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Park HE, Nebert L, King RM, Busby P, Myers JR. Influence of organic plant breeding on the rhizosphere microbiome of common bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1251919. [PMID: 37954997 PMCID: PMC10634438 DOI: 10.3389/fpls.2023.1251919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023]
Abstract
Introduction We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history. Methods Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set. Results Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens. Discussion The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.
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Affiliation(s)
- Hayley E. Park
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Lucas Nebert
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Ryan M. King
- National Clonal Germplasm Repository, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Posy Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
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Moura FT, Helene LCF, Ribeiro RA, Nogueira MA, Hungria M. The outstanding diversity of rhizobia microsymbionts of common bean (Phaseolus vulgaris L.) in Mato Grosso do Sul, central-western Brazil, revealing new Rhizobium species. Arch Microbiol 2023; 205:325. [PMID: 37659972 DOI: 10.1007/s00203-023-03667-w] [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: 06/22/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization. The phylogenetic tree of the 16S rRNA gene split the 13 strains into two large clades, seven in the R. etli and six in the R. tropici clade. The MLSA with four housekeeping genes (glnII, gyrB, recA, and rpoA) confirmed the phylogenetic allocation. Genomic comparisons indicated eight strains in five putative new species and the remaining five as R. phaseoli. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparing the putative new species and the closest neighbors ranged from 81.84 to 92.50% and 24.0 to 50.7%, respectively. Other phenotypic, genotypic, and symbiotic features were evaluated. Interestingly, some strains of both R. etli and R. tropici clades lost their nodulation capacity. The data support the description of the new species Rhizobium cerradonense sp. nov. (CNPSo 3464T), Rhizobium atlanticum sp. nov. (CNPSo 3490T), Rhizobium aureum sp. nov. (CNPSo 3968T), Rhizobium pantanalense sp. nov. (CNPSo 4039T), and Rhizobium centroccidentale sp. nov. (CNPSo 4062T).
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Affiliation(s)
- Fernanda Terezinha Moura
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70.040-020, Brazil
| | - Luisa Caroline Ferraz Helene
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
- Vittia Fertilizantes e Biológicos, São Joaquim da Barra, São Paulo, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Marco Antonio Nogueira
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Mariangela Hungria
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil.
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil.
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Wilkinson H, Coppock A, Richmond BL, Lagunas B, Gifford ML. Plant-Environment Response Pathway Regulation Uncovered by Investigating Non-Typical Legume Symbiosis and Nodulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:1964. [PMID: 37653881 PMCID: PMC10223263 DOI: 10.3390/plants12101964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Nitrogen is an essential element needed for plants to survive, and legumes are well known to recruit rhizobia to fix atmospheric nitrogen. In this widely studied symbiosis, legumes develop specific structures on the roots to host specific symbionts. This review explores alternate nodule structures and their functions outside of the more widely studied legume-rhizobial symbiosis, as well as discussing other unusual aspects of nodulation. This includes actinorhizal-Frankia, cycad-cyanobacteria, and the non-legume Parasponia andersonii-rhizobia symbioses. Nodules are also not restricted to the roots, either, with examples found within stems and leaves. Recent research has shown that legume-rhizobia nodulation brings a great many other benefits, some direct and some indirect. Rhizobial symbiosis can lead to modifications in other pathways, including the priming of defence responses, and to modulated or enhanced resistance to biotic and abiotic stress. With so many avenues to explore, this review discusses recent discoveries and highlights future directions in the study of nodulation.
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Affiliation(s)
- Helen Wilkinson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alice Coppock
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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Xavier GR, Jesus EDC, Dias A, Coelho MRR, Molina YC, Rumjanek NG. Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:954. [PMID: 36840302 PMCID: PMC9962295 DOI: 10.3390/plants12040954] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.
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Affiliation(s)
| | | | - Anelise Dias
- Departamento de Fitotecnia, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, UFRRJ, Rodovia BR-465, Km 7, Seropédica 23890-000, RJ, Brazil
| | | | - Yulimar Castro Molina
- Programa de Pós-graduação em Microbiologia Agrícola, Universidade Federal de Lavras, UFLA, Trevo Rotatório Professor Edmir Sá Santos, Lavras 37203-202, MG, Brazil
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Sindhu SS, Sehrawat A, Glick BR. The involvement of organic acids in soil fertility, plant health and environment sustainability. Arch Microbiol 2022; 204:720. [DOI: 10.1007/s00203-022-03321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
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Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation. Int J Mol Sci 2022; 23:ijms231912035. [PMID: 36233333 PMCID: PMC9570480 DOI: 10.3390/ijms231912035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/27/2022] [Accepted: 10/07/2022] [Indexed: 01/10/2023] Open
Abstract
Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth.
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