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Ferrando L, Rariz G, Martínez-Pereyra A, Fernández-Scavino A. Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties. J Appl Microbiol 2024; 135:lxae157. [PMID: 38925647 DOI: 10.1093/jambio/lxae157] [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: 03/29/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIM Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Affiliation(s)
- Lucía Ferrando
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Gastón Rariz
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Andrea Martínez-Pereyra
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
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2
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Hata S, Tsuda R, Kojima S, Tanaka A, Kouchi H. Both incompatible and compatible rhizobia inhabit the intercellular spaces of leguminous root nodules. PLANT SIGNALING & BEHAVIOR 2023; 18:2245995. [PMID: 37573516 PMCID: PMC10424618 DOI: 10.1080/15592324.2023.2245995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
In addition to rhizobia, many types of co-existent bacteria are found in leguminous root nodules, but their habitats are unclear. To investigate this phenomenon, we labeled Bradyrhizobium diazoefficiens USDA122 and Bradyrhizobium sp. SSBR45 with Discosoma sp. red fluorescent protein (DsRed) or enhanced green fluorescent protein (eGFP). USDA122 enhances soybean growth by forming effective root nodules, but SSBR45 does not form any nodules. Using low-magnification laser scanning confocal microscopy, we found that infected cells in the central zone of soybean nodules appeared to be occupied by USDA122. Notably, high-magnification microscopy after co-inoculation of non-fluorescent USDA122 and fluorescence-labeled SSBR45 also revealed that SSBR45 inhabits the intercellular spaces of healthy nodules. More unexpectedly, co-inoculation of eGFP-labeled USDA122 and DsRed-labeled SSBR45 (and vice versa) revealed the presence of USDA122 bacteria in both the symbiosomes of infected cells and in the apoplasts of healthy nodules. We then next inspected nodules formed after a mixed inoculation of differently-labeled USDA122, without SSBR45, and confirmed the inhabitation of the both populations of USDA122 in the intercellular spaces. In contrast, infected cells were occupied by single-labeled USDA122. We also observed Mesorhizobium loti in the intercellular spaces of active wild-type nodules of Lotus japonicus using transmission electron microscopy. Compatible intercellular rhizobia have been described during nodule formation of several legume species and in some mutants, but our evidence suggests that this type of colonization may occur much more commonly in leguminous root nodules.
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Affiliation(s)
- Shingo Hata
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Risa Tsuda
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Serina Kojima
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiroshi Kouchi
- Division of Arts and Sciences, International Christian University, Mitaka, Japan
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3
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Hata S, Kojima S, Tsuda R, Kawajiri N, Kouchi H, Suzuki T, Uesaka K, Tanaka A. Characterization of photosynthetic Bradyrhizobium sp. strain SSBR45 isolated from the root nodules of Aeschynomene indica. PLANT SIGNALING & BEHAVIOR 2023; 18:2184907. [PMID: 36879507 PMCID: PMC10012927 DOI: 10.1080/15592324.2023.2184907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
We isolated a novel strain of Bradyrhizobium sp., SSBR45, from the nodulated roots of Aeschynomene indica and labeled it with Discosoma sp. red fluorescent protein (dsRED) or enhanced green fluorescent protein (eGFP) and determined its draft genomic sequence. The labeled SSBR45 stimulated the growth of A. indica markedly on a nitrogen-free medium, as observed by visualizing the fluorescent root nodules. The nodulated roots also exhibited high acetylene reduction activities. The SSBR45 genome included genes involved in nitrogen fixation, photosynthesis, and type IV secretion system; however, it did not consist of canonical nodABC genes and type III secretion system genes. SSBR45, a novel species of the genus Bradyrhizobium, consisted of an average nucleotide identity and average amino acid identity of 87% and 90%, respectively, with the closest strain B. oligotrophicum S58.
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Affiliation(s)
- Shingo Hata
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Serina Kojima
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Risa Tsuda
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | | | - Hiroshi Kouchi
- Division of Arts and Sciences, International Christian University, Mitaka, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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4
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Tamang A, Swarnkar M, Kumar P, Kumar D, Pandey SS, Hallan V. Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb. Microbiol Spectr 2023; 11:e0227923. [PMID: 37811959 PMCID: PMC10715050 DOI: 10.1128/spectrum.02279-23] [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: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Pawan Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dinesh Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
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5
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Wangthaisong P, Piromyou P, Songwattana P, Wongdee J, Teamtaisong K, Tittabutr P, Boonkerd N, Teaumroong N. The Type IV Secretion System (T4SS) Mediates Symbiosis between Bradyrhizobium sp. SUTN9-2 and Legumes. Appl Environ Microbiol 2023; 89:e0004023. [PMID: 37255432 PMCID: PMC10304904 DOI: 10.1128/aem.00040-23] [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: 01/10/2023] [Accepted: 04/22/2023] [Indexed: 06/01/2023] Open
Abstract
There has been little study of the type IV secretion system (T4SS) of bradyrhizobia and its role in legume symbiosis. Therefore, broad host range Bradyrhizobium sp. SUTN9-2 was selected for study. The chromosome of Bradyrhizobium sp. SUTN9-2 contains two copies of the T4SS gene, homologous with the tra/trb operons. A phylogenetic tree of the T4SS gene traG was constructed, which exemplified its horizontal transfer among Bradyrhizobium and Mesorhizobium genera. They also showed similar gene arrangements for the tra/trb operons. However, the virD2 gene was not observed in Mesorhizobium, except M. oppotunistum WSM2075. Interestingly, the orientation of copG, traG, and virD2 cluster was unique to the Bradyrhizobium genus. The phylogenetic tree of copG, traG, and virD2 demonstrated that copies 1 and 2 of these genes were grouped in different clades. In addition, the derived mutant and complementation strains of T4SS were investigated in representative legumes Genistoids, Dalbergioids, and Millettiods. When T4SS copy 1 (T4SS1) was deleted, the nodule number and nitrogenase activity decreased. This supports a positive effect of T4SS1 on symbiosis. In addition, delayed nodulation was observed 7 dpi, which was restored by the complementation of T4SS1. Therefore, T4SS plays an important role in the symbiotic interaction between Bradyrhizobium sp. SUTN9-2 and its leguminous hosts. IMPORTANCE SUTN9-2 is a broad host range strain capable of symbiosis with several legumes. Two copies of T4SS clusters belonging to the tra/trb operon are observed on chromosomes with different gene arrangements. We use phylogenetic tree and gene annotation analysis to predict the evolution of the tra/trb operon of rhizobia. Our finding suggests that the gene encoding the T4SS gene among Bradyrhizobium and Mesorhizobium may have coevolution. In addition, Bradyrhizobium has a uniquely arranged copG, traG, and virD2 gene cluster. The results of T4SS1 gene deletion and complementation revealed its positive effect on nodulation. Therefore, T4SS seems to be another determinant for symbiosis. This is the first report on the role of T4SS in Bradyrhizobium symbiosis.
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Affiliation(s)
- Praneet Wangthaisong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kamonluck Teamtaisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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6
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Promotion of Peanut (Arachis hypogaea L.) Growth by Plant Growth-Promoting Microorganisms. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Brazil is an important peanut producer, but despite its high production, there still needs to be an inoculant for the peanut crop. In addition, the use of microorganisms that promote plant growth (PGPM) is not common, and this crop is highly dependent on chemical fertilizers. An excellent alternative to reduce the use of fertilizers and chemical inputs in peanut crops while reducing the production cost and environmental impact is the use of PGPM. The objective of this study was to evaluate the effects of Azospirillum brasilense, Bacillus subtilis, Bradyrhizobium japonicum, and Trichoderma harzianum as single inoculants and co-inoculants on the growth promotion and productivity of peanuts in greenhouse and field conditions. In the greenhouse, the experiment was conducted with 12 treatments with six repetitions. In the field conditions, the experiment was conducted with five treatments with four repetitions. Both experiments were conducted in randomized blocks. In general, all the microorganisms evaluated in the present study promoted increases in root dry mass, shoot dry mass, phosphorus concentrations, and plant height in the greenhouse and under field conditions compared with the control. Interestingly, the mixtures of microorganisms inoculated in peanut plants did not promote greater plant growth and development compared with inoculations of the microorganisms separately. Specifically, in the field, the highest productivity was found for the inoculation of B. japonicum alone. The PGPM evaluated in the present study for peanut crops generally promoted some increases in productivity in greenhouse and field conditions.
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7
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Saini MR, Chandran LP, Barbadikar KM, Sevanthi AMV, Chawla G, Kaushik M, Mulani E, Phule AS, Govindannagari R, Sonth B, Sinha SK, Sundaram RM, Mandal PK. Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:939395. [PMID: 36483966 PMCID: PMC9724235 DOI: 10.3389/fpls.2022.939395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.
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Affiliation(s)
- Manish Ranjan Saini
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
- Kalinga Institute of Industrial Technology (KIIT) School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | | | - Amitha Mithra V. Sevanthi
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Gautam Chawla
- Division of Nematology, ICAR- Indian Agriculture Research Institute, New Delhi, India
| | - Megha Kaushik
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Ekta Mulani
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | | | - Bandeppa Sonth
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pranab Kumar Mandal
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
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Klepa MS, Helene LCF, O´Hara G, Hungria M. Bradyrhizobium cenepequi sp. nov., Bradyrhizobium semiaridum sp. nov., Bradyrhizobium hereditatis sp. nov. and Bradyrhizobium australafricanum sp. nov., symbionts of different leguminous plants of Western Australia and South Africa and definition of three novel symbiovars. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005446] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium
is a heterogeneous bacterial genus capable of establishing symbiotic associations with a broad range of legume hosts, including species of economic and environmental importance. This study was focused on the taxonomic and symbiovar definition of four strains – CNPSo 4026T, WSM 1704T, WSM 1738T and WSM 4400T – previously isolated from nodules of legumes in Western Australia and South Africa. The 16S rRNA gene phylogenetic tree allocated the strains to the
Bradyrhizobium elkanii
supergroup. The multilocus sequence analysis (MLSA) with partial sequences of six housekeeping genes – atpD, dnaK, glnII, gyrB, recA and rpoB – did not cluster the strains under study as conspecific to any described
Bradyrhizobium
species. Average nucleotide identity and digital DNA–DNA hybridization values were calculated for the four strains of this study and the closest species according to the MLSA phylogeny with the highest values being 95.46 and 62.20 %, respectively; therefore, both being lower than the species delineation cut-off values. The nodC and nifH phylogenies included strains WSM 1738T and WSM 4400T in the symbiovars retamae and vignae respectively, and also allowed the definition of three new symbiovars, sv. cenepequi, sv. glycinis, and sv. cajani. Analysis of morphophysiological characterization reinforced the identification of four novel proposed
Bradyrhizobium
species that are accordingly named as follows: Bradyrhizobium cenepequi sp. nov. (CNPSo 4026T=WSM 4798T=LMG 31653T), isolated from Vigna unguiculata; Bradyrhizobium semiaridum sp. nov. (WSM 1704T=CNPSo 4028T=LMG 31654T), isolated from Tephrosia gardneri; Bradyrhizobium hereditatis sp. nov. (WSM 1738T=CNPSo 4025T=LMG 31652T), isolated from Indigofera sp.; and Bradyrhizobium australafricanum sp. nov. (WSM 4400T=CNPSo 4015T=LMG 31648T) isolated from Glycine sp.
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Affiliation(s)
- Milena Serenato Klepa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Luisa Caroline Ferraz Helene
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
| | - Graham O´Hara
- Centre for Rhizobium Studies (CRS), Murdoch University 90 South St. Murdoch, WA, Australia
| | - Mariangela Hungria
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10011, 86057-970, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Distrito Federal, Brazil
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil
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Chen XL, Sun MC, Chong SL, Si JP, Wu LS. Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2022; 12:700200. [PMID: 35154169 PMCID: PMC8828500 DOI: 10.3389/fpls.2021.700200] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 05/10/2023]
Abstract
In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.
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Affiliation(s)
| | | | | | | | - Ling-shang Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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10
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Application of Recombinant Human scFv Antibody as a Powerful Tool to Monitor Nitrogen Fixing Biofertilizer in Rice and Legume. Microbiol Spectr 2021; 9:e0209421. [PMID: 34908451 PMCID: PMC8672896 DOI: 10.1128/spectrum.02094-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium is an endophytic bacterium under investigation as an efficient biofertilizer for sustainable legume-rice rotational cropping system. Monitoring and bio-imaging of this nitrogen fixing bacterium is essential for the study of plant-microbe evolution, soil microbiome, as well as quality control in organic farming. While phage display antibody technology has been widely used to generate recombinant antibody for myriad medical purposes, so far, this technology has been minimally applied in the agricultural sector. In this study, single-chain variable fragments (scFv) against two Bradyrhizobium strains SUTN9-2 (yiN92-1e10) and DOA9 (yiDOA9-162) were isolated from a human phage display antibody library. Specific binding of scFv was demonstrated by ELISA and confocal-immunofluorescence imaging techniques. Bradyrhizobium localization in both endophytic and bacteroid forms could be observed inside rice tissue and plant nodule, respectively. Moreover, successful application of the recombinant antibody for the evaluation of nodule occupancy was also demonstrated in comparison with standard GUS-staining method. The results of this study showed for the first time the potential use of human phage display scFv antibody for imaging and monitoring of Bradyrhizobium biofertilizer and thus could be further applied for point-of-detection of bacterial inoculum in the legume-rice rotational crop system. IMPORTANCE Human scFv antibody generated from phage display technology was successfully used for the generation of specific recombinant antibodies: yiN92-1e10 and yiDOA9-162 for the detection of Bradyrhizobium strains SUTN9-2 and DOA9, respectively. These two recombinant scFv antibodies could be used for precise detection of the rhizobia both in symbiosis with legume and endophyte in rice tissue by ELISA and immunofluorescent staining, during legume-rice rotational cropping system in the field. This methodology can be further employed for the study of other plant-microbe interactions and monitoring of biofertilizer in diverse sustainable cropping systems as well as in precision agriculture.
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11
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Identification of an Exopolysaccharide Biosynthesis Gene in Bradyrhizobium diazoefficiens USDA110. Microorganisms 2021; 9:microorganisms9122490. [PMID: 34946092 PMCID: PMC8707904 DOI: 10.3390/microorganisms9122490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/27/2023] Open
Abstract
Exopolysaccharides (EPS) play critical roles in rhizobium-plant interactions. However, the EPS biosynthesis pathway in Bradyrhizobium diazoefficiens USDA110 remains elusive. Here we used transposon (Tn) mutagenesis with the aim to identify genetic elements required for EPS biosynthesis in B. diazoefficiens USDA110. Phenotypic screening of Tn5 insertion mutants grown on agar plates led to the identification of a mutant with a transposon insertion site in the blr2358 gene. This gene is predicted to encode a phosphor-glycosyltransferase that transfers a phosphosugar onto a polyprenol phosphate substrate. The disruption of the blr2358 gene resulted in defective EPS synthesis. Accordingly, the blr2358 mutant showed a reduced capacity to induce nodules and stimulate the growth of soybean plants. Glycosyltransferase genes related to blr2358 were found to be well conserved and widely distributed among strains of the Bradyrhizobium genus. In conclusion, our study resulted in identification of a gene involved in EPS biosynthesis and highlights the importance of EPS in the symbiotic interaction between USDA110 and soybeans.
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Rai A, Jha MN, Singh D, Thapa S, Chaurasia SK, Jha G. Detection of endophytic association between Aeschynomene nodulating Bradyrhizobium sp. and traditional Desariya rice roots under rice-Aeschynomene ecosystem of chaur land, Bihar, India. Biol Futur 2021; 73:95-105. [PMID: 34773605 DOI: 10.1007/s42977-021-00105-0] [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: 12/31/2020] [Accepted: 11/02/2021] [Indexed: 11/27/2022]
Abstract
Engineering diazotrophic rice having either an integral component of diazotrophic microbes or placing microbial origin nif gene to the rice plant is the dream of biotechnologist. Rice-Aeschynomene ecosystem of pristine chaur land provides a suitable niche to search Rhizobium endophytes in rice. Accordingly, the work was initiated to search suitable endophytic Rhizobium strain for artificial symbiosis within the roots of Desariya rice and its source through morphological, biochemical and molecular approaches. Detection of Acetylene reduction assay (ARA) activity in sterilized Desariya rice root confirmed the presence of putative diazotrophic endophytes in rice root. Isolates from Aeschynomene aspera L. nodulating and Desariya rice endophytic Rhizobium were evaluated for growth, IAA, morphological and biochemical features. Carbon profiling pattern of both these isolates indicated that Desariya rice endophytic Rhizobium has its similarity with Aeschynomene aspera L. nodulating Rhizobium. 16S rRNA gene sequencing confirmed the presence of endophytic Bradyrhizobium sp. in Desariya rice roots and its similarity with Aeschynomene aspera L. nodulating Bradyrhizobium. Desariya rice Bradyrhizobium may be an ideal candidate in the future for creating artificial symbiosis in rice due to its similarity with Aeschynomene aspera L. Bradyrhizobium.
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Affiliation(s)
- Abhilasha Rai
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Manindra Nath Jha
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Devendra Singh
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
- ICAR-Central Arid Zone Research Institute, Jodhpur, Rajasthan, 342003, India.
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, MaunathBhanjan, Uttar Pradesh, 275103, India
| | - Sanjeet Kumar Chaurasia
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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13
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Hernández I, Taulé C, Pérez-Pérez R, Battistoni F, Fabiano E, Rivero D, Nápoles MC. Endophytic rhizobia promote the growth of Cuban rice cultivar. Symbiosis 2021. [DOI: 10.1007/s13199-021-00803-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Klasek SA, Brock MT, Morrison HG, Weinig C, Maignien L. Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure. Front Microbiol 2021; 12:645784. [PMID: 33897658 PMCID: PMC8058099 DOI: 10.3389/fmicb.2021.645784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.
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Affiliation(s)
- Scott A Klasek
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States.,Department of Botany, University of Wyoming, Laramie, WY, United States
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, United States
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, United States.,Program in Ecology, University of Wyoming, Laramie, WY, United States.,Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
| | - Loïs Maignien
- Marine Biological Laboratory, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States.,UMR 6197, Laboratory of Microbiology of Extreme Environments, Institut Européen de la Mer, Université de Bretagne Occidentale, Brest, France
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15
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Tian L, Wang E, Lin X, Ji L, Chang J, Chen H, Wang J, Chen D, Tran LSP, Tian C. Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding. BMC Genomics 2021; 22:278. [PMID: 33865333 PMCID: PMC8052703 DOI: 10.1186/s12864-021-07587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. RESULTS In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. CONCLUSIONS This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Enze Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Xiaolong Lin
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongping Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Dazhou Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
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16
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Lu L, Chang M, Han X, Wang Q, Wang J, Yang H, Guan Q, Dai S. Beneficial effects of endophytic Pantoea ananatis with ability to promote rice growth under saline stress. J Appl Microbiol 2021; 131:1919-1931. [PMID: 33754394 DOI: 10.1111/jam.15082] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 11/28/2022]
Abstract
AIMS Soil salinization severely inhibits plant growth, leading to a low crop yield. The aim of the current study was to isolate endophytic bacteria with the ability to promote rice growth under saline conditions. METHODS AND RESULTS We isolated eight salt-tolerant endophytic bacteria from rice roots. An isolated strain D1 was selected due to its ability to stimulate rice seed germination in the presence of NaCl, which was identified as Pantoea ananatis D1. It exhibited multiple plant growth-promoting traits including phosphate solubilization, production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore. Inoculation of P. ananatis D1 obviously enhanced the rice root and shoot growth under normal and saline conditions. It also significantly increased the contents of chlorophyll, total soluble protein, and proline in salt-stressed rice seedlings. Moreover P. ananatis D1 could ameliorate the oxidative stress in rice induced by NaCl and Na2 CO3 treatment. The malondialdehyde content and various antioxidant enzyme activities were decreased by P. ananatis D1 inoculation in salt-affected rice. In addition, P. ananatis D1 showed a positive potential for limiting the Na+ accumulation and enhancing the K+ uptake, leading to an increase of 1·2-1·7 fold in K+ /Na+ ratio under saline environment. CONCLUSIONS Pantoea ananatis D1 has the ability to improve the salt tolerance of rice seedlings. SIGNIFICANCE AND IMPACT OF THE STUDY The application of plant growth-promoting bacteria (PGPB) is an eco-friendly strategy to improve plant tolerance towards abiotic stresses. We demonstrated that P. ananatis D1 could be used as an effective halotolerant PGPB to enhance rice growth in different salt-affected soils.
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Affiliation(s)
- L Lu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.,College of Life Sciences, Northeast Forestry University, Harbin, China
| | - M Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.,College of Life Sciences, Northeast Forestry University, Harbin, China
| | - X Han
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Q Wang
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | - J Wang
- College of Life Sciences, Northeast Forestry University, Harbin, China
| | - H Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.,College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Q Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.,College of Life Sciences, Northeast Forestry University, Harbin, China
| | - S Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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17
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Okamoto T, Shinjo R, Nishihara A, Uesaka K, Tanaka A, Sugiura D, Kondo M. Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content. FRONTIERS IN PLANT SCIENCE 2021; 12:719259. [PMID: 34447404 PMCID: PMC8383490 DOI: 10.3389/fpls.2021.719259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 05/14/2023]
Abstract
Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.
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Affiliation(s)
- Takanori Okamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- *Correspondence: Takanori Okamoto
| | - Rina Shinjo
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Arisa Nishihara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Daisuke Sugiura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Motohiko Kondo
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Motohiko Kondo
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18
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Cai W, Ou F, Staehelin C, Dai W. Bradyrhizobium sp. strain ORS278 promotes rice growth and its quorum sensing system is required for optimal root colonization. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:656-666. [PMID: 32929871 DOI: 10.1111/1758-2229.12885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/10/2020] [Indexed: 05/25/2023]
Abstract
Many Gram-negative bacteria communicate by using homoserine lactones (HSLs) as quorum sensing (QS) signals in a cell density-dependent manner. In addition to fatty acyl-HSL (acyl-HSL) signals, certain strains, most of them associated with plants, produce non-canonical aryl-HSLs such as cinnamoyl-HSL. However, the role of aryl-HSL in endophytic associations remained elusive. Bradyrhizobium sp. strain ORS278 possesses a LuxI-LuxR type QS system and produces cinnamoyl-HSL as a QS signal. Here, we report that strain ORS278 promotes growth of domesticated rice (Oryza sativa). QS mutants unable to produce cinnamoyl-HSL exhibited reduced plant-growth promoting activity in comparison to the parent strain ORS278. Likewise, the QS mutants were impaired in their ability to colonize rice roots. These findings suggest that genes controlled by cinnamoyl-HSL play an important role in the association between rice and ORS278. However, biofilm production was not visibly altered in these mutants. In conclusion, our study highlights the importance of aryl-HSLs in endophytic plant-bacteria interactions.
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Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Fuwen Ou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Bioresources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
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19
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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20
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Banerjee G, Basak S, Roy T, Chattopadhyay P. Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp. FEMS Microbiol Ecol 2020; 95:5586991. [PMID: 31609448 DOI: 10.1093/femsec/fiz165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/13/2019] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
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Affiliation(s)
- Goutam Banerjee
- Department of Biochemistry, University of Calcutta, West Bengal 700019, India
| | - Swarnendu Basak
- Department of Medical Zoology, Kyung Hee University, School of Medicine, Seoul 02447, Republic of Korea
| | - Tathagato Roy
- Member of Jeevak Herb Welfare Society (registration number S/1L/78148 OF 2010-2011), Santiniketan, 731235, India.,Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, U.S
| | - Pritam Chattopadhyay
- Department of Biotechnology, Gauhati University, Guwahati, Assam 781014, India.,Department of Botany, M.U.C. Women's College, University of Bardhaman, Bardhaman, West Bengal 713104, India
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21
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Greetatorn T, Hashimoto S, Maeda T, Fukudome M, Piromyou P, Teamtisong K, Tittabutr P, Boonkerd N, Kawaguchi M, Uchiumi T, Teaumroong N. Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation. Microbes Environ 2020; 35:ME20049. [PMID: 32727975 PMCID: PMC7511792 DOI: 10.1264/jsme2.me20049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.
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Affiliation(s)
- Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Taro Maeda
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Mitsutaka Fukudome
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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22
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Liu X, Liu C, Gao W, Xue C, Guo Z, Jiang L, Li F, Liu Y. Impact of biochar amendment on the abundance and structure of diazotrophic community in an alkaline soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:944-951. [PMID: 31726576 DOI: 10.1016/j.scitotenv.2019.06.293] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
Abstract
Biological nitrogen (N) fixation contributes to the pool of plant-available N in soil and helps to minimize the use of inorganic N fertilizer in agricultural ecosystems. Although diazotrophs play an important role in the biological fixation of atmospheric N2 in a range of soil types, the knowledge of their response to biochar amendment is still limited. Here, using the nifH gene as a molecular marker, we investigated the short-term effect of biochar application on the abundance, community composition and activity of diazotroph in an alkaline soil. A field trial was established before soybean sowing in 2017 and five treatments were included: inorganic NPK fertilizer (CK); inorganic NPK fertilizer + wheat straw (CS); inorganic NPK fertilizer + low rate of biochar (B4); inorganic NPK fertilizer + high rate of biochar (B20); biochar compound fertilizer (BCF). The field trial was lasted for one crop season and samples were collected by soybean harvest. The results showed that biochar addition generally increased the concentration of soil organic carbon (SOC) and available phosphorous (AP), while B20 treatment significantly increased the total nitrogen (TN) and available potassium (AK). Biochar addition treatments increased the nifH gene abundance and altered the community structure of soil diazotrophs. The abundance of nifH gene was positively correlated with SOC, indicating that increasing SOC potentially affected diazotrophic population in the alkaline soil. Community structure of diazotrophs in the CS treatment was similar with the CK treatment; thus, there was no effect of crop straw on diazotroph community structure. In contrast, the application of biochar and biochar compound fertilizer altered the diazotroph community structure with shifts in the dominant genus, with higher Sinorhizobium in the biochar-amended treatments. SOC, C/N and AP were the key factors correlated with change in diazotroph community structure. Overall, our results suggest that the addition of biochar or biochar compound fertilizer could increase the abundance and alter the community structure of diazotrophs, which may benefit N fixation in alkaline agricultural soil. Conversely, the direct straw return had no effect on the abundance and community structure of diazotrophs.
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Affiliation(s)
- Xiaoyu Liu
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Cheng Liu
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Wenhui Gao
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Chen Xue
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Zonghao Guo
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi 830011, China
| | - Feng Li
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China.
| | - Yuan Liu
- Department of Bioengineering, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, China.
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Yoneyama T, Terakado-Tonooka J, Bao Z, Minamisawa K. Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. PLANTS 2019; 8:plants8100408. [PMID: 31614562 PMCID: PMC6843303 DOI: 10.3390/plants8100408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 01/16/2023]
Abstract
Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N2) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N2 fixation in non-leguminous plants. Identification of the involved N2-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N2 fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N2. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N2 by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.
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Affiliation(s)
- Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Junko Terakado-Tonooka
- National Agriculture and Food Research Organization, Kannondai 3-1-1, Tsukuba, Ibaraki 305-8666, Japan.
| | - Zhihua Bao
- School of Ecology and Environment, Inner Mongolia University, 235 West University Blvd., Hohhot 010021, Inner Mongolia, China.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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Hara S, Morikawa T, Wasai S, Kasahara Y, Koshiba T, Yamazaki K, Fujiwara T, Tokunaga T, Minamisawa K. Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses. Front Microbiol 2019; 10:407. [PMID: 30915047 PMCID: PMC6422874 DOI: 10.3389/fmicb.2019.00407] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/15/2019] [Indexed: 02/04/2023] Open
Abstract
Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using “omics” approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9–3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.
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Affiliation(s)
- Shintaro Hara
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takashi Morikawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sawa Wasai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | | | - Kiyoshi Yamazaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Biodiversity of Endophytic Fungi from Diverse Niches and Their Biotechnological Applications. ADVANCES IN ENDOPHYTIC FUNGAL RESEARCH 2019. [DOI: 10.1007/978-3-030-03589-1_6] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Potential of Rice Stubble as a Reservoir of Bradyrhizobial Inoculum in Rice-Legume Crop Rotation. Appl Environ Microbiol 2017; 83:AEM.01488-17. [PMID: 28916558 DOI: 10.1128/aem.01488-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/06/2017] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium encompasses a variety of bacteria that can live in symbiotic and endophytic associations with leguminous and nonleguminous plants, such as rice. Therefore, it can be expected that rice endophytic bradyrhizobia can be applied in the rice-legume crop rotation system. Some endophytic bradyrhizobial strains were isolated from rice (Oryza sativa L.) tissues. The rice biomass could be enhanced when supplementing bradyrhizobial strain inoculation with KNO3, NH4NO3, or urea, especially in Bradyrhizobium sp. strain SUTN9-2. In contrast, the strains which suppressed rice growth were photosynthetic bradyrhizobia and were found to produce nitric oxide (NO) in the rice root. The expression of genes involved in NO production was conducted using a quantitative reverse transcription-PCR (qRT-PCR) technique. The nirK gene expression level in Bradyrhizobium sp. strain SUT-PR48 with nitrate was higher than that of the norB gene. In contrast, the inoculation of SUTN9-2 resulted in a lower expression of the nirK gene than that of the norB gene. These results suggest that SUT-PR48 may accumulate NO more than SUTN9-2 does. Furthermore, the nifH expression of SUTN9-2 was induced in treatment without nitrogen supplementation in an endophytic association with rice. The indole-3-acetic acid (IAA) and 1-amino-cyclopropane-1-carboxylic acid (ACC) deaminase produced in planta by SUTN9-2 were also detected. Enumeration of rice endophytic bradyrhizobia from rice tissues revealed that SUTN9-2 persisted in rice tissues until rice-harvesting season. The mung bean (Vigna radiata) can be nodulated after rice stubbles were decomposed. Therefore, it is possible that rice stubbles can be used as an inoculum in the rice-legume crop rotation system under both low- and high-organic-matter soil conditions.IMPORTANCE This study shows that some rice endophytic bradyrhizobia could produce IAA and ACC deaminase and have a nitrogen fixation ability during symbiosis inside rice tissues. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobia. However, the NO-producing strains should be of concern due to a possible deleterious effect of NO on rice growth. In addition, this study reports the application of endophytic bradyrhizobia in rice stubbles, and the rice stubbles were used directly as an inoculum for a leguminous plant (mung bean). The degradation of rice stubbles leads to an increased number of SUTN9-2 in the soil and may result in increased mung bean nodulation. Therefore, the persistence of endophytic bradyrhizobia in rice tissues can be developed to use rice stubbles as an inoculum for mung bean in a rice-legume crop rotation system.
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Songwattana P, Noisangiam R, Teamtisong K, Prakamhang J, Teulet A, Tittabutr P, Piromyou P, Boonkerd N, Giraud E, Teaumroong N. Type 3 Secretion System (T3SS) of Bradyrhizobium sp. DOA9 and Its Roles in Legume Symbiosis and Rice Endophytic Association. Front Microbiol 2017; 8:1810. [PMID: 28979252 PMCID: PMC5611442 DOI: 10.3389/fmicb.2017.01810] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/05/2017] [Indexed: 11/15/2022] Open
Abstract
The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod, nif, and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod-box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (ΩrhcN) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four (Arachis hypogea, Vigna radiata, Crotalaria juncea, and Macroptilium atropurpureum) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one (Stylosanthes hamata) responded negatively (fewer nodules and less nitrogen fixation) and four species (Aeschynomene americana, Aeschynomene afraspera, Indigofera tinctoria, and Desmodium tortuosum) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice.
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Affiliation(s)
- Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Rujirek Noisangiam
- National Bureau of Agricultural Commodity and Food Standards, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Janpen Prakamhang
- Department of Applied Biology, Faculty of Sciences and Liberal Arts, Rajamangala University of Technology IsanNakhon Ratchasima, Thailand
| | - Albin Teulet
- Institut de Recherche pour le Développement, LSTM, UMR IRD/SupAgro/INRA/Univ. Montpellier/CIRADMontpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD/SupAgro/INRA/Univ. Montpellier/CIRADMontpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
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Rangjaroen C, Sungthong R, Rerkasem B, Teaumroong N, Noisangiam R, Lumyong S. Untapped Endophytic Colonization and Plant Growth-Promoting Potential of the Genus Novosphingobium to Optimize Rice Cultivation. Microbes Environ 2017; 32:84-87. [PMID: 28228608 PMCID: PMC5371080 DOI: 10.1264/jsme2.me16112] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With the aim of searching for potent diazotrophic bacteria that are free of public health concerns and optimize rice cultivation, the endophytic colonization and plant growth-promoting activities of some endophytic diazotrophic bacteria isolated from rice were evaluated. Among these bacteria, the emerging diazotrophic strains of the genus Novosphingobium effectively associated with rice plant interiors and consequently promoted the growth of rice, even with the lack of a nitrogen source. These results suggest that diazotrophic Novosphingobium is an alternative microbial resource for further development as a safe biological enhancer in the optimization of organic rice cultivation.
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Affiliation(s)
- Chakrapong Rangjaroen
- Microbiology Division, Department of Biology, Faculty of Science, Chiang Mai University
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29
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Guha S, Sarkar M, Ganguly P, Uddin MR, Mandal S, DasGupta M. Segregation of nod-containing and nod-deficient bradyrhizobia as endosymbionts of Arachis hypogaea and as endophytes of Oryza sativa in intercropped fields of Bengal Basin, India. Environ Microbiol 2016; 18:2575-90. [PMID: 27102878 DOI: 10.1111/1462-2920.13348] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 04/17/2016] [Indexed: 11/30/2022]
Abstract
Bradyrhizobial invasion in dalbergoid legumes like Arachis hypogaea and endophytic bacterial invasions in non-legumes like Oryza sativa occur through epidermal cracks. Here, we show that there is no overlap between the bradyrhizobial consortia that endosymbiotically and endophytically colonise these plants. To minimise contrast due to phylogeographic isolation, strains were collected from Arachis/Oryza intercropped fields and a total of 17 bradyrhizobia from Arachis (WBAH) and 13 from Oryza (WBOS) were investigated. 16SrRNA and concatenated dnaK-glnII-recA phylogeny clustered the nodABC-positive WBAH and nodABC-deficient WBOS strains in two distinct clades. The in-field segregation is reproducible under controlled conditions which limits the factors that influence their competitive exclusion. While WBAH renodulated Arachis successfully, WBOS nodulated in an inefficient manner. Thus, Arachis, like other Aeschynomene legumes support nod-independent symbiosis that was ineffectual in natural fields. In Oryza, WBOS recolonised endophytically and promoted its growth. WBAH however caused severe chlorosis that was completely overcome when coinfected with WBOS. This explains the exclusive recovery of WBOS in Oryza in natural fields and suggests Nod-factors to have a role in counterselection of WBAH. Finally, canonical soxY1 and thiosulphate oxidation could only be detected in WBOS indicating loss of metabolic traits in WBAH with adaptation of symbiotic lifestyle.
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Affiliation(s)
- Sohini Guha
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Monolina Sarkar
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Pritha Ganguly
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Md Raihan Uddin
- Department of Microbiology, University of Calcutta, Kolkata, 700019, India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta, Kolkata, 700019, India
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
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30
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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31
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Piromyou P, Songwattana P, Greetatorn T, Okubo T, Kakizaki KC, Prakamhang J, Tittabutr P, Boonkerd N, Teaumroong N, Minamisawa K. The Type III Secretion System (T3SS) is a Determinant for Rice-Endophyte Colonization by Non-Photosynthetic Bradyrhizobium. Microbes Environ 2015; 30:291-300. [PMID: 26582551 PMCID: PMC4676552 DOI: 10.1264/jsme2.me15080] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Plant associations by bradyrhizobia have been detected not only in leguminous plants, but also in non-leguminous species including rice. Bradyrhizobium sp. SUTN9-2 was isolated from Aeschynomene americana L., which is a leguminous weed found in the rice fields of Thailand. This strain promoted the highest total rice (Oryza sativa L. cultivar Pathum Thani 1) dry weight among the endophytic bradyrhizobial strains tested, and was, thus, employed for the further characterization of rice-Bradyrhizobium interactions. Some known bacterial genes involved in bacteria-plant interactions were selected. The expression of the type III secretion component (rhcJ), type IV secretion component (virD4), and pectinesterase (peces) genes of the bacterium were up-regulated when the rice root exudate was added to the culture. When SUTN9-2 was inoculated into rice seedlings, the peces, rhcJ, virD4, and exopolysaccharide production (fliP) genes were strongly expressed in the bacterium 6–24 h after the inoculation. The gene for glutathione-S-transferase (gst) was slightly expressed 12 h after the inoculation. In order to determine whether type III secretion system (T3SS) is involved in bradyrhizobial infections in rice plants, wild-type SUTN9-2 and T3SS mutant strains were inoculated into the original host plant (A. americana) and a rice plant (cultivar Pathum Thani 1). The ability of T3SS mutants to invade rice tissues was weaker than that of the wild-type strain; however, their phenotypes in A. americana were not changed by T3SS mutations. These results suggest that T3SS is one of the important determinants modulating rice infection; however, type IV secretion system and peces may also be responsible for the early steps of rice infection.
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Affiliation(s)
- Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
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