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de Almeida Leite R, Martins da Costa E, Cabral Michel D, do Amaral Leite A, de Oliveira-Longatti SM, de Lima W, Konstantinidis KT, de Souza Moreira FM. Genomic insights into organic acid production and plant growth promotion by different species of phosphate-solubilizing bacteria. World J Microbiol Biotechnol 2024; 40:311. [PMID: 39198273 DOI: 10.1007/s11274-024-04119-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
Bacteria can solubilize phosphorus (P) through the secretion of low-molecular-weight organic acids and acidification. However, the genes involved in the production of these organic acids are poorly understood. The objectives of this study were to verify the calcium phosphate solubilization and the production of low-molecular-weight organic acids by diverse genera of phosphate solubilizing bacterial strains (PSBS); to identify the genes related to the synthesis of the organic acids in the genomes of these strains and; to evaluate growth and nutrient accumulation of maize plants inoculated with PSBS and fertilized with Bayóvar rock phosphate. Genomic DNA was extracted for strain identification and annotation of genes related to the organic acids production. A greenhouse experiment was performed with five strains plus 150 mg dm- 3 P2O5 as Bayóvar rock phosphate (BRP) to assess phosphate solubilization contribution to maize growth and nutrition. Paraburkholderia fungorum UFLA 04-21 and Pseudomonas anuradhapurensis UFPI B5-8A solubilized over 60% of Ca phosphate and produced high amounts of citric/maleic and gluconic acids in vitro, respectively. Eleven organic acids were identified in total, although not all strains produced all acids. Besides, enzymes related to the organic acids production were found in all bacterial genomes. Plants inoculated with strains UFPI B5-6 (Enterobacter bugandensis), UFPI B5-8A, and UFLA 03-10 (Paenibacillus peoriae) accumulated more biomass than the plants fertilized with BRP only. Strains UFLA 03-10 and UFPI B5-8A increased the accumulation of most macronutrients, including P. Collectively, the results show that PSBS can increase maize growth and nutrient accumulation based on Bayóvar rock phosphate fertilization.
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Affiliation(s)
- Rafael de Almeida Leite
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil
| | - Elaine Martins da Costa
- Universidade Federal do Piauí, Campus Professora Cinobelina Elvas, Bom Jesus, Piauí, 64900-000, Brazil
| | - Daniele Cabral Michel
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil
| | - Aline do Amaral Leite
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil
| | - Silvia Maria de Oliveira-Longatti
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil
| | - Wellington de Lima
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, College of Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Fatima Maria de Souza Moreira
- Departamento de Ciência do Solo, Setor de Biologia, Microbiologia e Processos Biológicos do Solo, Universidade Federal de Lavras (UFLA), Caixa Postal 3037, Lavras, Minas Gerais, CEP 37200- 900, Brazil.
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Wallner A, Antonielli L, Mesguida O, Rey P, Compant S. Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability. BMC Genomics 2024; 25:720. [PMID: 39054421 PMCID: PMC11271205 DOI: 10.1186/s12864-024-10610-w] [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: 03/26/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses. RESULTS Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients. CONCLUSIONS Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.
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Affiliation(s)
- Adrian Wallner
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria.
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
| | - Ouiza Mesguida
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
- GreenCell, Biopôle Clermont-Limagne, Saint Beauzire, 63360, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
| | - Stéphane Compant
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
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Ali MA, Ahmed T, Ibrahim E, Rizwan M, Chong KP, Yong JWH. A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities. Heliyon 2024; 10:e31573. [PMID: 38841467 PMCID: PMC11152693 DOI: 10.1016/j.heliyon.2024.e31573] [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: 01/15/2024] [Revised: 05/08/2024] [Accepted: 05/19/2024] [Indexed: 06/07/2024] Open
Abstract
Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.
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Affiliation(s)
- Md. Arshad Ali
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Temoor Ahmed
- Xianghu Laboratory, Hangzhou, 311231, China
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- MEU Research Unit, Middle East University, Amman, Jordan
| | - Ezzeldin Ibrahim
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Vegetable Diseases Research, Plant Pathology Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Khim Phin Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, 23456, Alnarp, Sweden
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Li E, Liu K, Yang S, Li L, Ran K, Sun X, Qu J, Zhao L, Xin Y, Zhu F, Ma J, Song F, Li Z. Analysis of the complete genome sequence of Paenibacillus sp. lzh-N1 reveals its antagonistic ability. BMC Genomics 2024; 25:276. [PMID: 38481158 PMCID: PMC10938842 DOI: 10.1186/s12864-024-10206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Plant diseases caused by pathogenic fungi are devastating. However, commonly used fungicides are harmful to the environment, and some are becoming ineffective due to fungal resistance. Therefore, eco-friendly biological methods to control pathogenic fungi are urgently needed. RESULTS In this study, a strain, Paenibacillus sp. lzh-N1, that could inhibit the growth of the pathogenic fungus Mycosphaerella sentina (Fr) Schrorter was isolated from the rhizosphere soil of pear trees, and the complete genome sequence of the strain was obtained, annotated, and analyzed to reveal the genetic foundation of its antagonistic ability. The entire genome of this strain contained a circular chromosome of 5,641,488 bp with a GC content of 45.50%. The results of species identification show that the strain belongs to the same species as P. polymyxa Sb3-1 and P. polymyxa CJX518. Sixteen secondary metabolic biosynthetic gene clusters were predicted by antiSMASH, including those of the antifungal peptides fusaricidin B and paenilarvins. In addition, biofilm formation-related genes containing two potential gene clusters for cyclic lactone autoinducer, a gene encoding S-ribosylhomocysteine lyase (LuxS), and three genes encoding exopolysaccharide biosynthesis protein were identified. CONCLUSIONS Antifungal peptides and glucanase biosynthesized by Paenibacillus sp. lzh-N1 may be responsible for its antagonistic effect. Moreover, quorum sensing systems may influence the biocontrol activity of this strain directly or indirectly.
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Affiliation(s)
- Ee Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Kaiquan Liu
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Shuhan Yang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Ling Li
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 250353, Jinan, P. R. China
| | - Kun Ran
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Xiaoli Sun
- Shandong Institute of Pomology, 271000, Taian, P. R. China
| | - Jie Qu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Li Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Yuxiu Xin
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Zhu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Jingfang Ma
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China
| | - Feng Song
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
| | - Zhenghua Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, 253023, Dezhou, P. R. China.
- Shandong Engineering Laboratory of Swine Herd Health Big Data and Intelligent Monitoring, Dezhou University, 253023, Dezhou, P.R. China.
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Cui Y, Zhao D, Liu K, Mei X, Sun S, Du B, Ding Y. Abh, AbrB3, and Spo0A play distinct regulatory roles during polymyxin synthesis in Paenibacillus polymyxa SC2. Microbiol Spectr 2024; 12:e0229323. [PMID: 38054717 PMCID: PMC10782996 DOI: 10.1128/spectrum.02293-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Polymyxins are considered the last line of defense against multidrug-resistant bacteria. The regulatory mechanism of polymyxin synthesis is poorly studied in Paenibacillus polymyxa. In this study, we found that Abh and AbrB3 negatively regulated, whereas Spo0A positively regulated polymyxin synthesis in P. polymyxa SC2. In addition, a regulatory relationship between Abh, AbrB3, and Spo0A was revealed, which regulate polymyxin synthesis via multiple regulatory mechanisms in P. polymyxa.
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Affiliation(s)
- Yanru Cui
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Dongying Zhao
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Kai Liu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Xiangui Mei
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Shanshan Sun
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Binghai Du
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Yanqin Ding
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, State Key Laboratory of Crop Biology, National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
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6
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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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Li X, Ma S, Meng Y, Wei W, Peng C, Ling C, Fan S, Liu Z. Characterization of Antagonistic Bacteria Paenibacillus polymyxa ZYPP18 and the Effects on Plant Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:2504. [PMID: 37447065 DOI: 10.3390/plants12132504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
Paenibacillus polymyxa is a plant growth-promoting rhizobacteria (PGPR) that has significant biocontrol properties. Wheat sheath blight caused by Rhizoctonia cerealis is a significant soil-borne disease of wheat that causes significant losses in wheat production, and the biological control against the disease has received extensive attention. P. polymyxa ZYPP18 was identified using morphological and molecular characterization. An antagonistic activity experiment verified that ZYPP18 inhibits the growth of R. cerealis on artificial growth media. A detached leaf assay verified that ZYPP18 inhibits the expansion of wheat sheath blight on the detached leaf. ZYPP18 has been found to possess plant growth-promoting properties, as well as the ability to solubilize phosphate and generate indole-3-acetic acid. Results from hydroponic experiments showed that wheat seedlings treated with ZYPP18 grew faster. Additionally, pot experiments and field experiments demonstrated that ZYPP18 effectively controls the occurrence of wheat sheath blight. ZYPP18 reduced the incidence of wheat sheath blight in wheat seedlings by 37.37% and 37.90%, respectively. The control effect of ZYPP18 on wheat sheath blight was 56.30% and 65.57%, respectively. These findings provide evidence that P. polymyxa ZYPP18 is an effective biological factor that can control disease and promote plant growth.
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Affiliation(s)
- Xiangying Li
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Sujing Ma
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Yuan Meng
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Wei Wei
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Chen Peng
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Chunli Ling
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Susu Fan
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Zhenyu Liu
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
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8
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Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
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Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
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9
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Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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Kumar P, Rani S, Dahiya P, Kumar A, Dang AS, Suneja P. Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte. Front Microbiol 2022; 13:998821. [PMID: 36419432 PMCID: PMC9676466 DOI: 10.3389/fmicb.2022.998821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/13/2022] [Indexed: 09/04/2024] Open
Abstract
Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.
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Affiliation(s)
- Pradeep Kumar
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Simran Rani
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Priyanka Dahiya
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Ajit Kumar
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, India
| | - Amita Suneja Dang
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Pooja Suneja
- Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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11
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Xu S, Zhao Y, Peng Y, Shi Y, Xie X, Chai A, Li B, Li L. Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium. Front Microbiol 2022; 13:850084. [PMID: 35444623 PMCID: PMC9015054 DOI: 10.3389/fmicb.2022.850084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Many Rahnella strains have been widely described as plant growth-promoting rhizobacteria with the potential to benefit plant growth and protect plants from pathogens. R. aceris ZF458 is a beneficial plant bacterium isolated from swamp soil with the potential for biocontrol. Strain ZF458 has shown broad-spectrum antagonistic activities against a variety of plant pathogens and exhibited a dramatic effect on controlling Agrobacterium tumefaciens in sunflowers. The R. aceris ZF458 genome sequence contained a 4,861,340-bp circular chromosome and two plasmids, with an average G + C content of 52.20%. Phylogenetic analysis demonstrated that R. aceris ZF458 was closely related to R. aceris SAP-19. Genome annotation and comparative genomics identified the conservation and specificity of large numbers of genes associated with nitrogen fixation, plant growth hormone production, organic acid biosynthesis and pyrroloquinoline quinone production that specific to benefiting plants in strain ZF458. In addition, numerous conserved genes associated with environmental adaption, including the bacterial secretion system, selenium metabolism, two-component system, flagella biosynthesis, chemotaxis, and acid resistance, were also identified in the ZF458 genome. Overall, this was the first study to systematically analyze the genes linked with plant growth promotion and environmental adaption in R. aceris. The aim of this study was to derive genomic information that would provide an in-depth insight of the mechanisms of plant growth-promoting rhizobacteria, and could be further exploited to improve the application of R. aceris ZF458 in the agriculture field.
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Affiliation(s)
- Shuai Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yurong Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Peng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Jiang A, Zou C, Xu X, Ke Z, Hou J, Jiang G, Fan C, Gong J, Wei J. Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism. BMC Genomics 2022; 23:161. [PMID: 35209846 PMCID: PMC8876185 DOI: 10.1186/s12864-022-08330-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/19/2022] [Indexed: 01/25/2023] Open
Abstract
Background Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed. Results In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified. Conclusions This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08330-0.
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Affiliation(s)
- Aiming Jiang
- College of Agriculture, Guangxi University, Nanning, 530004, China.,College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Chengwu Zou
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiang Xu
- Institute of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China
| | - Zunwei Ke
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Jiangan Hou
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guihe Jiang
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Chunli Fan
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jianhua Gong
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, 530004, China.
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13
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Mülner P, Schwarz E, Dietel K, Herfort S, Jähne J, Lasch P, Cernava T, Berg G, Vater J. Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1. Pathogens 2021; 10:1485. [PMID: 34832640 PMCID: PMC8621861 DOI: 10.3390/pathogens10111485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Paenibacilli are efficient producers of potent agents against bacterial and fungal pathogens, which are of great interest both for therapeutic applications in medicine as well as in agrobiotechnology. Lipopeptides produced by such organisms play a major role in their potential to inactivate pathogens. In this work we investigated two lipopeptide complexes, the fusaricidins and the polymyxins, produced by Paenibacillus polymyxa strains DSM 32871 and M1 by MALDI-TOF mass spectrometry. The fusaricidins show potent antifungal activities and are distinguished by an unusual variability. For strain DSM 32871 we identified numerous yet unknown variants mass spectrometrically. DSM 32871 produces polymyxins of type E (colistins), while M1 forms polymyxins P. For both strains, novel but not yet completely characterized polymyxin species were detected, which possibly are glycosylated. These compounds may be of interest therapeutically, because polymyxins have gained increasing attention as last-resort antibiotics against multiresistant pathogenic Gram-negative bacteria. In addition, the volatilomes of DSM 32781 and M1 were investigated with a GC-MS approach using different cultivation media. Production of volatile organic compounds (VOCs) was strain and medium dependent. In particular, strain M1 manifested as an efficient VOC-producer that exhibited formation of 25 volatiles in total. A characteristic feature of Paenibacilli is the formation of volatile pyrazine derivatives.
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Affiliation(s)
- Pascal Mülner
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Elisa Schwarz
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
| | - Kristin Dietel
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
| | - Stefanie Herfort
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Jennifer Jähne
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Peter Lasch
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Joachim Vater
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
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Soni R, Keharia H. Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli. PLANTA 2021; 254:49. [PMID: 34383174 DOI: 10.1007/s00425-021-03695-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.
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Affiliation(s)
- Riteshri Soni
- Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India
| | - Hareshkumar Keharia
- Department of Biosciences, UGC Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat, 388 315, India.
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15
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Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome. Sci Rep 2021; 11:15545. [PMID: 34330961 PMCID: PMC8324883 DOI: 10.1038/s41598-021-94820-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/16/2021] [Indexed: 01/10/2023] Open
Abstract
Paenibacillus species are Gram-positive bacteria that have been isolated from a diverse array of plant species and soils, with some species exhibiting plant growth-promoting (PGP) activities. Here we report two strains (S02 and S25) of a novel Paenibacillus sp. that were isolated from perennial ryegrass (Lolium perenne) seeds. Comparative genomics analyses showed this novel species was closely related to P. polymyxa. Genomic analyses revealed that strains S02 and S25 possess PGP genes associated with biological nitrogen fixation, phosphate solubilisation and assimilation, as well as auxin production and transportation. Moreover, secondary metabolite gene cluster analyses identified 13 clusters that are shared by both strains and three clusters unique to S25. In vitro assays demonstrated strong bioprotection activity against phytopathogens (Colletotrichum graminicola and Fusarium verticillioides), particularly for strain S02. A transcriptomics analysis evaluating nitrogen fixation activity showed both strains carry an expressed nif operon, but strain S02 was more active than strain S25 in nitrogen-free media. Another transcriptomics analysis evaluating the interaction of strains with F. verticillioides showed strain S02 had increased expression of core genes of secondary metabolite clusters (fusaricidin, paenilan, tridecaptin and polymyxin) when F. verticillioides was present and absent, compared to S25. Such bioactivities make strain S02 a promising candidate to be developed as a combined biofertiliser/bioprotectant.
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16
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Sompark C, Singkhonrat J, Sakkayawong N. Biotransformation of Reactive Red 141 by Paenibacillus terrigena KKW2-005 and Examination of Product Toxicity. J Microbiol Biotechnol 2021; 31:967-977. [PMID: 34099601 PMCID: PMC9705871 DOI: 10.4014/jmb.2104.04041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022]
Abstract
A total of 37 bacterial isolates were obtained from dye-contaminated soil samples at a textile processing factory in Nakhon Ratchasima Province, Thailand, and the potential of the isolates to decolorize and biotransform azo dye Reactive Red 141 (RR141) was investigated. The most potent bacterium was identified as Paenibacillus terrigena KKW2-005, which showed the ability to decolorize 96.45% of RR141 (50 mg/l) within 20 h under static conditions at pH 8.0 and a broad temperature range of 30-40°C. The biotransformation products were analyzed by using UV-Vis spectrophotometry and Fourier-transform infrared spectroscopy. Gas chromatography-mass spectroscopy analysis revealed four metabolites generated from the reductive biodegradation, namely sodium 3-diazenylnaphthalene-1,5-disulfonate (I), sodium naphthalene-2-sufonate (II), 4-chloro-1,3,5-triazin-2-amine (III) and N1-(1,3,5-triazin-2-yl) benzene-1,4-diamine (IV). Decolorization intermediates reduced phytotoxicity as compared with the untreated dye. However, they had phytotoxicity when compared with control, probably due to naphthalene and triazine derivatives. Moreover, genotoxicity testing by high annealing temperature-random amplified polymorphic DNA technique exhibited different DNA polymorphism bands in seedlings exposed to the metabolites. They compared to the bands found in seedlings subjected to the untreated dye or distilled water. The data from this study provide evidence that the biodegradation of Reactive Red 141 by P. terrigena KKW2-005 was genotoxic to the DNA seedlings.
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Affiliation(s)
- Chalermwoot Sompark
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Nueng, Klong Luang, Pathum Thani, Thailand, 12120
| | - Jirada Singkhonrat
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Nueng, Klong Luang, Pathum Thani, Thailand, 12120
| | - Niramol Sakkayawong
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Nueng, Klong Luang, Pathum Thani, Thailand, 12120,Corresponding author Phone: +66-2564-4444 ext 2068 Fax: +66-2564-4500 E-mail:
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Pirttilä AM, Mohammad Parast Tabas H, Baruah N, Koskimäki JJ. Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits. Microorganisms 2021; 9:817. [PMID: 33924411 PMCID: PMC8069042 DOI: 10.3390/microorganisms9040817] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 12/02/2022] Open
Abstract
Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains available as products for agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, and mycorrhizal fungi, each having specific challenges in their production and use, with the main one being inconsistency of field performance. With the growing global concern about pollution, greenhouse gas accumulation, and increased need for plant-based foods, the demand for biofertilizers and biocontrol agents is expected to grow. What are the prospects of finding solutions to the challenges on existing tools? The inconsistent field performance could be overcome by using combinations of several different types of microbial strains, consisting various members of the full plant microbiome. However, a thorough understanding of each microbiological tool, microbial communities, and their mechanisms of action must precede the product development. In this review, we offer a brief overview of the available tools and consider various techniques and approaches that can produce information on new beneficial traits in biofertilizer and biocontrol strains. We also discuss innovative ideas on how and where to identify efficient new members for the biofertilizer and biocontrol strain family.
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Affiliation(s)
- Anna Maria Pirttilä
- Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland; (H.M.P.T.); (N.B.); (J.J.K.)
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Furlan JPR, Lopes R, Stehling EG. Whole-genome sequence-based analysis of the Paenibacillus aquistagni strain DK1, a polyethylene-degrading bacterium isolated from landfill. World J Microbiol Biotechnol 2021; 37:80. [PMID: 33839943 DOI: 10.1007/s11274-021-03045-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/29/2021] [Indexed: 11/25/2022]
Abstract
Polyethylene-degrading bacteria have been emerging as a rational and safe alternative in bioremediation strategies. In this context, some Paenibacillus species produce enzymes involved in the biodegradation of pollutants. Among the enzymes involved in the biodegradation of polyethylene, the alkane hydroxylases, encoded by alkB homologous genes, play a key role in this process. Therefore, this study aimed to identify and perform a genomic investigation of the first polyethylene-degrading Paenibacillus sp. strain, named DK1. The whole-genome sequence-based analysis revealed that the DK1 strain belonged to the species Paenibacillus aquistagni and shared a total of 4327 CDSs with P. aquistagni strain 11. On the other hand, a comparison of the gene clusters showed that DK1 strain harbored a genetic context surrounding the alkB-like gene similar to that found in Pseudomonas sp. strains. The percentage of similarity ranged from 47.88 to 99.76% among all complete amino acid sequences of AlkB-like proteins analyzed. Nevertheless, the predicted amino acid sequences of AlkB-like contained typical structural motifs of alkane hydroxylases, such as His boxes and the HYG motif. These findings associated with the previously reported phenotypic results highlighted the potential of P. aquistagni strain DK1 to biodegrade polyethylene. Therefore, further studies focusing on the biochemical and structural properties of the AlkB-like protein from Paenibacillus may also contribute to the development of sustainable bioremediation strategies.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ralf Lopes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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19
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Langendries S, Goormachtig S. Paenibacillus polymyxa, a Jack of all trades. Environ Microbiol 2021; 23:5659-5669. [PMID: 33684235 DOI: 10.1111/1462-2920.15450] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 02/05/2023]
Abstract
The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under different adverse conditions, which is often accompanied by improved growth conditions for residing plants. Furthermore, Paenibacillus is a member of the core microbiome of several agriculturally important crops, making its close association with plants an interesting research topic. This review covers the versatile interaction possibilities of P. polymyxa with plants and its applicability in industry and agriculture. Thanks to its array of produced compounds and traits, P. polymyxa is likely an efficient plant growth-promoting bacterium, with the potential of biofertilization, biocontrol and protection against abiotic stresses. By contrast, cases of phytotoxicity of P. polymyxa have been described as well, in which growth conditions seem to play a key role. Because of its adjustable character, we propose this bacterial species as an outstanding model for future studies on host-microbe communications and on the manner how the environment can influence these interactions.
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Affiliation(s)
- Sarah Langendries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
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20
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Soni R, Rawal K, Keharia H. Genomics assisted functional characterization of Paenibacillus polymyxa HK4 as a biocontrol and plant growth promoting bacterium. Microbiol Res 2021; 248:126734. [PMID: 33690069 DOI: 10.1016/j.micres.2021.126734] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/22/2021] [Accepted: 02/21/2021] [Indexed: 10/22/2022]
Abstract
The diseases caused by phytopathogens account for huge economic losses in the agricultural sector. Paenibacillus polymyxa is one of the agriculturally important biocontrol agents and plant growth promoting bacterium. This study describes the antifungal potential of P. polymyxa HK4 against an array of fungal phytopathogens and its ability to stimulate seed germination of cumin and groundnut under in vitro conditions. The cumin and groundnut seeds bacterized with HK4 exhibited enhanced germination efficiency in comparison to controls. The use of HK4 as a soil inoculant significantly promoted the shoot length and fresh weight of groundnut plants in pot studies. The draft genome analysis of HK4 revealed the genetic attributes for motility, root colonization, antagonism, phosphate solubilization, siderophore production and production of volatile organic compounds. The bacterium HK4 harnessed several hydrolytic enzymes that may assist its competence in the rhizosphere. The PCR amplification and sequence analysis of the conserved region of the fusA gene amplicon revealed the ability of HK4 to produce fusaricidin. Furthermore, the LC-ESI-MS/MS of crude cell pellet extract of HK4 confirmed the presence of fusaricidin as a major antifungal metabolite. This study demonstrated the potential of HK4 as a biocontrol agent and a plant growth promoter.
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Affiliation(s)
- Riteshri Soni
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India
| | - Khushboo Rawal
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India
| | - Hareshkumar Keharia
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India.
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21
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Abdullahi S, Haris H, Zarkasi KZ, Amir HG. Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004). J Basic Microbiol 2021; 61:293-304. [PMID: 33491813 DOI: 10.1002/jobm.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 11/10/2022]
Abstract
Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy metal tolerance traits. It was able to tolerate more than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and still maintained the ability to produce plant growth-promoting substances under metal stress conditions. To explore the genetic basis of these beneficial traits, the complete genome sequencing of 4M9 was carried out using Pacific Bioscience (PacBio) sequencing technology. The complete genome consisted of one chromosome of 4,654,430 bp with a GC content of 54.6% and one plasmid of 51,135 bp with a GC content of 49.4%. Genome annotation revealed several genes involved in plant growth-promoting traits, including the production of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes involved in heavy metals (As, Co, Zn, Cu, Mn, Se, Cd, and Fe) tolerance were detected. These support its potential as a heavy metal-tolerant plant growth-promoting bacterium and a good genetic resource that can be employed to improve phytoremediation efficiency of heavy metal-contaminated soil via biotechnological techniques. This, to the best of our knowledge, is the first report on the complete genome sequence of heavy metal-tolerant plant growth-promoting E. tabaci.
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Affiliation(s)
- Saidu Abdullahi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia.,Department of Botany, Ahmadu Bello University, Zaria, Nigeria
| | - Hazzeman Haris
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Kamarul Z Zarkasi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Hamzah G Amir
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
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Microbial dynamics in rearing trials of Hermetia illucens larvae fed coffee silverskin and microalgae. Food Res Int 2020; 140:110028. [PMID: 33648256 DOI: 10.1016/j.foodres.2020.110028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 02/01/2023]
Abstract
In the present study, Hermetia illucens larvae were reared on a main rearing substrate composed of a coffee roasting byproduct (coffee silverskin, Cs) enriched with microalgae (Schizochytrium limacinum or Isochrysis galbana) at various substitution levels. The microbial diversity of the rearing substrates, larvae, and frass (excrement from the larvae mixed with the substrate residue) were studied by the combination of microbial culturing on various growth media and metataxonomic analysis (Illumina sequencing). High counts of total mesophilic aerobes, bacterial spores, presumptive lactic acid bacteria, coagulase-positive cocci, and eumycetes were detected. Enterobacteriaceae counts were low in the rearing diets, whereas higher counts of this microbial family were observed in the larvae and frass. The microbiota of the rearing substrates was characterized by the presence of lactic acid bacteria, including the genera Lactobacillus, Leuconostoc and Weissella. The microbiota of the H. illucens larvae fed Cs was characterized by the dominance of Paenibacillus. H. illucens fed diets containing I. galbana were characterized by the presence of Enterococcus, Lysinibacillus, Morganella, and Paenibacillus, depending on the algae inclusion level, while H. illucens fed diets containing S. limacinum were characterized by high relative abundances of Brevundimonas, Enterococcus, Paracoccus, and Paenibacillus, depending on the algae inclusion level. Brevundimonas and Alcaligenes dominated in the frass from larvae fed I. galbana; the predominance of Brevundimonas was also observed in the frass from larvae fed Schyzochitrium-enriched diets. Based on the results of the present study, an effect of algae nutrient bioactive substances (e.g. polysaccharides, high-unsaturated fatty acids, taurine, carotenoids) on the relative abundance of some of the bacterial taxa detected in larvae may be hypothesized, thus opening new intriguing perspectives for the control of the entomopathogenic species and foodborne human pathogens potentially occurring in edible insects. Further studies are needed to support this hypothesis. Finally, new information on the microbial diversity occurring in insect frass was also obtained.
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Li JY, Gao TT, Wang Q. Comparative and Functional Analyses of Two Sequenced Paenibacillus polymyxa Genomes Provides Insights Into Their Potential Genes Related to Plant Growth-Promoting Features and Biocontrol Mechanisms. Front Genet 2020; 11:564939. [PMID: 33391337 PMCID: PMC7773762 DOI: 10.3389/fgene.2020.564939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
Many bacteria belonging to Paenibacillus polymyxa are plant growth-promoting rhizobacteria (PGPR) with the potential to promote plant growth and suppress phytopathogens and have been used as biological control agents (BCAs). However, the growth promotion and biocontrol mechanisms of P. polymyxa have not been thoroughly elucidated thus far. In this investigation, the genome sequences of two P. polymyxa strains, ZF129 and ZF197, with broad anti-pathogen activities and potential for growth promotion were comparatively studied. Comparative and functional analyses of the two sequenced P. polymyxa genomes showed that the ZF129 genome consists of one 5,703,931 bp circular chromosome and two 79,020 bp and 37,602 bp plasmids, designated pAP1 and pAP2, respectively. The complete genome sequence of ZF197 consists of one 5,507,169 bp circular chromosome and one 32,065 bp plasmid, designated pAP197. Phylogenetic analysis revealed that ZF129 is highly similar to two P. polymyxa strains, HY96-2 and SQR-21, while ZF197 is highly similar to P. polymyxa strain J. The genes responsible for secondary metabolite synthesis, plant growth-promoting traits, and systemic resistance inducer production were compared between strains ZF129 and ZF197 as well as other P. polymyxa strains. The results indicated that the variation of the corresponding genes or gene clusters between strains ZF129 and ZF197 may lead to different antagonistic activities of their volatiles or cell-free supernatants against Fusarium oxysporum. This work indicates that plant growth promotion by P. polymyxa is largely mediated by phytohormone production, increased nutrient availability and biocontrol mechanisms. This study provides an in-depth understanding of the genome architecture of P. polymyxa, revealing great potential for the application of this bacterium in the fields of agriculture and horticulture as a PGPR.
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Affiliation(s)
- Jin-Yi Li
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Tan-Tan Gao
- Key Laboratory for Northern Urban Agriculture, Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Qi Wang
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
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Huang WC, Hu Y, Zhang G, Li M. Comparative genomic analysis reveals metabolic diversity of different Paenibacillus groups. Appl Microbiol Biotechnol 2020; 104:10133-10143. [PMID: 33128615 DOI: 10.1007/s00253-020-10984-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/13/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.
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Affiliation(s)
- Wen-Cong Huang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yilun Hu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- Key Laboratory of Alpine Ecology, CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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25
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Soni R, Nanjani S, Keharia H. Genome analysis reveals probiotic propensities of Paenibacillus polymyxa HK4. Genomics 2020; 113:861-873. [PMID: 33096257 DOI: 10.1016/j.ygeno.2020.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/24/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022]
Abstract
The legislations on the usage of antibiotics as growth promoters and prophylactic agents have compelled to develop alternative tools to upsurge the animal protection and contain antibiotic usage. Probiotics have emerged as an effective antibiotic substitute in animal farming. The present study explores the probiotic perspective of Paenibacillus polymyxa HK4 interlinking the genotypic and phenotypic characteristics. The draft genome of HK4 revealed the presence of ORFs encoding the functions associated with tolerance to gastrointestinal stress and adhesion. The biosynthetic gene clusters encoding non-ribosomally synthesized peptides, polyketides and lanthipeptides such as fusaricidin, tridecaptin, polymyxin, paenilan and paenibacillin were annotated in HK4 genome. The strain harbored the chromosomal gene conferring the resistance to lincosamides. No functional gene encoding virulence or toxins could be identified in the genome of HK4. The genome analysis data was complemented by the in vitro experiments confirming its survival during gastrointestinal transit, antimicrobial potential and antibiotic sensitivity. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The draft-genome sequence of Paenibacillus polymyxa HK4 has been deposited as whole-genome shotgun project at GenBank under the accession number PRJNA603023.
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Affiliation(s)
- Riteshri Soni
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India
| | - Sandhya Nanjani
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India
| | - Hareshkumar Keharia
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India.
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26
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Zhou L, Zhang T, Tang S, Fu X, Yu S. Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol. Antonie van Leeuwenhoek 2020; 113:1539-1558. [PMID: 32816227 DOI: 10.1007/s10482-020-01461-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.
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Affiliation(s)
- Liangliang Zhou
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Ting Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural university, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Shan Tang
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Xueqin Fu
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, Jiangxi, People's Republic of China
| | - Shuijing Yu
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China.
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27
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Voichek M, Maaß S, Kroniger T, Becher D, Sorek R. Peptide-based quorum sensing systems in Paenibacillus polymyxa. Life Sci Alliance 2020; 3:3/10/e202000847. [PMID: 32764104 PMCID: PMC7425212 DOI: 10.26508/lsa.202000847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
Discovery of conserved communication systems in the agriculturally important Paenibacillus bacteria. These systems are widespread, and some species encode more than 25 different peptide-receptor pairs. Paenibacillus polymyxa is an agriculturally important plant growth–promoting rhizobacterium. Many Paenibacillus species are known to be engaged in complex bacteria–bacteria and bacteria–host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date, no quorum sensing systems have been described in Paenibacillus. Here, we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
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Affiliation(s)
- Maya Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Tobias Kroniger
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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28
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Wang C, Zhao D, Qi G, Mao Z, Hu X, Du B, Liu K, Ding Y. Effects of Bacillus velezensis FKM10 for Promoting the Growth of Malus hupehensis Rehd. and Inhibiting Fusarium verticillioides. Front Microbiol 2020; 10:2889. [PMID: 31998247 PMCID: PMC6965166 DOI: 10.3389/fmicb.2019.02889] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022] Open
Abstract
Bacillus velezensis is a novel species of Bacillus that has been widely investigated and used because of its direct or indirect growth improvement effect for many plants. B. velezensis FKM10 was previously isolated from rhizosphere soil of apple trees and shows potential as a plant growth-promoting and biocontrol bacterium. In this study, strain FKM10 was verified to inhibit some fungal pathogens of soil-borne plant diseases, produce siderophores to absorb ferric iron for plants, and degrade proteins. Pot experiments showed that the application of strain FKM10 could directly promote the growth of Malus hupehensis Rehd. by increasing biomass, promoting the absorption of nutrients, improving soil fertility, changing the soil microbial community structure, and reducing fungal diversity. The results of this study provided a basis for using strain FKM10 to improve crop yield and overcome diseases of plants. The mechanism of strain FKM10 to control the phytopathogenic fungus Fusarium verticillioides was studied by interoperation with RNA sequencing. Strain FKM10 can destroy the cell wall and cell membrane of F. verticillioides. The secretion of glucosidases, such as β-glucanase, might be one of the causes of the destruction of the fungal cell wall. The regulation of amino acid metabolism might also play an important role in the antibacterial process of strain FKM10. During the antibacterial process, strain FKM10 attacks F. verticillioides and strain FKM10 itself is also affected: the expression of spores is increased, the number of viable cells is decreased, and the ribonucleoprotein complex and flagellar assembly-related genes are downregulated. The results of this study indicate that both strain FKM10 and F. verticillioides have mutually inhibitory activities in a liquid environment. Comparative genome analysis of B. velezensis FKM10 reveals that the general features of their genomes are similar overall and contain the core genome for this species. The results of this study further reveal that B. velezensis can also serve as a basis for developing new biocontrol agents or microbial fertilizers.
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Affiliation(s)
- Chengqiang Wang
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Dongying Zhao
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Guozhen Qi
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Zhiquan Mao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiuna Hu
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Binghai Du
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Kai Liu
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yanqin Ding
- Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, College of Life Sciences, Shandong Agricultural University, Tai'an, China
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Pasari N, Gupta M, Eqbal D, Yazdani SS. Genome analysis of Paenibacillus polymyxa A18 gives insights into the features associated with its adaptation to the termite gut environment. Sci Rep 2019; 9:6091. [PMID: 30988376 PMCID: PMC6465253 DOI: 10.1038/s41598-019-42572-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/03/2019] [Indexed: 01/17/2023] Open
Abstract
Paenibacillus polymyxa A18 was isolated from termite gut and was identified as a potential cellulase and hemicellulase producer in our previous study. Considering that members belonging to genus Paenibacillus are mostly free-living in soil, we investigated here the essential genetic features that helped P. polymyxa A18 to survive in gut environment. Genome sequencing and analysis identified 4608 coding sequences along with several elements of horizontal gene transfer, insertion sequences, transposases and integrated phages, which add to its genetic diversity. Many genes coding for carbohydrate-active enzymes, including the enzymes responsible for woody biomass hydrolysis in termite gut, were identified in P. polymyxa A18 genome. Further, a series of proteins conferring resistance to 11 antibiotics and responsible for production of 4 antibiotics were also found to be encoded, indicating selective advantage for growth and colonization in the gut environment. To further identify genomic regions unique to this strain, a BLAST-based comparative analysis with the sequenced genomes of 47 members belonging to genus Paenibacillus was carried out. Unique regions coding for nucleic acid modifying enzymes like CRISPR/Cas and Type I Restriction-Modification enzymes were identified in P. polymyxa A18 genome suggesting the presence of defense mechanism to combat viral infections in the gut. In addition, genes responsible for the formation of biofilms, such as Type IV pili and adhesins, which might be assisting P. polymyxa A18 in colonizing the gut were also identified in its genome. In situ colonization experiment further confirmed the ability of P. polymyxa A18 to colonize the gut of termite.
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Affiliation(s)
- Nandita Pasari
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mayank Gupta
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Danish Eqbal
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India. .,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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30
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Du Y, Ma J, Yin Z, Liu K, Yao G, Xu W, Fan L, Du B, Ding Y, Wang C. Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis. BMC Genomics 2019; 20:283. [PMID: 30975079 PMCID: PMC6458615 DOI: 10.1186/s12864-019-5646-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/27/2019] [Indexed: 02/03/2023] Open
Abstract
Background Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis. Results A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis. Conclusions This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5646-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuhui Du
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Jinjin Ma
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, People's Republic of China
| | - Kai Liu
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Gan Yao
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Wenfeng Xu
- State Key Laboratory of Nutrition Resources Integrated Utilization, Linshu, People's Republic of China
| | - Lingchao Fan
- State Key Laboratory of Nutrition Resources Integrated Utilization, Linshu, People's Republic of China
| | - Binghai Du
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China
| | - Yanqin Ding
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.
| | - Chengqiang Wang
- College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.
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31
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Jeong H, Choi SK, Ryu CM, Park SH. Chronicle of a Soil Bacterium: Paenibacillus polymyxa E681 as a Tiny Guardian of Plant and Human Health. Front Microbiol 2019; 10:467. [PMID: 30930873 PMCID: PMC6429003 DOI: 10.3389/fmicb.2019.00467] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 02/21/2019] [Indexed: 01/25/2023] Open
Abstract
The Gram-positive rhizosphere bacterium Paenibacillus polymyxa promotes plant growth and produces various antibiotics. Herein, we review research on this species over the past two and a half decades, and focus on the mechanisms of P. polymyxa strain E681, isolated from barley roots in the South Korea in 1995. Strain E681 has outstanding growth-promoting effects on barley, cucumber, pepper, sesame, and Arabidopsis thaliana and produces antimicrobial compounds that protect plants against pathogenic fungi, oomycetes, and bacteria. Induced systemic resistance elicited by treating seeds or roots with strain E681 is a possible mechanism for protecting systemic plant tissues from biotic and other environmental stresses. Genome sequencing has broadened our horizons for antibiotic development and other industrial applications beyond agricultural use. At least six gene clusters for the biosynthesis of antibiotics have been discovered, including polymyxin (pmx), which was recently re-instated as an antibiotic of last resort against Gram-negative drug-resistant bacteria. Three groups of antibiotic synthetases include the gene clusters that encode one for the non-ribosomal peptide polymyxin, fusaricidin, and tridecaptin, another for the lantibiotic paenilan, and the third for a polyketide. We successfully introduced the pmx gene cluster into the surrogate host Bacillus subtilis and created polymyxin derivatives by domain swapping. Furthermore, various E681 derivatives, including a high fusaricidin producer and strains lacking multi-antibiotics production, have been constructed by random mutagenesis and genome engineering. Thus, E681 is an important bacterium that contributes to both plant and human health.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
| | - Seung-Hwan Park
- Infectious Disease Research Center, KRIBB, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea
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Paenibacillus polymyxa bioactive compounds for agricultural and biotechnological applications. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101092] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alkhalili RN, Canbäck B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. Int J Mol Sci 2018; 19:E2650. [PMID: 30200662 PMCID: PMC6165006 DOI: 10.3390/ijms19092650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 09/04/2018] [Indexed: 01/03/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified polycyclic peptides. Lanthipeptides that have antimicrobial activity are known as lantibiotics. Accordingly, the discovery of novel lantibiotics constitutes a possible solution for the problem of antibiotic resistance. We utilized the publicly available genome sequences and the bioinformatic tools tailored for the detection of lanthipeptides. We designed our strategy for screening of 252 firmicute genomes and detecting class-I lanthipeptide-coding gene clusters. The designed strategy resulted in identifying 69 class-I lanthipeptide sequences, of which more than 10% were putative novel. The identified putative novel lanthipeptides have not been annotated on the original or the RefSeq genomes, or have been annotated merely as coding for hypothetical proteins. Additionally, we identified bacterial strains that have not been previously recognized as lanthipeptide-producers. Moreover, we suggest corrections for certain firmicute genome annotations, and recommend lanthipeptide records for enriching the bacteriocin genome mining tool (BAGEL) databases. Furthermore, we propose Z-geobacillin, a putative class-I lanthipeptide coded on the genome of the thermophilic strain Geobacillus sp. ZGt-1. We provide lists of putative novel lanthipeptide sequences and of the previously unrecognized lanthipeptide-producing bacterial strains, so they can be prioritized for experimental investigation. Our results are expected to benefit researchers interested in the in vitro production of lanthipeptides.
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Affiliation(s)
- Rawana N Alkhalili
- Biotechnology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
| | - Björn Canbäck
- Department of Biology, Lund University, SE-221 00 Lund, Sweden.
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Yu WQ, Zheng GP, Qiu DW, Yan FC, Liu WZ, Liu WX. Draft genome sequence, disease-resistance genes, and phenotype of a Paenibacillus terrae strain (NK3-4) with the potential to control plant diseases. Genome 2018; 61:725-734. [PMID: 30184440 DOI: 10.1139/gen-2018-0113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5 458 568 bp and a G+C content of 47%. Moreover, 4 690 015 bp encoded 5090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected. They mainly encode 19 non-ribosomal peptide synthetases (NRPSs); one polyketide synthase/NRPSs hybrid enzyme; four Zn-dependent metalloproteases; three antilisterial bacteriocin subtilosin biosynthesis proteins (AlbA); four serine proteases; five pectate lyases; three beta-glucanases; and four 1,4-beta-xylanases. These include four novel NRPSs that have not been found in any species of Paenibacillus. Furthermore, five proteins exhibiting antifungal activity were identified from the antifungal extracellular protein component based on MS/MS and the strain NK3-4 predicted protein library. On the basis of these features, we propose that strain NK3-4 represents a promising biocontrol agent for protecting plant from diseases. The draft genome sequence described herein may provide the genetic basis for the characterization of the molecular mechanisms underlying the biocontrol functions. It may also facilitate the development of rational strategies for improving the strain.
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Affiliation(s)
- Wen Qing Yu
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.,b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China.,c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Gui Ping Zheng
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - De Wen Qiu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Feng Chao Yan
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wen Zhi Liu
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wan Xue Liu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
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Ambrosini A, Sant'Anna FH, Heinzmann J, de Carvalho Fernandes G, Bach E, Passaglia LMP. Paenibacillus helianthi sp. nov., a nitrogen fixing species isolated from the rhizosphere of Helianthus annuus L. Antonie van Leeuwenhoek 2018; 111:2463-2471. [PMID: 30073429 DOI: 10.1007/s10482-018-1135-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022]
Abstract
Three facultatively anaerobic endospore-forming bacteria were isolated from the rhizosphere of sunflowers grown in fields of Rio Grande do Sul State, Brazil. The designated type strain P26ET was previously identified as a sunflower growth promoting bacterium and is able to fix nitrogen and to excrete ammonia. According to analyses of 16S rRNA gene sequences, P26ET presented similarity values above 98.8% in relation to Paenibacillus azotifigens NF2-4-5T, Paenibacillus graminis RSA19T, Paenibacillus jilunlii Be17T, Paenibacillus salinicaeni LAM0A28T, and Paenibacillus sonchi X19-5T. Phylogenetic reconstructions based on 16S rRNA gene and core proteome data showed that the strains P26ET, P3E and P32E form a distinct clade, which did not include any type strain of the currently described Paenibacillus species. Also, genomic comparisons using average nucleotide identity (ANI), Orthologous ANI and in silico DNA-DNA hybridization revealed similarity ranges below the recommended thresholds when the three isolates from sunflower were compared to their close relatives. The DNA G + C content of strain P26ET was determined to be 49.4 mol%. The major cellular fatty acids are anteiso-C15:0 and iso-C15:0, representing about 58 and 14% of the total fatty acids in P26ET, respectively. Based on different taxonomic genomic metrics, phylogeny, and phenotypic data, we propose that strain P26ET (= DSM 102269 = BR10509) represents a novel species within the genus Paenibacillus, for which the name Paenibacillus helianthi sp. nov. is proposed.
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Affiliation(s)
- Adriana Ambrosini
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernando Hayashi Sant'Anna
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Júlia Heinzmann
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriela de Carvalho Fernandes
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Evelise Bach
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Luciane Maria Pereira Passaglia
- Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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Luo Y, Cheng Y, Yi J, Zhang Z, Luo Q, Zhang D, Li Y. Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism. Front Microbiol 2018; 9:1520. [PMID: 30050512 PMCID: PMC6052121 DOI: 10.3389/fmicb.2018.01520] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
Paenibacillus polymyxa (formerly known as Bacillus polymyxa) has been extensively studied for agricultural applications as a plant-growth-promoting rhizobacterium and is also an important biocontrol agent. Our team has developed the P. polymyxa strain HY96-2 from the tomato rhizosphere as the first microbial biopesticide based on P. polymyxa for controlling plant diseases around the world, leading to the commercialization of this microbial biopesticide in China. However, further research is essential for understanding its precise biocontrol mechanisms. In this paper, we report the complete genome sequence of HY96-2 and the results of a comparative genomic analysis between different P. polymyxa strains. The complete genome size of HY96-2 was found to be 5.75 Mb and 5207 coding sequences were predicted. HY96-2 was compared with seven other P. polymyxa strains for which complete genome sequences have been published, using phylogenetic tree, pan-genome, and nucleic acid co-linearity analysis. In addition, the genes and gene clusters involved in biofilm formation, antibiotic synthesis, and systemic resistance inducer production were compared between strain HY96-2 and two other strains, namely, SC2 and E681. The results revealed that all three of the P. polymyxa strains have the ability to control plant diseases via the mechanisms of colonization (biofilm formation), antagonism (antibiotic production), and induced resistance (systemic resistance inducer production). However, the variation of the corresponding genes or gene clusters between the three strains may lead to different antimicrobial spectra and biocontrol efficacies. Two possible pathways of biofilm formation in P. polymyxa were reported for the first time after searching the KEGG database. This study provides a scientific basis for the further optimization of the field applications and quality standards of industrial microbial biopesticides based on HY96-2. It may also serve as a reference for studying the differences in antimicrobial spectra and biocontrol capability between different biocontrol agents.
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Affiliation(s)
| | | | | | | | | | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Vater J, Herfort S, Doellinger J, Weydmann M, Borriss R, Lasch P. Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa
E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin. Chembiochem 2018; 19:744-753. [DOI: 10.1002/cbic.201700615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Joachim Vater
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Stefanie Herfort
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Joerg Doellinger
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Max Weydmann
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Rainer Borriss
- Humboldt Universität Berlin; Fachgebiet Phytomedizin; Lentzeallee 55-57 14195 Berlin Germany
- NordReet UG; Marienstrasse 27a 17489 Greifswald Germany
| | - Peter Lasch
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
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Shariati J V, Malboobi MA, Tabrizi Z, Tavakol E, Owlia P, Safari M. Comprehensive genomic analysis of a plant growth-promoting rhizobacterium Pantoea agglomerans strain P5. Sci Rep 2017; 7:15610. [PMID: 29142289 PMCID: PMC5688152 DOI: 10.1038/s41598-017-15820-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis. Strain P5 can be grouped closely with strains PG734 and 299 R using pan and core genes, respectively. All the predicted and annotated gene sequences were allocated to KEGG pathways. Accordingly, genes involved in plant growth-promoting (PGP) ability, including phosphate solubilization, IAA and siderophore production, acetoin and 2,3-butanediol synthesis and bacterial secretion, were assigned. This study provides an in-depth view of the PGP characteristics of strain P5, highlighting its potential use in agriculture as a biofertilizer.
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Affiliation(s)
- Vahid Shariati J
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Ali Malboobi
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. .,R&D Department, Green Biotech Inc., Suite 10, 47 Bu-Ali-Sina St. W, Bistoun Ave, Fatemi Sq, Tehran, Iran.
| | - Zeinab Tabrizi
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture Shiraz University, Shiraz, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Maryam Safari
- Energy and Environmental Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Park JE, Kim HR, Park SY, Choi SK, Park SH. Identification of the biosynthesis gene cluster for the novel lantibiotic paenilan fromPaenibacillus polymyxaE681 and characterization of its product. J Appl Microbiol 2017; 123:1133-1147. [DOI: 10.1111/jam.13580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/12/2017] [Accepted: 08/21/2017] [Indexed: 12/26/2022]
Affiliation(s)
- J.-E. Park
- Infectious Disease Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Yuseong-gu Daejeon Korea
- Department of Biosystems and Bioengineering; KRIBB School of Biotechnology; Korea University of Science and Technology (UST); Yuseong-gu Daejeon Korea
| | - H.-R. Kim
- Infectious Disease Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Yuseong-gu Daejeon Korea
| | - S.-Y. Park
- Infectious Disease Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Yuseong-gu Daejeon Korea
| | - S.-K. Choi
- Infectious Disease Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Yuseong-gu Daejeon Korea
- Department of Biosystems and Bioengineering; KRIBB School of Biotechnology; Korea University of Science and Technology (UST); Yuseong-gu Daejeon Korea
| | - S.-H. Park
- Infectious Disease Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Yuseong-gu Daejeon Korea
- Department of Biosystems and Bioengineering; KRIBB School of Biotechnology; Korea University of Science and Technology (UST); Yuseong-gu Daejeon Korea
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Vater J, Herfort S, Doellinger J, Weydmann M, Dietel K, Faetke S, Lasch P. Fusaricidins from Paenibacillus polymyxa M-1, a family of lipohexapeptides of unusual complexity-a mass spectrometric study. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:7-15. [PMID: 27714901 DOI: 10.1002/jms.3891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Paenibacillus polymyxa are rhizobacteria with a high potential to produce natural compounds of biotechnological and medical interest. Main products of P. polymyxa are fusaricidins, a large family of antifungal lipopeptides with a 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid side chain. We use the P. polymyxa strain M-1 as a model organism for the exploration of the biosynthetic potential of these rhizobacteria. Using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) about 40 new fusaricidins were detected which were fractionated by reversed-phase (rp) HPLC. Their structure was determined by MALDI-LIFT-TOF/TOF fragment analysis. The dominant fragment in the product ion spectra of fusaricidins appeared at m/z 256.3, 284.3 and 312.4, respectively, indicating variations in their fatty acid part. Two new subfamilies of fusaricidins were introduced which contain guanidino-3-hydroxyhepta- and nonadecanoic acid as fatty acid constituents. Apparently, the end-standing guanidine group is not modified as shown by direct infusion nano-electrospray ionization mass spectrometry (nano-ESI MS). The results of this study suggest that advanced mass spectrometry is the method of choice for investigating natural compounds of unusual diversity, like fusaricidins. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Joachim Vater
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Stefanie Herfort
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Joerg Doellinger
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Max Weydmann
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Kristin Dietel
- Abitep GmbH Berlin, Glienicker Weg 185, 12489, Berlin, Germany
| | | | - Peter Lasch
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
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Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203. [PMID: 27905924 PMCID: PMC5134293 DOI: 10.1186/s12934-016-0603-7] [Citation(s) in RCA: 445] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/11/2022] Open
Abstract
Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.
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Affiliation(s)
- Elliot Nicholas Grady
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
| | - Linda Liu
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Alex Richman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
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How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier. J Microbiol Methods 2016; 131:135-143. [PMID: 27780731 DOI: 10.1016/j.mimet.2016.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/20/2022]
Abstract
Paenibacillus riograndensis SBR5T is a plant growth-promoting bacterium isolated from the wheat rhizosphere. Its recalcitrance to genetic manipulation is a major bottleneck for molecular studies, as has been reported for other Paenibacillus environmental isolates. An efficient electroporation protocol was established by evaluating diverse parameters and optimizing the culture medium, culture growth phase, electroporation solution, recovery medium, DNA input, and electric field strength. Efficiencies of approximately 2.8×104transformantsμg-1 of plasmid DNA were obtained. The optimized protocol was tested with other Paenibacillus species, and the relevance of bypassing the restriction DNA defense system to transform Paenibacillus was highlighted. This protocol is the tool needed to deepen molecular studies with this strain and will aid in the manipulation of other new environmental isolates that also exhibit recalcitrant transformation difficulties.
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Comparative Genomic Analysis of Delftia tsuruhatensis MTQ3 and the Identification of Functional NRPS Genes for Siderophore Production. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3687619. [PMID: 27847812 PMCID: PMC5099486 DOI: 10.1155/2016/3687619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/17/2016] [Accepted: 10/03/2016] [Indexed: 11/18/2022]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are a group of rhizosphere bacteria that promote plant growth. Delftia tsuruhatensis MTQ3 is a member of PGPR that produces siderophores. The draft genome sequence of MTQ3 has been reported. Here, we analyzed the genome sequence of MTQ3 and performed a comparative genome analysis of four sequenced Delftia strains, revealing genetic relationships among these strains. In addition, genes responsible for bacteriocin and nonribosomal peptide synthesis were detected in the genomes of each strain. To reveal the functions of NRPS genes in siderophore production in D. tsuruhatensis MTQ3, three NRPS genes were knocked out to obtain the three mutants MTQ3-Δ1941, MTQ3-Δ1945, and MTQ3-Δ1946, which were compared with the wild-type strain. In qualitative and quantitative analyses using CAS assay, the mutants failed to produce siderophores. Accordingly, the NRPS genes in MTQ3 were functionally related to siderophore production. These results clarify one mechanism by which plant growth is promoted in MTQ3 and have important applications in agricultural production.
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Weselowski B, Nathoo N, Eastman AW, MacDonald J, Yuan ZC. Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production. BMC Microbiol 2016; 16:244. [PMID: 27756215 PMCID: PMC5069919 DOI: 10.1186/s12866-016-0860-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paenibacillus polymyxa is a plant-growth promoting rhizobacterium that could be exploited as an environmentally friendlier alternative to chemical fertilizers and pesticides. Various strains have been isolated that can benefit agriculture through antimicrobial activity, nitrogen fixation, phosphate solubilization, plant hormone production, or lignocellulose degradation. However, no single strain has yet been identified in which all of these advantageous traits have been confirmed. RESULTS P. polymyxa CR1 was isolated from degrading corn roots from southern Ontario, Canada. It was shown to possess in vitro antagonistic activities against the common plant pathogens Phytophthora sojae P6497 (oomycete), Rhizoctonia solani 1809 (basidiomycete fungus), Cylindrocarpon destructans 2062 (ascomycete fungus), Pseudomonas syringae DC3000 (bacterium), and Xanthomonas campestris 93-1 (bacterium), as well as Bacillus cereus (bacterium), an agent of food-borne illness. P. polymyxa CR1 enhanced growth of maize, potato, cucumber, Arabidopsis, and tomato plants; utilized atmospheric nitrogen and insoluble phosphorus; produced the phytohormone indole-3-acetic acid (IAA); and degraded and utilized the major components of lignocellulose (lignin, cellulose, and hemicellulose). CONCLUSIONS P. polymyxa CR1 has multiple beneficial traits that are relevant to sustainable agriculture and the bio-economy. This strain could be developed for field application in order to control pathogens, promote plant growth, and degrade crop residues after harvest.
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Affiliation(s)
- Brian Weselowski
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Naeem Nathoo
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Biology, Biological and Geological Sciences Building, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Alexander William Eastman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
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Yuan Z, Druzhinina IS, Labbé J, Redman R, Qin Y, Rodriguez R, Zhang C, Tuskan GA, Lin F. Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity. Sci Rep 2016; 6:32467. [PMID: 27572178 PMCID: PMC5004162 DOI: 10.1038/srep32467] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/09/2016] [Indexed: 12/18/2022] Open
Abstract
Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.
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Affiliation(s)
- Zhilin Yuan
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, P. R. China
| | - Irina S. Druzhinina
- Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | | | - Yuan Qin
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, P. R. China
| | - Russell Rodriguez
- Adaptive Symbiotic Technologies, Seattle, USA
- Depart of Biology, University of Washington, Seattle, USA
| | - Chulong Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, P. R. China
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Fucheng Lin
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, P. R. China
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Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species. Sci Rep 2016; 6:21329. [PMID: 26856413 PMCID: PMC4746698 DOI: 10.1038/srep21329] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/20/2016] [Indexed: 11/09/2022] Open
Abstract
Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR.
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López-Mondéjar R, Zühlke D, Větrovský T, Becher D, Riedel K, Baldrian P. Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:104. [PMID: 27186238 PMCID: PMC4867992 DOI: 10.1186/s13068-016-0518-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/04/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstruction in a screen of environmental isolates. Here, we provide a detailed description of the complex multi-component O199 enzymatic system involved in the degradation of lignocellulose. RESULTS We examined the genome and the proteome of O199 grown on complex lignocellulose (wheat straw) and on microcrystalline cellulose. The genome contained 476 genes with domains assigned to carbohydrate-active enzyme (CAZyme) families, including 100 genes coding for glycosyl hydrolases (GHs) putatively involved in cellulose and hemicellulose degradation. Moreover, 31 % of these CAZymes were expressed on cellulose and 29 % on wheat straw. Proteomic analyses also revealed a complex and complete set of enzymes for deconstruction of cellulose (at least 22 proteins, including 4 endocellulases, 2 exocellulases, 2 cellobiohydrolases and 2 β-glucosidases) and hemicellulose (at least 28 proteins, including 5 endoxylanases, 1 β-xylosidase, 2 xyloglucanases, 2 endomannanases, 2 licheninases and 1 endo-β-1,3(4)-glucanase). Most of these proteins were secreted extracellularly and had numerous carbohydrate-binding domains (CBMs). In addition, O199 also secreted a high number of substrate-binding proteins (SBPs), including at least 42 proteins binding carbohydrates. Interestingly, both plant lignocellulose and crystalline cellulose triggered the production of a wide array of hydrolytic proteins, including cellulases, hemicellulases, and other GHs. CONCLUSIONS Our data provide an in-depth analysis of the complex and complete set of enzymes and accessory non-catalytic proteins-GHs, CBMs, transporters, and SBPs-implicated in the high cellulolytic capacity shown by this bacterial strain. The large diversity of hydrolytic enzymes and the extracellular secretion of most of them supports the use of Paenibacillus O199 as a candidate for second-generation technologies using paper or lignocellulosic agricultural wastes.
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Affiliation(s)
- Rubén López-Mondéjar
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Daniela Zühlke
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Tomáš Větrovský
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Dörte Becher
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Katharina Riedel
- />Institute of Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17487 Greifswald, Germany
| | - Petr Baldrian
- />Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v. v. i., Průmyslová 595, 252 42 Vestec, Czech Republic
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Complete genome sequence of Paenibacillus beijingensis 7188(T) (=DSM 24997(T)), a novel rhizobacterium from jujube garden soil. J Biotechnol 2015; 206:75-6. [PMID: 25937453 DOI: 10.1016/j.jbiotec.2015.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 11/23/2022]
Abstract
We present here the complete genome sequence of a novel species Paenibacillus beijingensis 7188(T) (=DSM 24997(T)) from jujube rhizosphere soil that consists of one circular chromosome of 5,749,967 bp with a GC content of 52.5%. On the significance of first genome information in this species, the genome sequence of strain 7188(T) will provide a better comprehension of Paenibacillus species for the practical uses as a biofertilizer in agriculture.
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Eastman AW, Yuan ZC. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing. Front Microbiol 2015; 5:769. [PMID: 25653642 PMCID: PMC4301005 DOI: 10.3389/fmicb.2014.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/16/2014] [Indexed: 01/10/2023] Open
Abstract
Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects.
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Affiliation(s)
- Alexander W Eastman
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Government of Canada London, ON, Canada ; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario London, ON, Canada
| | - Ze-Chun Yuan
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, Government of Canada London, ON, Canada ; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario London, ON, Canada
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