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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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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: 4] [Impact Index Per Article: 4.0] [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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3
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Koza NA, Adedayo AA, Babalola OO, Kappo AP. Microorganisms in Plant Growth and Development: Roles in Abiotic Stress Tolerance and Secondary Metabolites Secretion. Microorganisms 2022; 10:microorganisms10081528. [PMID: 36013946 PMCID: PMC9415082 DOI: 10.3390/microorganisms10081528] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Crops aimed at feeding an exponentially growing population are often exposed to a variety of harsh environmental factors. Although plants have evolved ways of adjusting their metabolism and some have also been engineered to tolerate stressful environments, there is still a shortage of food supply. An alternative approach is to explore the possibility of using rhizosphere microorganisms in the mitigation of abiotic stress and hopefully improve food production. Several studies have shown that rhizobacteria and mycorrhizae organisms can help improve stress tolerance by enhancing plant growth; stimulating the production of phytohormones, siderophores, and solubilizing phosphates; lowering ethylene levels; and upregulating the expression of dehydration response and antioxidant genes. This article shows the secretion of secondary metabolites as an additional mechanism employed by microorganisms against abiotic stress. The understanding of these mechanisms will help improve the efficacy of plant-growth-promoting microorganisms.
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Affiliation(s)
- Ntombikhona Appear Koza
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Afeez Adesina Adedayo
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Science, North-West University, Mmabatho 2735, South Africa
- Correspondence: (O.O.B.); (A.P.K.); Tel.: +27-18-389-2568 (O.O.B.); +27-11-559-3182 (A.P.K.); Fax: +27-11-559-2605 (O.O.B.)
| | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Correspondence: (O.O.B.); (A.P.K.); Tel.: +27-18-389-2568 (O.O.B.); +27-11-559-3182 (A.P.K.); Fax: +27-11-559-2605 (O.O.B.)
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Mulk S, Wahab A, Yasmin H, Mumtaz S, El-Serehy HA, Khan N, Hassan MN. Prevalence of Wheat Associated Bacillus spp. and Their Bio-Control Efficacy Against Fusarium Root Rot. Front Microbiol 2022; 12:798619. [PMID: 35310393 PMCID: PMC8927631 DOI: 10.3389/fmicb.2021.798619] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/07/2021] [Indexed: 01/30/2023] Open
Abstract
Bacillus spp. are the most prevalent group of bacteria in nature. Their prevalence depends upon multiple factors, namely, sporulation, antagonism, and production of secondary metabolites. The development of an eco-friendly approach to cope with edible crops diseases is very substantial for humans. In the present study, 658 isolates were obtained from wheat grown in the wheat rice cropping system and tested for their antagonistic activity against four wheat root rot pathogens, namely, Fusarium oxysporum, Fusarium moniliforme, Macrophomina phaseolina, and Rhizoctonia solani. Out of 658, 106 isolates were found antagonistic to either single or multiple fungi. Out of 106 antagonistic bacteria, 62 (23%) were rhizospheric, 28 (14%) were root endospheric, and 16 (9%) were leaf endospheric. Based on mean inhibition against all fungi, the bacterial strains SM-39 and SM-93 showed maximum antagonistic activity. The 16S rRNA gene analysis revealed that most of the antagonistic bacteria exhibiting ≥48% antagonism were Bacillus spp. (98%), except two were Klebsiella spp. (2%). The bacterial strains exhibited phylogenetic lineage with the type strains of the respective genus based on the 16S rRNA gene sequences. In the net house experiment, Bacillus velezensis (SM-39) and Bacillus cabrialesii (SM-93) significantly suppressed Fusarium root rot severity in wheat (42–62%). Plants treated with these strains had lower electrolytic leakage (29–36%), as compared to untreated (44%). Relative water content was much higher (46–58%) for plants inoculated with these strains. These antagonistic strains also considerably colonized the wheat rhizosphere with a cell population of 5.8–6.9.log CFU/g of soil. The rhizosphere of wheat grown in the wheat-rice cropping system could be the potential habitat of effective biocontrol agents.
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Affiliation(s)
- Shah Mulk
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Abdul Wahab
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Humaira Yasmin,
| | - Saqib Mumtaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, Florida University, Gainesville, FL, United States
| | - Muhammad Nadeem Hassan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- *Correspondence: Muhammad Nadeem Hassan,
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Fatima I, Hakim S, Imran A, Ahmad N, Imtiaz M, Ali H, Islam EU, Yousaf S, Mirza MS, Mubeen F. Exploring biocontrol and growth-promoting potential of multifaceted PGPR isolated from natural suppressive soil against the causal agent of chickpea wilt. Microbiol Res 2022; 260:127015. [DOI: 10.1016/j.micres.2022.127015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 10/18/2022]
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Liu G, Liu X, Liu W, Gao K, Chen X, Wang ET, Zhao Z, Du W, Li Y. Biodiversity and Geographic Distribution of Rhizobia Nodulating With Vigna minima. Front Microbiol 2021; 12:665839. [PMID: 34017318 PMCID: PMC8129581 DOI: 10.3389/fmicb.2021.665839] [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: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Vigna minima is a climbing annual plant widely distributed in barren wilderness, grass land, and shrub bush of China and other countries such as Japan. However, the rhizobia nodulating with this plant has never been systematically studied. In order to reveal the biodiversity of nodulating rhizobia symbiosis with V. minima, a total of 874 rhizobium isolates were obtained from root nodules of the plant spread in 11 sampling sites of Shandong Peninsula, China, and they were designated as 41 haplotypes in the genus Bradyrhizobium based upon recA sequence analyses. By multilocus sequence analysis (MLSA) of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB), the 41 strains representing different recA haplotypes were classified into nine defined species and nine novel genospecies. Bradyrhizobium elkanii, Bradyrhizobium ferriligni, and Bradyrhizobium pachyrhizi were the predominant and universally distributed groups. The phylogeny of symbiotic genes of nodC and nifH showed similar topology and phylogenetic relationships, in which all the representative strains were classified into two clades grouped with strains nodulating with Vigna spp., demonstrating that Vigna spp. shared common nodulating groups in the natural environment. All the representative strains formed nodules with V. minima in a nodulation test performed in green house conditions. The correlation between V. minima nodulating rhizobia and soil characteristics analyzed by CANOCO indicates that available nitrogen, total nitrogen, and organic carbon in the soil samples were the main factors affecting the distribution of rhizobia isolated in this study. This study systematically uncovered the biodiversity and distribution characteristics of V. minima nodulating rhizobia for the first time, which provided novel information for the formation of the corresponding rhizobium community.
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Affiliation(s)
- Guohua Liu
- College of Life Science, Yantai University, Yantai, China
| | - Xiaoling Liu
- College of Life Science, Yantai University, Yantai, China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Kangning Gao
- College of Resources and Environment, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoli Chen
- The Fruit Trees Work Station of Penglai, Yantai, China
| | - En-Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenjun Zhao
- College of Life Science, Yantai University, Yantai, China
| | - Wenxiao Du
- College of Life Science, Yantai University, Yantai, China
| | - Yan Li
- College of Life Science, Yantai University, Yantai, China.,Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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Gunnabo AH, van Heerwaarden J, Geurts R, Wolde-Meskel E, Degefu T, Giller KE. Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia. MICROBIAL ECOLOGY 2021; 81:703-716. [PMID: 33098438 PMCID: PMC7982387 DOI: 10.1007/s00248-020-01620-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar "Nattoli". Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.
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Affiliation(s)
- A H Gunnabo
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - J van Heerwaarden
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - R Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - E Wolde-Meskel
- World Agroforestry Centre (ICRAF), Addis Ababa, Ethiopia
| | - T Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - K E Giller
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
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8
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Hakim S, Imran A, Mirza MS. Phylogenetic diversity analysis reveals Bradyrhizobium yuanmingense and Ensifer aridi as major symbionts of mung bean (Vigna radiata L.) in Pakistan. Braz J Microbiol 2021; 52:311-324. [PMID: 33141350 PMCID: PMC7966693 DOI: 10.1007/s42770-020-00397-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/27/2020] [Indexed: 11/26/2022] Open
Abstract
The present study was carried out to evaluate the diversity of rhizobia associated with nodules of mung bean in Pakistan, because this information is necessary for inoculum development. Based on sequence analysis of 16S rRNA gene of thirty-one bacteria, 11 were assigned to genus Bradyrhizobium, 17 to Ensifer, and 3 to Rhizobium. Phylogenetic analyses on the basis of 16S-23S ITS region, atpD, recA, nifH, and nodA of representative strains revealed that B. yuanmingense is the predominant species distributed throughout different mung bean-growing areas. Among the fast-growing rhizobia, Ensifer aridi was predominant in Faisalabad, Layyah, and Rawalpindi, while E. meliloti in Thal desert. Sequence variations and phylogeny of nifH and nodA genes suggested that these genes might have been co-evolved with the housekeeping genes and maintained by vertical gene transfer in rhizobia detected in the present study. Host infectivity assay revealed the successful nodulation of host by rhizobia related to genera Bradyrhizobium, Ensifer and Rhizobium. Among all, Bradyrhizobium and Ensifer spp. inoculation exhibited a significantly higher number of nodules (11-34 nodules plant-1) and nitrogenase activity (nodule ARA 60-110 μmol g-1 h-1). Contrary to the previous studies, our data reveal that B. yuanmingense and E. aridi are predominant species forming effective nodules in mung bean in Pakistan. Furthermore, to the best of our knowledge, this is the first report showing the effective symbiosis of E. aridi, E. meliloti, and Rhizobium pusense with mung bean. The diversity of rhizobia in different habitats revealed in the present study will contribute towards designing site-specific inocula for mung bean.
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Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
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Hakim S, Naqqash T, Nawaz MS, Laraib I, Siddique MJ, Zia R, Mirza MS, Imran A. Rhizosphere Engineering With Plant Growth-Promoting Microorganisms for Agriculture and Ecological Sustainability. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.617157] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The rhizosphere is undoubtedly the most complex microhabitat, comprised of an integrated network of plant roots, soil, and a diverse consortium of bacteria, fungi, eukaryotes, and archaea. The rhizosphere conditions have a direct impact on crop growth and yield. Nutrient-rich rhizosphere environments stimulate plant growth and yield and vice versa. Extensive cultivation exhaust most of the soils which need to be nurtured before or during the next crop. Chemical fertilizers are the major source of crop nutrients but their uncontrolled and widespread usage has posed a serious threat to the sustainability of agriculture and stability of an ecosystem. These chemicals are accumulated in the soil, drained in water, and emitted to the air where they persist for decades causing a serious threat to the overall ecosystem. Plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere convert many plant-unavailable essential nutrients e.g., nitrogen, phosphorous, zinc, etc. into available forms. PGPR produces certain plant growth hormones (such as auxin, cytokinin, and gibberellin), cell lytic enzymes (chitinase, protease, hydrolases, etc.), secondary metabolites, and antibiotics, and stress alleviating compounds (e.g., 1-Aminocyclopropane-1- carboxylate deaminase), chelating agents (siderophores), and some signaling compounds (e.g., N-Acyl homoserine lactones) to interact with the beneficial or pathogenic counterparts in the rhizosphere. These multifarious activities of PGPR improve the soil structure, health, fertility, and functioning which directly or indirectly support plant growth under normal and stressed environments. Rhizosphere engineering with these PGPR has a wide-ranging application not only for crop fertilization but developing eco-friendly sustainable agriculture. Due to severe climate change effects on plants and rhizosphere biology, there is growing interest in stress-resilient PGPM and their subsequent application to induce stress (drought, salinity, and heat) tolerance mechanism in plants. This review describes the three components of rhizosphere engineering with an explicit focus on the broader perspective of PGPM that could facilitate rhizosphere engineering in selected hosts to serve as an efficient component for sustainable agriculture.
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Han Q, Ma Q, Chen Y, Tian B, Xu L, Bai Y, Chen W, Li X. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. THE ISME JOURNAL 2020; 14:1915-1928. [PMID: 32336748 PMCID: PMC7367843 DOI: 10.1038/s41396-020-0648-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023]
Abstract
Rhizobia-legume symbiosis is an important type of plant-microbe mutualism; however, the establishment of this association is complicated and can be affected by many factors. The soybean rhizosphere has a specific microbial community, yet whether these organisms affect rhizobial nodulation has not been well investigated. Here, we analyzed the compositions and relationships of soybean rhizocompartment microbiota in three types of soil. First, we found that the rhizosphere community composition of soybean varied significantly in different soils, and the association network between rhizobia and other rhizosphere bacteria was examined. Second, we found that some rhizosphere microbes were correlated with the composition of bradyrhizobia and sinorhizobia in nodules. We cultivated 278 candidate Bacillus isolates from alkaline soil. Finally, interaction and nodulation assays showed that the Bacillus cereus group specifically promotes and suppresses the growth of sinorhizobia and bradyrhizobia, respectively, and alleviates the effects of saline-alkali conditions on the nodulation of sinorhizobia as well as affecting its colonization in nodules. Our findings demonstrate a crucial role of the bacterial microbiota in shaping rhizobia-host interactions in soybean, and provide a framework for improving the symbiotic efficiency of this system of mutualism through the use of synthetic bacterial communities.
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Affiliation(s)
- Qin Han
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China
| | - Qun Ma
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China
| | - Yong Chen
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China
| | - Bing Tian
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China
| | - Lanxi Xu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, 100193, China.
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, China.
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Favero VO, Carvalho RH, Motta VM, Leite ABC, Coelho MRR, Xavier GR, Rumjanek NG, Urquiaga S. Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean ( Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products. FRONTIERS IN PLANT SCIENCE 2020; 11:602645. [PMID: 33510747 PMCID: PMC7835340 DOI: 10.3389/fpls.2020.602645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/14/2020] [Indexed: 05/07/2023]
Abstract
The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.
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Affiliation(s)
| | | | | | | | | | | | - Norma Gouvêa Rumjanek
- Embrapa Agrobiology, Seropédica, Rio de Janeiro, Brazil
- *Correspondence: Norma Gouvêa Rumjanek,
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Hakim S, Mirza BS, Imran A, Zaheer A, Yasmin S, Mubeen F, Mclean JE, Mirza MS. Illumina sequencing of 16S rRNA tag shows disparity in rhizobial and non-rhizobial diversity associated with root nodules of mung bean (Vigna radiata L.) growing in different habitats in Pakistan. Microbiol Res 2019; 231:126356. [PMID: 31722286 DOI: 10.1016/j.micres.2019.126356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
In Rhizobium-legume symbiosis, the nodule is the most frequently studied compartment, where the endophytic/symbiotic microbiota demands critical investigation for development of specific inocula. We identified the bacterial diversity within root nodules of mung bean from different growing areas of Pakistan using Illumina sequencing of 16S rRNA gene. We observed specific OTUs related to specific site where Bradyrhizobium was found to be the dominant genus comprising of 82-94% of total rhizobia in nodules with very minor fraction of sequences from other rhizobia at three sites. In contrast, Ensifer (Sinorhizobium) was single dominant genus comprising 99.9% of total rhizobial sequences at site four. Among non-rhizobial sequences, the genus Acinetobacter was abundant (7-18% of total sequences), particularly in Bradyrhizobium-dominated nodule samples. Rhizobia and non-rhizobial PGPR isolated from nodule samples include Ensifer, Bradyrhizobium, Acinetobacter, Microbacterium and Pseudomonas strains. Co-inoculation of multi-trait PGPR Acinetobacter sp. VrB1 with either of the two rhizobia in field exhibited more positive effect on nodulation and plant growth than single-strain inoculation which favors the use of Acinetobacter as an essential component for development of mung bean inoculum. Furthermore, site-specific dominance of rhizobia and non-rhizobia revealed in this study may contribute towards decision making for development and application of specific inocula in different habitats.
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Affiliation(s)
- Sughra Hakim
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Babur S Mirza
- Missouri State University, Biology Department, Springfield, MO 65897, USA
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Ahmad Zaheer
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan; Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Fathia Mubeen
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan
| | - Joan E Mclean
- Utah Water Research Laboratory, Utah State University, Logan, Utah, USA
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan.
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Johnson G. High throughput DNA extraction of legume root nodules for rhizobial metagenomics. AMB Express 2019; 9:47. [PMID: 30969386 PMCID: PMC6458200 DOI: 10.1186/s13568-019-0771-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
A novel combination of tissue homogenization, cell lysis, and DNA purification techniques was developed for isolating total DNA from whole legume root nodules on an automated robotic system. Silica dehydrated root nodules from soy bean, Glycine max cv. Tara, and mung bean, Vigna radiata cv. Crystal, were homogenized in 96-well plates and were enzymatically and chemically lysed before being loaded into the AutoGenprep 965 for automated phenol–chloroform based DNA isolation. The resulting DNAs were of relatively high concentration, low fragmentation, and free of phenolic and polysaccharide contaminants. In contrast to manual methods, this adaptation of the Autogen Prep automated DNA extraction instrument allows for 100’s to 1000’s of samples to be prepared in a fraction of the time and cost.
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Qaisrani MM, Zaheer A, Mirza MS, Naqqash T, Qaisrani TB, Hanif MK, Rasool G, Malik KA, Ullah S, Jamal MS, Mirza Z, Karim S, Rasool M. A comparative study of bacterial diversity based on culturable and culture-independent techniques in the rhizosphere of maize ( Zea mays L.). Saudi J Biol Sci 2019; 26:1344-1351. [PMID: 31762594 PMCID: PMC6864194 DOI: 10.1016/j.sjbs.2019.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/22/2019] [Accepted: 03/31/2019] [Indexed: 11/29/2022] Open
Abstract
Objective Maize is an important crop for fodder, food and feed industry. The present study explores the plant-microbe interactions as alternative eco-friendly sustainable strategies to enhance the crop yield. Methodology Bacterial diversity was studied in the rhizosphere of maize by culture-dependent and culture-independent techniques by soil sampling, extraction of DNA, amplification of gene of interest, cloning of desired fragment and library construction. Results Culturable bacteria were identified as Achromobacter, Agrobacterium, Azospirillum, Bacillus, Brevibacillus, Bosea, Enterobacter, Microbacterium, Pseudomonas, Rhodococcus, Stenotrophomonas and Xanthomonas genera. For culture-independent approach, clone library of 16S ribosomal RNA gene was assembled and 100 randomly selected clones were sequenced. Majority of the sequences were related to Firmicutes (17%), Acidobacteria (16%), Actinobacteria (17%), Alpha-Proteobacteria (7%), Delta-proteobacteria (4.2%) and Gemmatimonadetes (4.2%) However, some of the sequences (30%) were novel that showed no homologies to phyla of cultured bacteria in the database. Diversity of diazotrophic bacteria in the rhizosphere investigated by analysis of PCR-amplified nifH gene sequence that revealed abundance of sequences belonging to genera Azoarcus (25%), Aeromonas (10%), Pseudomonas (10%). The diazotrophic genera Azotobacter, Agrobacterium and Zoogloea related nifH sequences were also detected but no sequence related to Azospirillum was found showing biasness of the growth medium rather than relative abundance of diazotrophs in the rhizosphere. Conclusion The study provides a foundation for future research on focussed isolation of the Azoarcus and other diazotrophs found in higher abundance in the rhizosphere.
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Affiliation(s)
- Muther Mansoor Qaisrani
- Department of Bioinformatics, Khwaja Fareed University of Engineering & IT, Rahim Yar Khan, Pakistan
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | | | - Ghulam Rasool
- Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Kauser Abdulla Malik
- Department of Biological Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Saleem Ullah
- Department of Bioinformatics, Khwaja Fareed University of Engineering & IT, Rahim Yar Khan, Pakistan
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center (KFMRC), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- King Fahd Medical Research Center (KFMRC), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Rasul M, Yasmin S, Suleman M, Zaheer A, Reitz T, Tarkka MT, Islam E, Mirza MS. Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice. Microbiol Res 2019; 223-225:1-12. [PMID: 31178042 DOI: 10.1016/j.micres.2019.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/07/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022]
Abstract
Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 μg mL-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 μg mL-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.
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Affiliation(s)
- Maria Rasul
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - M Suleman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Institute of Microbiology, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road, Lahore, Pakistan
| | - Thomas Reitz
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120 Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Mika T Tarkka
- UFZ - Helmholtz-Centre for Environmental Research, Soil Ecology Department, Theodor-Lieser-Straße 4, 06120 Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ejazul Islam
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - M Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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