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Nishida H, Shimoda Y, Win KT, Imaizumi-Anraku H. Rhizosphere frame system enables nondestructive live-imaging of legume-rhizobium interactions in the soil. JOURNAL OF PLANT RESEARCH 2023; 136:769-780. [PMID: 37402088 PMCID: PMC10421814 DOI: 10.1007/s10265-023-01476-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.
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Affiliation(s)
- Hanna Nishida
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Khin Thuzar Win
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.
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Wang R, Liu J, Jiang W, Ji P, Li Y. Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping. Front Microbiol 2022; 13:833968. [PMID: 35531271 PMCID: PMC9069006 DOI: 10.3389/fmicb.2022.833968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.
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Affiliation(s)
- Ruiting Wang
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Jinxin Liu
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Wanyi Jiang
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Yonggang Li
- Agricultural College, Northeast Agricultural University, Harbin, China
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Goyal RK, Mattoo AK, Schmidt MA. Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability. Front Microbiol 2021; 12:669404. [PMID: 34177848 PMCID: PMC8226219 DOI: 10.3389/fmicb.2021.669404] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.
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Affiliation(s)
- Ravinder K Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Maria Augusta Schmidt
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
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Burghardt LT. Evolving together, evolving apart: measuring the fitness of rhizobial bacteria in and out of symbiosis with leguminous plants. THE NEW PHYTOLOGIST 2020; 228:28-34. [PMID: 31276218 DOI: 10.1111/nph.16045] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/20/2019] [Indexed: 05/11/2023]
Abstract
Most plant-microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume-rhizobia nitrogen-fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high-throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life-cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia - and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.
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Affiliation(s)
- Liana T Burghardt
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN, 55108, USA
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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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Wasai S, Minamisawa K. Plant-Associated Microbes: From Rhizobia To Plant Microbiomes. Microbes Environ 2019; 33:1-3. [PMID: 29593170 PMCID: PMC5877334 DOI: 10.1264/jsme2.me3301rh] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Sawa Wasai
- Graduate School of Life Sciences, Tohoku University
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Chitin Prevalence and Function in Bacteria, Fungi and Protists. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:19-59. [DOI: 10.1007/978-981-13-7318-3_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Saeki Y, Nakamura M, Mason MLT, Yano T, Shiro S, Sameshima-Saito R, Itakura M, Minamisawa K, Yamamoto A. Effect of Flooding and the nosZ Gene in Bradyrhizobia on Bradyrhizobial Community Structure in the Soil. Microbes Environ 2017; 32:154-163. [PMID: 28592720 PMCID: PMC5478539 DOI: 10.1264/jsme2.me16132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 04/11/2017] [Indexed: 11/12/2022] Open
Abstract
We investigated the effects of the water status (flooded or non-flooded) and presence of the nosZ gene in bradyrhizobia on the bradyrhizobial community structure in a factorial experiment that examined three temperature levels (20°C, 25°C, and 30°C) and two soil types (andosol and gray lowland soil) using microcosm incubations. All microcosms were inoculated with Bradyrhizobium japonicum USDA6T, B. japonicum USDA123, and B. elkanii USDA76T, which do not possess the nosZ gene, and then half received B. diazoefficiens USDA110Twt (wt for the wild-type) and the other half received B. diazoefficiens USDA110ΔnosZ. USDA110Twt possesses the nosZ gene, which encodes N2O reductase; 110ΔnosZ, a mutant variant, does not. Changes in the community structure after 30- and 60-d incubations were investigated by denaturing-gradient gel electrophoresis and an image analysis. USDA6T and 76T strains slightly increased in non-flooded soil regardless of which USDA110T strain was present. In flooded microcosms with the USDA110Twt strain, USDA110Twt became dominant, whereas in microcosms with the USDA110ΔnosZ, a similar change in the community structure occurred to that in non-flooded microcosms. These results suggest that possession of the nosZ gene confers a competitive advantage to B. diazoefficiens USDA110T in flooded soil. We herein demonstrated that the dominance of B. diazoefficiens USDA110Twt within the soil bradyrhizobial population may be enhanced by periods of flooding or waterlogging systems such as paddy-soybean rotations because it appears to have the ability to thrive in moderately anaerobic soil.
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Affiliation(s)
- Yuichi Saeki
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Misato Nakamura
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Maria Luisa T. Mason
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
- College of Agriculture, Central Luzon State UniversityScience City of Muñoz, 3120 Nueva EcijaPhilippines
| | - Tsubasa Yano
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
| | - Sokichi Shiro
- Faculty of Life and Environmental Science, Shimane UniversityShimane 690–8504Japan
| | - Reiko Sameshima-Saito
- College of Agriculture, Academic Institute, Shizuoka UniversityShizuoka 422–8529Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku UniversitySendai, Miyagi 980–8577Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo UniversityKyoto 603–8555Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku UniversitySendai, Miyagi 980–8577Japan
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of MiyazakiMiyazaki 889–2192Japan
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