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Abraha HB, Ramesha RM, Ferdiansyah MK, Son H, Kim G, Park B, Jeong DY, Kim KP. Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution. Curr Microbiol 2024; 81:305. [PMID: 39133322 DOI: 10.1007/s00284-024-03819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.
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Affiliation(s)
- Haftom Baraki Abraha
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | | | | | - Hyeonro Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Gayeong Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Beomseok Park
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Do-Youn Jeong
- Microbial Institute for Fermentation Industry, Sunchang, 56048, South Korea
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.
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Saikat TA, Sayem Khan MA, Islam MS, Tasnim Z, Ahmed S. Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications. Heliyon 2024; 10:e34369. [PMID: 39114027 PMCID: PMC11305188 DOI: 10.1016/j.heliyon.2024.e34369] [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: 02/19/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.
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Affiliation(s)
| | - Md Abu Sayem Khan
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Zarin Tasnim
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sangita Ahmed
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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Wang T, Shi Y, Zheng M, Zheng J. Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group. Microorganisms 2024; 12:986. [PMID: 38792815 PMCID: PMC11124052 DOI: 10.3390/microorganisms12050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/04/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.
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Affiliation(s)
- Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiling Shi
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhuo Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (T.W.); (Y.S.); (M.Z.)
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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6
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Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [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: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
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Guler P, Bendori SO, Borenstein T, Aframian N, Kessel A, Eldar A. Arbitrium communication controls phage lysogeny through non-lethal modulation of a host toxin-antitoxin defence system. Nat Microbiol 2024; 9:150-160. [PMID: 38177304 DOI: 10.1038/s41564-023-01551-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Temperate Bacillus phages often utilize arbitrium communication to control lysis/lysogeny decisions, but the mechanisms by which this control is exerted remains largely unknown. Here we find that the arbitrium system of Bacillus subtilis phage ϕ3T modulates the host-encoded MazEF toxin-antitoxin system to this aim. Upon infection, the MazF ribonuclease is activated by three phage genes. At low arbitrium signal concentrations, MazF is inactivated by two phage-encoded MazE homologues: the arbitrium-controlled AimX and the later-expressed YosL proteins. At high signal, MazF remains active, promoting lysogeny without harming the bacterial host. MazF cleavage sites are enriched on transcripts of phage lytic genes but absent from the phage repressor in ϕ3T and other Spβ-like phages. Combined with low activation levels of MazF during infections, this pattern explains the phage-specific effect. Our results show how a bacterial toxin-antitoxin system has been co-opted by a phage to control lysis/lysogeny decisions without compromising host viability.
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Affiliation(s)
- Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shira Omer Bendori
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tom Borenstein
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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Dergham Y, Le Coq D, Bridier A, Sanchez-Vizuete P, Jbara H, Deschamps J, Hamze K, Yoshida KI, Noirot-Gros MF, Briandet R. Bacillus subtilis NDmed, a model strain for biofilm genetic studies. Biofilm 2023; 6:100152. [PMID: 37694162 PMCID: PMC10485040 DOI: 10.1016/j.bioflm.2023.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/20/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.
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Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hadi Jbara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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9
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Förster M, Rathmann I, Yüksel M, Power JJ, Maier B. Genome-wide transformation reveals extensive exchange across closely related Bacillus species. Nucleic Acids Res 2023; 51:12352-12366. [PMID: 37971327 PMCID: PMC10711437 DOI: 10.1093/nar/gkad1074] [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: 07/03/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.
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Affiliation(s)
- Mona Förster
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 47a, 50674 Köln, Germany
| | - Isabel Rathmann
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 47a, 50674 Köln, Germany
| | - Melih Yüksel
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 47a, 50674 Köln, Germany
| | - Jeffrey J Power
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 47a, 50674 Köln, Germany
| | - Berenike Maier
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 47a, 50674 Köln, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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10
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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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11
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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12
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Krucoń T, Ruszkowska Z, Pilecka W, Szych A, Drewniak Ł. Bioprospecting of the Antarctic Bacillus subtilis strain for potential application in leaching hydrocarbons and trace elements from contaminated environments based on functional and genomic analysis. ENVIRONMENTAL RESEARCH 2023; 227:115785. [PMID: 36997039 DOI: 10.1016/j.envres.2023.115785] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/02/2023] [Accepted: 03/26/2023] [Indexed: 05/08/2023]
Abstract
The production of secondary metabolites including biosurfactants by the Bacillus subtilis ANT_WA51 and the evaluation of its ability to leach metals and petroleum derivatives from the soil, using post-culture medium was investigated. The ANT_WA51 strain isolated from a pristine, harsh Antarctic environment produces the biosurfactants surfactin and fengycin, which reduce the surface tension of molasses-based post-culture medium to 26.6 mN m-1 at a critical micellization concentration (CMC) of 50 mg L-1 and a critical micelle dilution (CMD) of 1:19. The presence of biosurfactants and other secondary metabolites in the post-culture medium contributed to significant removal of xenobiotics from contaminated soils in the batch washing experiment - 70% hydrocarbons and 10-23% metals (Zn, Ni and Cu). The isolate's tolerance to different abiotic stresses, including freezing, freeze-thaw cycles, salinity (up to 10%), the presence of metals - Cr(VI), Pb(II), Mn(II), As(V) (up to 10 mM) and Mo(VI) (above 500 mM) and petroleum hydrocarbons (up to 20.000 mg kg-1) as well as the confirmed metabolic activity of these bacteria in toxic environments in the OxiTop® system indicate that they can be used directly in bioremediation. Comparative genomic analysis of this bacteria revealed a high similarity of its genome to the associated plant strains from America and Europe indicating the wide applicability of plant growth-promoting Bacillus subtilis and that the data can be extrapolated to a wide range of environmental strains. An important aspect of the study was to present the absence of inherent features which would indicate its clear pathogenicity enables its safe use in the environment. Based on the obtained results, we also conclude that the use of post-culture medium, obtained on low-cost byproducts like molasses, for leaching contaminants, especially hydrocarbons, is a promising bioremediation method that can be a replacement for the use of synthetic surfactants and provides a base for further large-scale research but the selection of an appropriate leaching may be dependent on the concentration of contaminants.
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Affiliation(s)
- Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Zuzanna Ruszkowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Weronika Pilecka
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Szych
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Łukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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13
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Bi X, Cheng Y, Xu X, Lv X, Liu Y, Li J, Du G, Chen J, Ledesma-Amaro R, Liu L. etiBsu1209: A comprehensive multiscale metabolic model for Bacillus subtilis. Biotechnol Bioeng 2023; 120:1623-1639. [PMID: 36788025 DOI: 10.1002/bit.28355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/08/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
Genome-scale metabolic models (GEMs) have been widely used to guide the computational design of microbial cell factories, and to date, seven GEMs have been reported for Bacillus subtilis, a model gram-positive microorganism widely used in bioproduction of functional nutraceuticals and food ingredients. However, none of them are widely used because they often lead to erroneous predictions due to their low predictive power and lack of information on regulatory mechanisms. In this work, we constructed a new version of GEM for B. subtilis (iBsu1209), which contains 1209 genes, 1595 metabolites, and 1948 reactions. We applied machine learning to fill gaps, which formed a relatively complete metabolic network able to predict with high accuracy (89.3%) the growth of 1209 mutants under 12 different culture conditions. In addition, we developed a visualization and code-free software, Model Tool, for multiconstraints model reconstruction and analysis. We used this software to construct etiBsu1209, a multiscale model that integrates enzymatic constraints, thermodynamic constraints, and transcriptional regulatory networks. Furthermore, we used etiBsu1209 to guide a metabolic engineering strategy (knocking out fabI and yfkN genes) for the overproduction of nutraceutical menaquinone-7, and the titer increased to 153.94 mg/L, 2.2-times that of the parental strain. To the best of our knowledge, etiBsu1209 is the first comprehensive multiscale model for B. subtilis and can serve as a solid basis for rational computational design of B. subtilis cell factories for bioproduction.
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Affiliation(s)
- Xinyu Bi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yang Cheng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xianhao Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
| | | | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Ministry of Education, Jiangnan University, Wuxi, China
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14
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Konno N, Iwasaki W. Machine learning enables prediction of metabolic system evolution in bacteria. SCIENCE ADVANCES 2023; 9:eadc9130. [PMID: 36630500 PMCID: PMC9833677 DOI: 10.1126/sciadv.adc9130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even "ongoing" evolution in extant bacterial species is predictable in our framework.
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Affiliation(s)
- Naoki Konno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
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15
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Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution. THE ISME JOURNAL 2023; 17:130-139. [PMID: 36224268 PMCID: PMC9751276 DOI: 10.1038/s41396-022-01325-5] [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: 10/08/2021] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
Bacterial transformation, a common mechanism of horizontal gene transfer, can speed up adaptive evolution. How its costs and benefits depend on the growth environment is poorly understood. Here, we characterize the distributions of fitness effects (DFE) of transformation in different conditions and test whether they predict in which condition transformation is beneficial. To determine the DFEs, we generate hybrid libraries between the recipient Bacillus subtilis and different donor species and measure the selection coefficient of each hybrid strain. In complex medium, the donor Bacillus vallismortis confers larger fitness effects than the more closely related donor Bacillus spizizenii. For both donors, the DFEs show strong effect beneficial transfers, indicating potential for fast adaptive evolution. While some transfers of B. vallismortis DNA show pleiotropic effects, various transfers are beneficial only under a single growth condition, indicating that the recipient can benefit from a variety of donor genes to adapt to varying growth conditions. We scrutinize the predictive value of the DFEs by laboratory evolution under different growth conditions and show that the DFEs correctly predict the condition at which transformation confers a benefit. We conclude that transformation has a strong potential for speeding up adaptation to varying environments by profiting from a gene pool shared between closely related species.
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16
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de Lima Ferreira JK, de Mello Varani A, Tótola MR, Fernandes Almeida M, de Sousa Melo D, Ferreira Silva E Batista C, Chalfun-Junior A, Pimenta de Oliveira KK, Wurdig Roesch LF, Satler Pylro V. Phylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914. Braz J Microbiol 2022; 53:2051-2063. [PMID: 36083529 PMCID: PMC9679098 DOI: 10.1007/s42770-022-00815-0] [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: 04/29/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023] Open
Abstract
Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.
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Affiliation(s)
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias E Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Sao Paulo, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Michelle Fernandes Almeida
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | - Dirceu de Sousa Melo
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | - Antonio Chalfun-Junior
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | | | | | - Victor Satler Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil.
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17
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Babar TK, Glare TR, Hampton JG, Hurst MRH, Narciso JO. Isolation, Purification, and Characterisation of a Phage Tail-Like Bacteriocin from the Insect Pathogenic Bacterium Brevibacillus laterosporus. Biomolecules 2022; 12:1154. [PMID: 36009048 PMCID: PMC9406221 DOI: 10.3390/biom12081154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
The Gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to the often-restricted growth of these endemic isolates, production can be an issue. Based on the previous work, it was hypothesised that the putative phages might be involved. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages’ tail-like structures. A soft agar overlay method with PEG 8000 precipitation was used to differentiate between the antagonistic activity of the putative phage and phage tail-like structures (bacteriocins). Assay tests authenticated the absence of putative phage activity. Using the same method, broad-spectrum antibacterial activity of Bl 1821L lysate against several Gram-positive bacteria was found. SDS-PAGE of sucrose density gradient purified and 10 kD MWCO concentrated lysate showed a prominent protein band of ~48 kD, and transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ~48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. Bioinformatic analysis also identified an xkdK homolog in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-l-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ~48 kD sequenced protein of Bl 1821L. Antagonistic activity of the purified ~48 kD phage tail-like protein in the assays differed remarkably from the crude lysate by causing a decrease of 34.2% in the number of viable cells of Bl 1951, 18 h after treatment as compared to the control. Overall, the identified inducible phage tail-like particle is likely to have implications for the in vitro growth of the insect pathogenic isolate Bl 1821L.
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Affiliation(s)
- Tauseef K. Babar
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
- Department of Entomology, Faculty of Agriculture Sciences & Technology, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Travis R. Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - John G. Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
| | - Mark R. H. Hurst
- Resilient Agriculture, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand
| | - Josefina O. Narciso
- Bio-Protection Research Centre, Lincoln University, Lincoln 7674, New Zealand
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18
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Damage-Induced Mutation Clustering in Gram-Positive Bacteria: Preliminary Data. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The phenomenon of a nonrandom distribution of mutations in a genome has been observed for many years. In fact, recent findings have indicated the presence of mutation clusters in different biological systems, including chemically treated yeast, transgenic mice, and human cancer cells. Until now, an asymmetrical distribution of mutations was only described in a single bacterial species. Here, we used ethyl methanesulfonate mutagenesis and a whole-genome sequencing approach to determine if this phenomenon is universal and not confined to Gram-negative bacteria. The Gram-positive bacterium Bacillus subtilis was selected for ethyl methanesulfonate treatment, followed by the next-generation sequencing of several mutagenized B. subtilis genomes. A nonrandom distribution of mutations was observed. This pilot study with a limited number of sequenced clones may indicate not only the universality of the phenomenon of mutation clusters but also the effectiveness of the use of a whole-genome sequencing approach in studying this phenomenon.
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19
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Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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20
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Abstract
Halotolerant plant-growth-promoting rhizobacteria (PGPR) could not only promote plant growth, but also help in counteracting the detrimental effects of salt stress. In the present study, a total of 76 bacteria were isolated from the rhizosphere, non-rhizospheric soil and endophytes of the halophyte Salsola tetrandra, collected from natural saline soils in Algeria. Phylogenetic analysis based on the 16S rDNA sequence of Gram-negative bacteria (n = 51) identified, showed seventeen representative isolates grouped into four genera (Pseudomonas, Acinetobacter, Enterobacter, and Providencia). These bacterial isolates that exhibited different PGPR traits were selected and tested for their ability to tolerate different abiotic stress (NaCl, PEG8000, and pH). The majority of isolates were drought tolerant (60% of PEG8000) and had an optimal growth at high pH values (pH 9 and 11) and some strains tolerated 2 M of NaCl. Strains identified as Enterobacter xiangfangensis BE1, Providencia rettgeri BR5 and Pseudomonas stutzeri MLR6 showed high capacity of adaptation on their PGP traits. The salt-tolerant isolates were finally chosen to promote growth and enhance salt tolerance, separately or combined, of Arabidopsis thaliana (Col-0) exposed or not to 0.1 M NaCl, by following fresh and root weight, primary root elongation and lateral root number. The best bacterial effect was recorded for the MLR6 strain in increasing shoot fresh weight and for BE1 in terms of root fresh weight in the absence of salt stress. At stressed conditions, all growth parameters declined. However, inoculation of Arabidopsis thaliana with the three bacterial strains (MLR6, BE1 and BR5), single or in co-culture, conferred an increase in the shoot weight, primary root length and lateral root number. The use of these strains separately or combined as biofertilizers seems to be a powerful tool in the development of sustainable agriculture in saline soils.
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21
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Silva M, Pontes A, Franco-Duarte R, Soares P, Sampaio JP, Sousa MJ, Brito PH. A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast. Mol Ecol 2022; 32:2396-2412. [PMID: 35298044 DOI: 10.1111/mec.16428] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content, or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix - Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.
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Affiliation(s)
- Margarida Silva
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Pontes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Maria João Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Patrícia H Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Kamali M, Guo D, Naeimi S, Ahmadi J. Perception of Biocontrol Potential of Bacillus inaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis. BIOLOGY 2022; 11:biology11010137. [PMID: 35053135 PMCID: PMC8773019 DOI: 10.3390/biology11010137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
Simple Summary Bacillus is a bacterial genus that is widely used as a promising alternative to chemical pesticides due to its protective activity toward economically important plant pathogens. Fusarium wilt of tomato is a serious fungal disease limiting tomato production worldwide. Recently, the newly isolated B. inaquosorum strain KR2-7 considerably suppressed Fusarium wilt of tomato plants. The present study was performed to perceive potential direct and indirect biocontrol mechanisms implemented by KR2-7 against this disease through genome and chemical analysis. The potential direct biocontrol mechanisms of KR2-7 were determined through the identification of genes involved in the synthesis of antibiotically active compounds suppressing tomato Fusarium wilt. Furthermore, the indirect mechanisms of this bacterium were perceived through recognizing genes that contributed to the resource acquisition or modulation of plant hormone levels. This is the first study that aimed at the modes of actions of B. inaquosorum against Fusarium wilt of tomatoes and the results strongly indicate that strain KR2-7 could be a good candidate for microbial biopesticide formulations to be used for biological control of plant diseases and plant growth promotion. Abstract Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.
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Affiliation(s)
- Maedeh Kamali
- College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China;
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
- Correspondence: ; Tel.: +852-3943-6298
| | - Shahram Naeimi
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran 19858-13111, Iran;
| | - Jafar Ahmadi
- Department of Genetics and Plant Breeding, Imam Khomeini International University, Qazvin 34149-16818, Iran;
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Li X, Yang Z, Wang Z, Li W, Zhang G, Yan H. Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity. Front Microbiol 2022; 12:755874. [PMID: 35095786 PMCID: PMC8792951 DOI: 10.3389/fmicb.2021.755874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.
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Affiliation(s)
- Xiangyang Li
- School of Sciences, Kaili University, Kaili, China
- Bacterial Genome Data Mining and Bioinformatic Analysis Center, Kaili University, Kaili, China
- *Correspondence: Xiangyang Li,
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili, China
| | - Zhao Wang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Weipeng Li
- School of Big Data Engineering, Kaili University, Kaili, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili, China
| | - Hongguang Yan
- School of Life and Health Science, Kaili University, Kaili, China
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24
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Kalamara M, Abbott JC, MacPhee CE, Stanley-Wall NR. Biofilm hydrophobicity in environmental isolates of Bacillus subtilis. MICROBIOLOGY-SGM 2021; 167. [PMID: 34486975 DOI: 10.1099/mic.0.001082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacterium Bacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation. B. subtilis NCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge about B. subtilis biofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library of B. subtilis soil isolates and acquired their whole genome sequences. We used our novel isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature of B. subtilis colony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason for the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.
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Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - James C Abbott
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Cait E MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
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25
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Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis. Microb Physiol 2021; 31:260-279. [PMID: 34438398 DOI: 10.1159/000517718] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022]
Abstract
Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., Bacillus subtilis and Staphylococcus aureus, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., Mycobacterium tuberculosis, Listeria monocytogenes, and Chlamydia trachomatis, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Thoma
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stefan Pan
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Laura Reinhardt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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26
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Abstract
Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.
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27
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Dat TTH, Cuc NTK, Cuong PV, Smidt H, Sipkema D. Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19070353. [PMID: 34206202 PMCID: PMC8307940 DOI: 10.3390/md19070353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to assess the diversity and antimicrobial activity of cultivable bacteria associated with Vietnamese sponges. In total, 460 bacterial isolates were obtained from 18 marine sponges. Of these, 58.3% belonged to Proteobacteria, 16.5% to Actinobacteria, 18.0% to Firmicutes, and 7.2% to Bacteroidetes. At the genus level, isolated strains belonged to 55 genera, of which several genera, such as Bacillus, Pseudovibrio, Ruegeria, Vibrio, and Streptomyces, were the most predominant. Culture media influenced the cultivable bacterial composition, whereas, from different sponge species, similar cultivable bacteria were recovered. Interestingly, there was little overlap of bacterial composition associated with sponges when the taxa isolated were compared to cultivation-independent data. Subsequent antimicrobial assays showed that 90 isolated strains exhibited antimicrobial activity against at least one of seven indicator microorganisms. From the culture broth of the isolated strain with the strongest activity (Bacillus sp. M1_CRV_171), four secondary metabolites were isolated and identified, including cyclo(L-Pro-L-Tyr) (1), macrolactin A (2), macrolactin H (3), and 15,17-epoxy-16-hydroxy macrolactin A (4). Of these, compounds 2-4 exhibited antimicrobial activity against a broad spectrum of reference microorganisms.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
| | - Nguyen Thi Kim Cuc
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
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28
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Domingo-Sananes MR, McInerney JO. Mechanisms That Shape Microbial Pangenomes. Trends Microbiol 2021; 29:493-503. [PMID: 33423895 DOI: 10.1016/j.tim.2020.12.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023]
Abstract
Analyses of multiple whole-genome sequences from the same species have revealed that differences in gene content can be substantial, particularly in prokaryotes. Such variation has led to the recognition of pangenomes, the complete set of genes present in a species - consisting of core genes, present in all individuals, and accessory genes whose presence is variable. Questions now arise about how pangenomes originate and evolve. We describe how gene content variation can arise as a result of the combination of several processes, including random drift, selection, gain/loss balance, and the influence of ecological and epistatic interactions. We believe that identifying the contributions of these processes to pangenomes will need novel theoretical approaches and empirical data.
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Affiliation(s)
- Maria Rosa Domingo-Sananes
- School of Life Sciences, University of Nottingham, Nottingham, UK; School of Science and Technology, Nottingham Trent University, Nottingham, UK.
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29
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Serrano E, Ramos C, Alonso JC, Ayora S. Recombination proteins differently control the acquisition of homeologous DNA during Bacillus subtilis natural chromosomal transformation. Environ Microbiol 2020; 23:512-524. [PMID: 33264457 DOI: 10.1111/1462-2920.15342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022]
Abstract
Natural chromosomal transformation (CT) plays a major role in prokaryote evolution, yet factors that govern the integration of DNA from related species remain poorly understood. We show that in naturally competent Bacillus subtilis cells the acquisition of homeologous sequences is governed by sequence divergence (SD). Integration initiates in a minimal efficient processing segment via homology-directed CT, and its frequency decreases log-linearly with increased SD up to 15%. Beyond this and up to 23% SD the interspecies boundaries prevail, the CT frequency marginally decreases, and short (<10-nucleotides) segments are integrated via homology-facilitated micro-homologous integration. Both mechanisms are RecA dependent. We identify the other recombination proteins required for the acquisition of homeologous DNA. The absence of AddAB, RecF, RecO, RuvAB or RecU, crucial for repair-by-recombination, did not affect CT. However, dprA, radA, recJ, recX or recD2 inactivation strongly decreased intraspecies and interspecies CT. Interspecies CT was not detected beyond ~8% SD in ΔdprA, ~10% in ΔrecJ, ΔradA, ΔrecX and ~14% in ΔrecD2 cells. We propose that DprA, RecX, RadA/Sms, RecJ and RecD2 accessory proteins are important for the generation of genetic diversity. Together with RecA, they facilitate gene acquisition from bacteria of related species.
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Affiliation(s)
- Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
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30
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Samarth DP, Kwon YM. Horizontal genetic exchange of chromosomally encoded markers between Campylobacter jejuni cells. PLoS One 2020; 15:e0241058. [PMID: 33104745 PMCID: PMC7588059 DOI: 10.1371/journal.pone.0241058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
Many epidemiological studies provide us with the evidence of horizontal gene transfer (HGT) contributing to the bacterial genomic diversity that benefits the bacterial populations with increased ability to adapt to the dynamic environments. Campylobacter jejuni, a major cause of acute enteritis in the U.S., often linked with severe post-infection neuropathies, has been reported to exhibit a non-clonal population structure and comparatively higher strain-level genetic variation. In this study, we provide evidence of the HGT of chromosomally encoded genetic markers between C. jejuni cells in the biphasic MH medium. We used two C. jejuni NCTC-11168 mutants harbouring distinct antibiotic-resistance genes [chloramphenicol (Cm) and kanamycin (Km)] present at two different neutral genomic loci. Cultures of both marker strains were mixed together and incubated for 5 hrs, then plated on MH agar plates supplemented with both antibiotics. The recombinant cells with double antibiotic markers were generated at the frequency of 0.02811 ± 0.0035% of the parental strains. PCR assays using locus-specific primers confirmed that transfer of the antibiotic-resistance genes was through homologous recombination. Also, the addition of chicken cecal content increased the recombination efficiency approximately up to 10-fold as compared to the biphasic MH medium (control) at P < 0.05. Furthermore, treating the co-culture with DNase I decreased the available DNA, which in turn significantly reduced recombination efficiency by 99.92% (P < 0.05). We used the cell-free supernatant of 16 hrs-culture of Wild-type C. jejuni as a template for PCR and found DNA sequences from six different genomic regions were easily amplified, indicating the presence of released chromosomal DNA in the culture supernatant. Our findings suggest that HGT in C. jejuni is facilitated in the chicken gut environment contributing to in vivo genomic diversity. Additionally, C. jejuni might have an active mechanism to release its chromosomal DNA into the extracellular environment, further expediting HGT in C. jejuni populations.
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Affiliation(s)
- Deepti Pranay Samarth
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- * E-mail:
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States of America
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31
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Balderas-Ruíz KA, Bustos P, Santamaria RI, González V, Cristiano-Fajardo SA, Barrera-Ortíz S, Mezo-Villalobos M, Aranda-Ocampo S, Guevara-García ÁA, Galindo E, Serrano-Carreón L. Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. AMB Express 2020; 10:163. [PMID: 32894363 PMCID: PMC7477031 DOI: 10.1186/s13568-020-01101-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/30/2020] [Indexed: 01/05/2023] Open
Abstract
Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains. ![]()
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32
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Fang H, Xu JB, Nie Y, Wu XL. Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats. Environ Microbiol 2020; 23:861-877. [PMID: 32715552 DOI: 10.1111/1462-2920.15176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.
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Affiliation(s)
- Hui Fang
- College of Engineering, Peking University, Beijing, 100871, China
| | - Jin-Bo Xu
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, 100871, China.,Institute of Ocean Research, Peking University, Beijing, 100871, China
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33
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Hurel J, Schbath S, Bougeard S, Rolland M, Petrillo M, Touzain F. DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples. BMC Bioinformatics 2020; 21:284. [PMID: 32631215 PMCID: PMC7336441 DOI: 10.1186/s12859-020-03611-5] [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: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Background The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a “GMO-free” label. In recent years, imports of undescribed GMOs have been detected. Their sequences are not described and therefore not detectable by conventional approaches, such as PCR. Results We developed DUGMO, a bioinformatics pipeline for the detection of genetically modified (GM) bacteria, including unknown GM bacteria, based on Illumina paired-end sequencing data. The method is currently focused on the detection of GM bacteria with – possibly partial – transgenes in pure bacterial samples. In the preliminary steps, coding sequences (CDSs) are aligned through two successive BLASTN against the host pangenome with relevant tuned parameters to discriminate CDSs belonging to the wild type genome (wgCDS) from potential GM coding sequences (pgmCDSs). Then, Bray-Curtis distances are calculated between the wgCDS and each pgmCDS, based on the difference of genomic vocabulary. Finally, two machine learning methods, namely the Random Forest and Generalized Linear Model, are carried out to target true GM CDS(s), based on six variables including Bray-Curtis distances and GC content. Tests carried out on a GM Bacillus subtilis showed 25 positive CDSs corresponding to the chloramphenicol resistance gene and CDSs of the inserted plasmids. On a wild type B. subtilis, no false positive sequences were detected. Conclusion DUGMO detects exogenous CDS, truncated, fused or highly mutated wild CDSs in high-throughput sequencing data, and was shown to be efficient at detecting GM sequences, but it might also be employed for the identification of recent horizontal gene transfers.
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Affiliation(s)
- Julie Hurel
- ANSES, Laboratoire de Ploufragan, GVB unit, 22440, Ploufragan, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Stéphanie Bougeard
- ANSES, Laboratoire de Ploufragan, EPISABE unit, 22440, Ploufragan, France
| | - Mathieu Rolland
- ANSES, Laboratoire de la santé des végétaux, 49000, Angers, France
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Fabrice Touzain
- ANSES, Laboratoire de Ploufragan, GVB unit, 22440, Ploufragan, France.
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Polonca S. Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates. MICROBIAL ECOLOGY 2020; 79:853-864. [PMID: 31707464 DOI: 10.1007/s00248-019-01455-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.
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Affiliation(s)
- Stefanic Polonca
- Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia.
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Carvalho G, Fouchet D, Danesh G, Godeux AS, Laaberki MH, Pontier D, Charpentier X, Venner S. Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements. mBio 2020; 11:mBio.02443-19. [PMID: 32127449 PMCID: PMC7064763 DOI: 10.1128/mbio.02443-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.IMPORTANCE Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bacterial populations and (ii) the removal of infectious parasitic mobile genetic elements (MGEs). While the first one promotes genetic diversification, the other one promotes the removal of foreign DNA and thus genome stability, making these two functions apparently antagonistic. Using a computational model, we show that intermediate transformation rates, commonly observed in bacteria, allow the acquisition then removal of MGEs. The transient acquisition of costly MGEs with resistance genes maximizes bacterial fitness in environments with stochastic stress exposure. Thus, transformation would ensure both a strong dynamic of the bacterial genome in the short term and its long-term stabilization.
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Affiliation(s)
- Gabriel Carvalho
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - David Fouchet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Gonché Danesh
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Anne-Sophie Godeux
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Maria-Halima Laaberki
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- Université de Lyon, VetAgro Sup, Marcy-l'Étoile, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
- CNRS UMR5308, École Normale Supérieure de Lyon, University of Lyon, Villeurbanne, France
| | - Samuel Venner
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
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Ramos-Silva P, Serrano M, Henriques AO. From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile. Mol Biol Evol 2020; 36:2714-2736. [PMID: 31350897 PMCID: PMC6878958 DOI: 10.1093/molbev/msz175] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.
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Affiliation(s)
- Paula Ramos-Silva
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Lee IPA, Andam CP. Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle. BMC Microbiol 2019; 19:306. [PMID: 31881843 PMCID: PMC6935241 DOI: 10.1186/s12866-019-1664-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
Background Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources. Results The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production. Conclusions Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.
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Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Cheryl P Andam
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico. Int J Syst Evol Microbiol 2019; 69:3939-3945. [DOI: 10.1099/ijsem.0.003711] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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39
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Dunlap CA, Bowman MJ, Zeigler DR. Promotion of Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris to species status. Antonie van Leeuwenhoek 2019; 113:1-12. [PMID: 31721032 DOI: 10.1007/s10482-019-01354-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/26/2019] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis currently encompasses four subspecies, Bacillus subtilis subsp. subtilis, Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris. Several studies based on genomic comparisons have suggested these subspecies should be promoted to species status. Previously, one of the main reasons for leaving them as subspecies was the lack of distinguishing phenotypes. In this study, we used comparative genomics to determine the genes unique to each subspecies and used these to lead us to the unique phenotypes. The results show that one difference among the subspecies is they produce different bioactive secondary metabolites. B. subtilis subsp. spizizenii is shown conserve the genes to produce mycosubtilin, bacillaene and 3,3'-neotrehalosadiamine. B. subtilis subsp. inaquosorum is shown conserve the genes to produce bacillomycin F, fengycin and an unknown PKS/NRPS cluster. B. subtilis subsp. stercoris is shown conserve the genes to produce fengycin and an unknown PKS/NRPS cluster. While B. subtilis subsp. subtilis is shown to conserve the genes to produce 3,3'-neotrehalosadiamine. In addition, we update the chemotaxonomy and phenotyping to support their promotion to species status.
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Affiliation(s)
- Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL, USA.
| | - Michael J Bowman
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL, USA
| | - Daniel R Zeigler
- Bacillus Genetic Stock Center, The Ohio State University, Columbus, OH, USA
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Dunlap CA, Bowman MJ, Rooney AP. Iturinic Lipopeptide Diversity in the Bacillus subtilis Species Group - Important Antifungals for Plant Disease Biocontrol Applications. Front Microbiol 2019; 10:1794. [PMID: 31440222 PMCID: PMC6693446 DOI: 10.3389/fmicb.2019.01794] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/22/2019] [Indexed: 11/30/2022] Open
Abstract
Iturins and closely related lipopeptides constitute a family of antifungal compounds known as iturinic lipopeptides that are produced by species in the Bacillus subtilis group. The compounds that comprise the family are: iturin, bacillomycin D, bacillomycin F, bacillomycin L, mycosubtilin, and mojavensin. These lipopeptides are prominent in many Bacillus strains that have been commercialized as biological control agents against fungal plant pathogens and as plant growth promoters. The compounds are cyclic heptapeptides with a variable length alkyl sidechain, which confers surface activity properties resulting in an affinity for fungal membranes. Above a certain concentration, enough molecules enter the fungal cell membrane to create a pore in the cell wall, which leads to loss of cell contents and cell death. This study identified 330 iturinic lipopeptide clusters in publicly available genomes from the B. subtilis species group. The clusters were subsequently assigned into distinguishable types on the basis of their unique amino acid sequences and then verified by HPLC MS/MS analysis. The results show some lipopeptides are only produced by one species, whereas certain others can produce up to three. In addition, four species previously not known to produce iturinic lipopeptides were identified. The distribution of these compounds among the B. subtilis group species suggests that they play an important role in their speciation and evolution.
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Affiliation(s)
- Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
| | - Michael J Bowman
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
| | - Alejandro P Rooney
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL, United States
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Comparative Genome Assessment of the Two Novel Poly-γ-Glutamic Acid Producing Bacillus Strains. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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42
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Park CJ, Andam CP. Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus. Front Microbiol 2019; 10:552. [PMID: 30949149 PMCID: PMC6437091 DOI: 10.3389/fmicb.2019.00552] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 01/09/2023] Open
Abstract
Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes.
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Affiliation(s)
- Cooper J Park
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Cheryl P Andam
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
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Concepts of the last eukaryotic common ancestor. Nat Ecol Evol 2019; 3:338-344. [DOI: 10.1038/s41559-019-0796-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/03/2019] [Indexed: 12/27/2022]
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The first report of antifungal lipopeptide production by a Bacillus subtilis subsp. inaquosorum strain. Microbiol Res 2018; 216:40-46. [DOI: 10.1016/j.micres.2018.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/17/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022]
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A single mutation in rapP induces cheating to prevent cheating in Bacillus subtilis by minimizing public good production. Commun Biol 2018; 1:133. [PMID: 30272012 PMCID: PMC6123732 DOI: 10.1038/s42003-018-0136-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
Cooperation is beneficial to group behaviors like multicellularity, but is vulnerable to exploitation by cheaters. Here we analyze mechanisms that protect against exploitation of extracellular surfactin in swarms of Bacillus subtilis. Unexpectedly, the reference strain NCIB 3610 displays inherent resistance to surfactin-non-producing cheaters, while a different wild isolate is susceptible. We trace this interstrain difference down to a single amino acid change in the plasmid-borne regulator RapP, which is necessary and sufficient for cheater mitigation. This allele, prevalent in many Bacillus species, optimizes transcription of the surfactin operon to the minimum needed for full cooperation. When combined with a strain lacking rapP, NCIB 3610 acts as a cheater itself—except it does not harm the population at high proportions since it still produces enough surfactin. This strategy of minimal production is thus a doubly advantageous mechanism to limit exploitation of public goods, and is readily evolved from existing regulatory networks. Lyons and Kolter describe a single-point mutation in the plasmid-borne gene rapP of Bacillus subtilis that optimizes surfactin transcription to express the minimum required for cooperation. The decrease in the production of this public good significantly prevented the exploitation of cooperative traits by cheaters.
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