms used by Bacillus subtilis cells when they interact with Pseudomonas chlororaphis strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas chlororaphis T6SS that triggers sporulation in Bacillus subtilis. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor σW and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response permits bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector. IMPORTANCE The study of bacterial interactions is helping to define species-specific strategies used to modulate the competition dynamics underlying the development of community compositions. In this study, we deciphered the role of Pseudomonas T6SS when competing with Bacillus and the mechanism by which a T6SS-toxin modifies Bacillus physiology. We found that Pseudomonas triggers Bacillus sporulation by injecting through T6SS a toxin that we called Tse1. We found that Tse1 is a hydrolase that degrades Bacillus peptidoglycan and indirectly damages Bacillus membrane functionality. In addition, we demonstrated the mechanism by which Bacillus cells increase the sporulation rate upon recognition of the presence of Tse1. Interestingly, asporogenic Bacillus cells are more sensitive to T6SS activity, which led us to propose sporulation as a last resort of bacilli to overcome this family of toxins.
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Affiliation(s)
- Alicia I. Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
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13
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Jia S, Song C, Dong H, Yang X, Li X, Ji M, Chu J. Evaluation of efficacy and mechanism of Bacillus velezensis CB13 for controlling peanut stem rot caused by Sclerotium rolfsii. Front Microbiol 2023; 14:1111965. [PMID: 36876084 PMCID: PMC9978184 DOI: 10.3389/fmicb.2023.1111965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Peanut stem rot, caused by Sclerotium rolfsii, considerably affects crop productivity. Application of chemical fungicides harms the environment and induces drug resistance. Biological agents are valid and eco-friendly alternatives to chemical fungicides. Bacillus spp. are important biocontrol agents that are now widely used against several plant diseases. This study aimed to evaluate the efficacy and mechanism of a potential biocontrol agent Bacillus sp. for controlling peanut stem rot caused by S. rolfsii. Here, we isolated a strain of Bacillus from pig biogas slurry that considerably inhibits the radial growth of S. rolfsii. The strain CB13 was identified as Bacillus velezensis on the basis of morphological, physiological, biochemical characteristics and phylogenetic trees based on the 16S rDNA and gyrA, gyrB, and rpoB gene sequences. The biocontrol efficacy of CB13 was evaluated on the basis of colonization ability, induction of defense enzyme activity, and soil microbial diversity. The control efficiencies of B. velezensis CB13-impregnated seeds in four pot experiments were 65.44, 73.33, 85.13, and 94.92%. Root colonization was confirmed through green fluorescent protein (GFP)-tagging experiments. The CB13-GFP strain was detected in peanut root and rhizosphere soil, at 104 and 108 CFU/g, respectively, after 50 days. Furthermore, B. velezensis CB13 enhanced the defense response against S. rolfsii infection by inducing defense enzyme activity. MiSeq sequencing revealed a shift in the rhizosphere bacterial and fungal communities in peanuts treated with B. velezensis CB13. Specifically, the treatment enhanced disease resistance by increasing the diversity of soil bacterial communities in peanut roots, increasing the abundance of beneficial communities, and promoting soil fertility. Additionally, real-time quantitative polymerase chain reaction results showed that B. velezensis CB13 stably colonized or increased the content of Bacillus spp. in the soil and effectively inhibited S. rolfsii proliferation in soil. These findings indicate that B. velezensis CB13 is a promising agent for the biocontrol of peanut stem rot.
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Affiliation(s)
- Shu Jia
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- Sericultural Research Institute of Liaoning Province, Fengcheng, China
| | - Ce Song
- Sericultural Research Institute of Liaoning Province, Fengcheng, China
| | - Hai Dong
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xujie Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xinghai Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Mingshan Ji
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jin Chu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, China
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14
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Ioffe OY, Stetsenko OP, Kindzer SL, Kryvopustov MS, Tsiura YP, Prykhodko YS. APPLICATION OF PROBIOTIC ANTISEPSIS FOR PURULENT COMPLICATIONS IN PATIENTS WITH TYPE 2 DIABETES MELLITUS. WIADOMOSCI LEKARSKIE (WARSAW, POLAND : 1960) 2023; 76:1295-1301. [PMID: 37364088 DOI: 10.36740/wlek202305225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
OBJECTIVE The aim: To improve the results of surgical treatment of patients with type 2 diabetes and purulent-necrotic wounds by using probiotic antiseptics. PATIENTS AND METHODS Materials and methods: 66 patients with type 2 diabetes and purulent-necrotic complications took part in this study. Probiotic antiseptics were used for local treatment in the experimental group (n=31), and traditional antiseptics were used in the control group (n=35). The levels of pro-inflammatory markers in the blood (IL-6, TNF-a, CRP) were studied; microscopic material was taken to study the type of cytogram during bandaging, before wound treatment with antiseptics or debridement on admission to the hospital (1st day), on the 3rd day and on the 7th day. RESULTS Results: Analysis of dynamic changes in pro-inflammatory markers between the first and seventh days proved that only in the experimental group there was a statistically significant difference (IL-6 (Р=0.004), TNF-a (Р=0.001), CRP (Р=0.018)). Detection of regenerative-inflammatory and regenerative cytogram types on the 7th day in the experimental group had a statistically significant difference compared to the control group (p=0.002 and p<0.001, respectively). CONCLUSION Conclusions: the use of probiotic antisepsis accelerates wound healing in patients with type 2 diabetes and purulent-necrotic complications.
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Affiliation(s)
| | | | | | | | - Yuri P Tsiura
- BOGOMOLETS NATIONAL MEDICAL UNIVERSITY, KYIV, UKRAINE
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15
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Podnar E, Erega A, Danevčič T, Kovačec E, Lories B, Steenackers H, Mandic-Mulec I. Nutrient Availability and Biofilm Polysaccharide Shape the Bacillaene-Dependent Antagonism of Bacillus subtilis against Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0183622. [PMID: 36342318 PMCID: PMC9769773 DOI: 10.1128/spectrum.01836-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Salmonella enterica is one of the most common foodborne pathogens and, due to the spread of antibiotic resistance, new antimicrobial strategies are urgently needed to control it. In this study, we explored the probiotic potential of Bacillus subtilis PS-216 and elucidated the mechanisms that underlie the interactions between this soil isolate and the model pathogenic strain S. Typhimurium SL1344. The results reveal that B. subtilis PS-216 inhibits the growth and biofilm formation of S. Typhimurium through the production of the pks cluster-dependent polyketide bacillaene. The presence of S. Typhimurium enhanced the activity of the PpksC promoter that controls bacillaene production, suggesting that B. subtilis senses and responds to Salmonella. The level of Salmonella inhibition, overall PpksC activity, and PpksC induction by Salmonella were all higher in nutrient-rich conditions than in nutrient-depleted conditions. Although eliminating the extracellular polysaccharide production of B. subtilis via deletion of the epsA-O operon had no significant effect on inhibitory activity against Salmonella in nutrient-rich conditions, this deletion mutant showed an enhanced antagonism against Salmonella in nutrient-depleted conditions, revealing an intricate relationship between exopolysaccharide production, nutrient availability, and bacillaene synthesis. Overall, this work provides evidence on the regulatory role of nutrient availability, sensing of the competitor, and EpsA-O polysaccharide in the social outcome of bacillaene-dependent competition between B. subtilis and S. Typhimurium. IMPORTANCE Probiotic bacteria represent an alternative for controlling foodborne disease caused by Salmonella enterica, which constitutes a serious concern during food production due to its antibiotic resistance and resilience to environmental stress. Bacillus subtilis is gaining popularity as a probiotic, but its behavior in biofilms with pathogens such as Salmonella remains to be elucidated. Here, we show that the antagonism of B. subtilis is mediated by the polyketide bacillaene and that the production of bacillaene is a highly dynamic trait which depends on environmental factors such as nutrient availability and the presence of competitors. Moreover, the production of extracellular polysaccharides by B. subtilis further alters the influence of these factors. Hence, this work highlights the inhibitory effect of B. subtilis, which is condition-dependent, and the importance of evaluating probiotic strains under conditions relevant to the intended use.
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Affiliation(s)
- Eli Podnar
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andi Erega
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Danevčič
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Kovačec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Hans Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Ines Mandic-Mulec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Chair of Microprocess Engineering and Technology (COMPETE), University of Ljubljana, Ljubljana, Slovenia
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16
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Imai T, Tobe R, Honda K, Tanaka M, Kawamoto J, Mihara H. Group II truncated haemoglobin YjbI prevents reactive oxygen species-induced protein aggregation in Bacillus subtilis. eLife 2022; 11:70467. [PMID: 36125244 PMCID: PMC9536834 DOI: 10.7554/elife.70467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/19/2022] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress-mediated formation of protein hydroperoxides can induce irreversible fragmentation of the peptide backbone and accumulation of cross-linked protein aggregates, leading to cellular toxicity, dysfunction, and death. However, how bacteria protect themselves from damages caused by protein hydroperoxidation is unknown. Here, we show that YjbI, a group II truncated haemoglobin from Bacillus subtilis, prevents oxidative aggregation of cell-surface proteins by its protein hydroperoxide peroxidase-like activity, which removes hydroperoxide groups from oxidised proteins. Disruption of the yjbI gene in B. subtilis lowered biofilm water repellence, which associated with the cross-linked aggregation of the biofilm matrix protein TasA. YjbI was localised to the cell surface or the biofilm matrix, and the sensitivity of planktonically grown cells to generators of reactive oxygen species was significantly increased upon yjbI disruption, suggesting that YjbI pleiotropically protects labile cell-surface proteins from oxidative damage. YjbI removed hydroperoxide residues from the model oxidised protein substrate bovine serum albumin and biofilm component TasA, preventing oxidative aggregation in vitro. Furthermore, the replacement of Tyr63 near the haem of YjbI with phenylalanine resulted in the loss of its protein peroxidase-like activity, and the mutant gene failed to rescue biofilm water repellency and resistance to oxidative stress induced by hypochlorous acid in the yjbI-deficient strain. These findings provide new insights into the role of truncated haemoglobin and the importance of hydroperoxide removal from proteins in the survival of aerobic bacteria.
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Affiliation(s)
- Takeshi Imai
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Ryuta Tobe
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Koji Honda
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Mai Tanaka
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Hisaaki Mihara
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
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Xie S, Jiang L, Wu Q, Wan W, Gan Y, Zhao L, Wen J. Maize Root Exudates Recruit Bacillus amyloliquefaciens OR2-30 to Inhibit Fusarium graminearum Infection. PHYTOPATHOLOGY 2022; 112:1886-1893. [PMID: 35297645 DOI: 10.1094/phyto-01-22-0028-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacillus spp. can exert plant growth-promoting effects and biocontrol effects after effective colonization, and bacterial chemotaxis toward plant root exudates is the initial step to colonize. Under biotic stress, plants are able to alter their root exudates to attract or avoid different types of microbes. Hence, Bacillus chemotaxis toward root exudates after pathogen infection is crucial for exerting their beneficial effects. In this study, the Bacillus amyloliquefaciens OR2-30 strain, which exhibited greater chemotaxis ability toward maize root exudates after Fusarium graminearum infection, was screened from 156 rhizosphere microorganisms. The infected maize root exudates were further confirmed to improve the swarming and biofilm formation ability of the OR2-30 strain. Chemotaxis, swarming, and biofilm formation ability were able to influence bacterial colonization. Indeed, the the OR2-30 strain displayed more effective colonization ability in the maize rhizosphere after F. graminearum inoculation. Moreover, lipopeptides produced by OR2-30 were identified as iturins and responsible for suppressing F. graminearum growth. Further study showed that lipopeptides suppressed the growth of F. graminearum by inhibiting conidia formation and germination, inducing reactive oxygen species production and causing cell death in mycelium. Eventually, the OR2-30 strain increased maize resistance against F. graminearum. These results suggested that maize root exudates could recruit B. amyloliquefacines OR2-30 after F. graminearum infection, and that OR2-30 then suppresses the F. graminearum by producing lipopeptides, such as iturins, to protect maize.
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Affiliation(s)
- Shanshan Xie
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Lin Jiang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Qin Wu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Wenkun Wan
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yutian Gan
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Lingling Zhao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jiajia Wen
- The National Key Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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18
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Xu S, Cao Q, Liu Z, Chen J, Yan P, Li B, Xu Y. Transcriptomic Analysis Reveals the Role of tmRNA on Biofilm Formation in Bacillus subtilis. Microorganisms 2022; 10:microorganisms10071338. [PMID: 35889057 PMCID: PMC9319509 DOI: 10.3390/microorganisms10071338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus strains are widely distributed in terrestrial and marine environments, and some of them are used as biocontrol organisms for their biofilm-formation ability. In Bacillus subtilis, biofilm formation is fine-tuned by a complex network, a clear understanding of which still requires study. In bacteria, tmRNA, encoded by the ssrA gene, catalyzes trans-translation that can rescue ribosomes stalled on mRNA transcripts lacking a functional stop codon. tmRNA also affects physiological bioprocesses in some bacteria. In this study, we constructed a ssrA mutant in B. subtilis and found that the biofilm formation in the ssrA mutant was largely impaired. Moreover, we isolated a biofilm-formation suppressor of ssrA, in which the biofilm formation was restored to a level even stronger than that in the wild type. We further performed RNAseq assays with the wild type, ssrA mutant, and suppressor of ssrA for comparisons of their transcriptomes. By analyzing the transcriptomic data, we predicted the possible functions of some differentially expressed genes (DEGs) in the tmRNA regulation of biofilm formation in B. subtilis. Finally, we found that the overexpression of two DEGs, acoA and yhjR, could restore the biofilm formation in the ssrA mutant, indicating that AcoA and YhjR were immediate regulators involved in the tmRNA regulatory web controlling biofilm formation in B. subtilis. Our data can improve the knowledge about the molecular network involved in Bacillus biofilm formation and provide new targets for manipulation of Bacillus biofilms for future investigation.
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Affiliation(s)
- Shanshan Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Qianqian Cao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Zengzhi Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Junpeng Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
| | - Peiguang Yan
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Bingyu Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Health Science Center, Shenzhen University, Shenzhen 518055, China
- Correspondence: (B.L.); (Y.X.)
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China; (S.X.); (Q.C.); (Z.L.); (J.C.)
- Correspondence: (B.L.); (Y.X.)
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19
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Lamba S, Mundanda Muthappa D, Fanning S, Scannell AGM. Sporulation and Biofilms as Survival Mechanisms of Bacillus Species in Low-Moisture Food Production Environments. Foodborne Pathog Dis 2022; 19:448-462. [PMID: 35819266 DOI: 10.1089/fpd.2022.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Low-moisture foods (LMF) have clear advantages with respect to limiting the growth of foodborne pathogens. However, the incidences of Bacillus species in LMF reported in recent years raise concerns about food quality and safety, particularly when these foods are used as ingredients in more complex higher moisture products. This literature review describes the interlinked pathways of sporulation and biofilm formation by Bacillus species and their underlying molecular mechanisms that contribute to the bacteriums' persistence in LMF production environments. The long-standing challenges of food safety and quality in the LMF industry are also discussed with a focus on the bakery industry.
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Affiliation(s)
- Sakshi Lamba
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Dechamma Mundanda Muthappa
- UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
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20
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Li Y, Chen N, Wu Q, Liang X, Yuan X, Zhu Z, Zheng Y, Yu S, Chen M, Zhang J, Wang J, Ding Y. A Flagella Hook Coding Gene flgE Positively Affects Biofilm Formation and Cereulide Production in Emetic Bacillus cereus. Front Microbiol 2022; 13:897836. [PMID: 35756067 PMCID: PMC9226606 DOI: 10.3389/fmicb.2022.897836] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/10/2022] [Indexed: 12/22/2022] Open
Abstract
Bacillus cereus, an important foodborne pathogen, poses a risk to food safety and quality. Robust biofilm formation ability is one of the key properties that is responsible for the food contamination and food poisoning caused by B. cereus, especially the emetic strains. To investigate the mechanism of biofilm formation in emetic B. cereus strains, we screened for the mutants that fail to form biofilms by using random mutagenesis toward B. cereus 892-1, an emetic strain with strong biofilm formation ability. When knocking out flgE, a flagellar hook encoding gene, the mutant showed disappearance of flagellar structure and swimming ability. Further analysis revealed that both pellicle and ring presented defects in the null mutant compared with the wild-type and complementary strains. Compared with the flagellar paralytic strains ΔmotA and ΔmotB, the inhibition of biofilm formation by ΔflgE is not only caused by the inhibition of motility. Interestingly, ΔflgE also decreased the synthesis of cereulide. To our knowledge, this is the first report showing that a flagellar component can both affect the biofilm formation and cereulide production in emetic B. cereus, which can be used as the target to control the biohazard of emetic B. cereus.
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Affiliation(s)
- Yangfu Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Nuo Chen
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinmin Liang
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoming Yuan
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenjun Zhu
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Yin Zheng
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Shubo Yu
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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21
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Qin Y, Angelini LL, Chai Y. Bacillus subtilis Cell Differentiation, Biofilm Formation and Environmental Prevalence. Microorganisms 2022; 10:microorganisms10061108. [PMID: 35744626 PMCID: PMC9227780 DOI: 10.3390/microorganisms10061108] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling, spore-forming Gram-positive bacterium capable of cell differentiation. For decades, B. subtilis has been used as a model organism to study development of specialized cell types. In this minireview, we discuss cell differentiation in B. subtilis, covering both past research and recent progresses, and the role of cell differentiation in biofilm formation and prevalence of this bacterium in the environment. We review B. subtilis as a classic model for studies of endospore formation, and highlight more recent investigations on cell fate determination and generation of multiple cell types during biofilm formation. We present mechanistic details of how cell fate determination and mutually exclusive cell differentiation are regulated during biofilm formation.
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Affiliation(s)
- Yuxuan Qin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Q.); (Y.C.)
| | | | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA 02115, USA;
- Correspondence: (Y.Q.); (Y.C.)
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22
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Yu Z, Fu Y, Zhang W, Zhu L, Yin W, Chou SH, He J. The RNA Chaperone Protein Hfq Regulates the Characteristic Sporulation and Insecticidal Activity of Bacillus thuringiensis. Front Microbiol 2022; 13:884528. [PMID: 35479624 PMCID: PMC9037596 DOI: 10.3389/fmicb.2022.884528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus thuringiensis (Bt) is one of the most widely used bio-insecticides at present. It can produce many virulence factors and insecticidal crystal proteins during growth and sporulation. Hfq, on the other hand, is a bacterial RNA chaperone that can regulate the function of different kinds of RNAs, thereby affecting various bacterial phenotypes. To further explore the physiological functions of Hfq in Bt, we took BMB171 as the starting strain, knocked out one, two, or three hfq genes in its genome in different combinations, and compared the phenotypic differences between the deletion mutant strains and the starting strain. We did observe significant changes in several phenotypes, including motility, biofilm formation, sporulation, and insecticidal activity against cotton bollworm, among others. Afterward, we found through transcriptome studies that when all hfq genes were deleted, 32.5% of the genes in Bt were differentially transcribed, with particular changes in the sporulation-related and virulence-related genes. The above data demonstrated that Hfq plays a pivotal role in Bt and can regulate its various physiological functions. Our study on the regulatory mechanism of Hfq in Bt, especially the mining of the regulatory network of its sporulation and insecticidal activity, could lay a theoretical foundation for the better utilization of Bt as an effective insecticide.
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Affiliation(s)
- Zhaoqing Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wei Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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23
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Ghosh S, Nag M, Lahiri D, Sarkar T, Pati S, Kari ZA, Nirmal NP, Edinur HA, Ray RR. Engineered Biofilm: Innovative Nextgen Strategy for Quality Enhancement of Fermented Foods. Front Nutr 2022; 9:808630. [PMID: 35479755 PMCID: PMC9036442 DOI: 10.3389/fnut.2022.808630] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/11/2022] [Indexed: 11/22/2022] Open
Abstract
Microbial communities within fermented food (beers, wines, distillates, meats, fishes, cheeses, breads) products remain within biofilm and are embedded in a complex extracellular polymeric matrix that provides favorable growth conditions to the indwelling species. Biofilm acts as the best ecological niche for the residing microbes by providing food ingredients that interact with the fermenting microorganisms' metabolites to boost their growth. This leads to the alterations in the biochemical and nutritional quality of the fermented food ingredients compared to the initial ingredients in terms of antioxidants, peptides, organoleptic and probiotic properties, and antimicrobial activity. Microbes within the biofilm have altered genetic expression that may lead to novel biochemical pathways influencing their chemical and organoleptic properties related to consumer acceptability. Although microbial biofilms have always been linked to pathogenicity owing to its enhanced antimicrobial resistance, biofilm could be favorable for the production of amino acids like l-proline and L-threonine by engineered bacteria. The unique characteristics of many traditional fermented foods are attributed by the biofilm formed by lactic acid bacteria and yeast and often, multispecies biofilm can be successfully used for repeated-batch fermentation. The present review will shed light on current research related to the role of biofilm in the fermentation process with special reference to the recent applications of NGS/WGS/omics for the improved biofilm forming ability of the genetically engineered and biotechnologically modified microorganisms to bring about the amelioration of the quality of fermented food.
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Affiliation(s)
- Sreejita Ghosh
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, India
| | - Siddhartha Pati
- NatNov Bioscience Private Limited, Balasore, India
- Skills Innovation & Academic Network (SIAN) Institute, Association for Biodiversity Conservation and Research (ABC), Balasore, India
| | - Zulhisyam Abdul Kari
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Kota Bharu, Malaysia
| | | | - Hisham Atan Edinur
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India
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24
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Bremer E, Hoffmann T, Dempwolff F, Bedrunka P, Bange G. The many faces of the unusual biofilm activator RemA. Bioessays 2022; 44:e2200009. [PMID: 35289951 DOI: 10.1002/bies.202200009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.
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Affiliation(s)
- Erhard Bremer
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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25
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Antimicrobial Peptides as an Alternative for the Eradication of Bacterial Biofilms of Multi-Drug Resistant Bacteria. Pharmaceutics 2022; 14:pharmaceutics14030642. [PMID: 35336016 PMCID: PMC8950055 DOI: 10.3390/pharmaceutics14030642] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 12/03/2022] Open
Abstract
Bacterial resistance is an emergency public health problem worldwide, compounded by the ability of bacteria to form biofilms, mainly in seriously ill hospitalized patients. The World Health Organization has published a list of priority bacteria that should be studied and, in turn, has encouraged the development of new drugs. Herein, we explain the importance of studying new molecules such as antimicrobial peptides (AMPs) with potential against multi-drug resistant (MDR) and extensively drug-resistant (XDR) bacteria and focus on the inhibition of biofilm formation. This review describes the main causes of antimicrobial resistance and biofilm formation, as well as the main and potential AMP applications against these bacteria. Our results suggest that the new biomacromolecules to be discovered and studied should focus on this group of dangerous and highly infectious bacteria. Alternative molecules such as AMPs could contribute to eradicating biofilm proliferation by MDR/XDR bacteria; this is a challenging undertaking with promising prospects.
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26
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Mahapatra S, Yadav R, Ramakrishna W. Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde. J Appl Microbiol 2022; 132:3543-3562. [PMID: 35137494 DOI: 10.1111/jam.15480] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.
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27
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Wang R, Zhang W, Ding W, Liang Z, Long L, Wong WC, Qian PY. Profiling Signal Transduction in Global Marine Biofilms. Front Microbiol 2022; 12:768926. [PMID: 35069473 PMCID: PMC8776716 DOI: 10.3389/fmicb.2021.768926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Microbes use signal transduction systems in the processes of swarming motility, antibiotic resistance, virulence, conjugal plasmid transfer, and biofilm formation. However, the signal transduction systems in natural marine biofilms have hardly been profiled. Here we analyzed signal transduction genes in 101 marine biofilm and 91 seawater microbial metagenomes. The abundance of almost all signal transduction-related genes in biofilm microbial communities was significantly higher than that in seawater microbial communities, regardless of substrate types, locations, and durations for biofilm development. In addition, the dominant source microbes of signal transduction genes in marine biofilms were different from those in seawater samples. Co-occurrence network analysis on signal communication between microbes in marine biofilms and seawater microbial communities revealed potential inter-phyla interactions between microorganisms from marine biofilms and seawater. Moreover, phylogenetic tree construction and protein identity comparison displayed that proteins related to signal transductions from Red Sea biofilms were highly similar to those from Red Sea seawater microbial communities, revealing a possible biological basis of interspecies interactions between surface-associated and free-living microbial communities in a local marine environment. Our study revealed the special profile and enrichment of signal transduction systems in marine biofilms and suggested that marine biofilms participate in intercellular interactions of the local ecosystem where they were seeded.
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Affiliation(s)
- Ruojun Wang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhicong Liang
- Department of Mathematics, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Lexin Long
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wai Chuen Wong
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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28
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Antifungal Compounds of Plant Growth-Promoting Bacillus Species. Fungal Biol 2022. [DOI: 10.1007/978-3-031-04805-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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29
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Zhang H, Qian Y, Fan D, Tian Y, Huang X. Biofilm formed by Hansschlegelia zhihuaiae S113 on root surface mitigates the toxicity of bensulfuron-methyl residues to maize. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118366. [PMID: 34653590 DOI: 10.1016/j.envpol.2021.118366] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/20/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Bensulfuron-methyl (BSM) residues in soil threaten the rotation of BSM-sensitive crops. Microbial biofilms formed on crop roots could improve the ability of microbes to survive and protect crop roots. However, the research on biofilms with the purpose of mitigating or even eliminating BSM damage to sensitive crops is very limited. In this study, one BSM-degrading bacterium, Hansschlegelia zhihuaiae S113, colonized maize roots by forming a biofilm. Root exudates were associated with increased BSM degradation efficiency with strain S113 in rhizosphere soil relative to bulk soil, so the interactions among BSM degradation, root exudates, and biofilms may provide a new approach for the BSM-contaminated soil bioremediation. Root exudates and their constituent organic acids, including fumaric acid, tartaric acid, and l-malic acid, enhanced biofilm formation with 13.0-22.2% increases, owing to the regulation of genes encoding proteins responsible for cell motility/chemotaxis (fla/che cluster) and materials metabolism, thus promoting S113 population increases. Additionally, root exudates were also able to induce exopolysaccharide production to promote mature biofilm formation. Complete BSM degradation and healthy maize growth were found in BSM-contaminated rhizosphere soil treated with wild strain S113, compared to that treated with loss-of-function mutants ΔcheA-S113 (89.3%, without biofilm formation ability) and ΔsulE-S113 (22.1%, without degradation ability) or sterile water (10.7%, control). Furthermore, the biofilm mediated by organic acids, such as l-malic acid, exhibited a more favorable effect on BSM degradation and maize growth. These results showed that root exudates and their components (such as organic acids) can induce the biosynthesis of the biofilm to promote BSM degradation, emphasizing the contribution of root biofilm in reducing BSM damage to maize.
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Affiliation(s)
- Hao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China; College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, PR China; Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, Nanyang Normal University, Nanyang, 473061, PR China
| | - Yingying Qian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dandan Fan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yanning Tian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xing Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
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30
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Liu N, Chen B, Zhao X, Wen J, Qi G. Cations and surfactin serving as signal molecules trigger quorum sensing in Bacillus amyloliquefaciens. J Basic Microbiol 2021; 62:35-47. [PMID: 34825384 DOI: 10.1002/jobm.202100315] [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: 07/02/2021] [Revised: 10/31/2021] [Accepted: 11/06/2021] [Indexed: 11/06/2022]
Abstract
Microorganisms including Bacillus can produce signal molecules such as surfactin, resulting in the variation of membrane potential to trigger quorum sensing such as biofilm formation and sporulation in response to the environment stresses. However, biosynthesis of surfactin requires multiple resources such as huge enzyme complex, amino acids, fatty acids, and energy. Insufficient resources in the natural soil environment restrain biosynthesis of surfactin. When surfactin is inadequate, cations in soil might serve as substitutes to regulate quorum sensing. Our results showed that both surfactin and cations could lead to the variation of membrane potential, thus providing signals to trigger the quorum sensing such as growth, biofilm formation, and sporulation in Bacillus amyloliquefaciens. Neither KinC nor Abh was essential for surfactin or cations to trigger quorum sensing. The cation signaling pathway is only partially dependent on Spo0A, but the surfactin signaling pathway is fully dependent on this global regulator. Compared to surfactin, cations are less effective in promoting biofilm formation, but more effective to trigger sporulation in B. amyloliquefaciens. This study reveals a pathway through which cations regulate the quorum sensing in B. amyloliquefaciens in the case of insufficient surfactin in environment.
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Affiliation(s)
- Na Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bing Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiahong Wen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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31
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Zhang Y, Qi J, Wang Y, Wen J, Zhao X, Qi G. Comparative study of the role of surfactin-triggered signalling in biofilm formation among different Bacillus species. Microbiol Res 2021; 254:126920. [PMID: 34800863 DOI: 10.1016/j.micres.2021.126920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/18/2021] [Accepted: 09/13/2021] [Indexed: 01/12/2023]
Abstract
The signal molecule surfactin in biofilm formation has been extensively studied in B. subtilis, but there is rare reports in other Bacillus species. In this study, we compared the surfactin-Spo0A-SinI-SinR/SlrR signalling in regulating biofilm formation amongst four Bacillus species including B. subtilis, B. amyloliquefaciens, B. velezensis, and B. licheniformis. The role of surfactin in biofilm formation was dependent on Bacillus species and strains, and the importance of surfactin was as following: B. velezensis R9 = B. amyloliquefaciens WH1 > B. licheniformis 285-3 > B. subtilis CYY. The global regulator Spo0A was essential and very conservative for biofilm formation in all four Bacillus species. The regulators SinI and SinR played different roles to regulate biofilm formation in different Bacillus species. SinI had no obvious roles in B. velezensis, B. amyloliquefaciens and B. subtilis but had a positive role in B. licheniformis. SinR had no obvious roles in B. subtilis, but played a positive role in B. velezensis, B. amyloliquefaciens and B. licheniformis. The regulator SlrR played a positive role in the biofilm formation of all four Bacillus species. Collectively, surfactin, Spo0A and SlrR are essential for the biofilm formation in all four Bacillus species, and SinR and SinI plays different roles in different Bacillus species.
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Affiliation(s)
- Yan Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jishuai Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiahong Wen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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McLoon AL, Boeck ME, Bruckskotten M, Keyel AC, Søgaard-Andersen L. Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus. BMC Genomics 2021; 22:784. [PMID: 34724903 PMCID: PMC8561891 DOI: 10.1186/s12864-021-08051-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/30/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The Myxococcales are well known for their predatory and developmental social processes, and for the molecular complexity of regulation of these processes. Many species within this order have unusually large genomes compared to other bacteria, and their genomes have many genes that are unique to one specific sequenced species or strain. Here, we describe RNAseq based transcriptome analysis of the FruA regulon of Myxococcus xanthus and a comparative RNAseq analysis of two Myxococcus species, M. xanthus and Myxococcus stipitatus, as they respond to starvation and begin forming fruiting bodies. RESULTS We show that both species have large numbers of genes that are developmentally regulated, with over half the genome showing statistically significant changes in expression during development in each species. We also included a non-fruiting mutant of M. xanthus that is missing the transcriptional regulator FruA to identify the direct and indirect FruA regulon and to identify transcriptional changes that are specific to fruiting and not just the starvation response. We then identified Interpro gene ontologies and COG annotations that are significantly up- or down-regulated during development in each species. Our analyses support previous data for M. xanthus showing developmental upregulation of signal transduction genes, and downregulation of genes related to cell-cycle, translation, metabolism, and in some cases, DNA replication. Gene expression in M. stipitatus follows similar trends. Although not all specific genes show similar regulation patterns in both species, many critical developmental genes in M. xanthus have conserved expression patterns in M. stipitatus, and some groups of otherwise unstudied orthologous genes share expression patterns. CONCLUSIONS By identifying the FruA regulon and identifying genes that are similarly and uniquely regulated in two different species, this work provides a more complete picture of transcription during Myxococcus development. We also provide an R script to allow other scientists to mine our data for genes whose expression patterns match a user-selected gene of interest.
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Affiliation(s)
- Anna L McLoon
- Biology Department, Siena College, Loudonville, NY, USA
| | - Max E Boeck
- Biology Department, Regis University, Denver, CO, USA
| | - Marc Bruckskotten
- Center of Medical Genetics and Human Genetics, Philipps-University, Marburg, Germany
| | - Alexander C Keyel
- Department of Atmospheric and Environmental Sciences, University at Albany, Albany, NY, USA
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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Ribeiro M, Sousa CA, Simões M. Harnessing microbial iron chelators to develop innovative therapeutic agents. J Adv Res 2021; 39:89-101. [PMID: 35777919 PMCID: PMC9263657 DOI: 10.1016/j.jare.2021.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 01/19/2023] Open
Abstract
Microbial iron chelators as a new route to develop inspiring antimicrobials. Siderophore-mimicking antibiotics as a pathogen-targeted strategy. Effectiveness of iron chelators on antibiotic-resistant Gram-negative bacteria. Iron chelators and the treatment of iron overload diseases. Iron chelators as powerful tools for cancer therapy.
Background Aim of Review Key Scientific Concepts of Review
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Scholz AS, Baur SSM, Wolf D, Bramkamp M. An Stomatin, Prohibitin, Flotillin, and HflK/C-Domain Protein Required to Link the Phage-Shock Protein to the Membrane in Bacillus subtilis. Front Microbiol 2021; 12:754924. [PMID: 34777311 PMCID: PMC8581546 DOI: 10.3389/fmicb.2021.754924] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/27/2021] [Indexed: 11/28/2022] Open
Abstract
Membrane surveillance and repair is of utmost importance to maintain cellular integrity and allow cellular life. Several systems detect cell envelope stress caused by antimicrobial compounds and abiotic stresses such as solvents, pH-changes and temperature in bacteria. Proteins containing an Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH)-domain, including bacterial flotillins have been shown to be involved in membrane protection and membrane fluidity regulation. Here, we characterize a bacterial SPFH-domain protein, YdjI that is part of a stress induced complex in Bacillus subtilis. We show that YdjI is required to localize the ESCRT-III homolog PspA to the membrane with the help of two membrane integral proteins, YdjG/H. In contrast to classical flotillins, YdjI resides in fluid membrane regions and does not enrich in detergent resistant membrane fractions. However, similarly to FloA and FloT from B. subtilis, deletion of YdjI decreases membrane fluidity. Our data reveal a hardwired connection between phage shock response and SPFH proteins.
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Affiliation(s)
- Abigail Savietto Scholz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarah S. M. Baur
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Diana Wolf
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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Luo C, Liu J, Bilal M, Liu X, Wang X, Dong F, Liu Y, Zang S, Yin X, Yang X, Zhu T, Zhang S, Zhang W, Li B. Extracellular lipopeptide bacillomycin L regulates serial expression of genes for modulating multicellular behavior in Bacillus velezensis Bs916. Appl Microbiol Biotechnol 2021; 105:6853-6870. [PMID: 34477941 DOI: 10.1007/s00253-021-11524-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
In wild strains of Bacillus, a handful of extracellular natural products act as signals that can regulate multicellular behavior, but relatively little is known about molecular mechanisms' detail. We proposed a previously unreported molecular mechanism for triggering multicellularity in B. velezensis Bs916 by an endogenous cyclic lipopeptide, bacillomycin L. The genome-wide effect on gene expression was caused by the disruption of bacillomycin L gene cluster, and 100 µg/mL bacillomycin L was revealed by quantitative transcriptomics. A total of 878 differentially expressed genes among Bs916, Δbl, and Δbl + 100BL were identified and grouped into 9 functional categories. The transcription levels of 40 candidate genes were further evaluated by RT-qPCR analysis. The expression of eight candidate genes regulated by bacillomycin L in a dose-dependent manner was revealed by LacZ fusion experiment. Although the addition of bacillomycin L could not completely restore the expression levels of the differentially regulated genes in △bl, our results strongly suggest that bacillomycin L acts as a tuning signal of swarming motility and complex biofilm formation by indirectly regulating the expression levels of some two-component systems (TCSs) connector genes, particularly including several Raps that potentially regulate the phosphorylation levels of three major regulators ComA, DegU, and Spo0A.Key points• Proposed model for bacillomycin L regulation in B. velezensis Bs916.• Bacillomycin L can act as an extracellular signal to regulate the phosphorylation levels of three major regulators, ComA, DegU, and Spo0A and control the multicellular processes of vegetative growth, competent, motility, matrix production, sporulation, and autolysis.
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Affiliation(s)
- Chuping Luo
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Jiachen Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Muhammad Bilal
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xuehui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaohua Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Fei Dong
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Yuan Liu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China.,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shanshan Zang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiulian Yin
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Xueting Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tao Zhu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Shuangyu Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Weifeng Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Bin Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huai'an, 223003, China. .,Institute of Veterinary Medicine, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Gallegos-Monterrosa R, Christensen MN, Barchewitz T, Koppenhöfer S, Priyadarshini B, Bálint B, Maróti G, Kempen PJ, Dragoš A, Kovács ÁT. Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis. Commun Biol 2021; 4:468. [PMID: 33850233 PMCID: PMC8044106 DOI: 10.1038/s42003-021-01983-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Mathilde Nordgaard Christensen
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tino Barchewitz
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sonja Koppenhöfer
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.25055.370000 0000 9130 6822Present Address: Department of Biology, Memorial University of Newfoundland, St. John’s, NL Canada
| | - B. Priyadarshini
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Balázs Bálint
- grid.475919.7Seqomics Biotechnology Ltd., Mórahalom, Hungary
| | - Gergely Maróti
- grid.5018.c0000 0001 2149 4407Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Paul J. Kempen
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Dragoš
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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Dergham Y, Sanchez-Vizuete P, Le Coq D, Deschamps J, Bridier A, Hamze K, Briandet R. Comparison of the Genetic Features Involved in Bacillus subtilis Biofilm Formation Using Multi-Culturing Approaches. Microorganisms 2021; 9:microorganisms9030633. [PMID: 33803642 PMCID: PMC8003051 DOI: 10.3390/microorganisms9030633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Surface-associated multicellular assemblage is an important bacterial trait to withstand harsh environmental conditions. Bacillus subtilis is one of the most studied Gram-positive bacteria, serving as a model for the study of genetic pathways involved in the different steps of 3D biofilm formation. B. subtilis biofilm studies have mainly focused on pellicle formation at the air-liquid interface or complex macrocolonies formed on nutritive agar. However, only few studies focus on the genetic features of B. subtilis submerged biofilm formation and their link with other multicellular models at the air interface. NDmed, an undomesticated B. subtilis strain isolated from a hospital, has demonstrated the ability to produce highly structured immersed biofilms when compared to strains classically used for studying B. subtilis biofilms. In this contribution, we have conducted a multi-culturing comparison (between macrocolony, swarming, pellicle, and submerged biofilm) of B. subtilis multicellular communities using the NDmed strain and mutated derivatives for genes shown to be required for motility and biofilm formation in pellicle and macrocolony models. For the 15 mutated NDmed strains studied, all showed an altered phenotype for at least one of the different culture laboratory assays. Mutation of genes involved in matrix production (i.e., tasA, epsA-O, cap, ypqP) caused a negative impact on all biofilm phenotypes but favored swarming motility on semi-solid surfaces. Mutation of bslA, a gene coding for an amphiphilic protein, affected the stability of the pellicle at the air-liquid interface with no impact on the submerged biofilm model. Moreover, mutation of lytF, an autolysin gene required for cell separation, had a greater effect on the submerged biofilm model than that formed at aerial level, opposite to the observation for lytABC mutant. In addition, B. subtilis NDmed with sinR mutation formed wrinkled macrocolony, less than that formed by the wild type, but was unable to form neither thick pellicle nor structured submerged biofilm. The results are discussed in terms of the relevancy to determine whether genes involved in colony and pellicle formation also govern submerged biofilm formation, by regarding the specificities in each model.
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Affiliation(s)
- Yasmine Dergham
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (Y.D.); (P.S.-V.); (D.L.C.); (J.D.)
- Faculty of Science, Lebanese University, 1003 Beirut, Lebanon;
| | - Pilar Sanchez-Vizuete
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (Y.D.); (P.S.-V.); (D.L.C.); (J.D.)
| | - Dominique Le Coq
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (Y.D.); (P.S.-V.); (D.L.C.); (J.D.)
- Centre National de la Recherche Scientifique (CNRS), Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Julien Deschamps
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (Y.D.); (P.S.-V.); (D.L.C.); (J.D.)
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300 Fougères, France;
| | - Kassem Hamze
- Faculty of Science, Lebanese University, 1003 Beirut, Lebanon;
| | - Romain Briandet
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (Y.D.); (P.S.-V.); (D.L.C.); (J.D.)
- Correspondence:
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Sharipova MR, Mardanova AM, Rudakova NL, Pudova DS. Bistability and Formation of the Biofilm Matrix as Adaptive Mechanisms during the Stationary Phase of Bacillus subtilis. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172006017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Effects of an EPS Biosynthesis Gene Cluster of Paenibacillus polymyxa WLY78 on Biofilm Formation and Nitrogen Fixation under Aerobic Conditions. Microorganisms 2021; 9:microorganisms9020289. [PMID: 33573330 PMCID: PMC7911366 DOI: 10.3390/microorganisms9020289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/17/2022] Open
Abstract
Exopolysaccharides (EPS) are of high significance in bacterial biofilm formation. However, the effects of EPS cluster(s) on biofilm formation in Paenibacillus species are little known. In this study, we have shown that Paenibacillus polymyxa WLY78, a N2-fixing bacterium, can form biofilm. EPS is the major component of the extracellular matrix. The genome of P. polymyxa WLY78 contains two putative gene clusters (designated pep-1 cluster and pep-2 cluster). The pep-1 cluster is composed of 12 putative genes (pepO-lytR) co-located in a 13 kb region. The pep-2 cluster contains 17 putative genes (pepA-pepN) organized as an operon in a 20 kb region. Mutation analysis reveals that the pep-2 cluster is involved in EPS biosynthesis and biofilm formation. Disruption of the pep-2 cluster also leads to the enhancement of motility and change of the colony morphology. In contrast, disruption of the pep-1 cluster does not affect EPS synthesis or biofilm formation. More importantly, the biofilm allowed P. polymyxa WLY78 to fix nitrogen in aerobic conditions, suggesting that biofilm may provide a microaerobic environment for nitrogenase synthesis and activity.
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Hassanein WA, Reda FM, Moabed S, El Shafiey SN. Insecticidal impacts of Bacillus flexus S13 biofilm'extracellular matrix' on cowpea weevil, Callosobruchus maculatus. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Pinteus S, Lemos MFL, Alves C, Silva J, Pedrosa R. The marine invasive seaweeds Asparagopsis armata and Sargassum muticum as targets for greener antifouling solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141372. [PMID: 32853930 DOI: 10.1016/j.scitotenv.2020.141372] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/11/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Biofouling is a complex phenomenon that affects all maritime dependent industries. The accumulation of both micro and macro-organisms in immerged structures increases significantly the maintenance expenses, and thus the use of antifouling substances is inevitable. Although with recognized antifouling properties, the available antifouling coatings are known to induce negative impacts in aquatic ecosystems. Therefore, greener alternatives are urgently required. Living underwater, marine organisms are prone to biofouling and some have developed strategies to defend themselves against undesirable organisms, which include the production of bioactive substances. As a result, marine organisms are promising sources of natural antifouling substances. Within this framework, the marine invasive seaweeds Sargassum muticum and Asparagopsis armata were addressed for antifouling compounds biodiscovery. Both seaweeds revealed antifouling properties against microfoulers, namely algicidal and anti-biofilm activities; however Asparagopsis armata stand out for its capacity to inhibit marine bacteria and microalgae growth, to decrease biofilm formation, and for acting as a neurotransmitter disruptor through the inhibition of acetylcholinesterase activity. By addressing invasive species, the problematic of the biological material supply for industrial purposes is surpassed while mitigating the negative impacts of invasive species through specimen's collection.
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Affiliation(s)
- Susete Pinteus
- MARE - Marine and Environmental Sciences Centre, Polytechnic of Leiria, 2520-630 Peniche, Portugal..
| | - Marco F L Lemos
- MARE - Marine and Environmental Sciences Centre, Polytechnic of Leiria, 2520-630 Peniche, Portugal
| | - Celso Alves
- MARE - Marine and Environmental Sciences Centre, Polytechnic of Leiria, 2520-630 Peniche, Portugal
| | - Joana Silva
- MARE - Marine and Environmental Sciences Centre, Polytechnic of Leiria, 2520-630 Peniche, Portugal
| | - Rui Pedrosa
- MARE - Marine and Environmental Sciences Centre, Polytechnic of Leiria, 2520-630 Peniche, Portugal..
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Blake C, Christensen MN, Kovács ÁT. Molecular Aspects of Plant Growth Promotion and Protection by Bacillus subtilis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:15-25. [PMID: 32986513 DOI: 10.1094/mpmi-08-20-0225-cr] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bacillus subtilis is one of the most widely studied plant growth-promoting rhizobacteria. It is able to promote plant growth as well as control plant pathogens through diverse mechanisms, including the improvement of nutrient availability and alteration of phytohormone homeostasis as well as the production of antimicrobials and triggering induced systemic resistance, respectively. Even though its benefits for crop production have been recognized and studied extensively under laboratory conditions, the success of its application in fields varies immensely. It is widely accepted that agricultural application of B. subtilis often fails because the bacteria are not able to persist in the rhizosphere. Bacterial colonization of plant roots is a crucial step in the interaction between microbe and plant and seems, therefore, to be of great importance for its growth promotion and biocontrol effects. A successful root colonization depends thereby on both bacterial traits, motility and biofilm formation, as well as on a signal interplay with the plant. This review addresses current knowledge about plant-microbial interactions of the B. subtilis species, including the various mechanisms for supporting plant growth as well as the necessity for the establishment of the relationship.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
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Affiliation(s)
- Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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Ren P, Chen T, Liu N, Sun W, Hu G, Yu Y, Yu B, Ouyang P, Liu D, Chen Y. Efficient Biofilm-Based Fermentation Strategies by eDNA Formation for l-Proline Production with Corynebacterium glutamicum. ACS OMEGA 2020; 5:33314-33322. [PMID: 33403293 PMCID: PMC7774248 DOI: 10.1021/acsomega.0c05095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Biofilms could provide favorable conditions for the growth of cells during industrial fermentation. However, biofilm-immobilized fermentation has not yet been reported in Corynebacterium glutamicum (C. glutamicum), one of the main strains for amino acid production. This is mainly because C. glutamicum has a poor capability of adsorption onto materials or forming an extracellular polymeric substance (EPS). Here, an engineered strain, C. glutamicum Pro-ΔexeM, was created by removing the extracellular nuclease gene exeM, which effectively increased extracellular DNA (eDNA) in the EPS and cell adhesiveness onto carrier materials. In repeated-batch fermentation using the biofilm, l-proline production increased from 10.2 to 17.1 g/L. In summary, this research demonstrated that a synthetic C. glutamicum biofilm could be favorable for l-proline production, which could be extended to other industrial applications of C. glutamicum, and the strategy may also be applicable to the engineering of other strains.
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Affiliation(s)
- Peifang Ren
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Tianpeng Chen
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Na Liu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Wenjun Sun
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Guang Hu
- Nanjing
Iaso Biotherapeutics Co., Ltd., Nanjing 210000, P.R. China
| | - Ying Yu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Bin Yu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Pingkai Ouyang
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
| | - Dong Liu
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
| | - Yong Chen
- State
Key Laboratory of Materials-Oriented Chemical Engineering, College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
- National
Engineering Research Center for Biotechnology, College of Biotechnology
and Pharmaceutical Engineering, Nanjing
Tech University, Nanjing 211816, P.R. China
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44
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Wang R, Ding W, Long L, Lan Y, Tong H, Saha S, Wong YH, Sun J, Li Y, Zhang W, Qian PY. Exploring the Influence of Signal Molecules on Marine Biofilms Development. Front Microbiol 2020; 11:571400. [PMID: 33281767 PMCID: PMC7691533 DOI: 10.3389/fmicb.2020.571400] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/27/2020] [Indexed: 01/10/2023] Open
Abstract
Microbes respond to environmental stimuli through complicated signal transduction systems. In microbial biofilms, because of complex multiple species interactions, signals transduction systems are of an even higher complexity. Here, we performed a signal-molecule-treatment experiment to study the role of different signal molecules, including N-hexanoyl-L-homoserine lactone (C6-HSL), N-dodecanoyl-L-homoserine lactone (C12-HSL), Pseudomonas quinolone signal (PQS), and cyclic di-GMP (c-di-GMP), in the development of marine biofilms. Comparative metagenomics suggested a distinctive influence of these molecules on the microbial structure and function of multi-species biofilm communities in its developing stage. The PQS-treated biofilms shared the least similarity with the control and initial biofilms. The role of PQS in biofilm development was further explored experimentally with the strain Erythrobacter sp. HKB8 isolated from marine biofilms. Comparative transcriptomic analysis showed that 314 genes, such as those related to signal transduction and biofilm formation, were differentially expressed in the untreated and PQS-treated Erythrobacter sp. HKB8 biofilms. Our study demonstrated the different roles of signal molecules in marine biofilm development. In particular, the PQS-based signal transduction system, which is frequently detected in marine biofilms, may play an important role in regulating microbe-microbe interactions and the assemblage of biofilm communities.
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Affiliation(s)
- Ruojun Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lexin Long
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yi Lan
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Haoya Tong
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Subhasish Saha
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yue Him Wong
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jin Sun
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yongxin Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong.,The Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Kowloon, Hong Kong
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Thüring M, Ganapathy S, Schlüter MAC, Lechner M, Hartmann RK. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol 2020; 18:79-92. [PMID: 32862759 DOI: 10.1080/15476286.2020.1795408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Bacterial 6S RNA regulates transcription via binding to the active site of RNA polymerase holoenzymes. 6S RNA has been identified in the majority of bacteria, in most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two 6S RNA paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that the regulatory role of 6S RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed 6S RNA deletion mutants of the undomesticated B. subtilis wild-type strain NCIB 3610. We observed a strong phenotype for the ∆6S-2 RNA strain that showed increased biofilm formation on solid media and the ability to form surface-attached biofilms in liquid culture. This phenotype remained undetected in derived laboratory strains (168, PY79) that are defective in biofilm formation. Quantitative RT-PCR data revealed transcriptional upregulation of biofilm marker genes such as tasA, epsA and bslA in the ∆6S-2 RNA strain, particularly during transition from exponential to stationary growth phase. Salt stress, which blocks sporulation at a very early stage, was found to override the derepressed biofilm phenotype of the ∆6S-2 RNA strain. Furthermore, the ∆6S-2 RNA strain showed retarded swarming activity and earlier spore formation. Finally, the ∆6S-1&2 RNA double deletion strain showed a prolonged lag phase of growth under oxidative, high salt and alkaline stress conditions, suggesting that the interplay of both 6S RNAs in B. subtilis optimizes and fine-tunes transcriptomic adaptations, thereby contributing to the fitness of B. subtilis under the unsteady and temporarily harsh conditions encountered in natural habitats.
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Affiliation(s)
- Marietta Thüring
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Sweetha Ganapathy
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - M Amri C Schlüter
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Bioinformatics Core Facility , Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
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46
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Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation. Arch Microbiol 2020; 203:13-30. [PMID: 32785735 DOI: 10.1007/s00203-020-02012-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022]
Abstract
Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.
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47
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Verma N, Srivastava S, Malik R, Yadav JK, Goyal P, Pandey J. Computational investigation for modeling the protein-protein interaction of TasA (28-261)-TapA (33-253): a decisive process in biofilm formation by Bacillus subtilis. J Mol Model 2020; 26:226. [PMID: 32779018 DOI: 10.1007/s00894-020-04507-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/04/2020] [Indexed: 01/27/2023]
Abstract
Biofilms have a significant role in microbial persistence, antibiotic resistance, and chronic infections; consequently, there is a pressing need for development of novel "anti-biofilm strategies." One of the fundamental mechanisms involved in biofilm formation is protein-protein interactions of "amyloid-like proteins" (ALPs) in the extracellular matrix. Such interactions could be potential targets for development of novel anti-biofilm strategies; therefore, assessing the structural features of these interactions could be of great scientific value. Characterization of structural features the of protein-protein interaction with conventional structure biology tools including X-ray diffraction and nuclear magnetic resonance is technically challenging, expensive, and time-consuming. In contrast, modeling such interactions is time-efficient and economical, and might provide deeper understanding of structural basis of interactions. Although it is often acknowledged that molecular modeling methods have varying accuracy, their careful implementation with supplementary verification methods can provide valuable insight and directions for future studies. With this reasoning, during the present study, the protein-protein interaction of TasA(28-261)-TapA(33-253) (which is a decisive process for biofilm formation by Bacillus subtilis) was modeled using in silico approaches, viz., molecular modeling, protein-protein docking, and molecular dynamics simulations. Results obtained here identified amino acid residues present within intrinsically disordered regions of both proteins to be critical for interaction. These results were further supported with principal component analyses (PCA) and free energy landscape (FEL) analyses. Results presented here represent novel finding, and we hypothesize that amino acid residues identified during the present study could be targeted for inhibition of biofilm formation by B. subtilis.
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Affiliation(s)
- Nidhi Verma
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Pankaj Goyal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Janmejay Pandey
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan - Kishangarh, Ajmer, 305817, Rajasthan, India.
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48
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Zielińska A, Savietto A, de Sousa Borges A, Martinez D, Berbon M, Roelofsen JR, Hartman AM, de Boer R, Van der Klei IJ, Hirsch AKH, Habenstein B, Bramkamp M, Scheffers DJ. Flotillin-mediated membrane fluidity controls peptidoglycan synthesis and MreB movement. eLife 2020; 9:e57179. [PMID: 32662773 PMCID: PMC7360373 DOI: 10.7554/elife.57179] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
The bacterial plasma membrane is an important cellular compartment. In recent years it has become obvious that protein complexes and lipids are not uniformly distributed within membranes. Current hypotheses suggest that flotillin proteins are required for the formation of complexes of membrane proteins including cell-wall synthetic proteins. We show here that bacterial flotillins are important factors for membrane fluidity homeostasis. Loss of flotillins leads to a decrease in membrane fluidity that in turn leads to alterations in MreB dynamics and, as a consequence, in peptidoglycan synthesis. These alterations are reverted when membrane fluidity is restored by a chemical fluidizer. In vitro, the addition of a flotillin increases membrane fluidity of liposomes. Our data support a model in which flotillins are required for direct control of membrane fluidity rather than for the formation of protein complexes via direct protein-protein interactions.
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Affiliation(s)
- Aleksandra Zielińska
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Abigail Savietto
- Biozentrum, Ludwig-Maximilians-Universität MünchenMünchenGermany
- Institute for General Microbiology, Christian-Albrechts-UniversityKielGermany
| | - Anabela de Sousa Borges
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Melanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Joël R Roelofsen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Alwin M Hartman
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany
- Department of Pharmacy, Saarland UniversitySaarbrückenGermany
- Stratingh Institute for Chemistry, University of GroningenGroningenNetherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Ida J Van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Anna KH Hirsch
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI)SaarbrückenGermany
- Department of Pharmacy, Saarland UniversitySaarbrückenGermany
- Stratingh Institute for Chemistry, University of GroningenGroningenNetherlands
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Marc Bramkamp
- Biozentrum, Ludwig-Maximilians-Universität MünchenMünchenGermany
- Institute for General Microbiology, Christian-Albrechts-UniversityKielGermany
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
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49
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Wang X, Cao Z, Zhang M, Meng L, Ming Z, Liu J. Bioinspired oral delivery of gut microbiota by self-coating with biofilms. SCIENCE ADVANCES 2020; 6:eabb1952. [PMID: 32637620 PMCID: PMC7314526 DOI: 10.1126/sciadv.abb1952] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/08/2020] [Indexed: 05/05/2023]
Abstract
Transplanting beneficial bacteria to the gut microbiome can positively modulate the bacterial composition and remains of great interest in prevention and treatment. However, environmental assaults and rapid transit times in the gastrointestinal (GI) tract result in low oral bioavailability and limited intestinal colonization. Here, we describe a bioinspired strategy of self-coating with biofilms that endows the transplanted gut microbiota with superior resistance and adhesion capacity. Using clinical Bacillus subtilis as a model probiotic bacterium, biofilm-coated probiotics demonstrate substantially improved GI tract tolerance and mucoadhesion in mice and swine. In particular, coated probiotics exhibit a 125-fold higher oral bioavailability and a 17 times greater intestinal colonization than uncoated bacteria in the porcine model. With notable ability to survive and reside in the GI tract, coated bacteria further show a significantly enhanced decolonization effect in mice colonized with Staphylococcus aureus. Self-coating with biofilms suggests a robust platform for oral doses of gut microbiota.
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50
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Multiple and Overlapping Functions of Quorum Sensing Proteins for Cell Specialization in Bacillus Species. J Bacteriol 2020; 202:JB.00721-19. [PMID: 32071096 DOI: 10.1128/jb.00721-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In bacterial populations, quorum sensing (QS) systems participate in the regulation of specialization processes and regulate collective behaviors that mediate interactions and allow survival of the species. In Gram-positive bacteria, QS systems of the RRNPP family (Rgg, Rap, NprR, PlcR, and PrgX) consist of intracellular receptors and their cognate signaling peptides. Two of these receptors, Rap and NprR, have regained attention in Bacillus subtilis and the Bacillus cereus group. Some Rap proteins, such as RapH and Rap60, are multifunctional and/or redundant in function, linking the specialization processes of sporulation and competence, as well as global expression changes in the transition phase in B. subtilis NprR, an evolutionary intermediate between Rap and RRNPP transcriptional activators, is a bifunctional regulator that modulates sporulation initiation and activates nutrient scavenging genes. In this review, we discuss how these receptors switch between functions and connect distinct signaling pathways. Based on structural evidence, we propose that RapH and Rap60 should be considered moonlighting proteins. Additionally, we analyze an evolutionary and ecological perspective to understand the multifunctionality and functional redundancy of these regulators in both Bacillus spp. and non-Bacillus Firmicutes Understanding the mechanistic, structural, ecological, and evolutionary basis for the multifunctionality and redundancy of these QS systems is a key step for achieving the development of innovative technologies for health and agriculture.
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