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Denitrification by Bradyrhizobia under Feast and Famine and the Role of the bc1 Complex in Securing Electrons for N 2O Reduction. Appl Environ Microbiol 2023; 89:e0174522. [PMID: 36662572 PMCID: PMC9972998 DOI: 10.1128/aem.01745-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also must survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O2 tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N2O- over NO3- reduction in bradyrhizobia is retained under carbon limitation. Here, we show that starved cultures of a Bradyrhizobium strain with respiration rates 1 to 18% of well-fed cultures reduced all available N2O before touching provided NO3-. These organisms, which carry out complete denitrification, have the periplasmic nitrate reductase NapA but lack the membrane-bound nitrate reductase NarG. Proteomics showed similar levels of NapA and NosZ (N2O reductase), excluding that the lack of NO3- reduction was due to low NapA abundance. Instead, this points to a metabolic-level phenomenon where the bc1 complex, which channels electrons to NosZ via cytochromes, is a much stronger competitor for electrons from the quinol pool than the NapC enzyme, which provides electrons to NapA via NapB. The results contrast the general notion that NosZ activity diminishes under carbon limitation and suggest that bradyrhizobia carrying NosZ can act as strong sinks for N2O under natural conditions, implying that this criterion should be considered in the development of biofertilizers. IMPORTANCE Legume cropped farmlands account for substantial N2O emissions globally. Legumes are commonly inoculated with N2-fixing bacteria, rhizobia, to improve crop yields. Rhizobia belonging to Bradyrhizobium, the microsymbionts of several economically important legumes, are generally capable of denitrification but many lack genes encoding N2O reductase and will be N2O sources. Bradyrhizobia with complete denitrification will instead act as sinks since N2O-reduction efficiently competes for electrons over nitrate reduction in these organisms. This phenomenon has only been demonstrated under optimal conditions and it is not known how carbon substrate limitation, which is the common situation in most soils, affects the denitrification phenotype. Here, we demonstrate that bradyrhizobia retain their strong preference for N2O under carbon starvation. The findings add basic knowledge about mechanisms controlling denitrification and support the potential for developing novel methods for greenhouse gas mitigation based on legume inoculants with the dual capacity to optimize N2 fixation and minimize N2O emission.
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Competition for electrons favours N 2 O reduction in denitrifying Bradyrhizobium isolates. Environ Microbiol 2021; 23:2244-2259. [PMID: 33463871 DOI: 10.1111/1462-2920.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Bradyrhizobia are common members of soil microbiomes and known as N2 -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2 O. Inoculation with compatible rhizobia is often needed for optimal N2 -fixation, but the choice of inoculant may have consequences for N2 O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2 O. The N2 O-reducing isolates had strong preference for N2 O- over NO3 - -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3 - reductase) and Nos (N2 O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3 - reductase (Nar), reduced N2 O and NO3 - simultaneously. We propose that the control at the metabolic level, favouring N2 O reduction over NO3 - reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
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Molecular Characteristics of Rhizobia Isolated from Arachis hypogaea Grown under Stress Environment. SUSTAINABILITY 2020. [DOI: 10.3390/su12156259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The phenotypic and genotypic characterization of eight rhizobial isolates obtained from Arachis hypogaea nodules grown under stress environment was performed. Isolates were screened for their ability to tolerate different abiotic stresses (high temperature (60° C), salinity (1–5% (w/v) NaCl), and pH (1–12). The genomic analysis of 16S rRNA and housekeeping genes (atpD, recA, and glnII) demonstrated that native groundnut rhizobia from these stress soils are representatives of fast growers and phylogenetically related to Rhizobium sp. The phenotypic characterization (generation time, carbon source utilization) also revealed the isolates as fast-growing rhizobia. All the isolates can tolerate NaCl up to 3% and were able to grow between 20 and 37 °C with a pH between 5 to 10, indicating that the isolates were alkali and salt-tolerant. The tested isolates effectively utilize mono and disaccharides as carbon source. Out of eight, three rhizobial isolates (BN-20, BN-23, and BN-50) were able to nodulate their host plant, exhibiting their potential to be used as native groundnut rhizobial inoculum. The plant growth promoting characterization of all isolates revealed their effectiveness to solubilize inorganic phosphate (56–290 µg mL−1), synthesize indole acetic acid (IAA) (24–71 µg mL−1), and amplification of nitrogen fixing nifH gene, exploring their ability to be used as groundnut biofertilizer to enhance yield and N2-fixation for the resource poor farmers of rainfed Pothwar region.
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Genetic diversity analysis of some Egyptian Origanum and Thymus species using AFLP markers. J Genet Eng Biotechnol 2019; 17:13. [PMID: 31814081 PMCID: PMC6900380 DOI: 10.1186/s43141-019-0012-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the present investigation, two genera of family Labiatae (genus Origanum and genus Thymus including their available species in Egypt) were analyzed genetically on DNA level using amplified fragment length polymorphism (AFLP) markers. Four selective primer combinations (E-AGC/M-CAA, E-AGC/M-CAC, E-AGG/M-CTC, and E-ACC/M-CAT) were used to detect genetic variations (polymorphisms) within and between the studied plant species of each genus and with their cultivated relatives. RESULTS A total of 193 amplified fragments were obtained overall primer combinations with a disparity in the number of bands for each primer combination. The primer combination E-AGG/M-CTC exhibited a large number of amplicons (67) compared to the other primers with polymorphism percentage 69%. The polymorphism information content (PIC) was calculated for the four primer combinations showing a very high values ranging between 0.98 and 0.99. On the other hand, Thymus species (Thymus vulgaris, Thymus capitatus L., and Thymus decassatus Benth.) exhibited a total number of 171 amplicons for all primer combinations with an average of 42 bands. The primer combination E-AGG/M-CTC produced the largest number of bands (62 bands) with polymorphism percentage 35%, even though the primer combination AGC/M-CAA was more efficient to give high polymorphisms within Thymus species where it resulted in a total of 35 bands with polymorphism percentage 63%. The PIC values were calculated ranging from 0.96 to 0.99. CONCLUSION One can conclude that AFLP technique was informative and efficient technique to give a good coverage of Origanum and Thymus genomes. Furthermore, it was helpful to elucidate the genetic variations and phylogenetic relationships within the studied species as a basis for further studies on these genera and related species.
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Bacteria related to Bradyrhizobium yuanmingense from Ghana are effective groundnut micro-symbionts. APPLIED SOIL ECOLOGY : A SECTION OF AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2018; 127:41-50. [PMID: 29887673 PMCID: PMC5989812 DOI: 10.1016/j.apsoil.2018.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 03/02/2018] [Indexed: 05/27/2023]
Abstract
The identification of locally-adapted rhizobia for effective inoculation of grain legumes in Africa's semiarid regions is strategic for developing and optimizing cheap nitrogen fixation technologies for smallholder farmers. This study was aimed at selecting and characterising effective native rhizobia, from Ghanaian soils for groundnut (Arachis hypogaea L.) inoculation. From surface-disinfected root nodules of cowpea and groundnut plants grown on farmers' fields, 150 bacterial isolates were obtained, 30 of which were eventually found to nodulate groundnut plants. After testing the symbiotic potential of these isolates on groundnut on sterilized substrate, seven of them, designated as KNUST 1001-1007, were evaluated in an open field pot experiment using 15N-labelled soil. Although 15N dilution analyses did not indicate differences among treatments in the proportion of nitrogen (N) derived from the atmosphere (%Ndfa), all seven strains increased total N derived from N2 fixation by inoculated groundnut plants as compared to the non-inoculated control. Inoculation with KNUST 1002 led to total N accumulation as high as that of the groundnut reference strain 32H1. Genetic characterisation of the isolates by sequence analysis of 16S rRNA gene, 16S - 23S rRNA intergenic transcribed spacer (ITS) region and nodC gene revealed that isolates KNUST 1003 and 1007 were related to Rhizobium tropici, a common bean symbiont. The other five isolates, including KNUST 1002 belonged to the Bradyrhizobium genus, being closely related to Bradyrhizobium yuanmingense. Therefore, this study revealed novel native Ghanaian rhizobia with potential for the development of groundnut inoculants.
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Detection of the type III secretion system and its phylogenetic and symbiotic characterization in peanut bradyrhizobia isolated from Guangdong Province, China. Syst Appl Microbiol 2018; 41:437-443. [PMID: 29759900 DOI: 10.1016/j.syapm.2018.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
Abstract
The distribution of rhcRST and rhcJ-C1 fragments located in different loci of the type III secretion system (T3SS) gene cluster in the peanut-nodulating bradyrhizobia isolated from Guangdong Province, China was investigated by PCR-based sequencing. T3SS was detected in approximately one-third of the peanut bradyrhizobial strains and the T3SS-harboring strains belonging to different Bradyrhizobium genomic species. Diverse T3SS groups corresponding to different symbiotic gene types were defined among the 23 T3SS-harboring strains. The same or similar T3SS genes were detected in different genospecies, indicating that interspecies horizontal transfer of symbiotic genes had occurred in the Bradyrhizobium genus.
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Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa. Syst Appl Microbiol 2017; 40:215-226. [PMID: 28372899 PMCID: PMC5460907 DOI: 10.1016/j.syapm.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/05/2017] [Accepted: 02/12/2017] [Indexed: 11/30/2022]
Abstract
Groundnut is an economically important N2-fixing legume that can contribute about 100–190 kg N ha−1 to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.
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Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut. Int J Syst Evol Microbiol 2015; 65:4655-4661. [DOI: 10.1099/ijsem.0.000629] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.
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Wild peanut Arachis duranensis are nodulated by diverse and novel Bradyrhizobium species in acid soils. Syst Appl Microbiol 2014; 37:525-32. [PMID: 24985193 DOI: 10.1016/j.syapm.2014.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/17/2022]
Abstract
Aiming at learning the microsymbionts of Arachis duranensis, a diploid ancestor of cultivated peanut, genetic and symbiotic characterization of 32 isolates from root nodules of this plant grown in its new habitat Guangzhou was performed. Based upon the phylogeny of 16S rRNA, atpD and recA genes, diverse bacteria belonging to Bradyrhizobium yuanmingense, Bradyrhizobium elkanii, Bradyrhizobium iriomotense and four new lineages of Bradyrhizobium (19 isolates), Rhizobium/Agrobacterium (9 isolates), Herbaspirillum (2 isolates) and Burkholderia (2 isolates) were defined. In the nodulation test on peanut, only the bradyrhizobial strains were able to induce effective nodules. Phylogeny of nodC divided the Bradyrhizobium isolates into four lineages corresponding to the grouping results in phylogenetic analysis of housekeeping genes, suggesting that this symbiosis gene was mainly maintained by vertical gene transfer. These results demonstrate that A. duranensis is a promiscuous host preferred the Bradyrhizobium species with different symbiotic gene background as microsymbionts, and that it might have selected some native rhizobia, especially the novel lineages Bradyrhizobium sp. I and sp. II, in its new habitat Guangzhou. These findings formed a basis for further study on adaptation and evolution of symbiosis between the introduced legumes and the indigenous rhizobia.
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Multilocus sequence analyses reveal several unnamed Mesorhizobium genospecies nodulating Acacia species and Sesbania sesban trees in Southern regions of Ethiopia. Syst Appl Microbiol 2011; 34:216-26. [DOI: 10.1016/j.syapm.2010.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 08/14/2010] [Accepted: 09/28/2010] [Indexed: 11/17/2022]
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A study on the prevalence of bacteria that occupy nodules within single peanut plants. Curr Microbiol 2011; 62:1752-9. [PMID: 21442391 DOI: 10.1007/s00284-011-9924-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 03/16/2011] [Indexed: 11/26/2022]
Abstract
In this study, bacteria hosted in root nodules of single plants of legume Arachis hypogaea L. (peanut) cv Tegua Runner growing at field were isolated. The collection of nodule isolates included both fast and slow growing strains. Their genetic diversity was assessed in order to identify the more frequently rhizobial strain associated to nodules from single plants. Molecular fingerprinting of 213 nodular isolates indicated heterogeneity, absence of a dominant genotype and, therefore, of a unique strains highly competitive. Efficient nitrogen-fixing isolates were identified as Bradyrhizobium sp. by phylogenetic analysis of the sequences of their 16S rRNA genes. The genetic diversity of 68 peanut nodulating isolates from all the collected plants was also analyzed. Considering their ERIC-PCR profiles, they were grouped in eighteen different OTUs for 60% similarity cut-off. Results obtained in this study indicate that the genetic diversity of rhizobia occupying nodules from single plant is very high, without the presence of a dominant strain. Therefore, the identification of useful peanut rhizobia for agricultural purposes requires strongly the selection, among the diverse population, of a very competitive genotype in combination with a high-symbiotic performance.
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Interaction among Arachis hypogaea L. (peanut) and beneficial soil microorganisms: how much is it known? Crit Rev Microbiol 2010; 36:179-94. [PMID: 20214416 DOI: 10.3109/10408410903584863] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The leguminous crop Arachis hypogaea L. (peanut) is originally from South America and then was disseminated to tropical and subtropical regions. The dissemination of the crop resulted in peanut plants establishing a symbiotic nitrogen-fixing relationship with a wide diversity of indigenous soil bacteria. We present in this review, advances on the molecular basis for the crack-entry infection process involved in the peanut-rhizobia interaction, the diversity of rhizobial and fungal antagonistic bacteria associated with peanut plants, the effect of abiotic and biotic stresses on this interaction and the response of peanut to inoculation.
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Phenotypic and genotypic characterizations of rhizobia isolated from root nodules of peanut (Arachis hypogaea
L.
) grown in Moroccan soils. J Basic Microbiol 2009; 49:415-25. [DOI: 10.1002/jobm.200800359] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Genetic diversity ofBradyrhizobium japonicum within soybean growing regions of the north-eastern Great Plains of North America as determined by REP-PCR and ERIC-PCR profiling. Symbiosis 2009. [DOI: 10.1007/bf03179992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl Environ Microbiol 2008; 74:6987-96. [PMID: 18791003 PMCID: PMC2583495 DOI: 10.1128/aem.00875-08] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 09/07/2008] [Indexed: 01/12/2023] Open
Abstract
A highly supported maximum-likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix obtained from the concatenation of partial atpD, recA, glnII, and rpoB sequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified as B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense, or B. elkanii, whereas one represented a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the of B. japonicum I and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree.
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Competitiveness of a Bradyrhizobium sp. strain in soils containing indigenous rhizobia. Curr Microbiol 2007; 56:66-72. [PMID: 17899258 DOI: 10.1007/s00284-007-9041-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 08/04/2007] [Indexed: 11/28/2022]
Abstract
The success of rhizobial inoculation on plant roots is often limited by several factors, including environmental conditions, the number of infective cells applied, the presence of competing indigenous (native) rhizobia, and the inoculation method. Many approaches have been taken to solve the problem of inoculant competition by naturalized populations of compatible rhizobia present in soil, but so far without a satisfactory solution. We used antibiotic resistance and molecular profiles as tools to find a reliable and accurate method for competitiveness assay between introduced Bradyrhizobium sp. strains and indigenous rhizobia strains that nodulate peanut in Argentina. The positional advantage of rhizobia soil population for nodulation was assessed using a laboratory model in which a rhizobial population is established in sterile vermiculite. We observed an increase in nodule number per plant and nodule occupancy for strains established in vermiculite. In field experiments, only 9% of total nodules were formed by bacteria inoculated by direct coating of seed, whereas 78% of nodules were formed by bacteria inoculated in the furrow at seeding. In each case, the other nodules were formed by indigenous strains or by both strains (inoculated and indigenous). These findings indicate a positional advantage of native rhizobia or in-furrow inoculated rhizobia for nodulation in peanut.
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[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)]. Can J Microbiol 2006; 52:169-81. [PMID: 16604113 DOI: 10.1139/w05-092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.
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Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 2005; 55:1439-1452. [PMID: 16014464 DOI: 10.1099/ijs.0.63534-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR-RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500-1300 bp), and 58 strains contained double copies. UPGMA dendrograms generated from cluster analyses of the 16S and 23S rRNA gene PCR-RFLP data were in good agreement, and the combined distance matrices delineated 87 genotypes, indicating considerable genetic diversity among the isolates. Furthermore, partial sequence analysis of 67 representative strains revealed 46 16S rRNA gene sequence types, among which 12 were 100% similar to those of previously described species and 34 were novel sequences with 94-99% similarity to those of recognized species. The phylogenetic analyses suggested that strains indigenous to Ethiopia belonged to the genera Agrobacterium, Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium and Sinorhizobium. Many of the rhizobia isolated from previously uninvestigated indigenous woody legumes had novel 16S rRNA gene sequences and were phylogenetically diverse. This study clearly shows that the characterization of symbionts of unexplored legumes growing in previously unexplored biogeographical areas will reveal additional diversity.
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Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 2005; 55:569-575. [PMID: 15774626 DOI: 10.1099/ijs.0.63292-0] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Highly diverse Bradyrhizobium strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, atpD, glnII and recA sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely Bradyrhizobium japonicum and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name Bradyrhizobium canariense is proposed. B. canariense populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric B. japonicum bv. genistearum strains in soils of the Canary Islands. B. canariense strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not Glycine species, whereas acid-sensitive B. japonicum soybean isolates such as USDA 6T and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic nifH and nodC sequences, the biovarieties genistearum and glycinearum for the genistoid legume and soybean isolates, respectively, were proposed. B. canariense bv. genistearum strains display an overlapped host range with B. japonicum bv. genistearum isolates, both sharing monophyletic nifH and nodC alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. B. canariense is the sister species of B. japonicum, as inferred from a maximum-likelihood Bradyrhizobium species phylogeny estimated from congruent glnII+recA sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel Bradyrhizobium genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for B. canariense is BTA-1T (=ATCC BAA-1002T=LMG 22265T=CFNE 1008T).
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Abstract
AIMS To determine the effect that the presence of some beetles have on the species of bacteria found in their flour. METHODS AND RESULTS Bacteria were isolated from flour that either did not contain beetles, contained Tribolium beetles in different environments, or contained either Stegobium paniceum or Lasioderma serricorne. These bacteria were tentatively identified by both the gas chromatography-fatty acid methyl esters (GC-FAME) method and partial sequencing of the 16S rRNA gene. All samples contained Bacillus species including the controls, but the non-Tribolium beetles and a Tribolium beetle line known to have low benzoquinones also contained Enterococcus and Enterobacter species. Additionally an unidentified bacteria isolate in the Enterobacteriaceae was also found in the L. serricorne sample. Our results also suggest incongruent identifications when using the GC-FAME method vs sequencing. CONCLUSIONS Certain species of bacteria can be introduced by the presence of insect pests, but the diversity of species is far less in stocks of Tribolium beetles. SIGNIFICANCE AND IMPACT OF THE STUDY Stored product pests can alter the bacterial community. Isolated species from this study show a strong genetic relationship to each other, suggesting an isolated evolving system. A unique bacteria was also isolated. GC and sequencing methods of identification are compared.
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Phenotypic and Genotypic Characterization of Rhizobia from Diverse Geographical Origin that Nodulate Pachyrhizus species. Syst Appl Microbiol 2004; 27:737-45. [PMID: 15612632 DOI: 10.1078/0723202042369839] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Legumes from the genus Pachyrhizus, commonly known as yam bean, are cultivated in several countries from the American continent and constitute an alternative source for sustainable starch, oil and protein production. The endosymbionts of these legumes have been poorly studied although it is known that this legume is nodulated by fast and slow growing rhizobia. In this study we have analyzed a collection of strains isolated in several countries using different phenotypic and molecular methods. The results obtained by SDS-PAGE analysis, LPS profiling and TP-RAPD fingerprinting showed the high diversity of the strains analyzed, although all of them presented slow growth in yeast mannitol agar (YMA) medium. These results were confirmed using 16S-23S internal transcribed spacer (ITS) region and complete sequencing of the 16S rRNA gene, showing that most strains analyzed belong to different species of genus Bradyrhizobium. Three strains were closely related to B. elkanii and the rest of the strains were related to the phylogenetic group constituted by B. japonicum, B. liaoningense, B. yuanmingense and B. betae. These results support that the study of rhizobia nodulating unexplored legumes in different geographical locations will allow the discovery of new species able to establish legume symbioses.
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MESH Headings
- Bacterial Proteins/analysis
- Bacterial Proteins/isolation & purification
- Bradyrhizobium/chemistry
- Bradyrhizobium/classification
- Bradyrhizobium/genetics
- Bradyrhizobium/isolation & purification
- DNA Fingerprinting
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/isolation & purification
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Lipopolysaccharides/analysis
- Lipopolysaccharides/isolation & purification
- Molecular Sequence Data
- Pachyrhizus/microbiology
- Phylogeny
- Proteome/analysis
- Proteome/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Random Amplified Polymorphic DNA Technique
- Sequence Analysis, DNA
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Metabolic and genomic diversity of rhizobia isolated from field standing native and exotic woody legumes in southern Ethiopia. Syst Appl Microbiol 2004; 27:603-11. [PMID: 15490562 DOI: 10.1078/0723202041748145] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Eighty-seven rhizobial strains isolated from root nodules of field standing native and exotic woody legumes in southern Ethiopia were characterized using the Biolog method and AFLP fingerprinting technique. Cluster analysis of the metabolic and genomic fingerprints revealed 18 and 25 groups, respectively, demonstrating considerable diversity in rhizobial population indigenous to Ethiopian soils. While 25 strains (29%) were linked to members of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium or Sinorhizobium, the bulk of the strains formed several distinct groups in both methods and did not relate to reference species included in the study. In contrast to exotic species which formed symbiosis with strains of only one specific genomic group, indigenous host species nodulated by metabolically and genomically diverse groups. The results in this study support the view, that long-term association between the symbionts allows gradual differentiation and diversity in compatible rhizobial population resident in native soils. Lack of significant metabolic and genomic relatedness to the reference strains in our results suggested that test strains in our collection probably included 'unique' types, which belong to several yet undefined rhizobial species.
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Abstract
Genetic diversity of indigenous Bradyrhizobium japonicum population in Croatia was studied by using different PCR-based fingerprinting methods. Characteristic DNA profiles for 20 B. japonicum field isolates and two reference strains were obtained using random primers (RAPD) and two sets of repetitive primers (REP- and ERIC-PCR). In comparison with the REP, the ERIC primer set generates fingerprints of lower complexity, but still several strain-specific bands were detected. Different B. japonicum isolates could be more efficiently distinguished by using combined results from REP- and ERIC-PCR. The most polymorphic bands were observed after amplification with four different RAPD primers. Both methods, RAPD and rep-PCR, resulted in identical grouping of the strains. Cluster analysis, irrespective of the fingerprinting method used, revealed that all the isolates could be divided into three major groups. Within the major groups, the degree of relative similarity between B. japonicum isolates was dependent upon the method used. Our results indicate that both RAPD and rep-PCR fingerprinting can effectively distinguish different B. japonicum strains. RAPD fingerprinting proved to be slightly more discriminatory than rep-PCR.
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The Variable Part of the dnaK Gene as an Alternative Marker for Phylogenetic Studies of Rhizobia and Related Alpha Proteobacteria. Syst Appl Microbiol 2003; 26:483-94. [PMID: 14666974 DOI: 10.1078/072320203770865765] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DnaK is the 70 kDa chaperone that prevents protein aggregation and supports the refolding of damaged proteins. Due to sequence conservation and its ubiquity this chaperone has been widely used in phylogenetic studies. In this study, we applied the less conserved part that encodes the so-called alpha-subdomain of the substrate-binding domain of DnaK for phylogenetic analysis of rhizobia and related non-symbiotic alpha-Proteobacteria. A single 330 bp DNA fragment was routinely amplified from DNA templates isolated from the species of the genera, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium, but also from some non-symbiotic alpha Proteobacteria such as Blastochloris, Chelatobacter and Chelatococcus. Phylogenetic analyses revealed high congruence between dnaK sequences and 16S rDNA trees, but they were not identical. In contrast, the partition homogeneity tests revealed that dnaK sequence data could be combined with other housekeeping genes such as recA, atpD or glnA. The dnaK trees exhibited good resolution in the cases of the genera Mesorhizobium, Sinorhizobium and Rhizobium, even better than usually shown by 16S rDNA phylogeny. The dnaK phylogeny supported the close phylogenetic relationship of Rhizobium galegae and Agrobacterium tumefaciens (R. radiobacter) C58, which together formed a separate branch within the fast-growing rhizobia, albeit closer to the genus Sinorhizobium. The Rhizobium and Sinorhizobium genera carried an insertion composed of two amino acids, which additionally supported the phylogenetic affinity of these two genera, as well as their distinctness from the Mesorhizobium genus. Consistently with the phylogeny shown by 16S-23S rDNA intergenic region sequences, the dnaK trees divided the genus Bradyrhizobium into three main lineages, corresponding to B. japonicum, B. elkanii, and photosynthetic Bradyrhizobium strains that infect Aeschynomene plants. Our results suggest that the 330 bp dnaK sequences could be used as an additional taxonomic marker for rhizobia and related species (alternatively to the 16S rRNA gene phylogeny).
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Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR. Appl Environ Microbiol 2001; 67:3655-64. [PMID: 11472944 PMCID: PMC93068 DOI: 10.1128/aem.67.8.3655-3664.2001] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2000] [Accepted: 05/18/2001] [Indexed: 01/28/2023] Open
Abstract
In addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities or occur as endophytes, e.g., in rice. Two rhizobial strains which have been isolated from root nodules of the aquatic legumes Aeschynomene fluminensis (IRBG271) and Sesbania aculeata (IRBG74) were previously found to promote rice growth. In addition to analyzing their phylogenetic positions, we assessed the suitability of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (IGS) sequences for the differentiation of closely related rhizobial taxa and for the development of PCR protocols allowing the specific detection of strains in the environment. 16S rDNA sequence analysis (sequence identity, 99%) and phylogenetic analysis of IGS sequences showed that strain IRBG271 was related to but distinct from Bradyrhizobium elkanii. Rhizobium sp. (Sesbania) strain IRBG74 was located in the Rhizobium-Agrobacterium cluster as a novel lineage according to phylogenetic 16S rDNA analysis (96.8 to 98.9% sequence identity with Agrobacterium tumefaciens; emended name, Rhizobium radiobacter). Strain IRBG74 harbored four copies of rRNA operons whose IGS sequences varied only slightly (2 to 9 nucleotides). The IGS sequence analyses allowed intraspecies differentiation, especially in the genus Bradyrhizobium, as illustrated here for strains of Bradyrhizobium japonicum, B. elkanii, Bradyrhizobium liaoningense, and Bradyrhizobium sp. (Chamaecytisus) strain BTA-1. It also clearly differentiated fast-growing rhizobial species and strains, albeit with lower statistical significance. Moreover, the high sequence variability allowed the development of highly specific IGS-targeted nested-PCR assays. Strains IRBG74 and IRBG271 were specifically detected in complex DNA mixtures of numerous related bacteria and in the DNA of roots of gnotobiotically cultured or even of soil-grown rice plants after inoculation. Thus, IGS sequence analysis is an attractive technique for both microbial ecology and systematics.
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Abstract
Using high resolution molecular fingerprinting techniques like random amplification of polymorphic DNA, repetitive extragenic palindromic PCR and multilocus enzyme electrophoresis, a high bacterial diversity below the species and subspecies level (microdiversity) is revealed. It became apparent that bacteria of a certain species living in close association with different plants either as associated rhizosphere bacteria or as plant pathogens or symbiotic organisms, typically reflect this relationship in their genetic relatedness. The strain composition within a population of soil bacterial species at a given field site, which can be identified by these high resolution fingerprinting techniques, was markedly influenced by soil management and soil features. The observed bacterial microdiversity reflected the conditions of the habitat, which select for better adapted forms. In addition, influences of spatial separation on specific groupings of bacteria were found, which argue for the occurrence of isolated microevolution. In this review, examples are presented of bacterial microdiversity as influenced by different ecological factors, with the main emphasis on bacteria from the natural environment. In addition, information available from some of the first complete genome sequences of bacteria (Helicobacter pylori and Escherichia coli) was used to highlight possible mechanisms of molecular evolution through which mutations are created; these include mutator enzymes. Definitions of bacterial species and subspecies ranks are discussed in the light of detailed information from whole genome typing approaches.
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Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary islands. Syst Appl Microbiol 2000; 23:418-25. [PMID: 11108022 DOI: 10.1016/s0723-2020(00)80073-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.
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