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Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167774. [PMID: 37848152 DOI: 10.1016/j.scitotenv.2023.167774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.
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Affiliation(s)
- Yujia Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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Huang S, Zhang X, Song Z, Rahman MU, Fan B. Transcriptional Profiling and Transposon Mutagenesis Study of the Endophyte Pantoea eucalypti FBS135 Adapting to Nitrogen Starvation. Int J Mol Sci 2023; 24:14282. [PMID: 37762583 PMCID: PMC10532344 DOI: 10.3390/ijms241814282] [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: 08/17/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The research on plant endophytes has been drawing a lot of attention in recent years. Pantoea belongs to a group of endophytes with plant growth-promoting activity and has been widely used in agricultural fields. In our earlier studies, Pantoea eucalypti FBS135 was isolated from healthy-growing Pinus massoniana and was able to promote pine growth. P. eucalypti FBS135 can grow under extremely low nitrogen conditions. To understand the mechanism of the low-nitrogen tolerance of this bacterium, the transcriptome of FBS135 in the absence of nitrogen was examined in this study. We found that FBS135 actively regulates its gene expression in response to nitrogen deficiency. Nearly half of the number (4475) of genes in FBS135 were differentially expressed under this condition, mostly downregulated, while it significantly upregulated many transportation-associated genes and some nitrogen metabolism-related genes. In the downregulated genes, the ribosome pathway-related ones were significantly enriched. Meanwhile, we constructed a Tn5 transposon library of FBS135, from which four genes involved in low-nitrogen tolerance were screened out, including the gene for the host-specific protein J, RNA polymerase σ factor RpoS, phosphoribosamine-glycine ligase, and serine acetyltransferase. Functional analysis of the genes revealed their potential roles in the adaptation to nitrogen limitation. The results obtained in this work shed light on the mechanism of endophytes represented by P. eucalypti FBS135, at the overall transcriptional level, to an environmentally limited nitrogen supply and provided a basis for further investigation on this topic.
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Affiliation(s)
- Shengquan Huang
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Xiuyu Zhang
- Department of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zongwen Song
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Mati Ur Rahman
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
| | - Ben Fan
- Department of Forestry, Nanjing Forestry University, Nanjing 210037, China (M.U.R.)
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Wang S, Wang R, Zhao X, Ma G, Liu N, Zheng Y, Tan J, Qi G. Systemically engineering Bacillus amyloliquefaciens for increasing its antifungal activity and green antifungal lipopeptides production. Front Bioeng Biotechnol 2022; 10:961535. [PMID: 36159666 PMCID: PMC9490133 DOI: 10.3389/fbioe.2022.961535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/17/2022] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of antifungal lipopeptides iturin and fengycin has attracted broad interest; however, there is a bottleneck in its low yield in wild strains. Because the key metabolic mechanisms in the lipopeptides synthesis pathway remain unclear, genetic engineering approaches are all ending up with a single or a few gene modifications. The aim of this study is to develop a systematic engineering approach to improve the antifungal activity and biosynthesis of iturin and fengycin in Bacillus amyloliquefaciens. First, blocking the carbon overflow metabolic pathway to increase precursor supply of the branched-chain amino acids by knockout of bdh, disrupting sporulation to extend the stage for producing antifungal lipopeptides by deletion of kinA, blocking of siderophore synthesis to enhance the availability of amino acids and fatty acids by deletion of dhbF, and increasing Spo0A∼P by deletion of rapA, could improve the antifungal activity by 24%, 10%, 13% and 18%, respectively. Second, the double knockout strain ΔbdhΔkinA, triple knockout strain ΔbdhΔkinAΔdhbF and quadruple knockout strain ΔkinAΔbdhΔdhbFΔrapA could improve the antifungal activity by 38%, 44% and 53%, respectively. Finally, overexpression of sfp in ΔkinAΔbdhΔdhbFΔrapA further increased the antifungal activity by 65%. After purifying iturin and fengycin as standards for quantitative analysis of lipopeptides, we found the iturin titer was 17.0 mg/L in the final engineered strain, which was 3.2-fold of the original strain. After fermentation optimization, the titer of iturin and fengycin reached 31.1 mg/L and 175.3 mg/L in flask, and 123.5 mg/L and 1200.8 mg/L in bioreactor. Compared to the original strain, the iturin and fengycin titer in bioreactor increased by 22.8-fold and 15.9-fold in the final engineered strain, respectively. This study may pave the way for the commercial production of green antifungal lipopeptides, and is also favorable for understanding the regulatory and biosynthetic mechanism of iturin and fengycin.
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Affiliation(s)
- Susheng Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Wang
- Enshi Tobacco Technology Center, Enshi City, Hubei, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gaoqiang Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Na Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuqing Zheng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Tan
- Enshi Tobacco Technology Center, Enshi City, Hubei, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- *Correspondence: Gaofu Qi,
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Chen F, Ye J, Liu W, Chio C, Wang W, Qin W. Knockout of a highly GC-rich gene in Burkholderia pyrrocinia by recombineering with freeze-thawing transformation. MOLECULAR PLANT PATHOLOGY 2021; 22:843-857. [PMID: 33942460 PMCID: PMC8232026 DOI: 10.1111/mpp.13058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 05/12/2023]
Abstract
Genetic transformation is a valuable and essential method that provides powerful insights into the gene function of microorganisms and contributes to the construction of engineered bacteria. Here, we developed a novel genetic transformation system to easily knock out a highly GC-rich gene (74.71% GC) from Burkholderia pyrrocinia JK-SH007, a biocontrol strain of poplar canker disease. This system revealed a reliable selectable marker (trimethoprim resistance gene, Tmp) and a simplified, efficient transformation method (6,363.64 CFU/μg, pHKT2) that was developed via freeze-thawing. The knockout recombineering of B. pyrrocinia JK-SH007 was achieved through a suicide plasmid with a three-fragment mutagenesis construct. The three-fragment cassette for mutagenesis was generated by overlap extension and touchdown PCRs and composed of Tmp flanked by GC-rich upstream and downstream fragments from B. pyrrocinia JK-SH007. The mutant strain (ΔBpEG), which was verified by PCR, lost 93.3% of its ability to degrade carboxymethyl cellulose over 40 days. Overall, this system may contribute to future research on B. pyrrocinia traits.
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Affiliation(s)
- Feifei Chen
- College of Forestry and Co‐Innovation Center for Sustainable Forestry in Southern ChinaJiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjing Forestry UniversityNanjingJiangsuChina
- Department of BiologyLakehead UniversityThunder BayOntarioCanada
| | - Jianren Ye
- College of Forestry and Co‐Innovation Center for Sustainable Forestry in Southern ChinaJiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjing Forestry UniversityNanjingJiangsuChina
| | - Wanhui Liu
- College of Forestry and Co‐Innovation Center for Sustainable Forestry in Southern ChinaJiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjing Forestry UniversityNanjingJiangsuChina
| | - Chonlong Chio
- Department of BiologyLakehead UniversityThunder BayOntarioCanada
| | - Wendy Wang
- Department of BiologyLakehead UniversityThunder BayOntarioCanada
| | - Wensheng Qin
- Department of BiologyLakehead UniversityThunder BayOntarioCanada
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Cao X, Li Y, Fan J, Zhao Y, Borriss R, Fan B. Two Lysine Sites That Can Be Malonylated Are Important for LuxS Regulatory Roles in Bacillus velezensis. Microorganisms 2021; 9:microorganisms9061338. [PMID: 34205485 PMCID: PMC8233902 DOI: 10.3390/microorganisms9061338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
S-ribosylhomocysteine lyase (LuxS) has been shown to regulate bacterial multicellular behaviors, typically biofilm formation. However, the mechanisms for the regulation are still mysterious. We previously identified a malonylation modification on K124 and K130 of the LuxS in the plant growth-promoting rhizobacterium B. velezensis (FZB42). In this work, we investigated the effects of the two malonylation sites on biofilm formation and other biological characteristics of FZB42. The results showed that the K124R mutation could severely impair biofilm formation, swarming, and sporulation but promote AI-2 production, suggesting inhibitory effects of high-level AI-2 on the features. All mutations (K124R, K124E, K130R, and K130E) suppressed FZB42 sporulation but increased its antibiotic production. The double mutations generally had a synergistic effect or at least equal to the effects of the single mutations. The mutation of K130 but not of K124 decreased the in vitro enzymatic activity of LuxS, corresponding to the conservation of K130 among various Bacillus LuxS proteins. From the results, we deduce that an alternative regulatory circuit may exist to compensate for the roles of LuxS upon its disruption. This study broadens the understanding of the biological function of LuxS in bacilli and underlines the importance of the two post-translational modification sites.
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Affiliation(s)
- Xianming Cao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (Y.L.); (Y.Z.)
| | - Yulong Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (Y.L.); (Y.Z.)
| | - Jialu Fan
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China;
| | - Yinjuan Zhao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (Y.L.); (Y.Z.)
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, 10115 Berlin, Germany;
- Nord Reet UG, Marienstr. 27a, 17489 Greifswald, Germany
| | - Ben Fan
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (X.C.); (Y.L.); (Y.Z.)
- Correspondence:
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Fan B, Wang C, Ding X, Zhu B, Song X, Borriss R. AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5520604. [PMID: 31219564 PMCID: PMC6585148 DOI: 10.1093/database/baz071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/27/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
Since its isolation 20 years ago, many studies have been devoted to Bacillus velezensis FZB42 (former name Bacillus amyloliquefaciens subsp. plantarum FZB42), which has been gradually accepted as a model organism for Gram-positive rhizobacteria. FZB42 is different from another widely studied bacterial strain, Bacillus subtilis 168, in its many features that are closely associated with plants. FZB42 represents a large group of Bacillus isolates that are beneficial to plants and of great importance in agriculture. In this work a database for FZB42 named 'AmyloWiki' is built to integrate all information of FZB42 available to date. The information includes the genomic, transcriptomic, proteomic, post-translational data as well as FZB42 unique genes, protein regulators, mutant availability, publications and etc. The website is built up with PHP and MySQL with a function of keyword searching, browsing, data-downloading and other functions.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Bingyao Zhu
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, 10115 Berlin, Germany, and Nord Reet UG, Marienstr. 27a, 17489 Greifswald, Germany
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