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Nguyen LTT, Park AR, Van Le V, Hwang I, Kim JC. Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight. Appl Microbiol Biotechnol 2024; 108:49. [PMID: 38183485 DOI: 10.1007/s00253-023-12874-w] [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: 06/14/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 01/08/2024]
Abstract
Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.
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Affiliation(s)
- Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Inmin Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea.
- JAN153 Biotech Incorporated, Gwangju, 61186, Republic of Korea.
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Andreata MFL, Afonso L, Niekawa ETG, Salomão JM, Basso KR, Silva MCD, Alves LC, Alarcon SF, Parra MEA, Grzegorczyk KG, Chryssafidis AL, Andrade G. Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives. PLANTS (BASEL, SWITZERLAND) 2024; 13:2246. [PMID: 39204682 PMCID: PMC11360115 DOI: 10.3390/plants13162246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.
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Affiliation(s)
- Matheus F. L. Andreata
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Leandro Afonso
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Erika T. G. Niekawa
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Julio M. Salomão
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Kawany Roque Basso
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Maria Clara D. Silva
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Leonardo Cruz Alves
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Stefani F. Alarcon
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Maria Eugenia A. Parra
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | - Kathlen Giovana Grzegorczyk
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
| | | | - Galdino Andrade
- Microbial Ecology Laboratory, Department of Microbiology, State University of Londrina, Londrina 86057-970, Brazil; (M.F.L.A.); (L.A.); (E.T.G.N.); (J.M.S.); (K.R.B.); (M.C.D.S.); (L.C.A.); (S.F.A.); (M.E.A.P.); (K.G.G.)
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Li X, Tao H, Wang S, Zhang D, Xiong X, Cai Y. IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato ( Solanum tuberosum L.). Microorganisms 2024; 12:1530. [PMID: 39203372 PMCID: PMC11356661 DOI: 10.3390/microorganisms12081530] [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: 07/05/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L-1. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato.
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Affiliation(s)
- Xiaoyu Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.L.); (H.T.)
| | - Huan Tao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.L.); (H.T.)
| | - Shisong Wang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.L.); (H.T.)
| | - Di Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.L.); (H.T.)
| | - Xingyao Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yanfei Cai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; (X.L.); (H.T.)
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Rico-Jiménez M, Udaondo Z, Krell T, Matilla MA. Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica. mSystems 2024; 9:e0016524. [PMID: 38837409 PMCID: PMC11264596 DOI: 10.1128/msystems.00165-24] [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: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria. IMPORTANCE Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Zulema Udaondo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Funnicelli MIG, de Carvalho LAL, Teheran-Sierra LG, Dibelli SC, Lemos EGDM, Pinheiro DG. Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174577. [PMID: 38981540 DOI: 10.1016/j.scitotenv.2024.174577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.
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Affiliation(s)
- Michelli Inácio Gonçalves Funnicelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Lucas Amoroso Lopes de Carvalho
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Luis Guillermo Teheran-Sierra
- Agronomy Research Program, Colombian Oil Palm Research Center, Cenipalma, Calle 98 No. 70-91, Piso 14, Bogotá 111121, Colombia
| | - Sabrina Custodio Dibelli
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Molecular Biology Laboratory, Institute for Research in Bioenergy (IPBEN), São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
| | - Daniel Guariz Pinheiro
- Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil; Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil.
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Linda TM, Aliska J, Feronika N, Melisa I, Juliantari E. Production of Exopolysaccharides and İndole Acetic Acid (IAA) by Rhizobacteria and Their Potential against Drought Stress in Upland Rice. J Microbiol Biotechnol 2024; 34:1239-1248. [PMID: 38783698 PMCID: PMC11239409 DOI: 10.4014/jmb.2401.01035] [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: 01/31/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Peatlands are marginal agricultural lands due to highly acidic soil conditions and poor drainage systems. Drought stress is a big problem in peatlands as it can affect plants through poor root development, so technological innovations are needed to increase the productivity and sustainability of upland rice on peatlands. Rhizobacteria can overcome the effects of drought stress by altering root morphology, regulating stress-responsive genes, and producing exopolysaccharides and indole acetic acid (IAA). This study aimed to determine the ability of rhizobacteria in upland rice to produce exopolysaccharides and IAA, identify potential isolates using molecular markers, and prove the effect of rhizobacteria on viability and vigor index in upland rice. Rhizobacterial isolates were grown on yeast extract mannitol broth (YEMB) medium for exopolysaccharides production testing and Nutrient Broth (NB)+L-tryptophan medium for IAA production testing. The selected isolates identify using sequence 16S rRNA. The variables observed in testing the effect of rhizobacteria were germination ability, vigour index, and growth uniformity. EPS-1 isolate is the best production of exopolysaccharides (41.6 mg/ml) and IAA (60.83 ppm). The isolate EPS-1 was identified as Klebsiella variicola using 16S rRNA sequencing and phylogenetic analysis. The isolate EPS-1 can increase the viability and vigor of upland rice seeds. K. variicola is more adaptive and has several functional properties that can be developed as a potential bioagent or biofertilizer to improve soil nutrition, moisture and enhance plant growth. The use of rhizobacteria can reduce dependence on the use of synthetic materials with sustainable agriculture.
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Affiliation(s)
- Tetty Marta Linda
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University. Kampus Bina Widya Km. 12, 5 Simpang Baru Pekanbaru, Riau Province 28293, Indonesia
| | - Jusinta Aliska
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University. Kampus Bina Widya Km. 12, 5 Simpang Baru Pekanbaru, Riau Province 28293, Indonesia
| | - Nita Feronika
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University. Kampus Bina Widya Km. 12, 5 Simpang Baru Pekanbaru, Riau Province 28293, Indonesia
| | - Ineiga Melisa
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University. Kampus Bina Widya Km. 12, 5 Simpang Baru Pekanbaru, Riau Province 28293, Indonesia
| | - Erwina Juliantari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Riau University. Kampus Bina Widya Km. 12, 5 Simpang Baru Pekanbaru, Riau Province 28293, Indonesia
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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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Saha KK, Mandal S, Barman A, Mondal S, Chatterjee S, Mandal NC. Genomic insight of phosphate solubilization and plant growth promotion of two taxonomically distinct winter crops by Enterobacter sp. DRP3. J Appl Microbiol 2024; 135:lxae146. [PMID: 38877666 DOI: 10.1093/jambio/lxae146] [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: 12/14/2023] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 06/16/2024]
Abstract
AIMS Study of rhizospheric microbiome-mediated plant growth promotional attributes currently highlighted as a key tool for the development of suitable bio-inoculants for sustainable agriculture purposes. In this context, we have conducted a detailed study regarding the characterization of phosphate solubilizing potential by plant growth-promoting bacteria that have been isolated from the rhizosphere of a pteridophyte Dicranopteris sp., growing on the lateritic belt of West Bengal. METHODS AND RESULTS We have isolated three potent bacterial strains, namely DRP1, DRP2, and DRP3 from the rhizoids-region of Dicranopteris sp. Among the isolated strains, DRP3 is found to have the highest phosphate solubilizing potentiality and is able to produce 655.89 and 627.58 µg ml-1 soluble phosphate by solubilizing tricalcium phosphate (TCP) and Jordan rock phosphate, respectively. This strain is also able to solubilize Purulia rock phosphate moderately (133.51 µg ml-1). Whole-genome sequencing and further analysis of the studied strain revealed the presence of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase gdh gene along with several others that were well known for their role in phosphate solubilization. Further downstream, quantitative reverse transcriptase PCR-based expression study revealed 1.59-fold upregulation of PQQ-dependent gdh gene during the solubilization of TCP. Root colonization potential of the studied strain on two taxonomically distinct winter crops viz. Cicer arietinum and Triticum aestivum has been checked by using scanning electron microscopy. Other biochemical analyses for plant growth promotion traits including indole acetic acid production (132.02 µg ml-1), potassium solubilization (3 mg l-1), biofilm formation, and exopolymeric substances productions (1.88-2.03 µg ml-1) also has been performed. CONCLUSION This study highlighted the active involvement of PQQ-dependent gdh gene during phosphate solubilization from any Enterobacter group. Moreover, our study explored different roadmaps for sustainable farming methods and the preservation of food security without endangering soil health in the future.
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Affiliation(s)
- Kunal Kumar Saha
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Subhrangshu Mandal
- Stress Physiology and Environmental Microbiology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
| | - Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sangita Mondal
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Sumit Chatterjee
- Department of Biological Sciences, Bose Institute, Kolkata 700091, India
| | - Narayan Chandra Mandal
- Mycology and Plant Pathology Laboratory, Department of Botany, Visva Bharati, Santiniketan 731235, India
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9
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [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: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Ma MY, Hu LL, Xu WY, Zhang W. L-tryptophan anaerobic fermentation for indole acetic acid production: Bacterial enrichment and effects of zero valent iron. BIORESOURCE TECHNOLOGY 2024; 400:130691. [PMID: 38599347 DOI: 10.1016/j.biortech.2024.130691] [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: 01/24/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/12/2024]
Abstract
Indole acetic acid (IAA) as a plant hormone, was one of the valuable products of anaerobic fermentation. However, the enriching method remained unknown. Moreover, whether zero valent iron (ZVI) could enhance IAA production was unexplored. In this work, IAA producing bacteria Klebsiella (63 %) was enriched successfully. IAA average production rate and concentration were up to 3 mg/L/h and 56 mg/L. With addition of 1 g/L ZVI, IAA average production rate and concentration was increased for 2 and 3 folds. Mechanisms indicated ZVI increased Na+K+-ATP activity and electron transport activity for 2 folds and 1 fold. Moreover, macro transcription determined indole pyruvate pathway activity like primary-amine oxidase, indole pyruvate decarboxylase and aldehyde dehydrogenase were increased for 146 %, 187 %, and 557 %, respectively. Therefore, ZVI was suitable for enhancement IAA production from mixed culture anaerobic fermentation.
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Affiliation(s)
- Meng-Yao Ma
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Li-Li Hu
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Wen-Yan Xu
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China
| | - Wei Zhang
- Department of Environmental Science and Engineering, College of Resources and Environment, Anhui Agriculture University, Hefei, Anhui 230036, China.
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11
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Etesami H, Glick BR. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience. Microbiol Res 2024; 281:127602. [PMID: 38228017 DOI: 10.1016/j.micres.2024.127602] [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: 11/29/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.
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Affiliation(s)
- Hassan Etesami
- Soil Science Department, University of Tehran, Tehran, Iran.
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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12
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Qin Y, Khan Q, Yan JW, Wang YY, Pan YF, Huang Y, Wei JL, Guo DJ, Li YR, Dong DF, Xing YX. Molecular mechanism of endophytic bacteria DX120E regulating polyamine metabolism and promoting plant growth in sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 15:1334907. [PMID: 38476689 PMCID: PMC10927768 DOI: 10.3389/fpls.2024.1334907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Introduction Sugarcane endophytic nitrogen-fixing bacterium Klebsiella variícola DX120E displayed broad impact on growth, but the exact biological mechanism, especially polyamines (PAs) role, is still meager. Methods To reveal this relationship, the content of polyamine oxidase (PAO), PAs, reactive oxygen species (ROS)-scavenging antioxidative enzymes, phytohormones, 1-aminocyclopropane-1-carboxylic synthase (ACS), chlorophyll content, and biomass were determined in sugarcane incubated with the DX120E strain. In addition, expression levels of the genes associated with polyamine metabolism were measured by transcriptomic analysis. Results Genomic analysis of Klebsiella variícola DX120E revealed that 39 genes were involved in polyamine metabolism, transport, and the strain secrete PAs in vitro. Following a 7-day inoculation period, DX120E stimulated an increase in the polyamine oxidase (PAO) enzyme in sugarcane leaves, however, the overall PAs content was reduced. At 15 days, the levels of PAs, ROS-scavenging antioxidative enzymes, and phytohormones showed an upward trend, especially spermidine (Spd), putrescine (Put), catalase (CAT), auxin (IAA), gibberellin (GA), and ACS showed a significant up-regulation. The GO and KEGG enrichment analysis found a total of 73 differentially expressed genes, involving in the cell wall (9), stimulus response (13), peroxidase activity (33), hormone (14) and polyamine metabolism (4). Discussion This study demonstrated that endophytic nitrogen-fixing bacteria stimulated polyamine metabolism and phytohormones production in sugarcane plant tissues, resulting in enhanced growth. Dual RNA-seq analyses provided insight into the early-stage interaction between sugarcane seedlings and endophytic bacteria at the transcriptional level. It showed how diverse metabolic processes selectively use distinct molecules to complete the cell functions under present circumstances.
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Affiliation(s)
- Ying Qin
- College of Agriculture, Guangxi University, Nanning, China
| | - Qaisar Khan
- Ecology College, Lishui University, Lishui, China
| | - Jia-Wei Yan
- College of Agriculture, Guangxi University, Nanning, China
| | - Yu-Yi Wang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Fei Pan
- College of Agriculture, Guangxi University, Nanning, China
| | - Ying Huang
- College of Agriculture, Guangxi University, Nanning, China
| | - Jiang-Lu Wei
- Centre for Biotechnology Research, Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Dao-Jun Guo
- College of Life Sciences and Engineering, Hexi University, Zhangye, China
| | - Yang-Rui Li
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Deng-Feng Dong
- College of Agriculture, Guangxi University, Nanning, China
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
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Seitz VA, McGivem BB, Borton MA, Chaparro JM, Schipanski ME, Prenni JE, Wrighton KC. Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils. RESEARCH SQUARE 2024:rs.3.rs-3956430. [PMID: 38410449 PMCID: PMC10896397 DOI: 10.21203/rs.3.rs-3956430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils. Results Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs. Conclusions We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.
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14
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Chappell CL, Hoffman KL, Lorenzi PL, Tan L, Petrosino J, Gibbs R, Muzny D, Doddapaneni H, Ross MC, Menon VK, Surathu A, Javornik Cregeen SJ, Reyes AG, Okhuysen PC. Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples From Healthy Individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.572622. [PMID: 38187744 PMCID: PMC10769349 DOI: 10.1101/2023.12.20.572622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gut microbiota produce tryptophan metabolites (TMs) important to homeostasis. However, measuring TM levels in stool and determining their microbial sources can be difficult. Here, we measured TMs from the indole pathway in fecal samples from 21 healthy adults with the goal to: 1) determine fecal TM concentrations in healthy individuals; 2) link TM levels to bacterial abundance using 16S and whole genome shotgun (WGS) sequencing data; and 3) predict likely bacterial sources of TM production. Within our samples, we identified 151 genera (16S) and 592 bacterial species (WGS). Eight TMs were found in ≥17 fecal samples, including four in all persons. To our knowledge, we are the first to report fecal levels for indole-3-lactate, indole-3-propionate, and 3-indoleacrylate levels in healthy persons. Overall, indole, indole-3-acetate (IAA), and skatole accounted for 86% of the eight TMs measured. Significant correlations were found between seven TMs and 29 bacterial species. Predicted multiple TM sources support the notion of a complex network of TM production and regulation. Further, the data suggest key roles for Collinsella aerofaciens and IAA, a metabolite reported to maintain intestinal homeostasis through enhanced barrier integrity and anti-inflammatory/antioxidant activities. These findings extend our understanding of TMs and their relationship to the microbial species that act as effectors and/or regulators in the healthy intestine and may lead to novel strategies designed to manipulate tryptophan metabolism to prevent disease and/or restore health to the dysbiotic gut.
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15
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Zhou JL, Vadiveloo A, Chen DZ, Gao F. Regulation effects of indoleacetic acid on lipid production and nutrient removal of Chlorella pyrenoidosa in seawater-containing wastewater. WATER RESEARCH 2024; 248:120864. [PMID: 37979569 DOI: 10.1016/j.watres.2023.120864] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/12/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
The utilization of seawater supplemented with wastewater nutrients for microalgae cultivation represents a promising and cost-effective approach that combines the benefits of wastewater treatment and microalgal resource recovery. However, the high salt content in seawater poses a significant challenge, hindering microalgal growth and reducing the removal of nitrogen and phosphorus on a large scale. The phytohormone indoleacetic acid (IAA) was used in this study to enhance stress resistance and lipid production of Chlorella pyrenoidosa grown in seawater-wastewater medium. Compared to the control groups involving regular wastewater and seawater-containing wastewater without IAA, Chlorella pyrenoidosa cultivated in the seawater-containing wastewater supplemented with IAA exhibited remarkable outcomes. Specifically, microalgae in IAA-enhanced seawater-containing wastewater achieved the highest lipid productivity (22.67 mg L-1 d-1) along with impressive nitrogen (99.3 %) and phosphorus (97.3 %) removal rates. Moreover, their cell sedimentation ratio reached 76.6 %, indicating enhanced settling properties. Additionally, the physiological mechanism changes after exposure to seawater stress and IAA were revealed based on the changes in antioxidant enzymes, endogenous hormones, and fatty acid saturation. Furthermore, the transcriptomic analysis elucidated the molecular mechanisms underlying microalgal lipid synthesis and their response to antioxidant stress when exposed to seawater. The supplementation of IAA under seawater stress stimulated energy metabolism and the antioxidant response in microalgal cells, effectively mitigating the adverse effects of seawater stress and promoting overall algal lipid productivity. Overall, this study unveiled the potential of exogenous plant hormones, particularly IAA, in enhancing stress resistance and lipid productivity of microalgae grown in seawater-wastewater medium, which significantly contributed towards the efficient use of seawater resources for microalgae cultivation and biofuel production.
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Affiliation(s)
- Jin-Long Zhou
- School of Petrochemical Engineering & Environment, Zhejiang Ocean University, Zhoushan 316000, China; Zhejiang Key Laboratory of Petrochemical Environmental Pollution Control, Zhoushan, 316000, China
| | - Ashiwin Vadiveloo
- Centre for Water, Energy and Waste, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Dong-Zhi Chen
- School of Petrochemical Engineering & Environment, Zhejiang Ocean University, Zhoushan 316000, China; Zhejiang Key Laboratory of Petrochemical Environmental Pollution Control, Zhoushan, 316000, China
| | - Feng Gao
- School of Petrochemical Engineering & Environment, Zhejiang Ocean University, Zhoushan 316000, China; Zhejiang Key Laboratory of Petrochemical Environmental Pollution Control, Zhoushan, 316000, China.
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16
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Zaid DS, Li W, Yang S, Li Y. Identification of bioactive compounds of Bacillus velezensis HNA3 that contribute to its dual effects as plant growth promoter and biocontrol against post-harvested fungi. Microbiol Spectr 2023; 11:e0051923. [PMID: 37811935 PMCID: PMC10715170 DOI: 10.1128/spectrum.00519-23] [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: 02/03/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE The current study is an extension to our previous work on the plant growth-promoting rhizobacteria (PGPR) Bacillus velezensis HNA3 strain, which comes to confirm and reveals the huge stock of active secondary metabolites produced by HNA3. HNA3-emitted volatile organic compounds (VOCs) have demonstrated the capacity to impede the growth of phytopathogens affecting some fruits and vegetables, even in the absence of direct contact. Additionally, these volatiles enhanced soybean seed germination by breaking seed dormancy and inducing root system development. Furthermore, they promoted seedling growth, giving it prominence in soybean cultivation. The relevance of active volatiles derives from the fact that they can be developed as natural-safe biocontrol agents and plant promoters. This research validates the remarkable bioactivities exhibited by the Bacillus velezensis HNA3 and their potential applications in agriculture as an inoculant, encompassing biocontrol, plant growth promotion, and seed germination activities, thereby offering a safer alternative to hazardous chemicals.
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Affiliation(s)
- Doaa S. Zaid
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Desert Research Center, Ain Shams, Egypt
| | - Wenya Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Siyu Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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17
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Sondo M, Wonni I, Koïta K, Rimbault I, Barro M, Tollenaere C, Moulin L, Klonowska A. Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data. PLoS One 2023; 18:e0287084. [PMID: 38032916 PMCID: PMC10688718 DOI: 10.1371/journal.pone.0287084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
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Affiliation(s)
- Moussa Sondo
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Koïta
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Isabelle Rimbault
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Mariam Barro
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
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Ding WJ, Xu L, Zhao Y, Sun JQ. Aquibacillus rhizosphaerae sp. nov., an Indole Acetic Acid (IAA)-producing Halotolerant Bacterium Isolated from the Rhizosphere Soil of Kalidium cuspidatum. Curr Microbiol 2023; 80:404. [PMID: 37930394 DOI: 10.1007/s00284-023-03543-2] [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: 07/05/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
A bacterium (named strain LR5S19T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19T was Gram-stain-positive, motile with a polar flagellum, rod shaped, and spore forming at the terminal position in swollen sporangia, and it grew at 10-40 ℃ (optimum 30 ℃), pH 6.0-9.0 (optimum pH 7.0), and in the presence of 1.0-15.0% (w/v) NaCl (optimum 2.0%). The phylogenetic analysis of the 16S rRNA gene showed that strain LR5S19T shared the highest similarity (96.7%) with A. koreensis JCM 12387T, followed by A. kalidii HU2P27T (96.2%), A. sediminis BH258T (96.1%), and 'A. salsiterrae' 3ASR75-54T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19T and its closely related type strains were 69.3-73.8%, 65.4-72.4% and 19.2-20.3%, respectively. The major polar lipids in strain LR5S19T consisted of diphosphatidylglycerol, phosphatidylglycerol, and three unidentified phospholipids, while MK-7 was the major respiratory quinone. The major fatty acids of the strain were anteiso-C15:0 and iso-C15:0. Based on phylogenomic and phenotypic results, strain LR5S19T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19T (= CGMCC 1.62028T = KCTC 43434T). The comparative genomic analysis revealed that all eight members of Aquibacillus could utilize D-glucose via the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway and use the tricarboxylic acid cycle as the metabolic center. The potassium ion transport proteins and compatible solute synthesis pathways in all the members likely also help them cope with hypersaline environments.
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Affiliation(s)
- Wen-Jing Ding
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Zhao
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
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Cheng X, Li X, Tong M, Wu J, Chan LL, Cai Z, Zhou J. Indole-3-acetic acid as a cross-talking molecule in algal-bacterial interactions and a potential driving force in algal bloom formation. Front Microbiol 2023; 14:1236925. [PMID: 37928680 PMCID: PMC10623134 DOI: 10.3389/fmicb.2023.1236925] [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: 06/08/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Most signaling molecules are involved in inter-or intra-species communication, and signaling involving cross-kingdom cell-to-cell communication is limited. Howerver, algae and bacteria exchange nutrients and information in a range of interactions in marine environments. Multiple signaling molecules exist between algae and bacteria, including quorum-sensing molecules, nitric oxide, and volatile organic compounds. Recently, indole-3-acetic acid (IAA), an auxin hormone that is a well-studied signaling molecule in terrestrial ecosystems, was found to act as a cue in cross-kingdom communication between algae and bacteria in aquatic environments. To increase understanding of the roles of IAA in the phycosphere, the latest evidence regarding the ecological functions of IAA in cross-kingdom communication between algae and bacteria has been compiled in this review. The pathways of IAA biosynthesis, effects of IAA on algal growth & reproduction, and potential mechanisms at phenotypic and molecular levels are summarized. It is proposed that IAA is an important molecule regulating algal-bacterial interactions and acts as an invisible driving force in the formation of algal blooms.
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Affiliation(s)
- Xueyu Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xinyang Li
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Mengmeng Tong
- The Direction of Deep Sea Resource Exploration and Development Utilization, Hainan Institute of Zhejiang University, Sanya, China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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20
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Ogawa Y, Nishimura K, Obara K, Kamura T. Development of AlissAID system targeting GFP or mCherry fusion protein. PLoS Genet 2023; 19:e1010731. [PMID: 37315088 DOI: 10.1371/journal.pgen.1010731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 06/16/2023] Open
Abstract
Conditional control of target proteins using the auxin-inducible degron (AID) system provides a powerful tool for investigating protein function in eukaryotes. Here, we established an Affinity-linker based super-sensitive auxin-inducible degron (AlissAID) system in budding yeast by using a single domain antibody (a nanobody). In this system, target proteins fused with GFP or mCherry were degraded depending on a synthetic auxin, 5-Adamantyl-IAA (5-Ad-IAA). In AlissAID system, nanomolar concentration of 5-Ad-IAA induces target degradation, thus minimizing the side effects from chemical compounds. In addition, in AlissAID system, we observed few basal degradations which was observed in other AID systems including ssAID system. Furthermore, AlissAID based conditional knockdown cell lines are easily generated by using budding yeast GFP Clone Collection. Target protein, which has antigen recognition sites exposed in cytosol or nucleus, can be degraded by the AlissAID system. From these advantages, the AlissAID system would be an ideal protein-knockdown system in budding yeast cells.
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Affiliation(s)
- Yoshitaka Ogawa
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kohei Nishimura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keisuke Obara
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takumi Kamura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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Pantoja-Guerra M, Burkett-Cadena M, Cadena J, Dunlap CA, Ramírez CA. Lysinibacillus spp.: an IAA-producing endospore forming-bacteria that promotes plant growth. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01828-x. [PMID: 37138159 DOI: 10.1007/s10482-023-01828-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Lysinibacillus is a bacterial genus that has generated recent interest for its biotechnological potential in agriculture. Strains belonging to this group are recognized for their mosquitocidal and bioremediation activity. However, in recent years some reports indicate its importance as plant growth promoting rhizobacteria (PGPR). This research sought to provide evidence of the PGP activity of Lysinibacillus spp. and the role of the indole-3-acetic acid (IAA) production associated with this activity. Twelve Lysinibacillus spp. strains were evaluated under greenhouse conditions, six of which increased the biomass and root architecture of corn plants. In most cases, growth stimulation was evident at 108 CFU/mL inoculum concentration. All strains produced IAA with high variation between them (20-70 µg/mL). The bioinformatic identification of predicted genes associated with IAA production allowed the detection of the indole pyruvic acid pathway to synthesize IAA in all strains; additionally, genes for a tryptamine pathway were detected in two strains. Extracellular filtrates from all strain's cultures increased the corn coleoptile length in an IAA-similar concentration pattern, which demonstrates the filtrates had an auxin-like effect on plant tissue. Five of the six strains that previously showed PGPR activity in corn also promoted the growth of Arabidopsis thaliana (col 0). These strains induced changes in root architecture of Arabidopsis mutant plants (aux1-7/axr4-2), the partial reversion of mutant phenotype indicated the role of IAA on plant growth. This work provided solid evidence of the association of Lysinibacillus spp. IAA production with their PGP activity, which constitutes a new approach for this genus. These elements contribute to the biotechnological exploration of this bacterial genus for agricultural biotechnology.
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Affiliation(s)
- Manuel Pantoja-Guerra
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia.
- Facultad de Ciencias Agropecuarias, Unilasallista Corporación Universitaria, Caldas - Antioquia, Colombia.
| | | | | | - Christopher A Dunlap
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, 1815 N University, Peoria, IL, USA
| | - Camilo A Ramírez
- Universidad de Antioquia, Instituto de Biología, Medellín, Colombia
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22
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Su J, Wang Y, Bai M, Peng T, Li H, Xu HJ, Guo G, Bai H, Rong N, Sahu SK, He H, Liang X, Jin C, Liu W, Strube ML, Gram L, Li Y, Wang E, Liu H, Wu H. Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata 'Chachi'. MICROBIOME 2023; 11:61. [PMID: 36973820 PMCID: PMC10044787 DOI: 10.1186/s40168-023-01504-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The medicinal material quality of Citrus reticulata 'Chachi' differs depending on the bioactive components influenced by the planting area. Environmental factors, such as soil nutrients, the plant-associated microbiome and climatic conditions, play important roles in the accumulation of bioactive components in citrus. However, how these environmental factors mediate the production of bioactive components of medicinal plants remains understudied. RESULTS Here, a multi-omics approach was used to clarify the role of environmental factors such as soil nutrients and the root-associated microbiome on the accumulation of monoterpenes in the peel of C. reticulata 'Chachi' procured from core (geo-authentic product region) and non-core (non-geo-authentic product region) geographical regions. The soil environment (high salinity, Mg, Mn and K) enhanced the monoterpene content by promoting the expression of salt stress-responsive genes and terpene backbone synthase in the host plants from the core region. The microbial effects on the monoterpene accumulation of citrus from the core region were further verified by synthetic community (SynCom) experiments. Rhizosphere microorganisms activated terpene synthesis and promoted monoterpene accumulation through interactions with the host immune system. Endophyte microorganisms derived from soil with the potential for terpene synthesis might enhance monoterpene accumulation in citrus by providing precursors of monoterpenes. CONCLUSIONS Overall, this study demonstrated that both soil properties and the soil microbiome impacted monoterpene production in citrus peel, thus providing an essential basis for increasing fruit quality via reasonable fertilization and precision microbiota management. Video Abstract.
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Affiliation(s)
- Jianmu Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Mei Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Tianhua Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huisi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hui-Juan Xu
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Guifang Guo
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Haiyi Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ning Rong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanjun He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangxiu Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Canzhi Jin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark
| | - Yongtao Li
- Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Lorenzi AS, Bonatelli ML, Chia MA, Peressim L, Quecine MC. Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook. Microorganisms 2022; 10:microorganisms10102072. [PMID: 36296348 PMCID: PMC9610544 DOI: 10.3390/microorganisms10102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2022] Open
Abstract
Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.
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Affiliation(s)
- Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, UnB, Brasília 70910-900, DF, Brazil
| | - Maria Letícia Bonatelli
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH—UFZ, 04318 Leipzig, Germany
| | - Mathias Ahii Chia
- Department of Botany, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Leonardo Peressim
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, USP, Piracicaba 13418-900, SP, Brazil
- Correspondence:
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24
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Bellés-Sancho P, Liu Y, Heiniger B, von Salis E, Eberl L, Ahrens CH, Zamboni N, Bailly A, Pessi G. A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. FRONTIERS IN PLANT SCIENCE 2022; 13:991548. [PMID: 36247538 PMCID: PMC9554594 DOI: 10.3389/fpls.2022.991548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a nifA mutant compared to wild-type nodules. Here, we document the structural changes that a P. phymatum nifA mutant induces in common bean (Phaseolus vulgaris) nodules, eventually leading to hypernodulation. To investigate the role of the P. phymatum iaaMH genes during symbiosis, we monitored their expression in presence and absence of NifA over different stages of the symbiosis. The iaaMH genes were found to be under negative control of NifA in all symbiotic stages. While a P. phymatum iaaMH mutant produced the same number of nodules and nitrogenase activity as the wild-type strain, the nifA mutant produced more nodules than the wild-type that clustered into regularly-patterned root zones. Mutation of the iaaMH genes in a nifA mutant background reduced the presence of these nodule clusters on the root. We further show that the P. phymatum iaaMH genes are located in a region of the symbiotic plasmid with a significantly lower GC content and exhibit high similarity to two genes of the IAM pathway often used by bacterial phytopathogens to deploy IAA as a virulence factor. Overall, our data suggest that the increased abundance of rhizobial auxin in the non-fixing nifA mutant strain enables greater root infection rates and a role for bacterial auxin production in the control of early stage symbiotic interactions.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Elia von Salis
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Aurélien Bailly
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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25
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Zarei I, Koistinen VM, Kokla M, Klåvus A, Babu AF, Lehtonen M, Auriola S, Hanhineva K. Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition. Sci Rep 2022; 12:15018. [PMID: 36056162 PMCID: PMC9440220 DOI: 10.1038/s41598-022-19327-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 08/29/2022] [Indexed: 12/13/2022] Open
Abstract
The essential role of gut microbiota in health and disease is well recognized, but the biochemical details that underlie the beneficial impact remain largely undefined. To maintain its stability, microbiota participates in an interactive host-microbiota metabolic signaling, impacting metabolic phenotypes of the host. Dysbiosis of microbiota results in alteration of certain microbial and host metabolites. Identifying these markers could enhance early detection of certain diseases. We report LC-MS based non-targeted metabolic profiling that demonstrates a large effect of gut microbiota on mammalian tissue metabolites. It was hypothesized that gut microbiota influences the overall biochemistry of host metabolome and this effect is tissue-specific. Thirteen different tissues from germ-free (GF) and conventionally-raised (MPF) C57BL/6NTac mice were selected and their metabolic differences were analyzed. Our study demonstrated a large effect of microbiota on mammalian biochemistry at different tissues and resulted in statistically-significant modulation of metabolites from multiple metabolic pathways (p ≤ 0.05). Hundreds of molecular features were detected exclusively in one mouse group, with the majority of these being unique to specific tissue. A vast metabolic response of host to metabolites generated by the microbiota was observed, suggesting gut microbiota has a direct impact on host metabolism.
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Affiliation(s)
- Iman Zarei
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Ville M Koistinen
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Itäinen Pitkäkatu 4, 20014, Turku, Finland
| | - Marietta Kokla
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Ambrin Farizah Babu
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, 70211, Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
- LC-MS Metabolomics Center, Biocenter Kuopio, 70211, Kuopio, Finland
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, School of Medicine, Faculty of Health Science, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
- Food Chemistry and Food Development Unit, Department of Biochemistry, University of Turku, Itäinen Pitkäkatu 4, 20014, Turku, Finland.
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26
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Nonthakaew N, Panbangred W, Songnuan W, Intra B. Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets’ rhizosphere microbiome. Front Microbiol 2022; 13:967415. [PMID: 36090067 PMCID: PMC9453592 DOI: 10.3389/fmicb.2022.967415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.
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Affiliation(s)
- Napawit Nonthakaew
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
| | - Watanalai Panbangred
- Research, Innovation, and Partnerships Office (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
- *Correspondence: Bungonsiri Intra,
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27
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Boss BL, Wanees AE, Zaslow SJ, Normile TG, Izquierdo JA. Comparative genomics of the plant-growth promoting bacterium Sphingobium sp. strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata. BMC Genomics 2022; 23:508. [PMID: 35831788 PMCID: PMC9281055 DOI: 10.1186/s12864-022-08738-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Background The genus Sphingobium within the class Alpha-proteobacteria contains a small number of plant-growth promoting rhizobacteria (PGPR), although it is mostly comprised of organisms that play an important role in biodegradation and bioremediation in sediments and sandy soils. A Sphingobium sp. isolate was obtained from the rhizosphere of the beachgrass Ammophila breviligulata with a variety of plant growth-promoting properties and designated as Sphingobium sp. strain AEW4. Results Analysis of the 16S rRNA gene as well as full genome nucleotide and amino acid identities revealed that this isolate is most similar to Sphingobium xenophagum and Sphingobium hydrophobicum. Comparative genomics analyses indicate that the genome of strain AEW4 contains unique features that explain its relationship with a plant host as a PGPR, including pathways involved in monosaccharide utilization, fermentation pathways, iron sequestration, and resistance to osmotic stress. Many of these unique features are not broadly distributed across the genus. In addition, pathways involved in the metabolism of salicylate and catechol, phenyl acetate degradation, and DNA repair were also identified in this organism but not in most closely related organisms. Conclusion The genome of Sphingobium sp. strain AEW4 contains a number of distinctive features that are crucial to explain its role as a plant-growth promoting rhizobacterium, and comparative genomics analyses support its classification as a relevant Sphingobium strain involved in plant growth promotion of beachgrass and other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08738-8.
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Affiliation(s)
- Brianna L Boss
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Abanoub E Wanees
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Shari J Zaslow
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
| | - Tyler G Normile
- Department of Biology, Hofstra University, Hempstead, NY, 11549, USA
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28
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Panichikkal J, Mohanan DP, Koramkulam S, Krishnankutty RE. Chitosan nanoparticles augmented indole-3-acetic acid production by rhizospheric Pseudomonas monteilii. J Basic Microbiol 2022; 62:1467-1474. [PMID: 35510957 DOI: 10.1002/jobm.202100358] [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: 10/04/2021] [Revised: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 11/05/2022]
Abstract
Rhizospheric Pseudomonas spp. are widely used for upgrading sustainable agriculture because of their ability to execute multifaceted plant beneficial functions. In the current study, chitosan nanoparticles (CNPs) were used to analyze their effect on plant beneficial properties of rhizospheric Pseudomonas monteilii. The CNPs were characterized by transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis. The impact of CNPs on indole-3-acetic acid (IAA) production of P. monteilii was analyzed and quantified by spectrophotometric and confirmed high-performance liquid chromatography analysis. This revealed the beneficial effect of CNPs (1 mg/ml) by enhancing the IAA production of P. monteilii. In planta effect of varied bacterial IAA production was further demonstrated in Vigna unguiculata. Here, enhancement in shoot length (35.79 ± 0.37 cm), leaf number (7 ± 0.54), and fresh weight (3.07 ± 0.11 g) were observed in the plants treated with the culture filtrate collected from P. monteilii cultivated with 1 mg/ml CNPs. The results of the study highlight the beneficial effect of the CNPs to augment the rhizobacterial functioning by inducing the expression of plant beneficial properties.
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Affiliation(s)
- Jishma Panichikkal
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India
| | - Deepa P Mohanan
- International and Inter-University Centre for Nanoscience and Nanotechnology (IIUCNN), Mahatma Gandhi University, Kottayam, Kerala, India
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Kong WL, Wang WY, Zuo SH, Wu XQ. Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion. Front Microbiol 2022; 13:828990. [PMID: 35464970 PMCID: PMC9020876 DOI: 10.3389/fmicb.2022.828990] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Genomic information for bacteria within the genus Rahnella remains limited. Rahnella sp. JZ-GX1 was previously isolated from the Pinus massoniana rhizosphere in China and shows potential as a plant growth-promoting (PGP) bacterium. In the present work, we combined the GridION Nanopore ONT and Illumina sequencing platforms to obtain the complete genome sequence of strain JZ-GX1, and the application effects of the strain in natural field environment was assessed. The whole genome of Rahnella sp. JZ-GX1 comprised a single circular chromosome (5,472,828 bp, G + C content of 53.53%) with 4,483 protein-coding sequences, 22 rRNAs, and 77 tRNAs. Based on whole genome phylogenetic and average nucleotide identity (ANI) analysis, the JZ-GX1 strain was reidentified as R. victoriana. Genes related to indole-3-acetic acid (IAA), phosphorus solubilization, nitrogen fixation, siderophores, acetoin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, gamma-aminobutyric acid (GABA) production, spermidine and volatile organic compounds (VOCs) biosynthesis were present in the genome of strain JZ-GX1. In addition, these functions were also confirmed by in vitro experiments. Importantly, compared to uninoculated control plants, Pyrus serotina, Malus spectabilis, Populus euramericana (Dode) Guinier cv. “San Martino” (I-72 poplar) and Pinus elliottii plants inoculated with strain JZ-GX1 showed increased heights and ground diameters. These findings improve our understanding of R. victoriana JZ-GX1 as a potential biofertilizer in agriculture.
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Affiliation(s)
- Wei-Liang Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Wei-Yu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Sheng-Han Zuo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, China
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Kuzmina LY, Gilvanova EA, Galimzyanova NF, Arkhipova TN, Ryabova AS, Aktuganov GE, Sidorova LV, Kudoyarova GR, Melent’ev AI. Characterization of the Novel Plant Growth-Stimulating Strain Advenella kashmirensis IB-K1 and Evaluation of Its Efficiency in Saline Soil. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Wang J, Tang X, Mo Z, Mao Y. Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed. Front Microbiol 2022; 13:857901. [PMID: 35401438 PMCID: PMC8984609 DOI: 10.3389/fmicb.2022.857901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can influence host adaptation. Previous studies on the Pyropia microbiome were focused on the microbial components or the function of specific microbial lineages, which frequently exclude metabolic information and contained only a small fraction of the overall community. Here, we performed a genome-centric analysis to study the metabolic potential of the Pyropia haitanensis phycosphere bacteria. We reconstructed 202 unique metagenome-assembled genomes (MAGs) comprising all major taxa present within the P. haitanensis microbiome. The addition of MAGs to the genome tree containing all publicly available Pyropia-associated microorganisms increased the phylogenetic diversity by 50% within the bacteria. Metabolic reconstruction of the MAGs showed functional redundancy across taxa for pathways including nitrate reduction, taurine metabolism, organophosphorus, and 1-aminocyclopropane-1-carboxylate degradation, auxin, and vitamin B12 synthesis. Some microbial functions, such as auxin and vitamin B12 synthesis, that were previously assigned to a few Pyropia-associated microorganisms were distributed across the diverse epiphytic taxa. Other metabolic pathways, such as ammonia oxidation, denitrification, and sulfide oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- Junhao Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
- Yazhou Bay Innovation Research Institute, Hainan Tropical Ocean University, Sanya, China
- Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources of Hainan Province, Hainan Tropical Ocean University, Sanya, China
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Metabacillus dongyingensis sp. nov. Is Represented by the Plant Growth-Promoting Bacterium BY2G20 Isolated from Saline-Alkaline Soil and Enhances the Growth of Zea mays L. under Salt Stress. mSystems 2022; 7:e0142621. [PMID: 35229649 PMCID: PMC9040632 DOI: 10.1128/msystems.01426-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A novel plant growth-promoting rhizobacterium (PGPR), which was designated strain BY2G20, was isolated from saline-alkaline soil in Dongying, China. Strain BY2G20 can grow at a NaCl range from 0 to 7% and a pH range from 7 to 9 and can prevent the growth of the phytopathogen Ralstonia solanacearum. Based on its phenotypic and genomic characteristics and phylogenetic analysis, strain BY2G20 represents a novel species of the genus Metabacillus, for which the name Metabacillus dongyingensis sp. nov. is proposed. Comparative genomic analysis of strain BY2G20 with its closely related species exhibited a high level of evolutionary plasticity derived by horizontal gene transfer, which facilitated adaptative evolution. Different evolutionary constraints have operated on the diverse functions of BY2G20, with the gene adapted to saline-alkaline ecosystems experiencing functional constraints. We determined the genetic properties of saline-alkaline tolerance and plant growth promotion, such as cation-proton antiporters, cation transporters, osmoprotectant synthesis and transport, H+-transporting F1F0-ATPase, indole-3-acetic acid production, and secondary metabolite synthesis. We also evaluated the effects of strain BY2G20 on the growth of Zea mays L. (maize) under salt stress. The physiological parameters of maize such as plant height, stem diameter, dry biomass, and fresh biomass were significantly higher after inoculating strain BY2G20 under salt stress, indicating that inoculation with BY2G20 enhanced the growth of maize in saline areas. This study demonstrates that M. dongyingensis sp. nov. BY2G20 is a potential candidate for organic agriculture biofertilizers in saline-alkaline areas. IMPORTANCE Plant growth and yield are adversely affected by soil salinity. PGPRs can promote plant growth and enhance plant tolerance to salt stress. In this study, a saline-alkaline tolerant PGPR strain BY2G20 was isolated from the rhizosphere of Ulmus pumila in Dongying, China. Strain BY2G20 represents a novel species within the genus Metabacillus based on phenotypic, genomic, and phylogenetic analysis. Genomic components have undergone different functional constraints, and the disparity in the evolutionary rate may be associated with the adaptation to a specific niche. Genomic analysis revealed numerous adaptive features of strain BY2G20 to a saline-alkaline environment and rhizosphere, especially genes related to salt tolerance, pH adaptability, and plant growth promotion. Our work also exhibited that inoculation of strain BY2G20 enhanced the growth of maize under salt stress. This study demonstrates that PGPRs play an important role in stimulating salt tolerance in plants and can be used as biofertilizers to enhance the growth of crops in saline-alkaline areas.
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Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. Microbiol Spectr 2022; 10:e0207221. [PMID: 35230132 PMCID: PMC9045143 DOI: 10.1128/spectrum.02072-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective. IMPORTANCED. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.
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Lv Y, Li Y, Liu X, Xu K. A positive response of ginger root zone and rhizome development to suitable sowing depth. PROTOPLASMA 2022; 259:327-342. [PMID: 34075471 DOI: 10.1007/s00709-021-01647-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Sowing depth significantly affects ginger (Zingiber officinale Roscoe) yields, and sowing depth can affect rhizosphere community structure through root exudates. However, the relationship between the reaction process in root zone and ginger rhizome development is unclear. In this study, we investigated the rhizome and root development and rhizosphere environment at different sowing depths (2 cm (SD2), 5 cm (SD5), and 10 cm (SD10)). It was found that SD10 significantly increased ginger yield, which is related to the development of vascular bundles and the expression of aquaporin. PLS-PM analysis found that root length, root absorption capacity, and soil enzymes have the strongest correlation with yield, while root diameter is negatively correlated with yield. Under SD10, the increase of auxin and ethylene content together with the expression of ARF7, LBD16, and PIN1 promoted the development of lateral roots. In addition, SD10 increased the secretion of root organic acids, amino acids, and carbohydrates, which in turn promoted the development of rhizosphere bacteria. The promotion of SD10 on nitrogen cycle and nitrogen fixation ability in turn promoted the development of ginger.
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Affiliation(s)
- Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, 271018, China
- Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, 271018, China
- State Key Laboratory of Crop Biology, Tai'an, 271018, China
| | - Yanyan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaohui Liu
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, 271018, China.
- Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, 271018, China.
- State Key Laboratory of Crop Biology, Tai'an, 271018, China.
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Uzma M, Iqbal A, Hasnain S. Drought tolerance induction and growth promotion by indole acetic acid producing Pseudomonas aeruginosa in Vigna radiata. PLoS One 2022; 17:e0262932. [PMID: 35120147 PMCID: PMC8815908 DOI: 10.1371/journal.pone.0262932] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/07/2022] [Indexed: 11/18/2022] Open
Abstract
Drought accompanied with reduced precipitation is one of the key manacles to global agricultural throughput and is expected to escalate further hence posing major challenges to future food safety. For a sustainable agricultural environment, drought resistant plant growth promoting rhizobacteria (PGPR) are new encouraging prospect, which are inexpensive and have no side effects, as those of synthetic fertilizers. In the present study, five strains of Pseudomonas aeruginosa, the strain MK513745, strain MK513746, strain MK513747, strain MK513748, and strain MK513749 were used as drought tolerant PGPR with multiple traits of IAA production, N fixation, P solubilization, siderophore producing capabilities. The strain MK513745 and strain MK513749 produced higher quantities of indole acetic acid (116±0.13 and 108±0.26 μg ml-1). MK513749 yielded 12 different indole compounds in GCMS analysis. The strain MK513748 yielded maximum S.I. (3.33mm) for phosphate solubilizing test. Maximum nitrogen concentration was produced (0.18 μg ml-1) by strain MK513746. Percent siderophore units ranged from 2.65% to 2.83% as all five pseudomonas strains were siderophore positive. In all growth experiments of plant microbe interaction two varieties of Vigna radiata (AZRI-06, NM-11) plants inoculated with P. aeruginosa strains under drought stress responded significantly (P<0.05) better than control stressed plants. Maximum shoot length was enhanced up-to 125%, pod/plant 172%, number of grains 65%, 100 seed weight 95%, 100 seed straw weight 124% and total yield 293% were recorded in plants inoculated with drought stress tolerant PGPR in both varieties as compared to respective stressed control plants. Photosynthetic activity, membrane stability (45%), water content (68%) and antioxidant efficacy (19%) were improved with PGPR inoculations. The variety NM-11 (V2) was more tolerant to drought stress with inoculations of Pseudomonas strains than AZRI-06 (V1). Inoculations with these indole acetic acid producing strains would be suitable for plant growth promotion in areas facing water deficiency.
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Affiliation(s)
- Malika Uzma
- Department of Microbiology and Molecular Genetics, The Women University, Multan, Pakistan
| | - Atia Iqbal
- Department of Microbiology and Molecular Genetics, The Women University, Multan, Pakistan
| | - Shahida Hasnain
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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Sun YC, Sun P, Xue J, Du Y, Yan H, Wang LW, Yi XX, Sun JG, Zhang X, Gao JL. Arthrobacter wenxiniae sp. nov., a novel plant growth-promoting rhizobacteria species harbouring a carotenoids biosynthetic gene cluster. Antonie van Leeuwenhoek 2022; 115:353-364. [PMID: 35088183 DOI: 10.1007/s10482-021-01701-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/10/2021] [Indexed: 10/19/2022]
Abstract
A bacterial strain, designated AETb3-4T was isolated from the rhizosphere of lily. Comparison of 16S rRNA gene sequences showed that the sequence from strain AETb3-4T exhibits high sequence similarity with those of Arthrobacter silviterrae KIS14-16T (97.9%), Arthrobacter livingstonensis LI2T (97.2%) and Arthrobacter stackebrandtii CCM 2783T (97.0%). Whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between strain AETb3-4T and the reference strains A. silviterrae DSM 27180T, A. livingstonensis L12T and A. stackebrandtii DSM 16005T were below 83.6% and 27.7%, respectively, values which are considerably below the proposed thresholds for the species delineation, consistent with the proposal that strain AETb3-4T represents a novel species. The genome size of strain AETb3-4T is 4.33 Mb and the genomic DNA G + C content is 67.3%. The main polar lipids were identified as phosphatidylglycerol, diphosphatidylglycero, phosphatidylinositol and an unidentified glycolipid. The major fatty acids (> 10%) were identified as anteiso-C15: 0 and anteiso-C17: 0. The predominant menaquinone was found to be menaquinone 9 (MK-9) (H2) (82.2%). Phenotypic tests allowed the strain to be differentiated from its close phylogenetic neighbors. Based on the results obtained, it is proposed that the strain AETb3-4T (= CFCC 16390T = LMG 31708T) represents a novel species in the genus Arthrobacter, for which the names Arthrobacter wenxiniae sp. nov. is proposed. In addition, the novel strain AETb3-4T has multiple plant growth-promoting characters including ACC-deaminase activity and production of IAA. Furthermore, the genome contains secondary metabolite biosynthesis gene clusters, including a carotenoid biosynthetic gene cluster, suggesting potential capacities for secondary metabolite synthesis. These data suggest that strain AETb3-4T may have potential applications both in medicine and sustainable agriculture.
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Affiliation(s)
- Yu-Chen Sun
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Pengbo Sun
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Cancer Consortium(DKTK), German Cancer Research Center(DKFZ), 69120, Heidelberg, Germany
| | - Jing Xue
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yunpeng Du
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Li-Wei Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Xin-Xin Yi
- College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xiuhai Zhang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Jun-Lian Gao
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Szymaniak D, Ciarka K, Marcinkowska K, Praczyk T, Gwiazdowska D, Marchwińska K, Walkiewicz F, Pernak J. Bifunctional Double-Salt Ionic Liquids Containing both 4-Chloro-2-Methylphenoxyacetate and l-Tryptophanate Anions with Herbicidal and Antimicrobial Activity. ACS OMEGA 2021; 6:33779-33791. [PMID: 34926926 PMCID: PMC8679003 DOI: 10.1021/acsomega.1c05048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
The goal of this research was to obtain and characterize ionic liquids based on a bisammonium cation and both 4-chloro-2-methylphenoxyacetate (MCPA) and l-tryptophanate anions. The concept of including two structurally different anions was utilized to achieve improved biological activity, while crucial functional traits could be designed by modifying the cation. The synthesis process was efficient and resulted in high yields. Subsequent analyses (nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) spectroscopy, and high-performance liquid chromatography (HPLC)) confirmed the chemical structure, purity, and molar ratio of ions in the obtained compounds. The described compounds are novel and have not been previously described in the literature. Evaluations of physicochemical properties indicated that the obtained double-salt ionic liquids (DSILs) exhibited high thermal stability, high solubility in water, and surface activity. A biological activity assessment using greenhouse tests revealed that the herbicidal efficiency of the studied DSILs was notably increased compared to the reference commercial herbicide (even by ∼50% in the case of oilseed rape), which could be attributed to their high wettability toward hydrophobic surfaces. The compounds also efficiently inhibited the growth of several microbial species, with minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC)/minimum fungicidal concentration (MFC) values at the level of several μg·mL-1. The length of the spacer and alkyl substituent in the cation notably influenced the physicochemical and biological properties of the DSILs, which allowed us to design the structures of the obtained compounds in accordance with needs. The presented results confirm the high application potential of the described DSILs and provide a new and promising path for obtaining new and efficient plant-protection agents.
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Affiliation(s)
- Daria Szymaniak
- Faculty
of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, Poznań 60-965, Poland
| | - Kamil Ciarka
- PPC
ADOB, ul. Kołodzieja
11, Poznań 61-070, Poland
| | - Katarzyna Marcinkowska
- Institute
of Plant Protection, National Research Institute, ul. Węgorka 20, Poznań 60-318, Poland
| | - Tadeusz Praczyk
- Institute
of Plant Protection, National Research Institute, ul. Węgorka 20, Poznań 60-318, Poland
| | - Daniela Gwiazdowska
- Department
of Natural Science and Quality Assurance, Institute of Quality Science, Poznan University of Economics and Business, al. Niepodległości
10, Poznań 61-875, Poland
| | - Katarzyna Marchwińska
- Department
of Natural Science and Quality Assurance, Institute of Quality Science, Poznan University of Economics and Business, al. Niepodległości
10, Poznań 61-875, Poland
| | - Filip Walkiewicz
- Faculty
of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, Poznań 60-965, Poland
| | - Juliusz Pernak
- Faculty
of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, ul. Berdychowo 4, Poznań 60-965, Poland
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Li X, Zhang B, Hu Y, Zhao Y. New Insights Into Gut-Bacteria-Derived Indole and Its Derivatives in Intestinal and Liver Diseases. Front Pharmacol 2021; 12:769501. [PMID: 34966278 PMCID: PMC8710772 DOI: 10.3389/fphar.2021.769501] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
The interaction between host and microorganism widely affects the immune and metabolic status. Indole and its derivatives are metabolites produced by the metabolism of tryptophan catalyzed by intestinal microorganisms. By activating nuclear receptors, regulating intestinal hormones, and affecting the biological effects of bacteria as signaling molecules, indole and its derivatives maintain intestinal homeostasis and impact liver metabolism and the immune response, which shows good therapeutic prospects. We reviewed recent studies on indole and its derivatives, including related metabolism, the influence of diets and intestinal commensal bacteria, and the targets and mechanisms in pathological conditions, especially progress in therapeutic strategies. New research insights into indoles will facilitate a better understanding of their druggability and application in intestinal and liver diseases.
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Affiliation(s)
- Xiaojing Li
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Binbin Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiyang Hu
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Clinical Pharmacology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Zhao
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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39
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From Lab to Farm: Elucidating the Beneficial Roles of Photosynthetic Bacteria in Sustainable Agriculture. Microorganisms 2021; 9:microorganisms9122453. [PMID: 34946055 PMCID: PMC8707939 DOI: 10.3390/microorganisms9122453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Photosynthetic bacteria (PSB) possess versatile metabolic abilities and are widely applied in environmental bioremediation, bioenergy production and agriculture. In this review, we summarize examples of purple non-sulfur bacteria (PNSB) through biofertilization, biostimulation and biocontrol mechanisms to promote plant growth. They include improvement of nutrient acquisition, production of phytohormones, induction of immune system responses, interaction with resident microbial community. It has also been reported that PNSB can produce an endogenous 5-aminolevulinic acid (5-ALA) to alleviate abiotic stress in plants. Under biotic stress, these bacteria can trigger induced systemic resistance (ISR) of plants against pathogens. The nutrient elements in soil are significantly increased by PNSB inoculation, thus improving fertility. We share experiences of researching and developing an elite PNSB inoculant (Rhodopseudomonas palustris PS3), including strategies for screening and verifying beneficial bacteria as well as the establishment of optimal fermentation and formulation processes for commercialization. The effectiveness of PS3 inoculants for various crops under field conditions, including conventional and organic farming, is presented. We also discuss the underlying plant growth-promoting mechanisms of this bacterium from both microbial and plant viewpoints. This review improves our understanding of the application of PNSB in sustainable crop production and could inspire the development of diverse inoculants to overcome the changes in agricultural environments created by climate change.
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40
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Han H, Safe S, Jayaraman A, Chapkin RS. Diet-Host-Microbiota Interactions Shape Aryl Hydrocarbon Receptor Ligand Production to Modulate Intestinal Homeostasis. Annu Rev Nutr 2021; 41:455-478. [PMID: 34633858 PMCID: PMC8667662 DOI: 10.1146/annurev-nutr-043020-090050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated basic-helix-loop-helix transcription factor that binds structurally diverse ligands and senses cues from environmental toxicants and physiologically relevant dietary/microbiota-derived ligands. The AhR is an ancient conserved protein and is widely expressed across different tissues in vertebrates and invertebrates. AhR signaling mediates a wide range of cellular functions in a ligand-, cell type-, species-, and context-specific manner. Dysregulation of AhR signaling is linked to many developmental defects and chronic diseases. In this review, we discuss the emerging role of AhR signaling in mediating bidirectional host-microbiome interactions. We also consider evidence showing the potential for the dietary/microbial enhancement ofhealth-promoting AhR ligands to improve clinical pathway management in the context of inflammatory bowel diseases and colon tumorigenesis.
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Affiliation(s)
- Huajun Han
- Program in Integrative Nutrition and Complex Diseases and Department of Nutrition, Texas A&M University, College Station, Texas 77843, USA;
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Stephen Safe
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition and Complex Diseases and Department of Nutrition, Texas A&M University, College Station, Texas 77843, USA;
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
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41
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Lin H, Li Y, Hill RT. Microalgal and bacterial auxin biosynthesis: implications for algal biotechnology. Curr Opin Biotechnol 2021; 73:300-307. [PMID: 34619482 DOI: 10.1016/j.copbio.2021.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/03/2021] [Accepted: 09/12/2021] [Indexed: 12/21/2022]
Abstract
Optimization of microalgal growth and high-value metabolite production are key steps in microalgal mass culture for the algae industry. An emerging technology is the use of phytohormones, like indole-3-acetic acid (IAA), to promote microalgal growth. This requires an understanding of the biosynthesis of IAA in microalgae-bacteria associations and its function in regulating algal physiology and metabolite production. We review the current advances in understanding of microalgal and bacterial auxin biosynthesis and their implications for algal biotechnology.
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Affiliation(s)
- Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA.
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42
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Insight into the Metabolic Profiles of Pb(II) Removing Microorganisms. Molecules 2021; 26:molecules26134008. [PMID: 34209142 PMCID: PMC8271443 DOI: 10.3390/molecules26134008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 11/17/2022] Open
Abstract
The objective of the study was to gather insight into the metabolism of lead-removing microorganisms, coupled with Pb(II) removal, biomass viability and nitrate concentrations for Pb(II) bioremoval using an industrially obtained microbial consortium. The consortium used for study has proven to be highly effective at removing aqueous Pb(II) from solution. Anaerobic batch experiments were conducted with Luria-Bertani broth as rich growth medium over a period of 33 h, comparing a lower concentration of Pb(II) with a higher concentration at two different nutrient concentrations. Metabolite profiling and quantification were conducted with the aid of both liquid chromatography coupled with tandem mass spectroscopy (UPLC-HDMS) in a “non-targeted” fashion and high-performance liquid chromatography (HPLC) in a “targeted” fashion. Four main compounds were identified, and a metabolic study was conducted on each to establish their possible significance for Pb(II) bioremoval. The study investigates the first metabolic profile to date for Pb(II) bioremoval, which in turn can result in a clarified understanding for development on an industrial and microbial level.
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43
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Kaur J, Sharma J. Orchid Root Associated Bacteria: Linchpins or Accessories? FRONTIERS IN PLANT SCIENCE 2021; 12:661966. [PMID: 34249034 PMCID: PMC8264303 DOI: 10.3389/fpls.2021.661966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/19/2021] [Indexed: 05/28/2023]
Abstract
Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.
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Affiliation(s)
- Jaspreet Kaur
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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44
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Ulrich K, Kube M, Becker R, Schneck V, Ulrich A. Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance. Front Microbiol 2021; 12:687463. [PMID: 34220780 PMCID: PMC8245107 DOI: 10.3389/fmicb.2021.687463] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.
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Affiliation(s)
- Kristina Ulrich
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | | | - Regina Becker
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Volker Schneck
- Johann Heinrich von Thünen Institute, Institute of Forest Genetics, Waldsieversdorf, Germany
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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45
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Isolation and Characterization of Beneficial Bacteria from Food Process Wastes. Microorganisms 2021; 9:microorganisms9061156. [PMID: 34072245 PMCID: PMC8227246 DOI: 10.3390/microorganisms9061156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Significant quantities of food waste are accumulated globally on an annual basis, with approximately one-third of the food produced (equivalent to 1.3 billion tons of food) being wasted each year. A potential food waste recycling application is its utilization as a soil conditioner or fertilizer, whereby it increases the soil organic content and microbial biomass. This study evaluated the effectiveness of food waste as a microbial resource by analyzing the microbial community composition and isolating plant growth-promoting bacteria (PGPB) in food waste obtained from various sources. High-throughput sequencing identified 393 bacterial operational taxonomic units in the food process waste (FPW) samples. Moreover, the results showed that Firmicutes was abundant in the waste samples, followed by Bacteroidetes and Proteobacteria. A total of 92 bacteria were isolated from FPW. Moreover, the cultivable strains isolated from FPW belonged to the genus Bacillus, followed by Streptomyces and Proteus. Six isolated bacteria exhibited beneficial traits, including indole acetic acid production, antifungal resistance and extracellular lysis. FPW is a valuable microbial resource for isolation of PGPB, and its use as a fertilizer may enable a reduction in chemical fertilizer usage, thereby mitigating the corresponding adverse environmental impacts on sustainable crop development.
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46
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Batista BD, Dourado MN, Figueredo EF, Hortencio RO, Marques JPR, Piotto FA, Bonatelli ML, Settles ML, Azevedo JL, Quecine MC. The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom). Arch Microbiol 2021; 203:3869-3882. [PMID: 34013419 DOI: 10.1007/s00203-021-02361-z] [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] [Received: 11/10/2020] [Revised: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 12/28/2022]
Abstract
Strains of Bacillus thuringiensis (Bt) are commonly commercialized as bioinoculants for insect pest control, but their benefits go beyond their insecticidal property: they can act as plant growth-promoters. Auxins play a major role in the plant growth promotion. However, the mechanism of auxin production by the Bacilli group, and more specifically by Bt strains, is unclear. In previous work, the plant growth-promoting rhizobacterium (PGPR) B. thuringiensis strain RZ2MS9 increased the corn roots. This drew our attention to the strain's auxin production trait, earlier detected in vitro. Here, we demonstrate that in its genome, RZ2MS9 harbours the complete set of genes required in two pathways that are used for Indole acetic acid (IAA) production. We also detected that the strain produces almost five times more IAA during the stationary phase. The bacterial application increased the shoot dry weight of the Micro-Tom (MT) tomato by 24%. The application also modified MT root architecture, with an increase of 26% in the average lateral root length and inhibition of the axial root. At the cellular level, RZ2MS9-treated MT plants presented elongated root cortical cells with intensified mitotic activity. Altogether, these are the best characterized auxin-associated phenotypes. Besides that, no growth alteration was detected in the auxin-insensitive diageotropic (dgt) plants either with or without the RZ2MS9 inoculation. Our results suggest that auxins play an important role in the ability of B. thuringiensis RZ2MS9 to promote MT growth and provide a better understanding of the auxin production mechanism by a Bt strain.
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Affiliation(s)
- Bruna Durante Batista
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Manuella Nóbrega Dourado
- Department of Microbiology, Biomedicine Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Everthon Fernandes Figueredo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - Renata Ockner Hortencio
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - João Paulo Rodrigues Marques
- Laboratory of Nuclear Instrumentation, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Angelo Piotto
- Department of Crop Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Maria Letícia Bonatelli
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.,Bioinformatics Core, University of California, Davis, CA, USA
| | | | - João Lucio Azevedo
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, 11 Pádua Dias Av., Piracicaba, SP, 13418-900, Brazil.
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47
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Gao JL, Sun P, Sun YC, Xue J, Wang G, Wang LW, Du Y, Zhang X, Sun JG. Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root. Antonie van Leeuwenhoek 2021; 114:1213-1224. [PMID: 34002321 DOI: 10.1007/s10482-021-01593-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022]
Abstract
A novel Gram-stain-negative, aerobic and rod-shaped bacterium with a single polar flagellum or a stalk at the end of the cell, was isolated from maize roots in the Fangshan District of Beijing, People's Republic of China. The new strain designated 774T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3T, Caulobacter zeae 410Tand Caulobacter radices 695T, all with sequence similarities of 99.9%. The genome size of strain774T was 5.4 Mb, comprising 5042 predicted genes with a DNA G+C content of 68.7%.Three striking lasso peptide biosynthetic gene clusters and two IAA synthesis genes belonging to the TPM pathway were also found in the genome of strain 774T. The average nucleotide identity values and digital DNA-DNA hybridization values of the strain774T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774T were identified as C16: 0 (27.7%), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) (12.6%) and summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) (42.9%).The major polar lipids consisted of phosphatidyl-glycerol and glycolipids. The predominant ubiquinone was identified as Quinone 10. Based on the polyphasic characterization, strain 774T represents a novel species of the genus Caulobacter, for which the name Caulobacter endophyticus sp. nov. is proposed with 774T (= CGMCC 1.16558T = DSM 106777T) as the type strain.
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Affiliation(s)
- Jun-Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Pengbo Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Yu-Chen Sun
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China.,College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Li-Wei Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Yunpeng Du
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Xiuhai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China.
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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48
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Abdullahi S, Haris H, Zarkasi KZ, Amir HG. Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004). J Basic Microbiol 2021; 61:293-304. [PMID: 33491813 DOI: 10.1002/jobm.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 11/10/2022]
Abstract
Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy metal tolerance traits. It was able to tolerate more than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and still maintained the ability to produce plant growth-promoting substances under metal stress conditions. To explore the genetic basis of these beneficial traits, the complete genome sequencing of 4M9 was carried out using Pacific Bioscience (PacBio) sequencing technology. The complete genome consisted of one chromosome of 4,654,430 bp with a GC content of 54.6% and one plasmid of 51,135 bp with a GC content of 49.4%. Genome annotation revealed several genes involved in plant growth-promoting traits, including the production of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes involved in heavy metals (As, Co, Zn, Cu, Mn, Se, Cd, and Fe) tolerance were detected. These support its potential as a heavy metal-tolerant plant growth-promoting bacterium and a good genetic resource that can be employed to improve phytoremediation efficiency of heavy metal-contaminated soil via biotechnological techniques. This, to the best of our knowledge, is the first report on the complete genome sequence of heavy metal-tolerant plant growth-promoting E. tabaci.
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Affiliation(s)
- Saidu Abdullahi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia.,Department of Botany, Ahmadu Bello University, Zaria, Nigeria
| | - Hazzeman Haris
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Kamarul Z Zarkasi
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
| | - Hamzah G Amir
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, Penang, Malaysia
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49
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Castillo-Alfonso F, Rojas MM, Salgado-Bernal I, Carballo ME, Olivares-Hernández R, González-Bacerio J, Guisán JM, Del Monte-Martínez A. Optimization of theoretical maximal quantity of cells to immobilize on solid supports in the rational design of immobilized derivatives strategy. World J Microbiol Biotechnol 2021; 37:9. [PMID: 33392828 DOI: 10.1007/s11274-020-02972-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/29/2020] [Indexed: 11/24/2022]
Abstract
Current worldwide challenges are to increase the food production and decrease the environmental contamination by industrial emissions. For this, bacteria can produce plant growth promoter phytohormones and mediate the bioremediation of sewage by heavy metals removal. We developed a Rational Design of Immobilized Derivatives (RDID) strategy, applicable for protein, spore and cell immobilization and implemented in the RDID1.0 software. In this work, we propose new algorithms to optimize the theoretical maximal quantity of cells to immobilize (tMQCell) on solid supports, implemented in the RDIDCell software. The main modifications to the preexisting algorithms are related to the sphere packing theory and exclusive immobilization on the support surface. We experimentally validated the new tMQCell parameter by electrostatic immobilization of ten microbial strains on AMBERJET® 4200 Cl- porous solid support. All predicted tMQCell match the practical maximal quantity of cells to immobilize with a 10% confidence. The values predicted by the RDIDCell software are more accurate than the values predicted by the RDID1.0 software. 3-indolacetic acid (IAA) production by one bacterial immobilized derivative was higher (~ 2.6 μg IAA-like indoles/108 cells) than that of the cell suspension (1.5 μg IAA-like indoles/108 cells), and higher than the tryptophan amount added as indole precursor. Another bacterial immobilized derivative was more active (22 μg Cr(III)/108 cells) than the resuspended cells (14.5 μg Cr(III)/108 cells) in bioconversion of Cr(VI) to Cr(III). Optimized RDID strategy can be used to synthesize bacterial immobilized derivatives with useful biotechnological applications.
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Affiliation(s)
- Freddy Castillo-Alfonso
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba.,Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, 05348, Mexico, Mexico
| | - Marcia M Rojas
- Departamento de Microbiología y Virología, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba
| | - Irina Salgado-Bernal
- Departamento de Microbiología y Virología, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba
| | - María E Carballo
- Departamento de Microbiología y Virología, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba
| | - Roberto Olivares-Hernández
- Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, 05348, Mexico, Mexico
| | - Jorge González-Bacerio
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba. .,Departamento de Bioquímica, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba.
| | - José M Guisán
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco, 28049, Madrid, Spain
| | - Alberto Del Monte-Martínez
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25, #455, e/J e I, Vedado, 10400, Havana, Cuba.
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50
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Török N, Tanaka M, Vécsei L. Searching for Peripheral Biomarkers in Neurodegenerative Diseases: The Tryptophan-Kynurenine Metabolic Pathway. Int J Mol Sci 2020; 21:E9338. [PMID: 33302404 PMCID: PMC7762583 DOI: 10.3390/ijms21249338] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/28/2020] [Accepted: 11/29/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases are multifactorial, initiated by a series of the causative complex which develops into a certain clinical picture. The pathogenesis and disease course vary from patient to patient. Thus, it should be likewise to the treatment. Peripheral biomarkers are to play a central role for tailoring a personalized therapeutic plan for patients who suffered from neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis, among others. Nevertheless, the use of biomarkers in clinical practice is still underappreciated and data presented in biomarker research for clinical use is still uncompelling, compared to the abundant data available for drug research and development. So is the case with kynurenines (KYNs) and the kynurenine pathway (KP) enzymes, which have been associated with a wide range of diseases including cancer, autoimmune diseases, inflammatory diseases, neurologic diseases, and psychiatric disorders. This review article discusses current knowledge of KP alterations observed in the central nervous system as well as the periphery, its involvement in pathogenesis and disease progression, and emerging evidence of roles of microbiota in the gut-brain axis, searching for practical peripheral biomarkers which ensure personalized treatment plans for neurodegenerative diseases.
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Affiliation(s)
- Nóra Török
- MTA-SZTE, Neuroscience Research Group, Semmelweis u. 6, H-6725 Szeged, Hungary; (N.T.); (M.T.)
| | - Masaru Tanaka
- MTA-SZTE, Neuroscience Research Group, Semmelweis u. 6, H-6725 Szeged, Hungary; (N.T.); (M.T.)
- Department of Neurology, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary
| | - László Vécsei
- MTA-SZTE, Neuroscience Research Group, Semmelweis u. 6, H-6725 Szeged, Hungary; (N.T.); (M.T.)
- Department of Neurology, Interdisciplinary Excellence Centre, Faculty of Medicine, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary
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