1
|
Lin B, He D, Wen W, Lin B, Li Y, Chen X. Whole genome sequencing and functional analysis of porcine-borne Bacillus coagulans LYBC06. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2155568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Biaosheng Lin
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
- Key Laboratory of Fujian Universities Preventive Veterinary Medicine and Biotechnology, Biotechnology and Health products, Engineering Technology Research Center, Longyan University, Longyan, Fujian, PR China
| | - Dingyan He
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
| | - Wenying Wen
- Food Inspection Laboratory, Quality Measurement Inspection and Testing Center, Wuping County Market Supervisory Authority, Wuping, Fujian, PR China
| | - Bin Lin
- Project Management Office, Agricultural and Social Development Section, Longyan Science and Technology Bureau, Longyan, Fujian, PR China
| | - Yan Li
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
| | - Xiaohong Chen
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
| |
Collapse
|
2
|
Zanditenas E, Trebicz-Geffen M, Kolli D, Domínguez-García L, Farhi E, Linde L, Romero D, Chapman M, Kolodkin-Gal I, Ankri S. Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity. NPJ Biofilms Microbiomes 2023; 9:77. [PMID: 37813896 PMCID: PMC10562373 DOI: 10.1038/s41522-023-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
Collapse
Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Divya Kolli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Einan Farhi
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Liat Linde
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Matthew Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [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: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
Collapse
Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
| |
Collapse
|
5
|
Carroll LM, Pierneef R, Mathole A, Atanda A, Matle I. Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking. Microbiol Spectr 2022; 10:e0070022. [PMID: 35475639 PMCID: PMC9241823 DOI: 10.1128/spectrum.00700-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/06/2022] [Indexed: 12/22/2022] Open
Abstract
Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B. cereus sensu lato by (i) using WGS to characterize B. cereus sensu lato strains isolated during routine surveillance of meat products across South Africa (n = 25) and (ii) comparing the genomes sequenced here to all publicly available, high-quality B. cereus sensu lato genomes (n = 2,887 total genomes). Strains sequenced here were collected from meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 23) and (ii) imports held at port of entry (n = 2). The 25 strains sequenced here were partitioned into 15 lineages via in silico seven-gene multilocus sequence typing (MLST). While none of the South African B. cereus sensu lato strains sequenced here were identical to publicly available genomes, six MLST lineages contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale (≤3 core single nucleotide polymorphisms). Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus sensu lato can spread intra- and internationally via foodstuffs. IMPORTANCE Nationwide foodborne pathogen surveillance programs that use high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, Bacillus cereus sensu lato is often overlooked during large-scale routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus sensu lato surveillance and source tracking in foodstuffs. In this preliminary proof-of-concept study, we applied WGS to B. cereus sensu lato strains collected via South Africa's national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus sensu lato can be disseminated intra- and internationally via the agro-food supply chain. Our results showcase that WGS has the potential to be used for source tracking of B. cereus sensu lato in foods, although future WGS and metadata collection efforts are needed to ensure that B. cereus sensu lato surveillance initiatives are on par with those of other foodborne pathogens.
Collapse
Affiliation(s)
- Laura M. Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Aletta Mathole
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Abimbola Atanda
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Itumeleng Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| |
Collapse
|
6
|
Cohen-Cymberknoh M, Kolodkin-Gal D, Keren-Paz A, Peretz S, Brumfeld V, Kapishnikov S, Suissa R, Shteinberg M, McLeod D, Maan H, Patrauchan M, Zamir G, Kerem E, Kolodkin-Gal I. Calcium carbonate mineralization is essential for biofilm formation and lung colonization. iScience 2022; 25:104234. [PMID: 35521519 PMCID: PMC9062676 DOI: 10.1016/j.isci.2022.104234] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/18/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Biofilms are differentiated microbial communities held together by an extracellular matrix. μCT X-ray revealed structured mineralized areas within biofilms of lung pathogens belonging to two distant phyla - the proteobacteria Pseudomonas aeruginosa and the actinobacteria Mycobacterium abscessus. Furthermore, calcium chelation inhibited the assembly of complex bacterial structures for both organisms with little to no effect on cell growth. The molecular mechanisms promoting calcite scaffold formation were surprisingly conserved between the two pathogens as biofilm development was similarly impaired by genetic and biochemical inhibition of calcium uptake and carbonate accumulation. Moreover, chemical inhibition and mutations targeting mineralization significantly reduced the attachment of P. aeruginosa to the lung, as well as the subsequent damage inflicted by biofilms to lung tissues, and restored their sensitivity to antibiotics. This work offers underexplored druggable targets for antibiotics to combat otherwise untreatable biofilm infections.
Collapse
Affiliation(s)
- Malena Cohen-Cymberknoh
- Pediatric Pulmonary Unit and Cystic fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Dror Kolodkin-Gal
- Department of Experimental Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- National Center for Antibiotic Resistance and Infection Control, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Shani Peretz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Vlad Brumfeld
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Kapishnikov
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ronit Suissa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel
| | - Daniel McLeod
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Gideon Zamir
- Department of Experimental Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eitan Kerem
- Pediatric Pulmonary Unit and Cystic fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
7
|
Maan H, Gilhar O, Porat Z, Kolodkin-Gal I. Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production. Front Cell Infect Microbiol 2021; 11:722778. [PMID: 34557426 PMCID: PMC8454505 DOI: 10.3389/fcimb.2021.722778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/01/2022] Open
Abstract
Beneficial and probiotic bacteria play an important role in conferring immunity of their hosts to a wide range of bacterial, viral, and fungal diseases. Bacillus subtilis is a Gram-positive bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great importance for the elimination of pathogens and establishing beneficial host-associated communities. In this work, we used B. subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and imaging flow cytometry (IFC) analysis supported the notion that Arabidopsis thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin, plipastatin, and the polyketide bacillaene. IFC was more robust in quantifying the inducing effects of A. thaliana, considering the overall heterogeneity of the population. Our results highlight IFC as a useful tool to study the effect of association with a plant host on bacterial gene expression. Furthermore, the common regulation of multiple biosynthetic clusters for antibiotic production by the plant can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
Collapse
Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omri Gilhar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
8
|
Robas M, Probanza A, González D, Jiménez PA. Mercury and Antibiotic Resistance Co-Selection in Bacillus sp. Isolates from the Almadén Mining District. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168304. [PMID: 34444052 PMCID: PMC8392408 DOI: 10.3390/ijerph18168304] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022]
Abstract
Antibiotic resistance (AR) in the environment is of great global concern and a threat to public health. Soil bacteria, including Bacillus spp., could act as recipients and reservoirs of AR genes of clinical, livestock, or agricultural origin. These genes can be shared between bacteria, some of which could be potentially human pathogens. This process can be favored in conditions of abiotic stress, such as heavy metal contamination. The Almadén mining district (Ciudad Real, Spain) is one of the environments with the highest mercury (Hg) contamination worldwide. The link between heavy metal contamination and increased AR in environmental bacteria seems clear, due to co-resistance and co-selection phenomena. In the present study, 53 strains were isolated from rhizospheric and bulk soil samples in Almadén. AR was tested using Vitek® 2 and minimum inhibitory concentration (MIC) values were obtained and interpreted based on the criteria of the Clinical and Laboratory Standards Institute (CLSI) guidelines. Based on the resistance profiles, five different antibiotypes were established. The Hg minimum bactericidal concentration (MBC) of each strain was obtained using the plating method with increasing concentrations of HgCl2. A total of 72% of Bacillus spp. showed resistance to two or more commonly used antibiotics. A total of 38 isolates expressed AR to cephalosporins. Finally, the environmental co-selection of AR to cephalosporins and tetracyclines by selective pressure of Hg has been statistically demonstrated.
Collapse
|
9
|
Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
Collapse
Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
10
|
Hou Q, Keren-Paz A, Korenblum E, Oved R, Malitsky S, Kolodkin-Gal I. Weaponizing volatiles to inhibit competitor biofilms from a distance. NPJ Biofilms Microbiomes 2021; 7:2. [PMID: 33402677 PMCID: PMC7785731 DOI: 10.1038/s41522-020-00174-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
Collapse
Affiliation(s)
- Qihui Hou
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- grid.13992.300000 0004 0604 7563Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- grid.13992.300000 0004 0604 7563Metabolic Profiling Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
11
|
Vereecke D, Zhang Y, Francis IM, Lambert PQ, Venneman J, Stamler RA, Kilcrease J, Randall JJ. Functional Genomics Insights Into the Pathogenicity, Habitat Fitness, and Mechanisms Modifying Plant Development of Rhodococcus sp. PBTS1 and PBTS2. Front Microbiol 2020; 11:14. [PMID: 32082278 PMCID: PMC7002392 DOI: 10.3389/fmicb.2020.00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/06/2020] [Indexed: 01/05/2023] Open
Abstract
Pistachio Bushy Top Syndrome (PBTS) is a recently emerged disease that has strongly impacted the pistachio industry in California, Arizona, and New Mexico. The disease is caused by two bacteria, designated PBTS1 that is related to Rhodococcus corynebacterioides and PBTS2 that belongs to the species R. fascians. Here, we assessed the pathogenic character of the causative agents and examined their chromosomal sequences to predict the presence of particular functions that might contribute to the observed co-occurrence and their effect on plant hosts. In diverse assays, we confirmed the pathogenicity of the strains on "UCB-1" pistachio rootstock and showed that they can also impact the development of tobacco species, but concurrently inconsistencies in the ability to induce symptoms were revealed. We additionally evidence that fas genes are present only in a subpopulation of pure PBTS1 and PBTS2 cultures after growth on synthetic media, that these genes are easily lost upon cultivation in rich media, and that they are enriched for in an in planta environment. Analysis of the chromosomal sequences indicated that PBTS1 and PBTS2 might have complementary activities that would support niche partitioning. Growth experiments showed that the nutrient utilization pattern of both PBTS bacteria was not identical, thus avoiding co-inhabitant competition. PBTS2 appeared to have the potential to positively affect the habitat fitness of PBTS1 by improving its resistance against increased concentrations of copper and penicillins. Finally, mining the chromosomes of PBTS1 and PBTS2 suggested that the bacteria could produce cytokinins, auxins, and plant growth-stimulating volatiles and that PBTS2 might interfere with ethylene levels, in support of their impact on plant development. Subsequent experimentation supported these in silico predictions. Altogether, our data provide an explanation for the observed pathogenic behavior and unveil part of the strategies used by PBTS1 and PBTS2 to interact with plants.
Collapse
Affiliation(s)
- Danny Vereecke
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Isolde M Francis
- Department of Biology, California State University, Bakersfield, CA, United States
| | - Paul Q Lambert
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jolien Venneman
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Rio A Stamler
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - James Kilcrease
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jennifer J Randall
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| |
Collapse
|