1
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Lv F, Zhan Y, Feng H, Sun W, Yin C, Han Y, Shao Y, Xue W, Jiang S, Ma Y, Hu H, Wei J, Yan Y, Lin M. Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associated Pseudomonas stutzeri A1501. mSphere 2024; 9:e0076223. [PMID: 38747590 PMCID: PMC11332353 DOI: 10.1128/msphere.00762-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/10/2024] [Indexed: 06/26/2024] Open
Abstract
The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is nifM, encoding an isomerase necessary for nitrogenase reductase solubility; amtB, encoding an ammonium transporter; oprB, encoding a carbohydrate porin; and cheZ, encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways. IMPORTANCE Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated Pseudomonas stutzeri A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins' mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haichao Feng
- College of Agriculture, Henan University, Kaifeng, Henan, China
| | - Wenyue Sun
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyan Yin
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yueyue Han
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Xue
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haonan Hu
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinfeng Wei
- College of Agriculture, Henan University, Kaifeng, Henan, China
| | - Yongliang Yan
- Biotechnology Research Institute/National Key Laboratory of Agricultural Microbiology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Lin
- College of Agriculture, Henan University, Kaifeng, Henan, China
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He H, Zheng W, Xiao S, Gong L, Li H, Zhou K, Zhang L, Tu Q, Zhu YZ, Zhang Y. Deciphering the Nitrogen Fixation Gene Cluster in Vibrio natriegens: A Study on Optimized Expression and Application of Nitrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12618-12629. [PMID: 38778776 DOI: 10.1021/acs.jafc.4c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Microbial nitrogen fixation presents a viable alternative to chemical fertilizers, yet the limited colonization and specificity of naturally occurring nitrogen-fixing microorganisms present significant challenges to their widespread application. In this study, we identified a nitrogen fixation gene cluster (VNnif) in Vibrio natriegens (VN) and tested its nitrogenase activity through the acetylene reduction assay. We investigated the potential utilization of nitrogenase by incorporating the nitrogenase gene cluster from VN into plant growth-promoting rhizosphere bacteria Pseudomonas protegens CHA0 and enhancing its activity to 48.16 nmol C2H2/mg/h through promoter replacement and cluster rearrangement. The engineered strain CHA0-PVNnif was found to positively impact the growth of Arabidopsis thaliana col-0 and Triticum aestivum L. (wheat). This study expanded the role of plant growth-promoting rhizobacteria (PGPR) and provided a research foundation for enhancing nitrogenase activity.
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Affiliation(s)
- Haocheng He
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weijin Zheng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life and Geographic Sciences, Kashi University, Kashi 844099, China
| | - Shuai Xiao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liang Gong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - He Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Kexuan Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Letian Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi Zhun Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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3
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Gao Y, Li Y, Shang J, Zhang W. Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states. WATER RESEARCH 2024; 252:121225. [PMID: 38309070 DOI: 10.1016/j.watres.2024.121225] [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: 09/11/2023] [Revised: 01/25/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.
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Affiliation(s)
- Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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5
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Enright AL, Banta AB, Ward RD, Rivera Vazquez J, Felczak MM, Wolfe MB, TerAvest MA, Amador-Noguez D, Peters JM. The genetics of aerotolerant growth in an alphaproteobacterium with a naturally reduced genome. mBio 2023; 14:e0148723. [PMID: 37905909 PMCID: PMC10746277 DOI: 10.1128/mbio.01487-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE The inherent complexity of biological systems is a major barrier to our understanding of cellular physiology. Bacteria with markedly fewer genes than their close relatives, or reduced genome bacteria, are promising biological models with less complexity. Reduced genome bacteria can also have superior properties for industrial use, provided the reduction does not overly restrict strain robustness. Naturally reduced genome bacteria, such as the alphaproteobacterium Zymomonas mobilis, have fewer genes but remain environmentally robust. In this study, we show that Z. mobilis is a simplified genetic model for Alphaproteobacteria, a class with important impacts on the environment, human health, and industry. We also identify genes that are only required in the absence of atmospheric oxygen, uncovering players that maintain and utilize the cellular energy state. Our findings have broad implications for the genetics of Alphaproteobacteria and industrial use of Z. mobilis to create biofuels and bioproducts.
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Affiliation(s)
- Amy L. Enright
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julio Rivera Vazquez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Magdalena M. Felczak
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Michael B. Wolfe
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michaela A. TerAvest
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Venkataraman M, Yñigez-Gutierrez A, Infante V, MacIntyre A, Fernandes-Júnior PI, Ané JM, Pfleger B. Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes. ACS Synth Biol 2023; 12:3623-3634. [PMID: 37988619 PMCID: PMC10754042 DOI: 10.1021/acssynbio.3c00414] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. This work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.
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Affiliation(s)
- Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Audrey Yñigez-Gutierrez
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - April MacIntyre
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Valent BioSciences, Libertyville, Illinois 60048, United States
| | - Paulo Ivan Fernandes-Júnior
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Brazilian Agricultural Research Corporation (Embrapa), Tropical Semi-Arid Research Center (Embrapa Semiárido), Petrolina, Pernambuco 56302-970, Brazil
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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7
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Robicheau BM, Tolman J, Rose S, Desai D, LaRoche J. Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities. FEMS Microbiol Ecol 2023; 99:fiad122. [PMID: 37951299 PMCID: PMC10656255 DOI: 10.1093/femsec/fiad122] [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: 02/28/2023] [Revised: 07/30/2023] [Accepted: 11/09/2023] [Indexed: 11/13/2023] Open
Abstract
We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Sonja Rose
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
- Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
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Zayed O, Hewedy OA, Abdelmoteleb A, Ali M, Youssef MS, Roumia AF, Seymour D, Yuan ZC. Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction. Biomolecules 2023; 13:1443. [PMID: 37892125 PMCID: PMC10605003 DOI: 10.3390/biom13101443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.
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Affiliation(s)
- Omar Zayed
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Omar A. Hewedy
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Ali Abdelmoteleb
- Botany Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo 11753, Egypt;
| | - Mohamed S. Youssef
- Botany and Microbiology Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ahmed F. Roumia
- Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt;
| | - Danelle Seymour
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
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9
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Mehmood N, Saeed M, Zafarullah S, Hyder S, Rizvi ZF, Gondal AS, Jamil N, Iqbal R, Ali B, Ercisli S, Kupe M. Multifaceted Impacts of Plant-Beneficial Pseudomonas spp. in Managing Various Plant Diseases and Crop Yield Improvement. ACS OMEGA 2023; 8:22296-22315. [PMID: 37396244 PMCID: PMC10308577 DOI: 10.1021/acsomega.3c00870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023]
Abstract
The modern agricultural system has issues with the reduction of agricultural productivity due to a wide range of abiotic and biotic stresses. It is also expected that in the future the entire world population may rapidly increase and will surely demand more food. Farmers now utilize a massive quantity of synthetic fertilizers and pesticides for disease management and to increase food production. These synthetic fertilizers badly affect the environment, the texture of the soil, plant productivity, and human health. However, agricultural safety and sustainability depend on an ecofriendly and inexpensive biological application. In contrast to synthetic fertilizers, soil inoculation with plant-growth-promoting rhizobacteria (PGPR) is one of the excellent alternative options. In this regard, we focused on the best PGPR genera, Pseudomonas, which exists in the rhizosphere as well as inside the plant's body and plays a role in sustainable agriculture. Many Pseudomonas spp. control plant pathogens and play an effective role in disease management through direct and indirect mechanisms. Pseudomonas spp. fix the amount of atmospheric nitrogen, solubilize phosphorus and potassium, and also produce phytohormones, lytic enzymes, volatile organic compounds, antibiotics, and secondary metabolites during stress conditions. These compounds stimulate plant growth by inducing systemic resistance and by inhibiting the growth of pathogens. Furthermore, pseudomonads also protect plants during different stress conditions like heavy metal pollution, osmosis, temperature, oxidative stress, etc. Now, several Pseudomonas-based commercial biological control products have been promoted and marketed, but there are a few limitations that hinder the development of this technology for extensive usage in agricultural systems. The variability among the members of Pseudomonas spp. draws attention to the huge research interest in this genus. There is a need to explore the potential of native Pseudomonas spp. as biocontrol agents and to use them in biopesticide development to support sustainable agriculture.
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Affiliation(s)
- Najaf Mehmood
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Mahnoor Saeed
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Sana Zafarullah
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Sajjad Hyder
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Zarrin Fatima Rizvi
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Amjad Shahzad Gondal
- Department
of Plant Pathology, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Nuzhat Jamil
- Department
of Botany, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Rashid Iqbal
- Department
of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur Pakistan, Bahawalpur 63100, Pakistan
| | - Baber Ali
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sezai Ercisli
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- HGF
Agro, Ata Teknokent, Erzurum TR-25240, Türkiye
| | - Muhammed Kupe
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
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10
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Lu C, Hei R, Song X, Fan Z, Guo D, Luo J, Ma Y. Metal oxide nanoparticles inhibit nitrogen fixation and rhizosphere colonization by inducing ROS in associative nitrogen-fixing bacteria Pseudomonas stutzeri A1501. CHEMOSPHERE 2023:139223. [PMID: 37327828 DOI: 10.1016/j.chemosphere.2023.139223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/26/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the increasing-used MONPs, including TiO2, Al2O3, and ZnO nanoparticles (TiO2NP, Al2O3NP, and ZnONP, respectively), on nitrogenase activity was studied at the concentrations ranging from 0 to 10 mg L-1 using associative rhizosphere nitrogen-fixing bacteria Pseudomonas stutzeri A1501. Nitrogen fixation capacity was inhibited by MONPs in an increasing degree of TiO2NP < Al2O3NP < ZnONP. Realtime qPCR analysis showed that the expressions of nitrogenase synthesis-related genes, including nifA and nifH, were inhibited significantly when MONPs were added. MONPs could cause the explosion of intracellular ROS, and ROS not only changed the permeability of the membrane but also inhibited the expression of nifA and biofilm formation on the root surface. The repressed nifA gene could inhibit transcriptional activation of nif-specific genes, and ROS reduced the biofilm formation on the root surface which had a negative effect on resisting environmental stress. This study demonstrated that MONPs, including TiO2NP, Al2O3NP, and ZnONP, inhibited bacterial biofilm formation and nitrogen fixation in the rice rhizosphere, which might have a negative effect on the nitrogen cycle in bacteria-rice system.
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Affiliation(s)
- Chao Lu
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| | - Ruonan Hei
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Xiuchao Song
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Zixian Fan
- GenScript Biotech, Nanjing, 210003, China
| | - Dejie Guo
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China
| | - Jia Luo
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
| | - Yan Ma
- National Agricultural Experimental Station for Agricultural Environment, Luhe, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, PR China.
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11
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Hao F, Chen S, Yuan H, Yan X, Yang D. Effects of Rhizosphere Microorganisms on the Uptake and Translocation of Organic Compounds in Maize Seedlings. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6830-6837. [PMID: 37097808 DOI: 10.1021/acs.jafc.3c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The plant root is a key pathway to absorb insecticides from soil and is colonized by beneficial and pathogenic microbial communities. Our study demonstrated that colonizing roots by nitrogen-fixing bacterium Pseudomonas stutzeri and pathogenic Fusarium graminearum and Pythium ultimum increased the uptake of insecticides into maize roots from soil. An alteration in the permeability of root cells contributed to this increased uptake. For the subsequent root-to-shoot translocation, the relationship between translocation and log P of the compound satisfied a Gaussian distribution. Relatively beneficial P. stutzeri can promote maize seedling growth and increase translocation, whereas Fusarium and Pythium pathogens can retard the seedling growth and reduce the translocation. Furthermore, the relationship between the concentration difference (difference of an insecticide from inoculation treatment to control) and log P also showed a Gaussian distribution. The maximum concentration difference from the Gaussian equation can be applied to assess the capacity of rhizosphere microorganisms to influence translocation.
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Affiliation(s)
- Fengjiao Hao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Shuning Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Huizhu Yuan
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Xiaojing Yan
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Daibin Yang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
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12
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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13
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Oyetibo GO, Adebusoye SA, Ilori MO, Amund OO. Heavy metals assessment of ecosystem polluted with wastewaters and taxonomic profiling of multi-resistant bacteria with potential for petroleum hydrocarbon catabolism in nitrogen-limiting medium. World J Microbiol Biotechnol 2023; 39:84. [PMID: 36693977 DOI: 10.1007/s11274-023-03524-4] [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: 06/01/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
The coexistence of heavy metals (HMs) and petroleum hydrocarbons (PHs) exacerbates ecotoxicity and impair the drivers of eco-functionalities that stimulate essential nutrients for the productivity of the impacted environment. Profiling the bacteria that stem the ecological impact via HMs sequestration and PHs catabolism with nitrogen fixation is imperative to bioremediation of the polluted sites. The sediment of site that was consistently contaminated with industrial wastewaters was analysed for ecological toxicants and the bacterial strains that combined HMs resistance with PHs catabolism in a nitrogen-limiting system were isolated from the sediment and characterized. The geochemistry of the samples revealed the co-occurrence of the above-benchmark concentrations of HMs with the derivatives of hydrocarbons. Notwithstanding, nickel and mercury (with 5% each of the total metal concentrations in the polluted site) exhibited probable effect concentrations on the biota and thus hazardous to the ecosystem. Approx. 31% of the bacterial community, comprising unclassified Planococcaceae, unclassified Bradyrhizobiaceae, Rhodococcus, and Bacillus species, resisted 160 µmol Hg2+ in the nitrogen-limiting system within 24 h post-inoculation. The bacterial strains adopt volatilization, and sometimes in combination with adsorption/bioaccumulation strategies to sequester Hg2+ toxicity while utilizing PHs as sources of carbon and energy. Efficient metabolism of petroleum biomarkers (> 87%) and Hg2+ sequestration (≥ 75% of 40 µmol Hg2+) displayed by the selected bacterial strains portend the potential applicability of the bacilli for biotechnological restoration of the polluted site.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria. .,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.
| | - Sunday A Adebusoye
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Matthew O Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Institute of Maritime Studies, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, 101017, Lagos State, Nigeria.,Office of the Vice Chancellor, Elizade University, Ilara-Mokin, Ondo State, Nigeria
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14
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Lv F, Zhan Y, Lu W, Ke X, Shao Y, Ma Y, Zheng J, Yang Z, Jiang S, Shang L, Ma Y, Cheng L, Elmerich C, Yan Y, Lin M. Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri. iScience 2022; 25:105663. [PMID: 36505936 PMCID: PMC9730152 DOI: 10.1016/j.isci.2022.105663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Ke
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zheng
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhimin Yang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liguo Shang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yao Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | | | - Yongliang Yan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Corresponding author
| | - Min Lin
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Corresponding author
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15
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Alam KM, Yan Y, Lin M, Islam MA, Gaber A, Hossain A. Insight rifampicin-resistant (rpoB) mutation in Pseudomonas stutzeri leads to enhance the biosynthesis of secondary metabolites to survive against harsh environments. Arch Microbiol 2022; 204:437. [PMID: 35768665 DOI: 10.1007/s00203-022-03064-9] [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: 02/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 11/02/2022]
Abstract
In this study, a wild-type and five distinct rifampicin-resistant (Rifr) rpoB mutants of Pseudomonas stutzeri (i.e., Q518R, D521Y, D521V, H531R and I614T) ability were investigated against harsh environments (particularly nutritional complexity). Among these, the robust Rifr phenotype of P. Stutzeri was associated only with base replacements of the amino deposits. The use of carboxylic and amino acids significantly increased in various Rifr mutants than that of wild type of P. stutzeri. The assimilation of carbon and nitrogen (N) sources of Rifr mutants' confirmed that the organism maintains the adaptation in nutritionally complex environments. Acetylene reduction assay at different times also found the variability for N-fixation in all strains. Among them, the highest nitrogenase activity was determined in mutant 'D521V'. The assimilation of carbon and nitrogen sources of P. stutzeri and its Rifr mutants ensures that the organism maintains the adaptability in nutritionally complex environments through fixing more nitrogen.
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Affiliation(s)
- Khandakar Mohiul Alam
- Soils and Nutrition Division, Bangladesh Sugarcrop Research Institute, Pabna, 6620, Bangladesh
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Md Ariful Islam
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Pabna, 6600, Bangladesh
| | - Ahmed Gaber
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh.
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16
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Shao Y, Yin C, Lv F, Jiang S, Wu S, Han Y, Xue W, Ma Y, Zheng J, Zhan Y, Ke X, Lu W, Lin M, Shang L, Yan Y. The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of pslA in Pseudomonas stutzeri A1501. Genes (Basel) 2022; 13:genes13050867. [PMID: 35627252 PMCID: PMC9141998 DOI: 10.3390/genes13050867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas stutzeri A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the Pseudomonas genus; however, the function of AlgU in P. stutzeri A1501 is still unclear. In this work, we mainly investigated the role of algU in EPS production, biofilm formation and nitrogenase activity in A1501. The algU mutant ΔalgU showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the ΔalgU mutant. The transcriptional level of pslA, a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the algU mutant and was upregulated by 2.8-fold in the algU-overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of pslA. The DNase I footprinting assays indicated that AlgU could directly bind to the pslA promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the pslA promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of pslA, and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
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Affiliation(s)
- Yahui Shao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Changyan Yin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Fanyang Lv
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shanshan Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shaoyu Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yueyue Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yiyuan Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Juan Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Liguo Shang
- School of Basic Medicine, GuangXi University of Chinese Medicine, Nanning 530200, China
- Correspondence: (L.S.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
- Correspondence: (L.S.); (Y.Y.)
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17
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Mokabel S, Olama Z, Ali S, El-Dakak R. The Role of Plant Growth Promoting Rhizosphere Microbiome as Alternative Biofertilizer in Boosting Solanum melongena L. Adaptation to Salinity Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050659. [PMID: 35270129 PMCID: PMC8912713 DOI: 10.3390/plants11050659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 05/07/2023]
Abstract
Recent ecological perturbations are presumed to be minimized by the application of biofertilizers as a safe alternative to chemical fertilizers. The current study aims to use bioinoculum (I) as an alternative biofertilizer and to alleviate salinity stress in the cultivar Solanum melongena L. Baldi. The salinity drench was 200 mM NaCl (S), which was used with different treatments (0; I; S; S + I) in pots prefilled with clay and sand (1:2). Results showed that salinity stress inhibited both plant fresh and dry weights, water content, and photosynthetic pigments. The content of root spermine (Spm), spermidine (Spd), and puterscine (Put) decreased. However, addition of the bioinoculum to salt-treated plants increased pigment content (80.35, 39.25, and 82.44% for chl a, chl b, and carotenoids, respectively). Similarly, K+, K+/Na+, Ca2+, P, and N contents were significantly enhanced. Increases were recorded for Spm + Spd and Put in root and shoot (8.4-F, 1.6-F and 2.04-F, 2.13-F, respectively). RAPD PCR showed gene expression upregulation of photosystem II D2 protein, glutathione reductase, glutathione-S-transferase, protease I, and protease II. The current work recommends application of the selected bioinoculum as a green biofertilizer and biopesticide. Additionally, the studied eggplant cultivar can be regarded as a source of salt tolerance genes in agricultural fields.
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Affiliation(s)
- Souhair Mokabel
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
| | - Zakia Olama
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
| | - Safaa Ali
- Nucleic Acid Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications (SRTA-City), Alexandria 21934, Egypt;
| | - Rehab El-Dakak
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt; (S.M.); (Z.O.)
- Correspondence:
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18
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Roychoudhury T, Ray B, Seal A. Metabolically dependent consortia in biofilm: A new horizon for green agriculture. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Pseudomonas mediated nutritional and growth promotional activities for sustainable food security. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100084. [PMID: 34917993 PMCID: PMC8645841 DOI: 10.1016/j.crmicr.2021.100084] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Fluorescent and non-fluorescent species of Pseudomonas are important for plant growth promotion, phytopathogenic control and plant disease management. Pseudomonas belong to Pseudomonadaceae family (10 groups on the basis of rRNA-DNA hybridization) classified into 6-subgroups of rRNA gene homology and RFLP. Pseudomonas species produce antagonistic mechanism such as ISR and compounds like cell wall degradation enzymes, and antibiotics to maintain a mutualistic relationship with the associated plant. Pseudomonas sp. synthesize auxins having properties similar to phytohormones like IAA, which act as signaling molecules for regulating plant growth.
Numerous microbial communities show synergistic and antagonistic interactions among themselves, resulting in benefit and harm to either or both the associated members. The association holds accountability for nutrients recycling and energy drift, resulting in the availability of macronutrients unavailable and insoluble forms of rhizospheric nutrients, crucial for vital processes in plants, e.g., act as co-factors of various phyto-enzyme and redox mediators. Plant growth promoting rhizobacteria are known to enhance plant growth by increasing these macronutrients availability during their plant root colonization. In comparison to any other genera, Pseudomonas is the most favored bioinoculant due to its significant properties in both plant growth and phytopathogen control during its synergistic association with the host plant. These properties include siderophore production, phosphate solubilization, nitrogen fixation, phenazines, antibiotics, and induced systemic resistance carried out by various Pseudomonas species like Pseudomonas fluorescens, Pseudomonas putida, and Pseudomonas syringae. The association of Pseudomonas with crop plants procures several secretory and electron-based feedback mechanisms in order to regulate the plant growth and phytopathogen control activities through the secretion of several phytohormones (auxins, gibberellins, Indole-3-acetic acid), secondary metabolites (flavonoids) and enzymes (aminocyclopropane-1-carboxylate, phenylalanine ammonia-lyase). Ecologically significant applications of Pseudomonas in biocontrol and bioaugmentation are crucial for maintaining food security.
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Niepsch D, Clarke LJ, Tzoulas K, Cavan G. Distinguishing atmospheric nitrogen compounds (nitrate and ammonium) in lichen biomonitoring studies. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:2021-2036. [PMID: 34870671 DOI: 10.1039/d1em00274k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen speciation, i.e. distinguishing nitrate (NO3-) and ammonium (NH4+), is commonly undertaken in soil studies, but has not been conducted extensively for lichens. Lichen total nitrogen contents (N wt%) reflect airborne atmospheric nitrogen loadings, originating from anthropogenic sources (e.g. vehicular and agricultural/livestock emissions). Albeit nitrogen being an essential lichen nutrient, nitrogen compound (i.e. NO3- and NH4+) concentrations in the atmosphere can have deleterious effects on lichens. Moreover, N wt% do not provide information on individual nitrogen compounds, i.e. NO3- and NH4+ which are major constituents of atmospheric particulate matter (e.g. PM10 and PM2.5). This study presents a novel method to separate and quantify NO3- and NH4+ extracted from lichen material. An optimal approach was identified by testing different strengths and volumes of potassium chloride (KCl) solutions and variable extraction times, i.e. the use of 3% KCl for 6 hours can achieve a same-day extraction and subsequent ion chromatography (IC) analysis for reproducible lichen nitrate and ammonium concentration determinations. Application of the method was undertaken by comparing urban and rural Xanthoria parietina samples to investigate the relative importance of the two nitrogen compounds in contrasting environments. Findings presented showed that lichen nitrogen compound concentrations varied in rural and urban X. parietina samples, suggesting different atmospheric nitrogen loadings from potentially different sources (e.g. agricultural and traffic) and varied deposition patterns (e.g. urban layout impacts). Despite potential impacts of nitrogen compounds on lichen metabolism, the approach presented here can be used for quantification of two different nitrogen compounds in lichen biomonitoring studies that will provide specific information on spatial and temporal variability of airborne NO3- and NH4+ concentrations that act as precursors of particulate matter, affecting air quality and subsequently human health.
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Affiliation(s)
- Daniel Niepsch
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK.
| | - Leon J Clarke
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK.
| | - Konstantinos Tzoulas
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK.
| | - Gina Cavan
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, M1 5GD, UK.
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21
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Liu X, Liu Y, Wang Y, Wang D, Johnson KS, Xie Z. The Hypoxia-Associated Localization of Chemotaxis Protein CheZ in Azorhizorbium caulinodans. Front Microbiol 2021; 12:731419. [PMID: 34737727 PMCID: PMC8563088 DOI: 10.3389/fmicb.2021.731419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Spatial organization of chemotactic proteins is important for cooperative response to external stimuli. However, factors affecting the localization dynamics of chemotaxis proteins are less studied. According to some reports, the polar localization of chemotaxis system I is induced by hypoxia and starvation in Vibrio cholerae. However, in V. cholerae, the chemotaxis system I is not involved in flagellum-mediated chemotaxis, and it may play other alternative cellular functions. In this study, we found that the polar localization of CheZ, a phosphatase regulating chemotactic movement in Azorhizobium caulinodans ORS571, can also be affected by hypoxia and cellular energy-status. The conserved phosphatase active site D165 and the C-terminus of CheZ are essential for the energy-related localization, indicating a cross link between hypoxia-related localization changes and phosphatase activity of CheZ. Furthermore, three of five Aer-like chemoreceptors containing PAS domains participate in the cellular localization of CheZ. In contrast to carbon starvation, free-living nitrogen fixation can alleviate the role of nitrogen limitation and hypoxia on polar localization of CheZ. These results showed that the localization changes induced by hypoxia might be a strategy for bacteria to adapt to complex environment.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yixuan Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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Rios-Galicia B, Villagómez-Garfias C, De la Vega-Camarillo E, Guerra-Camacho JE, Medina-Jaritz N, Arteaga-Garibay RI, Villa-Tanaca L, Hernández-Rodríguez C. The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria. 3 Biotech 2021; 11:447. [PMID: 34631348 DOI: 10.1007/s13205-021-02983-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/04/2021] [Indexed: 01/02/2023] Open
Abstract
The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co2+, Fe3+, Mo2 +, V5+, Zn2+), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.
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Affiliation(s)
- Bibiana Rios-Galicia
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Catalina Villagómez-Garfias
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Esaú De la Vega-Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Jairo Eder Guerra-Camacho
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Nora Medina-Jaritz
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - Ramón Ignacio Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Boulevard de la Biodiversidad No. 400, Rancho Las Cruces, 47600 Tepatitlán de Morelos, Jalisco Mexico
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomás, 11340 Ciudad de México, Mexico
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Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future. BIOLOGY 2021; 10:biology10100961. [PMID: 34681060 PMCID: PMC8533330 DOI: 10.3390/biology10100961] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023]
Abstract
Simple Summary Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today. Abstract Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.
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Rudra B, Gupta RS. Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546867 DOI: 10.1099/ijsem.0.005011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas. Within this large cluster 18-30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae. This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans. Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas, which has priority over the name Oblitimonas. We are also proposing transfer of the deep-branching Pseudomonas hussainii, for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas, respectively. In addition, we are also reclassifying 'Pseudomonas acidophila' as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).
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Affiliation(s)
- Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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Master regulator NtrC controls the utilization of alternative nitrogen sources in Pseudomonas stutzeri A1501. World J Microbiol Biotechnol 2021; 37:177. [PMID: 34524580 PMCID: PMC8443478 DOI: 10.1007/s11274-021-03144-w] [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: 06/11/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022]
Abstract
Pseudomonas stutzeri A1501 is a model strain used to study associative nitrogen fixation, and it possesses the nitrogen regulatory NtrC protein in the core genome. Nitrogen sources represent one of the important factors affecting the efficiency of biological nitrogen fixation in the natural environment. However, the regulation of NtrC during nitrogen metabolism in P. stutzeri A1501 has not been clarified. In this work, a phenotypic analysis of the ntrC mutant characterized the roles of NtrC in nitrogen metabolism and the oxidative stress response of P. stutzeri A1501. To systematically identify NtrC-controlled gene expression, RNA-seq was performed to further analyse the gene expression differences between the wild-type strain and the ∆ntrC mutant under nitrogen fixation conditions. A total of 1431 genes were found to be significantly altered by ntrC deletion, among which 147 associative genes had NtrC-binding sites, and the pathways for nitrogen fixation regulation, nitrogenous compound acquisition and catabolism and nitrate assimilation were discussed. Furthermore, the oxidative stress-related gene (katB), which was upregulated by ntrC deletion, was suggested to be a potential target gene of NtrC, thus highlighting the importance of NtrC in nitrogenase protection against oxygen damage. Based on these findings, we propose that NtrC is a high-ranking element in the regulatory network of P. stutzeri A1501 that controls a variety of nitrogen metabolic and oxidative stress responsive traits required for adaptation to complex rhizosphere environments.
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A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri. NPJ Biofilms Microbiomes 2021; 7:54. [PMID: 34210981 PMCID: PMC8249394 DOI: 10.1038/s41522-021-00230-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing biofilms remain largely unknown. Here, we examined the roles of multiple signalling systems in the regulation of biofilm formation by root-associated diazotrophic P. stutzeri A1501. Physiological analysis, construction of mutant strains and microscale thermophoresis experiments showed that RpoN is a regulatory hub coupling nitrogen fixation and biofilm formation by directly activating the transcription of pslA, a major gene involved in the synthesis of the Psl exopolysaccharide component of the biofilm matrix and nifA, the transcriptional activator of nif gene expression. Genetic complementation studies and determination of the copy number of transcripts by droplet digital PCR confirmed that the regulatory ncRNA RsmZ serves as a signal amplifier to trigger biofilm formation by sequestering the translational repressor protein RsmA away from pslA and sadC mRNAs, the latter of which encodes a diguanylate cyclase that synthesises c-di-GMP. Moreover, RpoS exerts a braking effect on biofilm formation by transcriptionally downregulating RsmZ expression, while RpoS expression is repressed posttranscriptionally by RsmA. These findings provide mechanistic insights into how the Rpo/Gac/Rsm regulatory networks fine-tune nitrogen-fixing biofilm formation in response to the availability of nutrients.
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Bueno Batista M, Brett P, Appia-Ayme C, Wang YP, Dixon R. Disrupting hierarchical control of nitrogen fixation enables carbon-dependent regulation of ammonia excretion in soil diazotrophs. PLoS Genet 2021; 17:e1009617. [PMID: 34111137 PMCID: PMC8219145 DOI: 10.1371/journal.pgen.1009617] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/22/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022] Open
Abstract
The energetic requirements for biological nitrogen fixation necessitate stringent regulation of this process in response to diverse environmental constraints. To ensure that the nitrogen fixation machinery is expressed only under appropriate physiological conditions, the dedicated NifL-NifA regulatory system, prevalent in Proteobacteria, plays a crucial role in integrating signals of the oxygen, carbon and nitrogen status to control transcription of nitrogen fixation (nif) genes. Greater understanding of the intricate molecular mechanisms driving transcriptional control of nif genes may provide a blueprint for engineering diazotrophs that associate with cereals. In this study, we investigated the properties of a single amino acid substitution in NifA, (NifA-E356K) which disrupts the hierarchy of nif regulation in response to carbon and nitrogen status in Azotobacter vinelandii. The NifA-E356K substitution enabled overexpression of nitrogenase in the presence of excess fixed nitrogen and release of ammonia outside the cell. However, both of these properties were conditional upon the nature of the carbon source. Our studies reveal that the uncoupling of nitrogen fixation from its assimilation is likely to result from feedback regulation of glutamine synthetase, allowing surplus fixed nitrogen to be excreted. Reciprocal substitutions in NifA from other Proteobacteria yielded similar properties to the A. vinelandii counterpart, suggesting that this variant protein may facilitate engineering of carbon source-dependent ammonia excretion amongst diverse members of this family.
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Affiliation(s)
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich, United Kingdom
| | - Corinne Appia-Ayme
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Li Q, He X, Liu P, Zhang H, Wang M, Chen S. Synthesis of nitrogenase by Paenibacillus sabinae T27 in presence of high levels of ammonia during anaerobic fermentation. Appl Microbiol Biotechnol 2021; 105:2889-2899. [PMID: 33745008 DOI: 10.1007/s00253-021-11231-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 01/19/2023]
Abstract
Biological nitrogen fixation is usually inhibited by fixed nitrogen. Paenibacillus sabinae T27, a Gram-positive, spore-forming diazotroph, possesses high nitrogenase activity and has 3 copies of nifH (nifH, nifH2, nifH3), a copy of nifDK, and multiple nifHDK-like genes. In this study, we found that P. sabinae T27 showed nitrogenase activities not only in low (0-3 mM) concentrations of NH4+ but also in high (30-300 mM) concentrations of NH4+, no matter whether this bacterium was grown in a flask or in a fermenter on scale cultivation. qRT-PCR and western blotting analyses supported that Fe protein and MoFe protein were synthesized under both low (0-3 mM) and high (30-300 mM) concentrations of NH4+. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed that MoFe protein was encoded by nifDK and Fe protein was encoded by both nifH and nifH2. The cross-reaction suggested the purified Fe and MoFe components from P. sabinae T27 grown in both nitrogen-limited and nitrogen-excess conditions were active. This is the first time to report that diazotrophs show nitrogenase activity in presence of high (30-300 mM) concentrations of NH4+. Our study will provide a clue for studying the mechanisms of nitrogen fixation in presence of the high concentration of NH4+. KEY POINTS: • P. sabinae T27 can synthesize active nitrogenase in presence of high levels of ammonia. •Fe and MoFe proteins of nitrogenase purified in absence of ammonia are the same as those purified from the high concentration of ammonia. • Fe protein is encoded by nifH and nifH2, and MoFe protein is encoded by nifDK.
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Affiliation(s)
- Qin Li
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Xiaojuan He
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Pengxi Liu
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Haowei Zhang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Mingyang Wang
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People's Republic of China.
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Bioelectrochemical Fixation of Nitrogen to Extracellular Ammonium by Pseudomonas stutzeri. Appl Environ Microbiol 2021; 87:e0199820. [PMID: 33310714 DOI: 10.1128/aem.01998-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diazotrophs can produce bioavailable nitrogen from inert N2 gas by bioelectrochemical nitrogen fixation (e-BNF), which is emerging as an energy-saving and highly selective strategy for agriculture and industry. However, current e-BNF technology is impeded by requirements for NH4+ assimilation inhibitors to facilitate intracellular ammonia secretion and precious metal catalysts to generate H2 as the energy-carrying intermediate. Here, we initially demonstrate inhibitor- and catalystless extracellular NH4+ production by the diazotroph Pseudomonas stutzeri A1501 using an electrode as the sole electron donor. Multiple lines of evidence revealed that P. stutzeri produced 2.32 ± 0.25 mg/liter extracellular NH4+ at a poised potential of -0.3 V (versus standard hydrogen electrode [SHE]) without the addition of inhibitors or expensive catalysts. The electron uptake mechanism was attributed to the endogenous electron shuttle phenazine-1-carboxylic acid, which was excreted by P. stutzeri and mediated electron transfer from electrodes into cells to directly drive N2 fixation. The faradaic efficiency was 20% ± 3%, which was 2 to 4 times that of previous e-BNF attempts using the H2-mediated pathway. This study reports a diazotroph capable of producing secretable NH4+ via extracellular electron uptake, which has important implications for optimizing the performance of e-BNF systems and exploring the novel nitrogen-fixing mode of syntrophic microbial communities in the natural environment. IMPORTANCE Ammonia greatly affects global ecology, agriculture, and the food industry. Diazotrophs with an enhanced capacity of extracellular NH4+ excretion have been proven to be more beneficial to the growth of microalgae and plants, whereas most previously reported diazotrophs produce intracellular organic nitrogen in the absence of chemical suppression and genetic manipulation. Here, we demonstrate that Pseudomonas stutzeri A1501 is capable of extracellular NH4+ production without chemical suppression or genetic manipulation when the extracellular electrode is used as the sole electron donor. We also reveal the electron uptake pathway from the extracellular electron-donating partner to P. stutzeri A1501 via redox electron shuttle phenazines. Since both P. stutzeri A1501 and potential electron-donating partners (such as electroactive microbes and natural semiconductor minerals) are abundant in diverse soils and sediments, P. stutzeri A1501 has broader implications on the improvement of nitrogen fertilization in the natural environment.
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Draft Genome Sequence of Pseudomonas sp. Strain T2.31D-1, Isolated from a Drilling Core Sample Obtained 414 Meters below Surface in the Iberian Pyrite Belt. Microbiol Resour Announc 2021; 10:10/1/e01165-20. [PMID: 33414307 PMCID: PMC8407707 DOI: 10.1128/mra.01165-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We report the draft genome of Pseudomonas sp. strain T2.31D-1, which was isolated from a drilling core sample obtained 414 m below surface in the Iberian Pyrite Belt. The genome consists of a 4.7-Mb chromosome, with 4,428 coding sequences, one rRNA operon, and 59 tRNA genes, and a 31.8-kb plasmid. We report the draft genome of Pseudomonas sp. strain T2.31D-1, which was isolated from a drilling core sample obtained 414 m below surface in the Iberian Pyrite Belt. The genome consists of a 4.7-Mb chromosome with 4,428 coding sequences, 1 rRNA operon, 59 tRNA genes, and a 31.8-kb plasmid.
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Lami MJ, Adler C, Caram-Di Santo MC, Zenoff AM, de Cristóbal RE, Espinosa-Urgel M, Vincent PA. Pseudomonas stutzeri MJL19, a rhizosphere-colonizing bacterium that promotes plant growth under saline stress. J Appl Microbiol 2020; 129:1321-1336. [PMID: 32367524 DOI: 10.1111/jam.14692] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023]
Abstract
AIMS The aim of this study was to find and use rhizobacteria able to confer plants advantages to deal with saline conditions. METHODS AND RESULTS We isolated 24 different bacterial species from the rhizosphere of halophyte plants growing in Santiago del Estero, Argentina salt flat. Four strains were selected upon their ability to grow in salinity and their biochemical traits associated with plant growth promotion. Next, we tested the adhesion on soybean seeds surface and root colonization with the four selected isolates. Isolate 19 stood out from the rest and was selected for further experiments. This strain showed positive chemotaxis towards soybean root exudates and a remarkable ability to form biofilm both in vitro conditions and on soybean roots. Interestingly, this trait was enhanced in high saline conditions, indicating the extremely adapted nature of the bacterium to high salinity. In addition, this strain positively impacted on seed germination, plant growth and general plant health status also under saline stress. CONCLUSIONS A bacterium isolate with outstanding ability to promote seed germination and plant growth under saline conditions was found. SIGNIFICANCE AND IMPACT OF THE STUDY The experimental approach allowed us to find a suitable bacterial candidate for a biofertilizer intended to alleviate saline stress on crops. This would allow the use of soil now considered inadequate for agriculture and thus prevent further advancement of agriculture frontiers into areas of environmental value.
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Affiliation(s)
- M J Lami
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
- Department of Environmental Protection, Estación Experimental Del Zaidín, CSIC, Granada, Spain
| | - C Adler
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
| | - M C Caram-Di Santo
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
| | - A M Zenoff
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
| | - R E de Cristóbal
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
| | - M Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental Del Zaidín, CSIC, Granada, Spain
| | - P A Vincent
- Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET-UNT), Instituto de Química Biológica 'Dr. Bernabé Bloj', Tucumán, Argentina
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Lu C, Yang Z, Liu J, Liao Q, Ling W, Waigi MG, Odinga ES. Chlorpyrifos inhibits nitrogen fixation in rice-vegetated soil containing Pseudomonas stutzeri A1501. CHEMOSPHERE 2020; 256:127098. [PMID: 32470732 DOI: 10.1016/j.chemosphere.2020.127098] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/30/2020] [Accepted: 05/14/2020] [Indexed: 05/28/2023]
Abstract
Chlorpyrifos, a common organophosphorus pesticide, is widely used for agricultural pest control and can inhibit nitrogen-fixing bacteria biomass in paddy. In this study, the additions of chlorpyrifos (1 and 8 mg kg-1) to soil, with or without Pseudomonas stutzeri A1501, resulted in a significant decrease in nitrogen fixation, despite insignificant effects on the abundances of P. stutzeri A1501 and bacteria in soil. Toxic effect of chlorpyrifos on P. stutzeri A1501 nitrogenase activity in medium was also observed, accompanied by a significant reduction in the expression of nitrogen-fixing related genes (nifA and nifH). Furthermore, rhizosphere colonization and biofilm formation by P. stutzeri A1501 were repressed by chlorpyrifos, leading to decreased nitrogenase activity in the rhizosphere. Biofilm formation in medium was inhibited by bacterial hyperkinesis and reduction of extracellular polymeric substance, including exopolysaccharides and proteins. Together, these findings showed that chlorpyrifos-induced production of reactive oxygen species (ROS) which was directly responsible for reduced nitrogenase activity in the medium, soil, and rhizosphere by inhibiting the expressions of nitrogen-fixing related genes. Furthermore, the inhibition of biofilm formation by chlorpyrifos or ROS likely aggravated the reduction in rhizospherere nitrogenase activity. These findings provide potentially valuable insights into the toxicity of chlorpyrifos on nitrogen-fixing bacteria and its mechanisms. Furthermore, for sustainable rice production, it is necessary to evaluate whether other pesticides affect nitrogen fixation and select pesticides that do not inhibit nitrogen fixation.
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Affiliation(s)
- Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhimin Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qihang Liao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Emmanuel Stephen Odinga
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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Mahajan SG, Nandre VS, Salunkhe RC, Shouche YS, Kulkarni MV. Chemotaxis and physiological adaptation of an indigenous abiotic stress tolerant plant growth promoting Pseudomonas stutzeri: Amelioration of salt stress to Cicer arietinum. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Liu Y, Shang L, Zhan Y, Lin M, Liu Z, Yan Y. Genome-Wide Analysis of Sugar Transporters Identifies the gtsA Gene for Glucose Transportation in Pseudomonas stutzeri A1501. Microorganisms 2020; 8:microorganisms8040592. [PMID: 32325908 PMCID: PMC7232493 DOI: 10.3390/microorganisms8040592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various carbon sources. However, sugars are not a preferred carbon source for P. stutzeri A1501. The P. stutzeri A1501 genome has been sequenced, allowing for the homology-based in silico identification of genes potentially encoding sugar-transport systems by using established microbial sugar transporters as a template sequence. Genomic analysis revealed that there were 10 sugar transporters in P. stutzeri A1501, most of which belong to the ATP-binding cassette (ABC) family (5/10); the others belong to the phosphotransferase system (PTS), major intrinsic protein (MIP) family, major facilitator superfamily (MFS) and the sodium solute superfamily (SSS). These systems might serve for the import of glucose, galactose, fructose and other types of sugar. Growth analysis showed that the only effective medium was glucose and its corresponding metabolic system was relatively complete. Notably, the loci of glucose metabolism regulatory systems HexR, GltR/GtrS, and GntR were adjacent to the transporters ABCMalEFGK, ABCGtsABCD, and ABCMtlEFGK, respectively. Only the ABCGtsABCD expression was significantly upregulated under both glucose-sufficient and -limited conditions. The predicted structure and mutant phenotype data of the key protein GtsA provided biochemical evidence that P. stutzeri A1501 predominantly utilized the ABCGtsABCD transporter for glucose uptake. We speculate that gene absence and gene diversity in P. stutzeri A1501 was caused by sugar-deficient environmental factors and hope that this report can provide guidance for further analysis of similar bacterial lifestyles.
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Affiliation(s)
- Yaqun Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Liguo Shang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Zhu Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Correspondence: (Z.L.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
- Correspondence: (Z.L.); (Y.Y.)
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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Hu G, Hu T, Zhan Y, Lu W, Lin M, Huang Y, Yan Y. NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli. AMB Express 2019; 9:156. [PMID: 31555995 PMCID: PMC6761216 DOI: 10.1186/s13568-019-0881-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) can finely control the expression of target genes at the posttranscriptional level in prokaryotes. Regulatory small RNAs (sRNAs) designed to control target gene expression for applications in metabolic engineering and synthetic biology have been successfully developed and used. However, the effect on the heterologous expression of species- or strain-specific ncRNAs in other bacterial strains remains poorly understood. In this work, a Pseudomonas stutzeri species-specific regulatory ncRNA, NfiS, which has been shown to play an important role in the response to oxidative stress as well as osmotic stress in P. stutzeri A1501, was cloned and transferred to the Escherichia coli strain Trans10. Recombinant NfiS-expressing E. coli, namely, Trans10-nfiS, exhibited significant enhancement of tolerance to oxidative stress. To map the possible gene regulatory networks mediated by NfiS in E. coli under oxidative stress, a microarray assay was performed to delineate the transcriptomic differences between Trans10-nfiS and wild-type E. coli under H2O2 shock treatment conditions. In all, 1184 genes were found to be significantly altered, and these genes were divided into mainly five functional categories: stress response, regulation, metabolism related, transport or membrane protein and unknown function. Our results suggest that the P. stutzeri species-specific ncRNA NfiS acts as a regulator that integrates adaptation to H2O2 with other cellular stress responses and helps protect E. coli cells against oxidative damage.
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The Pseudomonas stutzeri-Specific Regulatory Noncoding RNA NfiS Targets katB mRNA Encoding a Catalase Essential for Optimal Oxidative Resistance and Nitrogenase Activity. J Bacteriol 2019; 201:JB.00334-19. [PMID: 31262840 PMCID: PMC6755748 DOI: 10.1128/jb.00334-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas stutzeri A1501 is a versatile nitrogen-fixing bacterium capable of living in diverse environments and coping with various oxidative stresses. NfiS, a regulatory noncoding RNA (ncRNA) involved in the control of nitrogen fixation in A1501, was previously shown to be required for optimal resistance to H2O2; however, the precise role of NfiS and the target genes involved in the oxidative stress response is entirely unknown. In this work, we systematically investigated the NfiS-based mechanisms underlying the response of this bacterium to H2O2 at the cellular and molecular levels. A mutant strain carrying a deletion of nfiS showed significant downregulation of oxidative stress response genes, especially katB, a catalase gene, and oxyR, an essential regulator for transcription of catalase genes. Secondary structure prediction revealed two binding sites in NfiS for katB mRNA. Complementation experiments using truncated nfiS genes showed that each of two sites is functional, but not sufficient, for NfiS-mediated regulation of oxidative stress resistance and nitrogenase activities. Microscale thermophoresis assays further indicated direct base pairing between katB mRNA and NfiS at both sites 1 and 2, thus enhancing the half-life of the transcript. We also demonstrated that katB expression is dependent on OxyR and that both OxyR and KatB are essential for optimal oxidative stress resistance and nitrogenase activities. H2O2 at low concentrations was detoxified by KatB, leaving O2 as a by-product to support nitrogen fixation under O2-insufficient conditions. Moreover, our data suggest that the direct interaction between NfiS and katB mRNA is a conserved and widespread mechanism among P. stutzeri strains.IMPORTANCE Protection against oxygen damage is crucial for survival of nitrogen-fixing bacteria due to the extreme oxygen sensitivity of nitrogenase. This work exemplifies how the small ncRNA NfiS coordinates oxidative stress response and nitrogen fixation via base pairing with katB mRNA and nifK mRNA. Hence, NfiS acts as a molecular link to coordinate the expression of genes involved in oxidative stress response and nitrogen fixation. Our study provides the first insight into the biological functions of NfiS in oxidative stress regulation and adds a new regulation level to the mechanisms that contribute to the oxygen protection of the MoFe nitrogenase.
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NfiR, a New Regulatory Noncoding RNA (ncRNA), Is Required in Concert with the NfiS ncRNA for Optimal Expression of Nitrogenase Genes in Pseudomonas stutzeri A1501. Appl Environ Microbiol 2019; 85:AEM.00762-19. [PMID: 31076427 PMCID: PMC6606865 DOI: 10.1128/aem.00762-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
Biological nitrogen fixation is an energy-expensive process requiring the hydrolysis of 16 ATPs. Consequently, the expression of nif genes is highly regulated at both transcriptional and posttranscriptional levels through complex regulatory networks. Global regulation involves a number of regulatory proteins, such as the nif-specific activator NifA and the global nitrogen regulator NtrC, as well as various regulatory ncRNAs. We show that the two P. stutzeri ncRNAs, namely NfiS and NfiR (for nitrogen fixation condition-inducible ncRNA), optimize nitrogen fixation and environmental stress responses. NfiS and NfiR respond differently to various environmental signals and differ in their secondary structures. In addition, the two ncRNAs target the mRNAs of nifK and nifD, respectively. Such ncRNA-based posttranscriptional regulation of nitrogenase expression might be an evolved survival strategy, particularly in nitrogen-limiting environments. This study not only highlights the significant roles of regulatory ncRNAs in the coordination and fine tuning of various physiological processes but also provides a new paradigm for posttranscriptional regulation in nitrogen-fixing bacteria. Expression of nitrogenase genes (nifHDK) is strictly regulated at both transcriptional and posttranscriptional levels. Efficient nitrogenase activity requires maintaining sufficient levels of nif mRNAs, yet the underlying mechanism is not fully understood due to its complexity. We have previously shown that a novel regulatory noncoding RNA (ncRNA), NfiS, optimizes nitrogen fixation through targeting nifK mRNA in Pseudomonas stutzeri A1501. Here, we report the identification and characterization of a second ncRNA inducible under nitrogen fixation conditions (nitrogen-free and microaerobic conditions), termed NfiR (for nitrogen fixation condition-inducible ncRNA), the expression of which is dependent on two global regulators, NtrC and Hfq. Comparative phenotypic and proteomic analyses of an nfiR mutant identify a role of NfiR in regulating the expression of nitrogenase genes. Further microscale thermophoresis and genetic complementation showed that an 11-nucleotide (nt) sequence in the stem-loop structure of NfiR (nucleotides 12 to 22) pairs with its counterpart in the coding region of nifD mRNA (nucleotides 1194 to 1207) by eight nucleotides. Significantly, deletion of nfiR caused a 60% reduction of nitrogenase activity, and the half-life of nifD mRNA was reduced from 20 min for the wild type to 15 min for the ΔnfiR mutant. With regard to nitrogenase activity and stability of the nifD and nifK transcripts, phenotypes were more severe for the double deletion mutant lacking nfiR and nfiS, suggesting that NfiR, in concert with NfiS, optimizes nitrogenase production at the posttranscriptional level. IMPORTANCE Biological nitrogen fixation is an energy-expensive process requiring the hydrolysis of 16 ATPs. Consequently, the expression of nif genes is highly regulated at both transcriptional and posttranscriptional levels through complex regulatory networks. Global regulation involves a number of regulatory proteins, such as the nif-specific activator NifA and the global nitrogen regulator NtrC, as well as various regulatory ncRNAs. We show that the two P. stutzeri ncRNAs, namely NfiS and NfiR (for nitrogen fixation condition-inducible ncRNA), optimize nitrogen fixation and environmental stress responses. NfiS and NfiR respond differently to various environmental signals and differ in their secondary structures. In addition, the two ncRNAs target the mRNAs of nifK and nifD, respectively. Such ncRNA-based posttranscriptional regulation of nitrogenase expression might be an evolved survival strategy, particularly in nitrogen-limiting environments. This study not only highlights the significant roles of regulatory ncRNAs in the coordination and fine tuning of various physiological processes but also provides a new paradigm for posttranscriptional regulation in nitrogen-fixing bacteria.
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Raimi AR, Ezeokoli OT, Adeleke RA. High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment. 3 Biotech 2019; 9:108. [PMID: 30863692 DOI: 10.1007/s13205-019-1643-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/20/2019] [Indexed: 02/03/2023] Open
Abstract
The genetic and predicted functional diversity of bacterial communities in 12 commercial biofertiliser products were evaluated using high-throughput sequencing of the 16S rRNA gene. Proteobacteria, Firmicutes and Bacteroides dominated the bacterial communities, with the genera Pseudomonas, Lactobacillus, Bacillus, Bradyrhizobium and Rhizobium being prevalent. The manufacturer-specified species were detected in relatively high abundance in two of the products while a few or none of the specified species were detected in some products. A number of unspecified microbes were detected, including potential human and crop pathogens such as Alcaligenes, Clostridium, Escherichia-Shigella and Proteus. The functional prediction unravelled high prevalence of enzyme-coding genes such as nitrogenase, NifT, alkaline phosphatase and reductases of nitric oxide, nitrate and nitrite which contribute to nitrogen-fixation, phosphorus solubilisation and degradation of nitrates and nitrites. In addition, toxins such as leukocidin/hemolysin and colicin V protein that cause product quality damage were highly predicted in over 67% of the products. Overall, high-throughput sequence analysis of bacterial communities in biofertiliser products revealed that majority of the products were of poor quality. This result justifies the need for regular quality assessment and improvement in quality control systems during biofertiliser formulation.
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Jing X, Cui Q, Li X, Yin J, Ravichandran V, Pan D, Fu J, Tu Q, Wang H, Bian X, Zhang Y. Engineering Pseudomonas protegens Pf-5 to improve its antifungal activity and nitrogen fixation. Microb Biotechnol 2018; 13:118-133. [PMID: 30461205 PMCID: PMC6984399 DOI: 10.1111/1751-7915.13335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 11/26/2022] Open
Abstract
In agricultural production, sustainability is currently one of the most significant concerns. The genetic modification of plant growth‐promoting rhizobacteria may provide a novel way to use natural bacteria as microbial inoculants. In this study, the root‐colonizing strain Pseudomonas protegens Pf‐5 was genetically modified to act as a biocontrol agent and biofertilizer with biological nitrogen fixation activity. Genetic inactivation of retS enhanced the production of 2,4‐diacetylphloroglucinol, which contributed for the enhanced antifungal activity. Then, the entire nitrogenase island with native promoter from Pseudomonas stutzeri DSM4166 was introduced into a retS mutant strain for expression. Root colonization patterns assessed via confocal laser scanning microscopy confirmed that GFP‐tagged bacterial were mainly located on root surfaces and at the junctions between epidermal root cells. Moreover, under pathogen and N‐limited double treatment conditions, the fresh weights of seedlings inoculated with the recombinant retS mutant‐nif strain were increased compared with those of the control. In conclusion, this study has innovatively developed an eco‐friendly alternative to the agrochemicals that will benefit global plant production significantly.
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Affiliation(s)
- Xiaoshu Jing
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Jia Yin
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Vinothkannan Ravichandran
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Deng Pan
- Jinan Yian Biology Institute, Shandong Yian Biological Engineering Co. Ltd., Jinan, 250100, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Xiaoying Bian
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, 266237, Qingdao, China
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Ke X, Feng S, Wang J, Lu W, Zhang W, Chen M, Lin M. Effect of inoculation with nitrogen-fixing bacterium Pseudomonas stutzeri A1501 on maize plant growth and the microbiome indigenous to the rhizosphere. Syst Appl Microbiol 2018; 42:248-260. [PMID: 30477902 DOI: 10.1016/j.syapm.2018.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022]
Abstract
Plant growth promoting diazotrophs with the ability to associate with plant roots are in common use as inoculants to benefit crop yield and to mitigate chemical nitrogen fertilization. However, limited information is available in understanding to what extent the plant growth-promoting effect of the inoculum has on the plant's nitrogen acquisition as well as on the impact of inoculation on the indigenous rhizosphere microbial population. Here we reported on experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15N dilution technique under two water regime conditions. The effects of inoculation and different water regimes were also assessed for the maize rhizospheric and surface soil communities by MiSeq community sequencing combined with qPCR of functional genes and transcripts (nifH and amoA) related to nitrogen cycling. Results support maize inoculated with P. stutzeri A1501 grew better and accumulated more nitrogen with a lower δ15N signature after 60 days than did plants inoculated with nifH-mutant and sterilized A1501 cells (non N2-fixing controls). Inoculant contribution to the plant was estimated to range from 0.30 to 0.82g N/plant, depending on water conditions. Inoculation with P. stutzeri A1501 significantly altered the composition of the diazotrophic community that P. stutzeri became dominant in the rhizosphere, and also increased the population of indigenous diazotrophs and ammonia oxidizers and functional genes transcripts. Redundancy analysis revealed that soil compartment and A1501 inoculation treatments were the main factors affecting the distribution of the diazotrophic community.
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Affiliation(s)
- Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Feng
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Life Science and Engineering College, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Majeed A, Kaleem Abbasi M, Hameed S, Yasmin S, Hanif MK, Naqqash T, Imran A. Pseudomonas sp. AF-54 containing multiple plant beneficial traits acts as growth enhancer of Helianthus annuus L. under reduced fertilizer input. Microbiol Res 2018; 216:56-69. [PMID: 30269857 DOI: 10.1016/j.micres.2018.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/12/2018] [Accepted: 08/10/2018] [Indexed: 12/23/2022]
Abstract
Plant growth promoting rhizobacteria (PGPR) are capable to increase the growth and yield of crops in eco-friendly and sustainable manner. To evaluate the response of sunflower towards inoculation with PGPR, a sunflower root associated bacterium AF-54 isolated from Diyar Gali Himalayan Mountain region, Azad Jammu and Kashmir (AJK), identified as Pseudomonas sp. by 16S rRNA sequence analysis and was characterized using polyphasic approach. The bacterium produced 23.9 μgmL-1 indole-3-acetic acid in tryptophan-supplemented medium, showed 44.28 nmoles mg-1 protein h-1 nitrogenase activity through acetylene reduction assay and released 48.80 μg mL-1 insoluble phosphorus in Pikovskaya's broth. During P-solubilization, the pH of the Pikovskaya's medium decreased from 7 to 3.04 due to the production of acetic acid, malic acid and gluconic acid. Pseudomonas sp. AF-54 showed metabolic versatility by utilizing 79 carbon sources from BIOLOG GN2 plates and resistance to many antibiotics. Furthermore, it inhibited the growth of Fusarium oxysporum in dual culture assay. To evaluate the plant-inoculation response, series of experiments conducted in hydroponic, sterilized soil and fields at AJK, and Faisalabad where inoculated plants with reduced fertilizer showed a significant increase in growth, yield, oil contents and achene NP uptake as compared to non-inoculated control. AF-54 showed extensive root colonization in sterilized and non-sterile conditions documented through yfp-labeling and fluorescent in situ hybridization coupled with confocal laser scanning microscopy. This study concludes that the Pseudomonas sp. strain AF-54 containing multiple plant growth promoting traits can be a potential candidate for biofertilizer production to enhance sunflower crop yield with reduced application of chemical (NP) fertilizers.
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Affiliation(s)
- Afshan Majeed
- Department of Soil and Environmental Sciences, The University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan; National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - M Kaleem Abbasi
- Department of Soil and Environmental Sciences, The University of Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Sohail Hameed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan; Academics and Coordination (Biology), Pakistan Atomic Energy Commission, Islamabad, Pakistan; Department of Biosciences, University of Wah Research Lab. Complex, University of Wah, Wah Cantt, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan
| | - Muhammad Kashif Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan; Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Tahir Naqqash
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan; Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad, Pakistan.
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Global investigation of an engineered nitrogen-fixing Escherichia coli strain reveals regulatory coupling between host and heterologous nitrogen-fixation genes. Sci Rep 2018; 8:10928. [PMID: 30026566 PMCID: PMC6053447 DOI: 10.1038/s41598-018-29204-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 07/06/2018] [Indexed: 11/08/2022] Open
Abstract
Transfer of nitrogen fixation (nif) genes from diazotrophs to amenable heterologous hosts is of increasing interest to genetically engineer nitrogen fixation. However, how the non-diazotrophic host maximizes opportunities to fine-tune the acquired capacity for nitrogen fixation has not been fully explored. In this study, a global investigation of an engineered nitrogen-fixing Escherichia coli strain EN-01 harboring a heterologous nif island from Pseudomonas stutzeri was performed via transcriptomics and proteomics analyses. A total of 1156 genes and 206 discriminative proteins were found to be significantly altered when cells were incubated under nitrogen-fixation conditions. Pathways for regulation, metabolic flux and oxygen protection to nitrogenase were particularly discussed. An NtrC-dependent regulatory coupling between E. coli nitrogen regulation system and nif genes was established. Additionally, pentose phosphate pathway was proposed to serve as the primary route for glucose catabolism and energy supply to nitrogenase. Meanwhile, HPLC analysis indicated that organic acids produced by EN-01 might have negative effects on nitrogenase activity. This study provides a global view of the complex network underlying the acquired nif genes in the recombinant E. coli and also provides clues for the optimization and redesign of robust nitrogen-fixing organisms to improve nitrogenase efficiency by overcoming regulatory or metabolic obstacles.
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Mohammed WS, Ziganshina EE, Shagimardanova EI, Gogoleva NE, Ziganshin AM. Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae). Sci Rep 2018; 8:10073. [PMID: 29968731 PMCID: PMC6030058 DOI: 10.1038/s41598-018-27342-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.
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Affiliation(s)
- Waleed S Mohammed
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Elvira E Ziganshina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Natalia E Gogoleva
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Iffis B, St-Arnaud M, Hijri M. Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities. FRONTIERS IN PLANT SCIENCE 2017; 8:1381. [PMID: 28848583 PMCID: PMC5550799 DOI: 10.3389/fpls.2017.01381] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/25/2017] [Indexed: 05/30/2023]
Abstract
Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.
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Wang D, Xu A, Elmerich C, Ma LZ. Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions. ISME JOURNAL 2017; 11:1602-1613. [PMID: 28338674 DOI: 10.1038/ismej.2017.30] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/26/2016] [Accepted: 01/22/2017] [Indexed: 12/14/2022]
Abstract
The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air-liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air. The two kinds of biofilms both contained large ovoid shape 'cells' that were multiple living bacteria embedded in a sac of extracellular polymeric substances (EPSs). We proposed to name such large 'cells' as A1501 cyst. Our results suggest that the EPS, especially exopolysaccharides enabled the encased bacteria to fix nitrogen while grown under aerobic condition. The formation of A1501 cysts was reversible in response to the changes of carbon or nitrogen source status. A1501 cyst formation depended on nitrogen-limiting signaling and the presence of sufficient carbon sources, yet was independent of an active nitrogenase. The pellicles formed by Azospirillum brasilense, another free-living nitrogen-fixing rhizobacterium, which also exhibited nitrogenase activity and contained the large EPS-encapsuled A1501 cyst-like 'cells'. Our data imply that free-living nitrogen-fixing bacteria could convert the easy-used carbon sources to exopolysaccharides in order to enable nitrogen fixation in a natural aerobic environment.
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Affiliation(s)
- Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Dahal B, NandaKafle G, Perkins L, Brözel VS. Diversity of free-Living nitrogen fixing Streptomyces in soils of the badlands of South Dakota. Microbiol Res 2017; 195:31-39. [DOI: 10.1016/j.micres.2016.11.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 11/04/2016] [Accepted: 11/12/2016] [Indexed: 11/25/2022]
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Babaei P, Marashi SA, Asad S. Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501. MOLECULAR BIOSYSTEMS 2016; 11:3022-32. [PMID: 26302703 DOI: 10.1039/c5mb00086f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pseudomonas stutzeri A1501 is an endophytic bacterium capable of nitrogen fixation. This strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen and phytohormones. These interesting features encouraged us to study the metabolism of this microorganism at the systems-level. In this work, we present the first genome-scale metabolic model (iPB890) for P. stutzeri, involving 890 genes, 1135 reactions, and 813 metabolites. A combination of automatic and manual approaches was used in the reconstruction process. Briefly, using the metabolic networks of Pseudomonas aeruginosa and Pseudomonas putida as templates, a draft metabolic network of P. stutzeri was reconstructed. Then, the draft network was driven through an iterative and curative process of gap filling. In the next step, the model was evaluated using different experimental data such as specific growth rate, Biolog substrate utilization data and other experimental observations. In most of the evaluation cases, the model was successful in correctly predicting the cellular phenotypes. Thus, we posit that the iPB890 model serves as a suitable platform to explore the metabolism of P. stutzeri.
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Affiliation(s)
- Parizad Babaei
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
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50
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Iffis B, St-Arnaud M, Hijri M. Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes. Environ Microbiol 2016; 18:2689-704. [DOI: 10.1111/1462-2920.13438] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bachir Iffis
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal; 4101 Rue Sherbrooke Est Montréal QC H1X 2B2 Canada
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