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Yu J, Zhang Y, Liu H, Liu Y, Mohsin A, Liu Z, Zheng Y, Xing J, Han J, Zhuang Y, Guo M, Wang Z. Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights. Microb Cell Fact 2024; 23:88. [PMID: 38519954 PMCID: PMC10960403 DOI: 10.1186/s12934-024-02358-5] [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: 01/14/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood. RESULTS This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis. CONCLUSIONS This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.
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Affiliation(s)
- Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Hao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yuxuan Liu
- Department of Chemical Engineering for Energy Resources, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Zebo Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jianmin Xing
- Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China.
| | - Zejian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China.
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Li Q, Huang Z, Zhong Z, Bian F, Zhang X. Integrated Genomics and Transcriptomics Provide Insights into Salt Stress Response in Bacillus subtilis ACP81 from Moso Bamboo Shoot ( Phyllostachys praecox) Processing Waste. Microorganisms 2024; 12:285. [PMID: 38399690 PMCID: PMC10893186 DOI: 10.3390/microorganisms12020285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Salt stress is detrimental to the survival of microorganisms, and only a few bacterial species produce hydrolytic enzymes. In this study, we investigated the expression of salt stress-related genes in the salt-tolerant bacterial strain Bacillus subtilis ACP81, isolated from bamboo shoot processing waste, at the transcription level. The results indicate that the strain could grow in 20% NaCl, and the sub-lethal concentration was 6% NaCl. Less neutral protease and higher cellulase and β-amylase activities were observed for B. subtilis ACP81 under sub-lethal concentrations than under the control concentration (0% NaCl). Transcriptome analysis showed that the strain adapted to high-salt conditions by upregulating the expression of genes involved in cellular processes (membrane synthesis) and defense systems (flagellar assembly, compatible solute transport, glucose metabolism, and the phosphotransferase system). Interestingly, genes encoding cellulase and β-amylase-related (malL, celB, and celC) were significantly upregulated and were involved in starch and sucrose metabolic pathways, and the accumulated glucose was effective in mitigating salt stress. RT-qPCR was performed to confirm the sequencing data. This study emphasizes that, under salt stress conditions, ACP81 exhibits enhanced cellulase and β-amylase activities, providing an important germplasm resource for saline soil reclamation and enzyme development.
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Affiliation(s)
- Qiaoling Li
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Zhiyuan Huang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Zheke Zhong
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Fangyuan Bian
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
| | - Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou 310012, China; (Q.L.); (Z.H.); (Z.Z.); (F.B.)
- National Long-Term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou 310012, China
- Engineering Research Center of Biochar of Zhejiang Province, Hangzhou 310012, China
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Hu B, Flemetakis E, Liu Z, Hänsch R, Rennenberg H. Significance of nitrogen-fixing actinorhizal symbioses for restoration of depleted, degraded, and contaminated soil. TRENDS IN PLANT SCIENCE 2023; 28:752-764. [PMID: 37002002 DOI: 10.1016/j.tplants.2023.03.005] [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: 09/21/2022] [Revised: 02/09/2023] [Accepted: 03/09/2023] [Indexed: 06/17/2023]
Abstract
Atmospheric nitrogen (N2)-fixing legume trees are frequently used for the restoration of depleted, degraded, and contaminated soils. However, biological N2 fixation (BNF) can also be performed by so-called actinorhizal plants. Actinorhizal plants include a high diversity of woody species and therefore can be applied in a broad spectrum of environments. In contrast to N2-fixing legumes, the potential of actinorhizal plants for soil restoration remains largely unexplored. In this Opinion, we propose related basic research requirements for the characterization of environmental stress responses that determine the restoration potential of actinorhizal plants for depleted, degraded, and contaminated soils. We identify advantages and unexplored processes of actinorhizal plants and describe a mainly uncharted avenue of future research for this important group of plant species.
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Affiliation(s)
- Bin Hu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China.
| | - Emmanouil Flemetakis
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China; Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Zhenshan Liu
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China
| | - Robert Hänsch
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China; Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106 Braunschweig, Germany.
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University No. 2, Tiansheng Road, Beibei District, 400715 Chongqing, PR China
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Zhang J, Li Y, Du S, Deng Z, Liang Q, Song G, Wang H, Yan M, Wang X. Transcriptomic and proteomic analysis reveals (E)-2-hexenal modulates tomato resistance against Botrytis cinerea by regulating plant defense mechanism. PLANT MOLECULAR BIOLOGY 2023; 111:505-522. [PMID: 37027117 DOI: 10.1007/s11103-023-01339-3] [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: 10/03/2022] [Accepted: 02/07/2023] [Indexed: 06/19/2023]
Abstract
In a previous study, we observed that (E)-2-hexenal stimulated systemic resistance against B. cinerea in tomato plants. However, the molecular mechanisms underlying (E)-2-hexenal-mediated regulation of systemic immunity against B. cinerea remained unclear. In the current study, the global mechanism underlying (E)-2-hexenal-meidated regulation of biotic stress tolerance in tomato was investigated using RNA-seq- and LC-MS/MS- integrated transcriptomic and proteomic analyses. Compared to control plants, (E)-2-hexenal-treated plants exhibited reduced susceptibility to B. cinerea, with a 50.51% decrease in lesion diameters. Meanwhile, (E)-2-hexenal vapor fumigation significantly increased total phenolic content and activities of various antioxidant enzymes peroxidase (POD), phenylalanine ammonia lyase (PAL), and lipoxygenase (LOX). A total of 233 differentially expressed genes (DEGs) and 400 differentially expressed proteins (DEPs), respectively, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that (E)-2-hexenal treatment markedly affected the expression of genes involved in multiple metabolic pathways, especially glutathione metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling pathway. Notably, proteomic analysis revealed modulation of the activities of several defense response proteins, such as pathogenesis-related (PR) proteins (Solyc02g031950.3.1, Solyc02g031920.4.1, and Solyc04g064870.3.1), peroxidases (Solyc06g050440.3.1, Solyc01g105070.3.1, Solyc01g015080.3.1, Solyc03g025380.3.1 and Solyc06g076630.3.1). Our results provide a comprehensive analysis of the effects of (E)-2-hexenal treatment on the transcriptome and proteome of tomato plants, which might be used as a reference in further studies on plant defense responses against pathogens.
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Affiliation(s)
- Jihong Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China.
| | - Yuqiong Li
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Shenglong Du
- College of Chemical Engineering and Technology, Xiangtan University, Xiangtan, 411105, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310022, China
| | - Quanwu Liang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Ge Song
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Haihua Wang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, College of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA30602, USA
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Papadopoulou E, Rodriguez de Evgrafov MC, Kalea A, Tsapekos P, Angelidaki I. Adaptive laboratory evolution to hypersaline conditions of lactic acid bacteria isolated from seaweed. N Biotechnol 2023; 75:21-30. [PMID: 36870677 DOI: 10.1016/j.nbt.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Seaweed biomass has been proposed as a promising alternative carbon source for fermentation processes using microbial factories. However, the high salinity content of seaweed biomass is a limiting factor in large scale fermentation processes. To address this shortcoming, three bacterial species (Pediococcus pentosaceus, Lactobacillus plantarum, and Enterococcus faecium) were isolated from seaweed biomass and evolved to increasing concentrations of NaCl. Following the evolution period, P. pentosaceus reached a plateau at the initial NaCl concentration, whereas L. plantarum, and E. faecium showed a 1.29 and 1.75-fold increase in their salt tolerance, respectively. The impact that salt evolution had on lactic acid production using hypersaline seaweed hydrolysate was investigated. Salinity evolved L. plantarum produced 1.18-fold more lactic acid than the wild type, and salinity evolved E. faecium was able to produce lactic acid, while the wild type could not. No differences in lactic acid production were observed between the P. pentosaceus salinity evolved and wild type strains. Evolved lineages were analyzed for the molecular mechanisms underlying the observed phenotypes. Mutations were observed in genes affecting the ion balance in the cell, the composition of the cell membrane and proteins acting as regulators. This study demonstrates that bacterial isolates from saline niches are promising microbial factories for the fermentation of saline substrates, without the requirement of previous desalination steps, while preserving high final product yields.
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Affiliation(s)
- Eleftheria Papadopoulou
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | | | - Argyro Kalea
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Panagiotis Tsapekos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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Kucho KI, Asukai K, Nguyen TV. NAD + Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes Environ 2023; 38. [PMID: 36858533 PMCID: PMC10037102 DOI: 10.1264/jsme2.me22093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Frankia spp. are multicellular actinobacteria that fix atmospheric dinitrogen (N2) not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species, called actinorhizal plants. To identify novel Frankia genes involved in N2 fixation, we previously isolated mutants of Frankia casuarinae that cannot fix N2. One of these genes, mutant N3H4, did not induce nodulation when inoculated into the host plant Casuarina glauca. Cell lineages that regained the ability to fix N2 as free-living cells were isolated from the mutant cell population. These restored strains also regained the ability to stimulate nodulation. A comparative ana-lysis of the genomes of mutant N3H4 and restored strains revealed that the mutant carried a mutation (Thr584Ile) in the glutamine-dependent NAD+ synthetase gene (Francci3_3146), while restored strains carried an additional suppressor mutation (Asp478Asn) in the same gene. Under nitrogen-depleted conditions, the concentration of NAD(H) was markedly lower in the mutant strain than in the wild type, whereas it was higher in restored strains. These results indicate that glutamine-dependent NAD+ synthetase plays critical roles in both free-living and symbiotic N2 fixation in Frankia.
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Affiliation(s)
- Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University
| | - Koya Asukai
- Graduate School of Science and Engineering, Kagoshima University
| | - Thanh Van Nguyen
- Graduate School of Science and Engineering, Kagoshima University
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Yu J, Wang Z, Wang J, Mohisn A, Liu H, Zhang Y, Zhuang Y, Guo M. Physiological metabolic topology analysis of Halomonas elongata DSM 2581 T in response to sodium chloride stress. Biotechnol Bioeng 2022; 119:3509-3525. [PMID: 36062959 DOI: 10.1002/bit.28222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/06/2022]
Abstract
The halophilic bacterium Halomonas elongata DSM 2581T generally adapts well to high level of salinity by biosynthesizing ectoine, which functions as an important compatible solute protecting the cell against external salinity environment. Halophilic bacteria have specific metabolic activities under high-salt conditions and are gradually applied in various industries. The present study focuses on investigating the physiological and metabolic mechanism of Halomonas elongata DSM 2581T driven by the external salinity environment. The physiological metabolic dynamics under salt stress were investigated to evaluate the effect of NaCl stress on the metabolism of H. elongata. The obtained results demonstrated that ectoine biosynthesis transited from a non-growth-related process to a growth-related process when the NaCl concentration varied from 1% to 13% (w/v). The maximum biomass (Xm =41.37 g/L), and highest ectoine production (Pm =12.91 g/L) were achieved under 8% NaCl. Moreover, the maximum biomass (Xm ) and the maximum specific growth rates (μm ) showed a first rising and then declining trend with the increased NaCl stress. Furthermore, the transcriptome analysis of H. elongata under different NaCl concentrations demonstrated that both 8% and 13% NaCl conditions resulted in increased expressions of genes involved in the pentose phosphate pathway (PPP), Entner-Doudoroff (ED) pathway, Flagellar assembly pathway and ectoine metabolism, but negatively affected the tricarboxylic acid (TCA) cycle and Fatty acid metabolism. At last, the proposed possible adaptation mechanism under the optimum NaCl concentration in H. elongata was described. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Junxiong Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Zejian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Jing Wang
- Department of Chemical Engineering for Energy Resources, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Ali Mohisn
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Hao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237, China
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Chetri SPK, Rahman Z, Thomas L, Lal R, Gour T, Agarwal LK, Vashishtha A, Kumar S, Kumar G, Kumar R, Sharma K. Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives. J Basic Microbiol 2022; 62:764-778. [PMID: 35638879 DOI: 10.1002/jobm.202200043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/17/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.
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Affiliation(s)
| | - Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, New Delhi, Delhi, India
| | - Ratan Lal
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Tripti Gour
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Akanksha Vashishtha
- Department of Plant Protection, CCS University, Meerut, Uttar Pradesh, India
| | - Sachin Kumar
- Department of Botany, Shri Venkateshwara College, University of Delhi, New Delhi, Delhi, India
| | - Gaurav Kumar
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Botany, Hindu College, University of Delhi, New Delhi, Delhi, India
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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Ondrasek G, Rathod S, Manohara KK, Gireesh C, Anantha MS, Sakhare AS, Parmar B, Yadav BK, Bandumula N, Raihan F, Zielińska-Chmielewska A, Meriño-Gergichevich C, Reyes-Díaz M, Khan A, Panfilova O, Seguel Fuentealba A, Romero SM, Nabil B, Wan C(C, Shepherd J, Horvatinec J. Salt Stress in Plants and Mitigation Approaches. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060717. [PMID: 35336599 PMCID: PMC8950276 DOI: 10.3390/plants11060717] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/26/2022] [Accepted: 02/26/2022] [Indexed: 02/07/2023]
Abstract
Salinization of soils and freshwater resources by natural processes and/or human activities has become an increasing issue that affects environmental services and socioeconomic relations. In addition, salinization jeopardizes agroecosystems, inducing salt stress in most cultivated plants (nutrient deficiency, pH and oxidative stress, biomass reduction), and directly affects the quality and quantity of food production. Depending on the type of salt/stress (alkaline or pH-neutral), specific approaches and solutions should be applied to ameliorate the situation on-site. Various agro-hydrotechnical (soil and water conservation, reduced tillage, mulching, rainwater harvesting, irrigation and drainage, control of seawater intrusion), biological (agroforestry, multi-cropping, cultivation of salt-resistant species, bacterial inoculation, promotion of mycorrhiza, grafting with salt-resistant rootstocks), chemical (application of organic and mineral amendments, phytohormones), bio-ecological (breeding, desalination, application of nano-based products, seed biopriming), and/or institutional solutions (salinity monitoring, integrated national and regional strategies) are very effective against salinity/salt stress and numerous other constraints. Advances in computer science (artificial intelligence, machine learning) provide rapid predictions of salinization processes from the field to the global scale, under numerous scenarios, including climate change. Thus, these results represent a comprehensive outcome and tool for a multidisciplinary approach to protect and control salinization, minimizing damages caused by salt stress.
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Affiliation(s)
- Gabrijel Ondrasek
- Faculty of Agriculture, The University of Zagreb, Svetosimunska c. 25, 10000 Zagreb, Croatia; (J.S.); (J.H.)
- Correspondence:
| | - Santosha Rathod
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, India; (S.R.); (C.G.); (M.S.A.); (A.S.S.); (B.P.); (N.B.)
| | | | - Channappa Gireesh
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, India; (S.R.); (C.G.); (M.S.A.); (A.S.S.); (B.P.); (N.B.)
| | | | - Akshay Sureshrao Sakhare
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, India; (S.R.); (C.G.); (M.S.A.); (A.S.S.); (B.P.); (N.B.)
| | - Brajendra Parmar
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, India; (S.R.); (C.G.); (M.S.A.); (A.S.S.); (B.P.); (N.B.)
| | | | - Nirmala Bandumula
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, India; (S.R.); (C.G.); (M.S.A.); (A.S.S.); (B.P.); (N.B.)
| | - Farzana Raihan
- Department of Forestry and Environmental Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh;
| | - Anna Zielińska-Chmielewska
- Department of Business Activity and Economic Policy, Institute of Economics, Poznań University of Economics and Business, Al. Niepodległości 10, 61-875 Poznań, Poland;
| | - Cristian Meriño-Gergichevich
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4780000, Chile;
| | - Marjorie Reyes-Díaz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4780000, Chile;
| | - Amanullah Khan
- Department of Agronomy, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar 25130, Pakistan;
| | - Olga Panfilova
- Russian Research Institute of Fruit Crop Breeding (VNIISPK), 302530 Zhilina, Orel District, Orel Region, Russia;
| | - Alex Seguel Fuentealba
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Temuco 4780000, Chile;
| | | | - Beithou Nabil
- Mechanical and Industrial Engineering Department, Applied Science Private University, Amman 11931, Jordan;
| | - Chunpeng (Craig) Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Jonti Shepherd
- Faculty of Agriculture, The University of Zagreb, Svetosimunska c. 25, 10000 Zagreb, Croatia; (J.S.); (J.H.)
| | - Jelena Horvatinec
- Faculty of Agriculture, The University of Zagreb, Svetosimunska c. 25, 10000 Zagreb, Croatia; (J.S.); (J.H.)
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10
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Chen Q, Xie H, Wei G, Guo X, Zhang J, Lu X, Tang Z. Metabolic differences of two constructive species in saline-alkali grassland in China. BMC PLANT BIOLOGY 2022; 22:53. [PMID: 35081916 PMCID: PMC8790901 DOI: 10.1186/s12870-021-03401-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/14/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Salinization of soil is an urgent problem that restricts agroforestry production and environmental protection. Substantial accumulation of metal ions or highly alkaline soil alters plant metabolites and may even cause plant death. To explore the differences in the response strategies between Suaeda salsa (S. salsa) and Puccinellia tenuiflora (P. tenuiflora), two main constructive species that survive in saline-alkali soil, their metabolic differences were characterized. RESULT Metabolomics was conducted to study the role of metabolic differences between S. salsa and P. tenuiflora under saline-alkali stress. A total of 68 significantly different metabolites were identified by GC-MS, including 9 sugars, 13 amino acids, 8 alcohols, and 34 acids. A more detailed analysis indicated that P. tenuiflora utilizes sugars more effectively and may be saline-alkali tolerant via sugar consumption, while S. salsa utilizes mainly amino acids, alcohols, and acids to resist saline-alkali stress. Measurement of phenolic compounds showed that more C6C3C6-compounds accumulated in P. tenuiflora, while more C6C1-compounds, phenolic compounds that can be used as signalling molecules to defend against stress, accumulated in S. salsa. CONCLUSIONS Our observations suggest that S. salsa resists the toxicity of saline-alkali stress using aboveground organs and that P. tenuiflora eliminates this toxicity via roots. S. salsa has a stronger habitat transformation ability and can provide better habitat for other plants.
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Affiliation(s)
- Qi Chen
- School of Life Sciences Nantong University, Nantong, China
| | - Huansong Xie
- School of Life Sciences Nantong University, Nantong, China
| | - Guanyun Wei
- School of Life Sciences Nantong University, Nantong, China
| | - Xiaorui Guo
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, China
| | - Jian Zhang
- School of Life Sciences Nantong University, Nantong, China
| | - Xueyan Lu
- Northeast Agricultural University, Harbin, China.
| | - Zhonghua Tang
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, China.
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11
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Shahbazi M, Tohidfar M, Azimzadeh Irani M. Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis. 3 Biotech 2021; 11:503. [PMID: 34881166 PMCID: PMC8602552 DOI: 10.1007/s13205-021-03050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/31/2021] [Indexed: 10/19/2022] Open
Abstract
The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03050-w.
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Affiliation(s)
- Mehrdad Shahbazi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
| | - Masoud Tohidfar
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
| | - Maryam Azimzadeh Irani
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983969411 Tehran, Iran
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12
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Chen C, Huang K, Li X, Tian H, Yu H, Huang J, Yuan H, Zhao S, Shao L. Effects of CcpA against salt stress in Lactiplantibacillus plantarum as assessed by comparative transcriptional analysis. Appl Microbiol Biotechnol 2021; 105:3691-3704. [PMID: 33852024 DOI: 10.1007/s00253-021-11276-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Lactiplantibacillus plantarum is frequently exposed to salt stress during industrial applications. Catabolite control protein (CcpA) controls the transcription of many genes, but its role in the response to salt stress remains unclear. In this study, we used transcriptome analyses to investigate differences in the logarithmic growth phases of Lactiplantibacillus plantarum ST-III and its ccpA-knockout mutant when grown with or without salt and glycine betaine (GB). The deletion of ccpA significantly affected bacterial growth under different conditions. Among the comparisons, the highest proportion of differentially expressed genes (64%) was observed in the comparison between the wild-type and ccpA mutant grown with NaCl, whereas the lowest proportion (6%) was observed in the comparison between the ccpA mutant strain cultures grown with NaCl alone or with GB together. Transcriptomic analyses showed that CcpA could regulate GB uptake, activate iron uptake, produce acetyl-CoA, and affect fatty acid composition to maintain membrane lipid homeostasis in the adaptation of high-salinity conditions. Conclusively, these results demonstrate the importance of CcpA as a master regulator of these processes in response to salt stress, and provide new insights into the complex regulatory network of lactic acid bacteria. KEY POINTS: • The absence of CcpA significantly affected growth of L. plantarum and its response to salt stress. • CcpA regulates compatible solutes absorption and ions transport to resist salt stress. • CcpA alters fatty acids composition to maintain membrane lipid homeostasis towards salt stress.
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Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Ke Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Xiaohong Li
- Shanghai Customs P. R. China Technical Center For Animal, Plant And Food Inspection And Quarantine, Shanghai, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Juan Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Shanshan Zhao
- College of Agriculture, Hebei University of Engineering, Handan, People's Republic of China
| | - Li Shao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China.
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13
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Maity PJ, Pawlowski K. Anthropogenic influences on the distribution of the Casuarina-Frankia symbiosis. Symbiosis 2021. [DOI: 10.1007/s13199-021-00765-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Ondrasek G, Rengel Z. Environmental salinization processes: Detection, implications & solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142432. [PMID: 33254867 DOI: 10.1016/j.scitotenv.2020.142432] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 05/27/2023]
Abstract
A great portion of Earth's freshwater and land resources are salt-affected and thus have restricted use or may become unsuitable for most human activities. Some of the recent scenarios warn that environmental salinization processes will continue to be exacerbated due to global climate change. The most relevant implications and side-effects in ecosystems under excessive salinity are destructive and long lasting (e.g. soil dispersion, water/soil hypersalinity, desertification, ruined biodiversity), often with non-feasible on site remediation, especially at larger scales. Agro-ecosystems are very sensitive to salinization; after a certain threshold is reached, yields and food quality start to deteriorate sharply. Additionally, salinity often coincides with numerous other environmental constrains (drought, waterlogging, pollution, acidity, nutrient deficiency, etc.) that progressively aggravate the threat to food security and general ecosystem resilience. Some well-proven, widely-used and cost-effective traditional ameliorative strategies (e.g. conservation agriculture, application of natural conditioners) help against salinity and other constraints, especially in developing countries. Remotely-sensed and integrated data of salt-affected areas combined with in situ and lab-based observations have never been so easy and rapid to acquire, precise and applicable on huge scales, representing a valuable tool for policy-makers and other stakeholders in implementing targeted measures to control and prevent ecosystem degradation (top-to-bottom approach). Continued progress in biotechnology and ecoengineering offers some of the most advanced and effective solutions against salinity (e.g. nanomaterials, marker-assisted breeding, genome editing, plant-microbial associations), albeit many knowledge gaps and ethical frontiers remain to be overcome before a successful transfer of these potential solutions to the industrial-scale food production can be effective.
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Affiliation(s)
- Gabrijel Ondrasek
- The University of Zagreb, Faculty of Agriculture, Svetosimunska c. 25, Croatia.
| | - Zed Rengel
- The University of Western Australia, UWA School of Agriculture and Environment, Stirling Highway 35, Perth, W. Australia, Australia; Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, Split, Croatia
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15
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Mansour S, Swanson E, Pesce C, Simpson S, Morris K, Thomas WK, Tisa LS. Draft Genome Sequences for the Frankia sp. strains CgS1, CcI156 and CgMI4, Nitrogen-Fixing Bacteria Isolated from Casuarina sp. in Egypt. J Genomics 2020; 8:84-88. [PMID: 33029225 PMCID: PMC7532629 DOI: 10.7150/jgen.51181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/05/2020] [Indexed: 02/04/2023] Open
Abstract
Frankia sp. strains CgS1, CcI156 and CgMI4 were isolated from Casuarina glauca and C. cunninghamiana nodules. Here, we report the 5.26-, 5.33- and 5.20-Mbp draft genome sequences of Frankia sp. strains CgS1, CcI156 and CgMI4, respectively. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.
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Affiliation(s)
- Samira Mansour
- Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Erik Swanson
- University of New Hampshire, Durham, New Hampshire, USA
| | - Céline Pesce
- University of New Hampshire, Durham, New Hampshire, USA.,Present address: HM Clause, Davis, California, USA
| | | | | | | | - Louis S Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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16
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Identification of salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains by genomic analysis. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01551-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Abstract
Purpose
The aim of this study was to identify salt tolerance-related genes of Lactobacillus plantarum D31 and T9 strains, isolated from Chinese traditional fermented food, by genomic analysis.
Methods
Tolerance of L. plantarum D31 and T9 strains was evaluated at different stress conditions (temperatures, acid, osmolality, and artificial gastrointestinal fluids). Draft genomes of the two strains were determined using the Illumina sequencing technique. Comparative genomic analysis and gene transcriptional analysis were performed to identify and validate the salt tolerance-related genes.
Results
Both L. plantarum D31 and T9 strains were able to withstand high osmotic pressure caused by 5.0% NaCl, and L. plantarum D31 even to tolerate 8.0% NaCl. L. plantarum D31 genome contained 3,315,786 bp (44.5% GC content) with 3106 predicted protein-encoding genes, while L. plantarum T9 contained 3,388,070 bp (44.1% GC content) with 3223 genes. Comparative genomic analysis revealed a number of genes involved in the maintenance of intracellular ion balance, absorption or synthesis of compatible solutes, stress response, and modulation of membrane composition in L. plantarum D31 and or T9 genomes. Gene transcriptional analysis validated that most of these genes were coupled with the stress-resistance phenotypes of the two strains.
Conclusions
L. plantarum D31 and T9 strains tolerated 5.0% NaCl, and D31 even tolerated 8.0% NaCl. The draft genomes of these two strains were determined, and comparative genomic analysis revealed multiple molecular coping strategies for the salt stress tolerance in L. plantarum D31 and T9 strains.
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17
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Wang X, Tang D, Wang W. Adaptation strategies of
Pseudomonas protegens
SN15‐2 to hyperosmotic growth environment. J Appl Microbiol 2020; 128:1720-1734. [DOI: 10.1111/jam.14582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- X. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - D. Tang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - W. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
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18
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Plant Growth-Promoting Active Metabolites from Frankia spp. of Actinorhizal Casuarina spp. Appl Biochem Biotechnol 2020; 191:74-91. [PMID: 31989439 DOI: 10.1007/s12010-020-03243-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
In agriculture, plant growth enrichment via plant growth stimulating microbes has been recognized as an emergency, it is used as an alternatives to chemical pesticides and growth stimulants. The phytopathogens cause various diseases such as blister bark; stem cankers, and pink and brown rot diseases besides affect the growth frequency of Casuarina spp. toward biotic and abiotic stresses. Bio-control and plant growth-promoting potential of native Frankia isolates from Casuarina spp. in Tamil Nadu, India, was not much explored. Hence, in the present study, we are investigating the plant growth improvement activity and phytopathogen control in Casuarina spp. The Frankia sp. DDNSF-01 and Frankia casuarinae DDNSF-02 were isolated and identified from the root nodules of Casuarina spp. Additionally, it is recognized for plant growth promoter activity and in vitro antimicrobial activity against phytopathogens including Pseudomonas sp. and Colletotrichum sp. The plant growth regulators including IAA, siderophore, ammonia production, and phosphate solubilization were found out. Therefore, the formation of the most significant plant growth-promoting phytohormone IAA was confirmed by UV, FT-IR, TLC, HPLC, HPTLC, and NMR spectrum. Bioactive metabolites including methyl 4-hydroxybenzoate, dodecanoic acid, and some novel flavonoids were identified. Therefore, various growth regulators such as L-aspartic acid, 1H-indole-3-carboxaldehyde were confirmed by GC-MS spectra. The present findings conclude Frankia spp. as efficient plant growth enhancement mediator and also inhibit the phytopathogens.
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19
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Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. Extremophiles 2019; 24:249-264. [PMID: 31820112 DOI: 10.1007/s00792-019-01150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022]
Abstract
The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432T and Egibacter rhizosphaerae EGI 80759T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10T has a closer phylogenetic relationship to Euzebya rosea DSW09T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2T and E. halophilus EGI 80432T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K+ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.
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20
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Stable Transformation of the Actinobacteria Frankia spp. Appl Environ Microbiol 2019; 85:AEM.00957-19. [PMID: 31152017 DOI: 10.1128/aem.00957-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022] Open
Abstract
A stable and efficient plasmid transfer system was developed for nitrogen-fixing symbiotic actinobacteria of the genus Frankia, a key first step in developing a genetic system. Four derivatives of the broad-host-range cloning vector pBBR1MCS were successfully introduced into different Frankia strains by a filter mating with Escherichia coli strain BW29427. Initially, plasmid pHKT1 that expresses green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 × 10-3, resulting in transformants that were tetracycline resistant and exhibited GFP fluorescence. The presence of the plasmid was confirmed by molecular approaches, including visualization on agarose gel and PCR. Several other pBBR1MCS plasmids were also introduced into F. casuarinae strain CcI3 and other Frankia strains at frequencies ranging from 10-2 to 10-4, and the presence of the plasmids was confirmed by PCR. The plasmids were stably maintained for over 2 years and through passage in a plant host. As a proof of concept, a salt tolerance candidate gene from the highly salt-tolerant Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. Endpoint reverse transcriptase PCR (RT-PCR) showed that the gene was expressed in F. casuarinae strain CcI3. The expression provided an increased level of salt tolerance for the transformant. These results represent stable plasmid transfer and exogenous gene expression in Frankia spp., overcoming a major hurdle in the field. This step in the development of genetic tools in Frankia spp. will open up new avenues for research on actinorhizal symbiosis.IMPORTANCE The absence of genetic tools for Frankia research has been a major hindrance to the associated field of actinorhizal symbiosis and the use of the nitrogen-fixing actinobacteria. This study reports on the introduction of plasmids into Frankia spp. and their functional expression of green fluorescent protein and a cloned gene. As the first step in developing genetic tools, this technique opens up the field to a wide array of approaches in an organism with great importance to and potential in the environment.
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21
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Nouioui I, Cortés-albayay C, Carro L, Castro JF, Gtari M, Ghodhbane-Gtari F, Klenk HP, Tisa LS, Sangal V, Goodfellow M. Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia. Front Microbiol 2019; 10:1457. [PMID: 31333602 PMCID: PMC6624747 DOI: 10.3389/fmicb.2019.01457] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carlos Cortés-albayay
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca, Spain
| | - Jean Franco Castro
- The Chilean Collection of Microbial Genetic Resources (CChRGM), Instituto de Investigaciones Agropecuarias (INIA) – Quilamapu, Chillán, Chile
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
- Laboratoire Microorganismes et Biomolécules Actives, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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22
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Liu X, Xu J, Zhu J, Du P, Sun A. Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens. Front Microbiol 2019; 10:94. [PMID: 30787912 PMCID: PMC6372562 DOI: 10.3389/fmicb.2019.00094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/16/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial contamination is considered the main cause of food spoilage. Pseudomonas fluorescens is a typical spoilage bacterium contributing to a large extent to the spoilage process of proteinaceous foods. RpoS is known as an alternative sigma factor controlling stress resistance and virulence in many pathogens. Our previous work revealed that RpoS contributes to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. RNA-seq transcriptomics analysis combined with quantitative proteomics analysis based on multiplexed isobaric tandem mass tag (TMT) labeling was performed in the P. fluorescens wild-type strain UK4 and its derivative carrying an rpoS mutation. A total of 375 differentially expressed coding sequences (DECs) and 212 differentially expressed proteins (DEPs) were identified. The DECs were further verified by qRT-PCR. The combined transcriptome and proteome analyses revealed the involvement of this regulator in several cellular processes, mainly including polysaccharide metabolism, intracellular secretion, extracellular structures, cell wall biogenesis, stress responses, and amino acid and biogenic amine metabolism, which may contribute to the biofilm formation, stress resistance, and spoilage activities of P. fluorescens. Moreover, we indeed observed that RpoS contributed to the production of the macrocolony biofilm's matrix. Our results provide insights into the regulatory network of RpoS and expand the knowledge about the role of RpoS in the functioning of P. fluorescens in food spoilage.
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Affiliation(s)
- Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jun Xu
- Hangzhou Lin'an District People's Hospital, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
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Ghedira K, Harigua-Souiai E, Ben Hamda C, Fournier P, Pujic P, Guesmi S, Guizani I, Miotello G, Armengaud J, Normand P, Sghaier H. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Sci Rep 2018; 8:759. [PMID: 29335550 PMCID: PMC5768760 DOI: 10.1038/s41598-017-18839-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
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Affiliation(s)
- Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
- Université de Carthage, Faculté des Sciences de Bizerte, Tunis, 7021, Tunisia
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Sihem Guesmi
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- National Agronomy Institute (INAT), Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- Associated with Laboratory "Biotechnology and Nuclear Technology" (LR16CNSTN01) & Laboratory "Biotechnology and Bio-Geo Resources Valorization" (LR11ES31), Sidi Thabet Technopark, 2020, Tunisia
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