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Araya S, Elia P, Quigley CV, Song Q. Genetic variation and genetic complexity of nodule occupancy in soybean inoculated with USDA110 and USDA123 rhizobium strains. BMC Genomics 2023; 24:520. [PMID: 37667205 PMCID: PMC10478483 DOI: 10.1186/s12864-023-09627-4] [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: 04/14/2023] [Accepted: 08/26/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Symbiotic nitrogen fixation differs among Bradyrhizobium japonicum strains. Soybean inoculated with USDA123 has a lower yield than strains known to have high nitrogen fixation efficiency, such as USDA110. In the main soybean-producing area in the Midwest of the United States, USDA123 has a high nodule incidence in field-grown soybean and is competitive but inefficient in nitrogen fixation. In this study, a high-throughput system was developed to characterize nodule number among 1,321 Glycine max and 69 Glycine soja accessions single inoculated with USDA110 and USDA123. RESULTS Seventy-three G. max accessions with significantly different nodule number of USDA110 and USDA123 were identified. After double inoculating 35 of the 73 accessions, it was observed that PI189939, PI317335, PI324187B, PI548461, PI562373, and PI628961 were occupied by USDA110 and double-strain nodules but not by USDA123 nodules alone. PI567624 was only occupied by USDA110 nodules, and PI507429 restricted all strains. Analysis showed that 35 loci were associated with nodule number in G. max when inoculated with strain USDA110 and 35 loci with USDA123. Twenty-three loci were identified in G. soja when inoculated with strain USDA110 and 34 with USDA123. Only four loci were common across two treatments, and each locus could only explain 0.8 to 1.5% of phenotypic variation. CONCLUSIONS High-throughput phenotyping systems to characterize nodule number and occupancy were developed, and soybean germplasm restricting rhizobium strain USDA123 but preferring USDA110 was identified. The larger number of minor effects and a small few common loci controlling the nodule number indicated trait genetic complexity and strain-dependent nodulation restriction. The information from the present study will add to the development of cultivars that limit USDA123, thereby increasing nitrogen fixation efficiency and productivity.
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Affiliation(s)
- Susan Araya
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Patrick Elia
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Charles V Quigley
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
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2
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Effector-Dependent and -Independent Molecular Mechanisms of Soybean-Microbe Interaction. Int J Mol Sci 2022; 23:ijms232214184. [PMID: 36430663 PMCID: PMC9695568 DOI: 10.3390/ijms232214184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Soybean is a pivotal staple crop worldwide, supplying the main food and feed plant proteins in some countries. In addition to interacting with mutualistic microbes, soybean also needs to protect itself against pathogens. However, to grow inside plant tissues, plant defense mechanisms ranging from passive barriers to induced defense reactions have to be overcome. Pathogenic but also symbiotic micro-organisms effectors can be delivered into the host cell by secretion systems and can interfere with the immunity system and disrupt cellular processes. This review summarizes the latest advances in our understanding of the interaction between secreted effectors and soybean feedback mechanism and uncovers the conserved and special signaling pathway induced by pathogenic soybean cyst nematode, Pseudomonas, Xanthomonas as well as by symbiotic rhizobium.
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3
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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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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. FRONTIERS IN PLANT SCIENCE 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Teulet A, Gully D, Rouy Z, Camuel A, Koebnik R, Giraud E, Lassalle F. Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium. Microb Genom 2020; 6:mgen000407. [PMID: 32783800 PMCID: PMC7643967 DOI: 10.1099/mgen.0.000407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/26/2020] [Indexed: 01/22/2023] Open
Abstract
Bradyrhizobium are abundant soil bacteria and the major symbiont of legumes. The recent availability of Bradyrhizobium genome sequences provides a large source of information for analysis of symbiotic traits. In this study, we investigated the evolutionary dynamics of the nodulation genes (nod) and their relationship with the genes encoding type III secretion systems (T3SS) and their effectors among bradyrhizobia. Based on the comparative analysis of 146 Bradyrhizobium genome sequences, we identified six different types of T3SS gene clusters. The two predominant cluster types are designated RhcIa and RhcIb and both belong to the RhcI-T3SS family previously described in other rhizobia. They are found in 92/146 strains, most of them also containing nod genes. RhcIa and RhcIb gene clusters differ in the genes they carry: while the translocon-encoding gene nopX is systematically found in strains containing RhcIb, the nopE and nopH genes are specifically conserved in strains containing RhcIa, suggesting that these last two genes might functionally substitute nopX and play a role related to effector translocation. Phylogenetic analysis suggests that bradyrhizobia simultaneously gained nod and RhcI-T3SS gene clusters via horizontal transfer or subsequent vertical inheritance of a symbiotic island containing both. Sequence similarity searches for known Nop effector proteins in bradyrhizobial proteomes revealed the absence of a so-called core effectome, i.e. that no effector is conserved among all Bradyrhizobium strains. However, NopM and SUMO proteases were found to be the main effector families, being represented in the majority of the genus. This study indicates that bradyrhizobial T3SSs might play a more significant symbiotic role than previously thought and provides new candidates among T3SS structural proteins and effectors for future functional investigations.
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Affiliation(s)
- Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Zoe Rouy
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Ralf Koebnik
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Florent Lassalle
- Department of Infectious Disease Epidemiology. Imperial College London, St Mary’s Hospital Campus, Praed Street, London W2 1NY, UK
- Pathogen and Microbes Program, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Present address: Pathogen and Microbes Program, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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6
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Mason MLT, Tabing BLC, Yamamoto A, Saeki Y. Influence of flooding and soil properties on the genetic diversity and distribution of indigenous soybean-nodulating bradyrhizobia in the Philippines. Heliyon 2018; 4:e00921. [PMID: 30480155 PMCID: PMC6240709 DOI: 10.1016/j.heliyon.2018.e00921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/03/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022] Open
Abstract
One of the strategies that is commonly used in the Philippines to improve the production of soybean is by inoculation. However, this technique often fails mainly due to the lack of information about the indigenous soybean rhizobia in the Philippines soil. In this study, the diversity of indigenous bradyrhizobia collected from the non-flooded and flooded soil conditions at 11 locations in the country was investigated using a local soybean cultivar as the host plant. The genetic variation among the 424 isolates was detected through Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment and sequence analysis for 16S rRNA gene, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene. All the isolates were classified under the Bradyrhizobium species namely B. elkanii, B. diazoefficiens, B. japonicum, B. yuanmingense and a considerable proportion of the isolates were clustered under Bradyrhizobium sp. The isolates which were classified under Bradyrhizobium sp. were thought to be endemic to Philippines soil as evidenced by their nucleotide divergence against the known rhizobia and the historical absence of rhizobia inoculation in the collection sites. The major influence on the distribution and diversity of soybean bradyrhizobia is attributed to the difference in the flooding period, followed by soil properties such as pH, soil type, and nutrient content. As determined, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.
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Affiliation(s)
- Maria Luisa Tabing Mason
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan.,College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines
| | - Baby Lyn Cortez Tabing
- College of Agriculture, Don Mariano Marcos Memorial State University-South Luzon Campus, Rosario, La Union, Philippines
| | - Akihiro Yamamoto
- Faculty of Agriculture, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan
| | - Yuichi Saeki
- Faculty of Agriculture, University of Miyazaki, Gakuenkibanadai Nishi, Miyazaki, Japan
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7
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Cooper B, Campbell KB, Beard HS, Garrett WM, Mowery J, Bauchan GR, Elia P. A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:334-343. [PMID: 29117782 DOI: 10.1094/mpmi-10-17-0243-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rhizobia colonize legumes and reduce N2 to NH3 in root nodules. The current model is that symbiotic rhizobia bacteroids avoid assimilating this NH3. Instead, host legume cells form glutamine from NH3, and the nitrogen is returned to the bacteroid as dicarboxylates, peptides, and amino acids. In soybean cells surrounding bacteroids, glutamine also is converted to ureides. One problem for soybean cultivation is inefficiency in symbiotic N2 fixation, the biochemical basis of which is unknown. Here, the proteomes of bacteroids of Bradyrhizobium elkanii USDA76 isolated from N2 fixation-efficient Peking and -inefficient Williams 82 soybean nodules were analyzed by mass spectrometry. Nearly half of the encoded bacterial proteins were quantified. Efficient bacteroids produced greater amounts of enzymes to form Nod factors and had increased amounts of signaling proteins, transporters, and enzymes needed to generate ATP to power nitrogenase and to acquire resources. Parallel investigation of nodule proteins revealed that Peking had no significantly greater accumulation of enzymes needed to assimilate NH3 than Williams 82. Instead, efficient bacteroids had increased amounts of enzymes to produce amino acids, including glutamine, and to form ureide precursors. These results support a model for efficient symbiotic N2 fixation in soybean where the bacteroid assimilates NH3 for itself.
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Affiliation(s)
- Bret Cooper
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Kimberly B Campbell
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Hunter S Beard
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | | | - Joseph Mowery
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Gary R Bauchan
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
| | - Patrick Elia
- 1 Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A.; and
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