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Khan N, Humm EA, Jayakarunakaran A, Hirsch AM. Reviewing and renewing the use of beneficial root and soil bacteria for plant growth and sustainability in nutrient-poor, arid soils. Front Plant Sci 2023; 14:1147535. [PMID: 37089637 PMCID: PMC10117987 DOI: 10.3389/fpls.2023.1147535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
A rapidly increasing human population coupled with climate change and several decades of over-reliance on synthetic fertilizers has led to two pressing global challenges: food insecurity and land degradation. Therefore, it is crucial that practices enabling both soil and plant health as well as sustainability be even more actively pursued. Sustainability and soil fertility encompass practices such as improving plant productivity in poor and arid soils, maintaining soil health, and minimizing harmful impacts on ecosystems brought about by poor soil management, including run-off of agricultural chemicals and other contaminants into waterways. Plant growth promoting bacteria (PGPB) can improve food production in numerous ways: by facilitating resource acquisition of macro- and micronutrients (especially N and P), modulating phytohormone levels, antagonizing pathogenic agents and maintaining soil fertility. The PGPB comprise different functional and taxonomic groups of bacteria belonging to multiple phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, among others. This review summarizes many of the mechanisms and methods these beneficial soil bacteria use to promote plant health and asks whether they can be further developed into effective, potentially commercially available plant stimulants that substantially reduce or replace various harmful practices involved in food production and ecosystem stability. Our goal is to describe the various mechanisms involved in beneficial plant-microbe interactions and how they can help us attain sustainability.
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Affiliation(s)
- Noor Khan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ethan A. Humm
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Akshaya Jayakarunakaran
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ann M. Hirsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Ann M. Hirsch,
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Kucho KI, Asukai K, Nguyen TV. NAD + Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes Environ 2023; 38. [PMID: 36858533 PMCID: PMC10037102 DOI: 10.1264/jsme2.me22093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Frankia spp. are multicellular actinobacteria that fix atmospheric dinitrogen (N2) not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species, called actinorhizal plants. To identify novel Frankia genes involved in N2 fixation, we previously isolated mutants of Frankia casuarinae that cannot fix N2. One of these genes, mutant N3H4, did not induce nodulation when inoculated into the host plant Casuarina glauca. Cell lineages that regained the ability to fix N2 as free-living cells were isolated from the mutant cell population. These restored strains also regained the ability to stimulate nodulation. A comparative ana-lysis of the genomes of mutant N3H4 and restored strains revealed that the mutant carried a mutation (Thr584Ile) in the glutamine-dependent NAD+ synthetase gene (Francci3_3146), while restored strains carried an additional suppressor mutation (Asp478Asn) in the same gene. Under nitrogen-depleted conditions, the concentration of NAD(H) was markedly lower in the mutant strain than in the wild type, whereas it was higher in restored strains. These results indicate that glutamine-dependent NAD+ synthetase plays critical roles in both free-living and symbiotic N2 fixation in Frankia.
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Affiliation(s)
- Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University
| | - Koya Asukai
- Graduate School of Science and Engineering, Kagoshima University
| | - Thanh Van Nguyen
- Graduate School of Science and Engineering, Kagoshima University
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Bender FR, Nagamatsu ST, Delamuta JRM, Ribeiro RA, Nogueira MA, Hungria M. Genetic variation in symbiotic islands of natural variant strains of soybean Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens differing in competitiveness and in the efficiency of nitrogen fixation. Microb Genom 2022; 8:000795. [PMID: 35438622 PMCID: PMC9453064 DOI: 10.1099/mgen.0.000795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022] Open
Abstract
Soybean is the most important legume cropped worldwide and can highly benefit from the biological nitrogen fixation (BNF) process. Brazil is recognized for its leadership in the use of inoculants and two strains, Bradyrhizobium japonicum CPAC 15 (=SEMIA 5079) and Bradyrhizobium diazoefficiens CPAC 7 (=SEMIA 5080) compose the majority of the 70 million doses of soybean inoculants commercialized yearly in the country. We studied a collection of natural variants of these two strains, differing in properties of competitiveness and efficiency of BNF. We sequenced the genomes of the parental strain SEMIA 566 of B. japonicum, of three natural variants of this strain (S 204, S 340 and S 370), and compared with another variant of this group, strain CPAC 15. We also sequenced the genome of the parental strain SEMIA 586 of B. diazoefficiens, of three natural variants of this strain (CPAC 390, CPAC 392 and CPAC 394) and compared with the genome of another natural variant, strain CPAC 7. As the main genes responsible for nodulation (nod, noe, nol) and BNF (nif, fix) in soybean Bradyrhizobium are located in symbiotic islands, our objective was to identify genetic variations located in this region, including single nucleotide polymorphisms (SNPs) and insertions and deletions (indels), that could be potentially related to their different symbiotic phenotypes. We detected 44 genetic variations in the B. japonicum strains and three in B. diazoefficiens. As the B. japonicum strains have gone through a longer period of adaptation to the soil, the higher number of genetic variations could be explained by survival strategies under the harsh environmental conditions of the Brazilian Cerrado biome. Genetic variations were detected in genes enconding proteins such as a dephospho-CoA kinase, related to the CoA biosynthesis; a glucosamine-fructose-6-phosphate aminotransferase, key regulator of the hexosamine biosynthetic pathway; a LysR family transcriptional regulator related to nodulation genes; and NifE and NifS proteins, directly related to the BNF process. We suggest potential genetic variations related to differences in the symbiotic phenotypes.
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Affiliation(s)
- Flavia Raquel Bender
- Department of Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, 86085-981, Londrina-PR, Brazil
| | - Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Jakeline Renata Marçon Delamuta
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, 86085-981, Londrina-PR, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Renan Augusto Ribeiro
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Marco Antonio Nogueira
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, 86085-981, Londrina-PR, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
| | - Mariangela Hungria
- Department of Biotechnology, Universidade Estadual de Londrina, C.P. 10011, 86057-970 Londrina, Paraná, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, 86085-981, Londrina-PR, Brazil
- CNPq, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001, Brasília, Federal District, Brazil
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Marappa N, Ramachandran L, Dharumadurai D, Nooruddin T. Plant Growth-Promoting Active Metabolites from Frankia spp. of Actinorhizal Casuarina spp. Appl Biochem Biotechnol 2020; 191:74-91. [PMID: 31989439 DOI: 10.1007/s12010-020-03243-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022]
Abstract
In agriculture, plant growth enrichment via plant growth stimulating microbes has been recognized as an emergency, it is used as an alternatives to chemical pesticides and growth stimulants. The phytopathogens cause various diseases such as blister bark; stem cankers, and pink and brown rot diseases besides affect the growth frequency of Casuarina spp. toward biotic and abiotic stresses. Bio-control and plant growth-promoting potential of native Frankia isolates from Casuarina spp. in Tamil Nadu, India, was not much explored. Hence, in the present study, we are investigating the plant growth improvement activity and phytopathogen control in Casuarina spp. The Frankia sp. DDNSF-01 and Frankia casuarinae DDNSF-02 were isolated and identified from the root nodules of Casuarina spp. Additionally, it is recognized for plant growth promoter activity and in vitro antimicrobial activity against phytopathogens including Pseudomonas sp. and Colletotrichum sp. The plant growth regulators including IAA, siderophore, ammonia production, and phosphate solubilization were found out. Therefore, the formation of the most significant plant growth-promoting phytohormone IAA was confirmed by UV, FT-IR, TLC, HPLC, HPTLC, and NMR spectrum. Bioactive metabolites including methyl 4-hydroxybenzoate, dodecanoic acid, and some novel flavonoids were identified. Therefore, various growth regulators such as L-aspartic acid, 1H-indole-3-carboxaldehyde were confirmed by GC-MS spectra. The present findings conclude Frankia spp. as efficient plant growth enhancement mediator and also inhibit the phytopathogens.
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Asukai K, Kucho KI. Characterization of Vesicle Differentiation Mutants of Frankia casuarinae. Microbes Environ 2020; 35:ME19150. [PMID: 32269204 PMCID: PMC7308572 DOI: 10.1264/jsme2.me19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/27/2020] [Indexed: 11/17/2022] Open
Abstract
The nitrogen-fixing actinobacterium Frankia develops unique multicellular structures called vesicles, which are the site of nitrogen fixation. These vesicles are surrounded by a thick hopanoid lipid envelope that protects nitrogenase against oxygen inactivation. The phenotypes of five mutants that form smaller numbers of vesicles were investigated. The vesicles of these mutants were smaller than those of the wild type and had a phase dark appearance. They induced the expression of a glutamine synthetase gene in hyphae cells in response to ammonium starvation. These results suggest that genes impaired in the mutants do not function in global nitrogen regulation, but specifically function in vesicle differentiation.
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Affiliation(s)
- Koya Asukai
- Graduate School of Science and Engineering, Kagoshima University, 1–21–35 Korimoto, Kagoshima 890–0065, Japan
| | - Ken-ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University, 1–21–35 Korimoto, Kagoshima 890–0065, Japan
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Affiliation(s)
- Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Pesce C, Oshone R, Hurst SG 4th, Kleiner VA, Tisa LS. Stable Transformation of the Actinobacteria Frankia spp. Appl Environ Microbiol 2019; 85:e00957-19. [PMID: 31152017 DOI: 10.1128/AEM.00957-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022] Open
Abstract
A stable and efficient plasmid transfer system was developed for nitrogen-fixing symbiotic actinobacteria of the genus Frankia, a key first step in developing a genetic system. Four derivatives of the broad-host-range cloning vector pBBR1MCS were successfully introduced into different Frankia strains by a filter mating with Escherichia coli strain BW29427. Initially, plasmid pHKT1 that expresses green fluorescent protein (GFP) was introduced into Frankia casuarinae strain CcI3 at a frequency of 4.0 × 10-3, resulting in transformants that were tetracycline resistant and exhibited GFP fluorescence. The presence of the plasmid was confirmed by molecular approaches, including visualization on agarose gel and PCR. Several other pBBR1MCS plasmids were also introduced into F. casuarinae strain CcI3 and other Frankia strains at frequencies ranging from 10-2 to 10-4, and the presence of the plasmids was confirmed by PCR. The plasmids were stably maintained for over 2 years and through passage in a plant host. As a proof of concept, a salt tolerance candidate gene from the highly salt-tolerant Frankia sp. strain CcI6 was cloned into pBBR1MCS-3. The resulting construct was introduced into the salt-sensitive F. casuarinae strain CcI3. Endpoint reverse transcriptase PCR (RT-PCR) showed that the gene was expressed in F. casuarinae strain CcI3. The expression provided an increased level of salt tolerance for the transformant. These results represent stable plasmid transfer and exogenous gene expression in Frankia spp., overcoming a major hurdle in the field. This step in the development of genetic tools in Frankia spp. will open up new avenues for research on actinorhizal symbiosis.IMPORTANCE The absence of genetic tools for Frankia research has been a major hindrance to the associated field of actinorhizal symbiosis and the use of the nitrogen-fixing actinobacteria. This study reports on the introduction of plasmids into Frankia spp. and their functional expression of green fluorescent protein and a cloned gene. As the first step in developing genetic tools, this technique opens up the field to a wide array of approaches in an organism with great importance to and potential in the environment.
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Cissoko M, Hocher V, Gherbi H, Gully D, Carré-Mlouka A, Sane S, Pignoly S, Champion A, Ngom M, Pujic P, Fournier P, Gtari M, Swanson E, Pesce C, Tisa LS, Sy MO, Svistoonoff S. Actinorhizal Signaling Molecules: Frankia Root Hair Deforming Factor Shares Properties With NIN Inducing Factor. Front Plant Sci 2018; 9:1494. [PMID: 30405656 PMCID: PMC6201211 DOI: 10.3389/fpls.2018.01494] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/25/2018] [Indexed: 05/22/2023]
Abstract
Actinorhizal plants are able to establish a symbiotic relationship with Frankia bacteria leading to the formation of root nodules. The symbiotic interaction starts with the exchange of symbiotic signals in the soil between the plant and the bacteria. This molecular dialog involves signaling molecules that are responsible for the specific recognition of the plant host and its endosymbiont. Here we studied two factors potentially involved in signaling between Frankia casuarinae and its actinorhizal host Casuarina glauca: (1) the Root Hair Deforming Factor (CgRHDF) detected using a test based on the characteristic deformation of C. glauca root hairs inoculated with F. casuarinae and (2) a NIN activating factor (CgNINA) which is able to activate the expression of CgNIN, a symbiotic gene expressed during preinfection stages of root hair development. We showed that CgRHDF and CgNINA corresponded to small thermoresistant molecules. Both factors were also hydrophilic and resistant to a chitinase digestion indicating structural differences from rhizobial Nod factors (NFs) or mycorrhizal Myc-LCOs. We also investigated the presence of CgNINA and CgRHDF in 16 Frankia strains representative of Frankia diversity. High levels of root hair deformation (RHD) and activation of ProCgNIN were detected for Casuarina-infective strains from clade Ic and closely related strains from clade Ia unable to nodulate C. glauca. Lower levels were present for distantly related strains belonging to clade III. No CgRHDF or CgNINA could be detected for Frankia coriariae (Clade II) or for uninfective strains from clade IV.
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Affiliation(s)
- Maimouna Cissoko
- Laboratoire Commun de Microbiologie, Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
| | - Valérie Hocher
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
| | - Hassen Gherbi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
| | - Alyssa Carré-Mlouka
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
- UMR 7245, Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Universités, Paris, France
| | - Seyni Sane
- Laboratoire de Botanique et de Biodiversité Végétale, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Sarah Pignoly
- Laboratoire Commun de Microbiologie, Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
| | - Antony Champion
- Laboratoire Commun de Microbiologie, Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
- UMR Diversité Adaptation et Développement des Plantes (DIADE), Institut de Recherche pour le Développement, Montpellier, France
| | - Mariama Ngom
- Laboratoire Commun de Microbiologie, Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
| | - Petar Pujic
- Ecologie Microbienne, UMR 5557 CNRS, Université Lyon 1, Villeurbanne, France
| | - Pascale Fournier
- Ecologie Microbienne, UMR 5557 CNRS, Université Lyon 1, Villeurbanne, France
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Tunis, Tunisia
| | - Erik Swanson
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Céline Pesce
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Mame Oureye Sy
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Sergio Svistoonoff
- Laboratoire Commun de Microbiologie, Institut de Recherche pour le Développement/Institut Sénégalais de Recherches Agricoles/Université Cheikh Anta Diop, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés Aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche pour le Développement/INRA/CIRAD, Université Montpellier/SupAgro, Montpellier, France
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