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Response of Soil Bacterial Community to Application of Organic and Inorganic Phosphate Based Fertilizers under Vicia faba L. Cultivation at Two Different Phenological Stages. SUSTAINABILITY 2020. [DOI: 10.3390/su12229706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It is essential to investigate to which extent and how specifically soil–plant–microbe interactions can be conditioned by different agricultural practices. Legumes such as Vicia faba is one of the essential functional group in intercropping and crop rotations due to its higher N fixing capacity. Hence, it is important to study the living microbial community of this legume. Further, it is also expected that fluctuations in soil microbial diversity and composition could be complemented by plant phenological stages and different fertilizer amendments. Thus, we investigated bacterial community composition in soil treated with phosphate-based inorganic and organic fertilizers, in the presence of Vicia faba plants at flowering and fruiting time using NGS 16S rRNA gene amplicon sequencing. Further, the evaluation of plant biomass parameters under different fertilizer treatments was also carried out. The presence of the Vicia faba plant increased the abundance of N fixing bacterial such as Bardyrhizobium, Microvirga (Rhizobiales), Arthrobacter, and Psuedoarthrobacter (Actinomycetales) in soil. Fluctuation in composition and diversity of bacterial community was further supplemented by plant phenological stages. These alterations could be due to changes that occurred in the plant nutrient requirement and varied root exudation patterns at a specific phenological stage. Further, fertilizer treatments also have a profound effect on the diversity and structure of the bacterial community. Organic fertilizers, especially vegetable tanned leather waste (VTLW), have a stronger effect on the composition and diversity of bacterial community compared to inorganic fertilizer (PT—triple superphosphate). Alpha-diversity was significantly decreased by both organic and inorganic amendments, especially a species evenness because each fertilizer tends to stimulate the growth of distinctive microbes that dominated the community of amended soil. Proteobacteria, Actinobacteria, and Cyanobacteria were the most abundant phyla, and Chelatococcus, Cyanobacteria, Sphingomonas, and Microvirga were a most abundant genus that contributed most in co-occurrence pattern, which suggests that these generalists are adapted to a variety of environments. These indicate that plant presence was a key, dominating factor, followed by fertilizers and time, in affecting soil bacterial diversity and composition. Plant recruits system (fertilization and time) -specific taxa due to differences in available nutrients and energy sources among different treatments during different growth stages. Further, fertilizer treatments did not have a stronger effect on plant production as compared to the effect on microbial community, which highlights that organic fertilizers did not tend to increase plant production. Thus, organic and inorganic amendments with matched macronutrients could have a similar impact on crop yields.
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Ramongolalaina C. Dual-luciferase assay and siRNA silencing for nodD1 to study the competitiveness of Bradyrhizobium diazoefficiens USDA110 in soybean nodulation. Microbiol Res 2020; 237:126488. [PMID: 32408049 DOI: 10.1016/j.micres.2020.126488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/29/2020] [Accepted: 04/15/2020] [Indexed: 11/13/2022]
Abstract
The symbiosis of soybean with Bradyrhizobium diazoefficiens USDA110, which always competes with other rhizobia in the field, is of great agronomic and environmental importance. Herein, a dual-luciferase reporter assay was utilized to monitor the dynamics of two dominant bradyrhizobia infecting roots of soybean. More explicitly, luciferase-tagged B. diazoefficiens USDA110 (USDA110-FLuc) and Bradyrhizobium elkanii USDA 94 (USDA94-RLuc) were designed, co-inoculated into soybean seeds, and observed for their colonization in root nodules by bioluminescence imaging. The results showed that USDA110-FLuc initiated infection earlier than USDA94-RLuc, but its occupancy in the nodules decreased as the plant grew. A nodulation test showed that nodD1 mutant USDA110 strains, including CRISPR engineered mutants, were less competitive than wild type. I constructed siRNAs to knockdown nodD1 at different target sites and transformed them into the bacteria. Surprisingly, although siRNAs - with 3' end target sites - were able to repress up to 65% of nodD1 expression, the profiling of total RNAs with a bioanalyzer revealed that 23S/16S-rRNA ratios of siRNA-transformed and wild type USDA110 strains were similar, but lower than that of nodD1 mutant. In short, the current work - while reporting the competitiveness of B. diazoefficiens USDA110 in early occupancy of soybean nodules and the gene nodD1 as a key determinant of this infection - gives an insight on siRNA silencing in microbes, and demonstrates a highly efficient imaging approach that could entail many new avenues for many biological research fields.
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Affiliation(s)
- Clarissien Ramongolalaina
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan; Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan.
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Shiro S, Kuranaga C, Yamamoto A, Sameshima-Saito R, Saeki Y. Temperature-Dependent Expression of NodC and Community Structure of Soybean-Nodulating Bradyrhizobia. Microbes Environ 2016; 31:27-32. [PMID: 26877137 PMCID: PMC4791112 DOI: 10.1264/jsme2.me15114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
In order to assess the physiological responses of bradyrhizobia and competition for the nodulation of soybean at different temperatures, we investigated the expression of the nodC gene at 20, 25, and 30°C and the abilities of bacteria to nodulate soybean in microcosms at day/night cultivation temperatures of 23/18°C, 28/23°C, and 33/28°C for 16/8 h. We tested five Bradyrhizobium USDA strains: B. diazoefficiens USDA 110(T) and 122, B. japonicum USDA 123, and B. elkanii USDA 31 and 76(T). The expression of nodC was up-regulated by increasing culture temperatures in USDA 110(T), 122, 31, and 76(T), but was down-regulated in USDA 123. The proportions of USDA 110(T) and 122 within the community were the greatest at 28/23°C. The population of USDA 31 increased, whereas that of USDA 123 decreased with increasing cultivation temperatures. On the other hand, infection by USDA 76(T) was not detected, and low numbers of USDA 76(T) nodules confirmed its poor nodulation ability. These results indicate that the competitiveness of and infection by USDA 110(T), 122, 123, and 31 for soybean nodulation depend on cultivation temperatures, and suggest that the temperature dependence of nodC expression affects the bradyrhizobial community structure.
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Affiliation(s)
- Sokichi Shiro
- Faculty of Life and Environmental Science, Shimane University1060 Nishikawatsu, Matsue, Shimane 690–8504Japan
| | - Chika Kuranaga
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University836 Otani, Suruga-ku, Shizuoka, Shizuoka 422–8529Japan
| | - Yuichi Saeki
- Faculty of Agriculture, University of Miyazaki1–1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki 889–2192Japan
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Lira MA, Nascimento LRS, Fracetto GGM. Legume-rhizobia signal exchange: promiscuity and environmental effects. Front Microbiol 2015; 6:945. [PMID: 26441880 PMCID: PMC4561803 DOI: 10.3389/fmicb.2015.00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/27/2015] [Indexed: 12/29/2022] Open
Abstract
Although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. Although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. This relative disparity in current knowledge is also apparent in the research on the effects of environmental stress on signal exchange; cool-climate stresses, such as low-soil temperature, comprise a relatively large body of research, whereas high-temperature stresses and drought are not nearly as well understood. Both tropical legumes and their environmental stress-induced effects are increasingly important due to global population growth (the demand for protein), climate change (increasing temperatures and more extreme climate behavior), and urbanization (and thus heavy metals). This knowledge gap for both legumes and their environmental stresses is compounded because whereas most temperate legume-rhizobia symbioses are relatively specific and cultivated under relatively stable environments, the converse is true for tropical legumes, which tend to be promiscuous, and grow in highly variable conditions. This review will clarify some of this missing information and highlight fields in which further research would benefit our current knowledge.
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Affiliation(s)
- Mario A. Lira
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
| | - Luciana R. S. Nascimento
- Agronomy Department, Federal Rural University of PernambucoRecife, Brazil
- National Council for Research and Scientific and Technological DevelopmentBrasília, Brazil
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Takeshima K, Hidaka T, Wei M, Yokoyama T, Minamisawa K, Mitsui H, Itakura M, Kaneko T, Tabata S, Saeki K, Oomori H, Tajima S, Uchiumi T, Abe M, Tokuji Y, Ohwada T. Involvement of a novel genistein-inducible multidrug efflux pump of Bradyrhizobium japonicum early in the interaction with Glycine max (L.) Merr. Microbes Environ 2013; 28:414-21. [PMID: 24225224 PMCID: PMC4070704 DOI: 10.1264/jsme2.me13057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/20/2013] [Indexed: 11/12/2022] Open
Abstract
The early molecular dialogue between soybean and the bacterium Bradyrhizobium japonicum is crucial for triggering their symbiotic interaction. Here we found a single large genomic locus that is widely separated from the symbiosis island and was conspicuously induced within minutes after the addition of genistein. This locus (named BjG30) contains genes for the multidrug efflux pump, TetR family transcriptional regulator, and polyhydroxybutyrate (PHB) metabolism. The induction of BjG30 by genistein was competitively inhibited by daidzein, although both genistein and daidzein are soybean-derived inducers of nodulation (nod) genes. Such a differential expression pattern is also observed in some legume-derived flavonoids, which structurally differ in the hydroxy/deoxy group at the 5-position. In addition, not only did the induction start far in advance of nodW and nodD1 after the addition of genistein, but the levels showed distinct concentration dependence, indicating that the induction pattern of BjG30 is completely different from that of nod genes. The deletion of genes encoding either the multidrug efflux pump or PHB metabolism, especially the former, resulted in defective nodulation performance and nitrogen-fixing capability. Taken together, these results indicate that BjG30, and especially its multidrug efflux pump, may play a key role in the early stage of symbiosis by balancing the dual functions of genistein as both a nod gene inducer and toxicant.
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Affiliation(s)
- Keisuke Takeshima
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Tatsuo Hidaka
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Min Wei
- School of Life Science, Lanzhou University, 222 Tianshui South Rd, Gansu, Lanzhou, 730000, China
| | - Tadashi Yokoyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3–8–1, Harumi-cho, Fuchu, Tokyo, 183–8538, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Science, Tohoku University, 2–1–1, Katahira, Aoba-ku, Sendai, Miyagi, 980–8577, Japan
| | - Takakazu Kaneko
- Faculty of Engineering, Kyoto Sangyo University, Kitaku, Kyoto, 603–8555, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2–6–7, Kazusa-kamatari, Kisarazu, Chiba, 292–0818, Japan
| | - Kazuhiko Saeki
- Department of Biological Science, Faculty of Science, Nara Women’s University, Kitauoyanishi-machi, Nara, 630–8506, Japan
| | - Hirofumi Oomori
- Graduate School of Science, Osaka University, 1–1, Machikaneyama, Toyonaka, 560–0043, Osaka, Japan
| | - Shigeyuki Tajima
- Department of Life Science, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761–0795, Japan
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Mikiko Abe
- Graduate School of Science and Engineering, Kagoshima University, 1–21–24, Korimoto, Kagoshima, 890–0065, Japan
| | - Yoshihiko Tokuji
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
| | - Takuji Ohwada
- Department of Agricultural and Life Sciences, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Nishi 2–11, Obihiro, Hokkaido, 080–8555, Japan
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Fotiadis CT, Dimou M, Georgakopoulos DG, Katinakis P, Tampakaki AP. Functional characterization of NopT1 and NopT2, two type III effectors of Bradyrhizobium japonicum. FEMS Microbiol Lett 2012; 327:66-77. [PMID: 22112296 DOI: 10.1111/j.1574-6968.2011.02466.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/08/2011] [Accepted: 11/15/2011] [Indexed: 12/16/2023] Open
Abstract
NopT1 and NopT2, putative type III effectors from the plant symbiotic bacterium Bradyrhizobium japonicum, are predicted to belong to a family of YopT/AvrPphB effectors, which are cysteine proteases. In the present study, we showed that both NopT1 and NopT2 indeed possess cysteine protease activity. When overexpressed in Escherichia coli, both NopT1 and NopT2 undergo autoproteolytic processing which is largely abolished in the presence of E-64, a papain family-specific inhibitor. Mutations of NopT1 disrupting either the catalytic triad or the putative autoproteolytic site reduce or markedly abolish the protease activity. Autocleavage likely occurs between residues K48 and M49, though another potential cleavage site is also possible. NopT1 also elicitis HR-like cell death when transiently expressed in tobacco plants and its cysteine protease activity is essential for this ability. In contrast, no macroscopic symptoms were observed for NopT2. Furthermore, mutational analysis provided evidence that NopT1 may undergo acylation inside plant cells and that this would be required for its capacity to elicit HR-like cell death in tobacco.
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Affiliation(s)
- Christos T Fotiadis
- Laboratory of General and Agricultural Microbiology, Department of Agricultural Biotechnology, Agricultural University of Athens, Athens, Greece
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Kaneko T, Maita H, Hirakawa H, Uchiike N, Minamisawa K, Watanabe A, Sato S. Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. Genes (Basel) 2011; 2:763-87. [PMID: 24710291 PMCID: PMC3927601 DOI: 10.3390/genes2040763] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/03/2022] Open
Abstract
The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
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Affiliation(s)
- Takakazu Kaneko
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Hiroko Maita
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Nobukazu Uchiike
- Faculty of Engineering, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
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