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Parker GD, Plymale A, Hager J, Hanley L, Yu XY. Studying microbially induced corrosion on glass using ToF-SIMS. Biointerphases 2024; 19:051004. [PMID: 39392276 DOI: 10.1116/6.0003883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 09/20/2024] [Indexed: 10/12/2024] Open
Abstract
Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.
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Affiliation(s)
- Gabriel D Parker
- Department of Chemistry, University of Illinois Chicago, 845 W Taylor St., Chicago, Illinois 60607
- Oak Ridge National Laboratory, Physical Science Directorate, Material Science and Technology Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
| | - Andrew Plymale
- Pacific Northwest National Laboratory, Energy and Environment Directorate, 902 Battelle Boulevard, Richland, Washington 99354
| | - Jacqueline Hager
- Pacific Northwest National Laboratory, Energy and Environment Directorate, 902 Battelle Boulevard, Richland, Washington 99354
| | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, 845 W Taylor St., Chicago, Illinois 60607
| | - Xiao-Ying Yu
- Oak Ridge National Laboratory, Physical Science Directorate, Material Science and Technology Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
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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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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [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: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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Koo YM, Heo AY, Choi HW. Isolation and Identification Antagonistic Bacterium Paenibacillus tianmuensis YM002 against Acidovorax citrulli. FRONTIERS IN PLANT SCIENCE 2023; 14:1173695. [PMID: 37377812 PMCID: PMC10292757 DOI: 10.3389/fpls.2023.1173695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/10/2023] [Indexed: 06/29/2023]
Abstract
In this study, we aimed to screen antagonistic microorganisms against Acidovorax citrulli, the causal agent of bacterial fruit blotch, which is known to induce sever diseases in cucurbit crops. From 240 bacterial strains isolated, only one unknown bacterial isolate, named YM002, showed significant antagonistic activity against A. citrulli KACC17909. Further experiments revealed that YM002 shows antagonistic activity against all tested A. citrulli strains, including KACC17000, KACC17001 and KACC17005, to different degrees. The phylogenetic analysis of 16S rRNA sequences identified YM002 as Paenibacillus tianmuensis. Importantly, pretreatment of cucumber (Cucumis sativus) leaves with YM002 enhanced disease resistance as observed by significantly reduced necrotic symptom development and bacterial growth. YM002-induced resistance accompanied by enhanced expression of defense-related genes, such as PAL1, PR1-1a and CTR1. Importantly, culture filtrate of YM002 significantly suppressed biofilm formation and swimming motility of A. citrulli, which is indispensable for its full virulence. In addition to its antagonistic activity, YM002 showed a various plant growth promotion (PGP)-related traits, such as production of ammonia production, amylase production, ACC deaminase production, inodole-3-acetic acid production, extracellular protease production, siderophore production, and zinc solubilization activities. Indeed, treatment of cucumber roots with YM002 significantly enhanced plant growth parameters, such as fresh and dry weight of leaves or roots. This study suggests the potential of YM002 as an effective PGPR with biological control activity against Acidovorax citrulli in cucumber plants.
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Affiliation(s)
- Young Mo Koo
- Department of Plant Medicals, College of Life Sciences and Biotechnology, Andong National University, Andong, Republic of Korea
- Institute of Cannabis Biotechnology, Andong National University, Andong, Republic of Korea
| | - A Yeong Heo
- Department of Plant Medicals, College of Life Sciences and Biotechnology, Andong National University, Andong, Republic of Korea
- Institute of Cannabis Biotechnology, Andong National University, Andong, Republic of Korea
| | - Hyong Woo Choi
- Department of Plant Medicals, College of Life Sciences and Biotechnology, Andong National University, Andong, Republic of Korea
- Institute of Cannabis Biotechnology, Andong National University, Andong, Republic of Korea
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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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Cardoso AF, da Silva RDSS, Prado IGDO, Bitencourt JAP, Gastauer M. Acquiring Iron-Reducing Enrichment Cultures: Environments, Methods and Quality Assessments. Microorganisms 2023; 11:microorganisms11020448. [PMID: 36838412 PMCID: PMC9959475 DOI: 10.3390/microorganisms11020448] [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: 11/14/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
Lateritic duricrusts cover iron ore deposits and form spatially restricted, unique canga ecosystems endangered by mining. Iron cycling, i.e., the dissolution and subsequent precipitation of iron, is able to restitute canga duricrusts, generating new habitats for endangered biota in post-mining landscapes. As iron-reducing bacteria can accelerate this iron cycling, we aim to retrieve microbial enrichment cultures suitable to mediate the large-scale restoration of cangas. For that, we collected water and sediment samples from the Carajás National Forest and cultivated the iron-reducing microorganisms therein using a specific medium. We measured the potential to reduce iron using ferrozine assays, growth rate and metabolic activity. Six out of seven enrichment cultures effectively reduced iron, showing that different environments harbor iron-reducing bacteria. The most promising enrichment cultures were obtained from environments with repeated flooding and drying cycles, i.e., periodically inundated grasslands and a plateau of an iron mining waste pile characterized by frequent soaking. Selected enrichment cultures contained iron-reducing and fermenting bacteria, such as Serratia and Enterobacter. We found higher iron-reducing potential in enrichment cultures with a higher cell density and microorganism diversity. The obtained enrichment cultures should be tested for canga restoration to generate benefits for biodiversity and contribute to more sustainable iron mining in the region.
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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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Dong H, Zhang F, Xu T, Liu Y, Du Y, Wang C, Liu T, Gao J, He Y, Wang X, Sun S, She Y. Culture-dependent and culture-independent methods reveal microbe-clay mineral interactions by dissimilatory iron-reducing bacteria in an integral oilfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156577. [PMID: 35688243 DOI: 10.1016/j.scitotenv.2022.156577] [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: 04/05/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Fe(III) may be reasonably considered as one of the most important electron acceptors in petroleum reservoir ecosystems. The microbial mineralization of clay minerals, especially montmorillonite, is also of great significance to the exploration of petroleum and gas reservoirs. The bioreduction mechanisms of iron-poor minerals in petroleum reservoirs have been poorly investigated. This study investigated the bioreduction of montmorillonite by dissimilatory iron-reducing bacteria (DIRB) in petroleum reservoirs based on culture-independent and culture-dependent methods. Microbial diversity analysis revealed that Halolactibacillus, Bacillus, Alkaliphilus, Shewanella, Clostridium, and Pseudomonas were the key genera involved in the bioreduction of Fe(III). Through the traditional culture-dependent method, most of the key genera were isolated from the samples collected from petroleum reservoirs. Traditional culture-dependent methods can be used to reveal the metabolic characteristics of microorganisms (such as iron-reduction efficiency) to further elucidate the roles of different species (B. subtilis and B. alkalitelluris) in the environment. Moreover, many species with high iron-reduction efficiencies and relatively low abundances in the samples, such as Tessaracoccus and Flaviflexus, were isolated from petroleum reservoirs for the first time. The combination of culture-dependent and culture-independent methods can be used to further the understanding of the microbial communities and the metabolic characteristics of DIRB in petroleum reservoirs. Structural alterations that occurred during the interactions of microorganisms and montmorillonite were revealed through scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The physical and chemical analysis results demonstrated that microorganisms from petroleum reservoirs can dissolve iron-poor montmorillonite and promote the release of interlayer water. The secondary minerals illite and clinoptilolite were observed in bioreduced smectite. The formation of secondary minerals was closely related to the dissolution degrees of minerals based on iron reduction.
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Affiliation(s)
- Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China.
| | - Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, College of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
| | - Ting Xu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Yulong Liu
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Ying Du
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Chen Wang
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Tiansheng Liu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Ji Gao
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Yanlong He
- College of Petroleum Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Xiaotong Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Sun
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Yuehui She
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China.
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Shah D, Khan MS, Aziz S, Ali H, Pecoraro L. Molecular and Biochemical Characterization, Antimicrobial Activity, Stress Tolerance, and Plant Growth-Promoting Effect of Endophytic Bacteria Isolated from Wheat Varieties. Microorganisms 2021; 10:microorganisms10010021. [PMID: 35056470 PMCID: PMC8777632 DOI: 10.3390/microorganisms10010021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 02/05/2023] Open
Abstract
Endophytic bacteria have been utilized as an alternative source to chemical fertilizers and pesticides to enhance plant productivity and defense mechanisms against biotic and abiotic stress. Five endophytic bacterial strains were isolated from the seeds of three different Pakistani wheat varieties (Ghaneemat-e-IBGE, Atta-Habib, and Siren). The isolated strains AH-1, S-5, S-7, GI-1, and GI-6 showed phylogenetic similarity with Bacillus altitudinis, B. aryabhattai, B. wiedmannii, Pseudomonas aeruginosa, and Burkholderia gladioli, respectively. All strains showed catalase activity (except AH-1) and Indole-3-acetic acid production, with the highest concentration (16.77 μg·mL-1) found for GI-6, followed by S-5 (11.5 μg·mL-1), nitrogen assimilation (except S-7), phosphorus solubilization (except S-7 and AH-1), and ability to produce siderophores, with maximum productions for GI-6 (31 ± 3.5 psu) and GI-1 (30 ± 2.9 psu). All five analyzed strains possessed antimicrobial activity, which was particularly strong in GI-6 and S-5 against Klebsiella pneumonia, Escherichia coli, and Bacillus subtilis. Increasing salinity stress with NaCl negatively affected the bacterial growth of all isolates. However, strains GI-6 and S-5 showed salt tolerance after three days of incubation. A drought tolerance test resulted in a negative impact of poly ethylene glycol on bacterial growth, which was, however, less pronounced in GI-6 strain. The GI-6 strain revealed growth-promoting effects on inoculated wheat plants.
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Affiliation(s)
- Dawood Shah
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar 25000, Pakistan; (D.S.); (M.S.K.); (S.A.); (H.A.)
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Mohammad Sayyar Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar 25000, Pakistan; (D.S.); (M.S.K.); (S.A.); (H.A.)
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar 25000, Pakistan; (D.S.); (M.S.K.); (S.A.); (H.A.)
| | - Haidar Ali
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar 25000, Pakistan; (D.S.); (M.S.K.); (S.A.); (H.A.)
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
- Correspondence: ; Tel.: +86-185-2082-4550
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Courchesne B, Schindler M, Mykytczuk NCS. Relationships Between the Microbial Composition and the Geochemistry and Mineralogy of the Cobalt-Bearing Legacy Mine Tailings in Northeastern Ontario. Front Microbiol 2021; 12:660190. [PMID: 34603222 PMCID: PMC8485068 DOI: 10.3389/fmicb.2021.660190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
Mine tailings host dynamic biogeochemical processes that can mobilize a range of elements from the host material and release them into the environment through acidic, neutral, or alkaline mine drainage. Here we use a combination of mineralogical, geochemical, and microbiological techniques that provide a better understanding of biogeochemical processes within the surficial layers of neutral cobalt and arsenic-rich tailings material at Cobalt, ON, Canada. Tailings material within 30-cm depth profiles from three tailings sites (sites A, B, and C) were characterized for their mineralogical, chemical and microbial community compositions. The tailings material at all sites contains (sulf)arsenides (safflorite, arsenopyrite), and arsenates (erythrite and annabergite). Site A contained a higher and lower amount of (sulf)arsenides and arsenates than site B, respectively. Contrary to site A and B, site C depicted a distinct zoning with (sulf)arsenides found in the deeper reduced zone, and arsenates occurring in the shallow oxidized zone. Variations in the abundance of Co+As+Sb+Zn (Co#), Fe (Fe#), total S (S#), and average valence of As indicated differences in the mineralogical composition of the tailings material. For example, material with a high Co#, lo Fe# and high average valence of As commonly have a higher proportion of secondary arsenate to primary (sulf)arsenide minerals. Microbial community profiling indicated that the Cobalt tailings are primarily composed of Actinobacteria and Proteobacteria, and known N, S, Fe, methane, and possible As-cycling bacteria. The tailings from sites B and C had a larger abundance of Fe and S-cycling bacteria (e.g., Sulfurifustis and Thiobacillus), which are more abundant at greater depths, whereas the tailings of site A had a higher proportion of potential As-cycling and -resistant genera (e.g., Methylocystis and Sphingomonas). A multi-variate statistical analysis showed that (1) distinct site-specific groupings occur for the Co # vs. Fe #, Co# vs. S#'s and for the microbial community structure and (2) microbial communities are statistically highly correlated to depth, S#, Fe#, pH and the average valence of As. The variation in As valence correlated well with the abundance of N, S, Fe, and methane-cycling bacteria. The results of this study provide insights into the complex interplay between minerals containing the critical element cobalt, arsenic, and microbial community structure in the Cobalt Mining Camp tailings.
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Affiliation(s)
| | - Michael Schindler
- Department of Geological Sciences, University of Manitoba, Winnipeg, MB, Canada
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Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4. Genes (Basel) 2021; 12:genes12071060. [PMID: 34356076 PMCID: PMC8303946 DOI: 10.3390/genes12071060] [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: 04/05/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 01/21/2023] Open
Abstract
The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.
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12
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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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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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Khan MS, Gao J, Chen X, Zhang M, Yang F, Du Y, Moe TS, Munir I, Xue J, Zhang X. The Endophytic Bacteria Bacillus velezensis Lle-9, Isolated from Lilium leucanthum, Harbors Antifungal Activity and Plant Growth-Promoting Effects. J Microbiol Biotechnol 2020; 30:668-680. [PMID: 32482932 PMCID: PMC9728359 DOI: 10.4014/jmb.1910.10021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/28/2020] [Indexed: 12/15/2022]
Abstract
Bacillus velezensis is an important plant growth-promoting rhizobacterium with immense potential in agriculture development. In the present study, Bacillus velezensis Lle-9 was isolated from the bulbs of Lilium leucanthum. The isolated strain showed antifungal activities against plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea and Fusarium fujikuroi. The highest percentage of growth inhibition i.e., 68.56±2.35% was observed against Fusarium oxysporum followed by 63.12 ± 2.83%, 61.67 ± 3.39% and 55.82 ± 2.76% against Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several were identified as antimicrobial agents such as diketopiperazines, cyclo-peptides, linear peptides, latrunculin A, 5α-hydroxy-6-ketocholesterol, (R)-S-lactoylglutathione, triamterene, rubiadin, moxifloxacin, 9-hydroxy-5Z,7E,11Z,14Zeicosatetraenoic acid, D-erythro-C18-Sphingosine, citrinin, and 2- arachidonoyllysophosphatidylcholine. The presence of these antimicrobial compounds in the bacterial culture might have contributed to the antifungal activities of the isolated B. velezensis Lle- 9. The strain showed plant growth-promoting traits such as production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation and phosphate solubilization. IAA production was accelerated with application of exogenous tryptophan concentrations in the medium. Further, the lily plants upon inoculation with Lle-9 exhibited improved vegetative growth, more flowering shoots and longer roots than control plants under greenhouse condition. The isolated B. velezensis strain Lle-9 possessed broad-spectrum antifungal activities and multiple plant growth-promoting traits and thus may play an important role in promoting sustainable agriculture. This strain could be developed and applied in field experiments in order to promote plant growth and control disease pathogens.
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Affiliation(s)
- Mohammad Sayyar Khan
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
- Genomics and Bioinformatics Division, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 5000 Khyber Pakhtunkhwa, Pakistan
| | - Junlian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - Xuqing Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - Mingfang Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - Fengping Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - Yunpeng Du
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - The Su Moe
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
- Pharmaceutical Research Laboratory, Biotechnology Research Department, Ministry of Education, Mandalay Division, Kyaukse 05151, Myanmar
| | - Iqbal Munir
- Genomics and Bioinformatics Division, Institute of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 5000 Khyber Pakhtunkhwa, Pakistan
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
| | - Xiuhai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 00097, P.R. China
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Isolation and Characterization of Plant Growth-Promoting Endophytic Bacteria Paenibacillus polymyxa SK1 from Lilium lancifolium. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8650957. [PMID: 32190683 PMCID: PMC7064867 DOI: 10.1155/2020/8650957] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 12/31/2019] [Indexed: 12/18/2022]
Abstract
Paenibacillus polymyxa is a plant growth-promoting rhizobacterium that has immense potential to be used as an environmentally friendly replacement of chemical fertilizers and pesticides. In the present study, Paenibacillus polymyxa SK1 was isolated from bulbs of Lilium lancifolium. The isolated endophytic strain showed antifungal activities against important plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea, and Fusarium fujikuroi. The highest percentage of growth inhibition, i.e., 66.67 ± 2.23%, was observed for SK1 against Botryosphaeria dothidea followed by 61.19 ± 3.12%, 60.71 ± 3.53%, and 55.54 ± 2.89% against Botrytis cinerea, Fusarium fujikuroi, and Fusarium oxysporum, respectively. The metabolite profiling of ethyl acetate fraction was assessed through the UHPLC-LTQ-IT-MS/MS analysis, and putative identification was done with the aid of the GNPS molecular networking workflow. A total of 29 compounds were putatively identified which included dipeptides, tripeptides, cyclopeptides (cyclo-(Leu-Leu), cyclo(Pro-Phe)), 2-heptyl-3-hydroxy 4-quinolone, 6-oxocativic acid, anhydrobrazilic acid, 1-(5-methoxy-1H-indol-3-yl)-2-piperidin-1-ylethane-1,2-dione, octadecenoic acid, pyochelin, 15-hydroxy-5Z,8Z,11Z, 13E-eicosatetraenoic acid, (Z)-7-[(2R,3S)-3-[(2Z,5E)-Undeca-2,5-dienyl]oxiran-2-yl]hept-5-enoic acid, arginylasparagine, cholic acid, sphinganine, elaidic acid, gossypin, L-carnosine, tetrodotoxin, and ursodiol. The high antifungal activity of SK1 might be attributed to the presence of these bioactive compounds. The isolated strain SK1 showed plant growth-promoting traits such as the production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, nitrogen fixation, and phosphate solubilization. IAA production was strongly correlated with the application of exogenous tryptophan concentrations in the medium. Furthermore, inoculation of SK1 enhanced plant growth of two Lilium varieties, Tresor and White Heaven, under greenhouse condition. In the light of these findings, the P. polymyxa SK1 may be utilized as a source of plant growth promotion and disease control in sustainable agriculture.
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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17
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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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18
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Zeng Q, Xie J, Li Y, Gao T, Xu C, Wang Q. Comparative genomic and functional analyses of four sequenced Bacillus cereus genomes reveal conservation of genes relevant to plant-growth-promoting traits. Sci Rep 2018; 8:17009. [PMID: 30451927 PMCID: PMC6242881 DOI: 10.1038/s41598-018-35300-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
Some Bacillus strains function as predominant plant-growth-promoting rhizobacteria. Bacillus cereus 905 is a rod-shaped Gram-positive bacterium isolated from wheat rhizosphere and is a rhizobacterium that exhibits significant plant-growth-promoting effects. Species belonging to the genus Bacillus are observed in numerous different habitats. Several papers on B. cereus are related to pathogens that causes food-borne illness and industrial applications. However, genomic analysis of plant-associated B. cereus has yet to be reported. Here, we conducted a genomic analysis comparing strain 905 with three other B. cereus strains and investigate the genomic characteristics and evolution traits of the species in different niches. The genome sizes of four B. cereus strains range from 5.38 M to 6.40 M, and the number of protein-coding genes varies in the four strains. Comparisons of the four B. cereus strains reveal 3,998 core genes. The function of strain-specific genes are related to carbohydrate, amino acid and coenzyme metabolism and transcription. Analysis of single nucleotide polymorphisms (SNPs) indicates local diversification of the four strains. SNPs are unevenly distributed throughout the four genomes, and function interpretation of regions with high SNP density coincides with the function of strain-specific genes. Detailed analysis indicates that certain SNPs contribute to the formation of strain-specific genes. By contrast, genes related to plant-growth-promoting traits are highly conserved. This study shows the genomic differences between four strains from different niches and provides an in-depth understanding of the genome architecture of these species, thus facilitating genetic engineering and agricultural applications in the future.
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Affiliation(s)
- Qingchao Zeng
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Jianbo Xie
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Yan Li
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Tantan Gao
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Cheng Xu
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Qi Wang
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China.
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Adhikari M, Yadav DR, Kim SW, Um YH, Kim HS, Lee SC, Song JY, Kim HG, Lee YS. Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen ( Acidovorax citrulli) with Rhizosphere Associated Bacteria. THE PLANT PATHOLOGY JOURNAL 2017; 33:170-183. [PMID: 28381964 PMCID: PMC5378438 DOI: 10.5423/ppj.oa.09.2016.0187] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/10/2016] [Accepted: 12/05/2016] [Indexed: 06/07/2023]
Abstract
Bacterial fruit blotch (BFB), which is caused by Acidovorax citrulli, is a serious threat to watermelon growers around the world. The present study was conducted to screen effective rhizobacterial isolates against 35 different A. citrulli isolates and determine their efficacy on BFB and growth parameters of watermelon. Two rhizobacterial isolates viz. Paenibacillus polymyxa (SN-22), Sinomonas atrocyanea (NSB-27) showed high inhibitory activity in the preliminary screening and were further evaluated for their effect on BFB and growth parameters of three different watermelon varieties under greenhouse conditions. The greenhouse experiment result revealed that SN-22 and NSB-27 significantly reduced BFB and had significant stimulatory effect on total chlorophyll content, plant height, total fresh weight and total dry weight compared to uninoculated plants across the tested three watermelon varieties. Analysis of the 16S ribosomal RNA (rRNA) sequences revealed that strains SN-22 belong to P. polymyxa and NSB-27 to S. atrocyanea with the bootstrap value of 99% and 98%, respectively. The isolates SN-22 and NSB-27 were tested for antagonistic and PGP traits. The result showed that the tested isolates produced siderophore, hydrolytic enzymes (protease and cellulose), chitinase, starch hydrolytic enzymes and they showed phosphate as well as zinc solubilizing capacity. This is the first report of P. polymyxa (SN-22) and S. atrocyanea (NSB-27) as biocontrol-plant growth promoting rhizobacteria on watermelon.
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Affiliation(s)
- Mahesh Adhikari
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Dil Raj Yadav
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sang Woo Kim
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Young Hyun Um
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Hyun Seung Kim
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Seong Chan Lee
- Protected Horticulture Research Station, National Institute of Horticultural and Herbal Science, Rural Development Administration, Haman 52054, Korea
| | - Jeong Young Song
- Department of Applied Biology, Chungnam National University, Daejeon 34134, Korea
| | - Hong Gi Kim
- Department of Applied Biology, Chungnam National University, Daejeon 34134, Korea
| | - Youn Su Lee
- Division of Biological Resources Sciences, Kangwon National University, Chuncheon 24341, Korea
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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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21
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Sperb ER, Tadra-Sfeir MZ, Sperotto RA, Fernandes GDC, Pedrosa FDO, de Souza EM, Passaglia LMP. Iron deficiency resistance mechanisms enlightened by gene expression analysis in Paenibacillus riograndensis SBR5. Res Microbiol 2016; 167:501-9. [PMID: 27130283 DOI: 10.1016/j.resmic.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/11/2016] [Accepted: 04/18/2016] [Indexed: 11/29/2022]
Abstract
Despite its importance in growth and cell division, iron metabolism is still poorly understood in microorganisms, especially in Gram-positive bacteria. In this work, we used RNA sequencing technology to elucidate global mechanisms involved in iron starvation resistance in Paenibacillus riograndensis SBR5, a potential plant growth-promoting bacterium. Iron deficiency caused several changes in gene expression, and 150 differentially expressed genes were found: 71 genes were overexpressed and 79 genes were underexpressed. Eight genes for which expression was at least twice as high or twice as low in iron-limited condition compared with iron-sufficient condition were chosen for RT-qPCR analysis to validate the RNA seq data. In general, most genes exhibited the same pattern of expression after 24 h of P. riograndensis growth under iron-limiting condition. Our results suggest that, during iron deficiency, bacteria express several genes related to nutrient uptake when they start to grow to obtain all of the molecules necessary for maintaining major cellular processes. However, once iron becomes highly limiting and is no longer able to sustain exponential growth, bacteria begin to express genes related to several processes, like sporulation and DNA protection, as a way of resisting this stress.
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Affiliation(s)
- Edilena Reis Sperb
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Prédio 43312, CEP 91501-970, Porto Alegre, RS, Brazil.
| | - Michelle Zibetti Tadra-Sfeir
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, C. P. 19046, CEP 81531-980, Curitiba, PR, Brazil.
| | - Raul Antônio Sperotto
- Setor de Genética e Biologia Molecular do Museu de Ciências Naturais (MCN), Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil.
| | - Gabriela de Carvalho Fernandes
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Prédio 43312, CEP 91501-970, Porto Alegre, RS, Brazil.
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, C. P. 19046, CEP 81531-980, Curitiba, PR, Brazil.
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, C. P. 19046, CEP 81531-980, Curitiba, PR, Brazil.
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Prédio 43312, CEP 91501-970, Porto Alegre, RS, Brazil.
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Kwon MJ, O’Loughlin EJ, Boyanov MI, Brulc JM, Johnston ER, Kemner KM, Antonopoulos DA. Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions. PLoS One 2016; 11:e0146689. [PMID: 26800443 PMCID: PMC4723079 DOI: 10.1371/journal.pone.0146689] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 12/21/2015] [Indexed: 11/23/2022] Open
Abstract
Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.
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Affiliation(s)
- Man Jae Kwon
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, United States of America
- Korea Institute of Science and Technology (KIST) – Gangneung Institute, Gangneung, 210–340, S. Korea
| | - Edward J. O’Loughlin
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, United States of America
| | - Maxim I. Boyanov
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, United States of America
| | - Jennifer M. Brulc
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, 60439, United States of America
| | - Eric R. Johnston
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, 60439, United States of America
| | - Kenneth M. Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, United States of America
| | - Dionysios A. Antonopoulos
- Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, United States of America
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, 60439, United States of America
- * E-mail:
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23
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Eastman AW, Heinrichs DE, Yuan ZC. Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genomics 2014; 15:851. [PMID: 25280501 PMCID: PMC4209062 DOI: 10.1186/1471-2164-15-851] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/22/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. RESULTS Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. CONCLUSIONS Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.
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Affiliation(s)
| | | | - Ze-Chun Yuan
- Southern Crop Protection & Food Research Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4 T3, Canada.
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24
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Hertlein G, Müller S, Garcia-Gonzalez E, Poppinga L, Süssmuth RD, Genersch E. Production of the catechol type siderophore bacillibactin by the honey bee pathogen Paenibacillus larvae. PLoS One 2014; 9:e108272. [PMID: 25237888 PMCID: PMC4169593 DOI: 10.1371/journal.pone.0108272] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/27/2014] [Indexed: 12/15/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood. This bacterial infection of honey bee brood is a notifiable epizootic posing a serious threat to global honey bee health because not only individual larvae but also entire colonies succumb to the disease. In the recent past considerable progress has been made in elucidating molecular aspects of host pathogen interactions during pathogenesis of P. larvae infections. Especially the sequencing and annotation of the complete genome of P. larvae was a major step forward and revealed the existence of several giant gene clusters coding for non-ribosomal peptide synthetases which might act as putative virulence factors. We here present the detailed analysis of one of these clusters which we demonstrated to be responsible for the biosynthesis of bacillibactin, a P. larvae siderophore. We first established culture conditions allowing the growth of P. larvae under iron-limited conditions and triggering siderophore production by P. larvae. Using a gene disruption strategy we linked siderophore production to the expression of an uninterrupted bacillibactin gene cluster. In silico analysis predicted the structure of a trimeric trithreonyl lactone (DHB-Gly-Thr)3 similar to the structure of bacillibactin produced by several Bacillus species. Mass spectrometric analysis unambiguously confirmed that the siderophore produced by P. larvae is identical to bacillibactin. Exposure bioassays demonstrated that P. larvae bacillibactin is not required for full virulence of P. larvae in laboratory exposure bioassays. This observation is consistent with results obtained for bacillibactin in other pathogenic bacteria.
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Affiliation(s)
- Gillian Hertlein
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Sebastian Müller
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Lena Poppinga
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | | | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
- Freie Universität Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
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Variation of rhizosphere bacterial community in watermelon continuous mono-cropping soil by long-term application of a novel bioorganic fertilizer. Microbiol Res 2014; 169:570-8. [DOI: 10.1016/j.micres.2013.10.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 09/01/2013] [Accepted: 10/21/2013] [Indexed: 11/21/2022]
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26
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Zhao L, Wang F, Zhang Y, Zhang J. Involvement of Trichoderma asperellum strain T6 in regulating iron acquisition in plants. J Basic Microbiol 2014; 54 Suppl 1:S115-24. [PMID: 24861576 DOI: 10.1002/jobm.201400148] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/12/2014] [Indexed: 11/06/2022]
Abstract
Iron (Fe) deficiency is a major plant nutritional disorder in many parts of the world, particularly in areas with saline soils. Among the numerous root-associated microbes that are beneficial for plant nutrient uptake, Trichoderma spp. are the most effective rhizosphere fungi for enhancing plant growth and plant resistance to biotic and abiotic stresses. To investigate the potential mechanisms of action of Trichoderma on insoluble Fe in the soil, which is difficult for plants to absorb and utilize, a high siderophore-producing strain of Trichoderma T6, was isolated from the rhizosphere of cucumber plants. The strain was identified as T. asperellum based on the morphological features and molecular phylogenetic analyses. Applying strain T6 to sterile soil could increase soil levels of Fe(2+) and siderophores, as well as increase Fe(2+) and Fe(3+)-chelate reductase (FCR) activity in cucumber tissues. Purified siderophore eluent (PSE) increased plant growth, thus confirming its role in plant growth promotion. Moreover, extracellular Fe(3+) reducing activity and three kinds of organic acids were detected in the culture filtrate of strain T6. These results indicate that strain T6 influences plant Fe absorption in several ways. Siderophore-based Fe chelation is effective in providing Fe to plants, organic acids, and Fe(3+) reducing enzymes may participate in the solubilization and reduction of insoluble Fe(3+) to Fe(2+).
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Affiliation(s)
- Lei Zhao
- College of Life Science, Shandong Normal University, Jinan, Shandong, P. R. China
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Wen Y, Wu X, Teng Y, Qian C, Zhan Z, Zhao Y, Li O. Identification and analysis of the gene cluster involved in biosynthesis of paenibactin, a catecholate siderophore produced by Paenibacillus elgii B69. Environ Microbiol 2011; 13:2726-37. [DOI: 10.1111/j.1462-2920.2011.02542.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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