scholarly journals Proposal of 'Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules

2020 ◽  
Vol 70 (10) ◽  
pp. 5453-5459 ◽  
Author(s):  
Adrien C. Meynier Pozzi ◽  
Aude Herrera-Belaroussi ◽  
Guillaume Schwob ◽  
Hector H. Bautista-Guerrero ◽  
Lorine Bethencourt ◽  
...  
Keyword(s):  
Root Nodules ◽  
Molecular Clusters ◽  
High Latitudes ◽  
Nitrogen Fixing ◽  
High Altitudes ◽  
Content Type ◽  
Link Type ◽  
Dicotyledonous Plants ◽  
Alpine Environments ◽  
Species Being

The members of the genus Frankia are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on Alnus spp. (Betulaceae), Myrica spp., Morella spp. and Comptonia spp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'Candidatus Frankia alpina' species for some strains present in nodules of Alnus alnobetula and A. incana that grow in alpine environments at high altitudes or in subarctic environments at high latitudes.

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

scholarly journals Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3950-3957 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Margo Cnockaert ◽  
Julie K. Ardley ◽  
Garth Maker ◽  
Ron Yates ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia , with the representative strain WSM5005T being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia . Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.

scholarly journals FrankiaDiversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity ofFrankiaPopulations in Corresponding Rhizosphere Soils

2017 ◽  
Vol 84 (5) ◽  
Author(s):  
Seifeddine Ben Tekaya ◽  
Trina Guerra ◽  
David Rodriguez ◽  
Jeffrey O. Dawson ◽  
Dittmar Hahn
Keyword(s):  
Host Plant ◽  
Root Nodule ◽  
Root Nodules ◽  
Actinorhizal Plants ◽  
Nodule Formation ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Rhizosphere Soils ◽  
Root Nodule Formation ◽  
Host Infection

ABSTRACTActinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genusFrankia, and specificFrankiataxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms, we observed that some host species were nodulated (Alnus glutinosa,Alnus cordata,Shepherdia argentea,Casuarina equisetifolia) while others were not (Alnus viridis,Hippophaë rhamnoides). Nodule populations were represented by eight different sequences ofnifHgene fragments. Two of these sequences characterized frankiae inS. argenteanodules, and three others characterized frankiae inA. glutinosanodules. Frankiae inA. cordatanodules were represented by five sequences, one of which was also found in nodules fromA. glutinosaandC. equisetifolia, while another was detected in nodules fromA. glutinosa. Quantitative PCR assays showed that vegetation generally increased the abundance of frankiae in soil, independently of the target gene (i.e.,nifHor the 23S rRNA gene). Targeted Illumina sequencing ofFrankia-specificnifHgene fragments detected 24 unique sequences from rhizosphere soils, 4 of which were also found in nodules, while the remaining 4 sequences in nodules were not found in soils. Seven of the 24 sequences from soils represented >90% of the reads obtained in most samples; the 2 most abundant sequences from soils were not found in root nodules, and only 2 of the sequences from soils were detected in nodules. These results demonstrate large differences between detectableFrankiapopulations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specificFrankiapopulations in soils.IMPORTANCEThe nitrogen-fixing actinobacteriumFrankiaforms root nodules on actinorhizal plants, with members of specificFrankiataxonomic clusters nodulating plants in corresponding host infection groups. We assessedFrankiadiversity in root nodules of different host plant species, and we related specific populations to the abundance and relative distribution of indigenous frankiae in rhizosphere soils. Large differences were observed between detectableFrankiapopulations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specificFrankiapopulations in soils but rather results from plants potentially selecting frankiae from the soil for root nodule formation. These data also highlight the necessity of using a combination of different assessment tools so as to adequately address methodological constraints that could produce contradictory data sets.

Azospirillum humicireducens sp. nov., a nitrogen-fixing bacterium isolated from a microbial fuel cell

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2618-2624 ◽  
Author(s):  
Shungui Zhou ◽  
Luchao Han ◽  
Yueqiang Wang ◽  
Guiqin Yang ◽  
Li Zhuang ◽  
...  
Keyword(s):  
Fuel Cell ◽  
Microbial Fuel Cell ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-negative, facultative anaerobic, motile, spiral, straight-to-slightly curved rod-shaped and nitrogen-fixing strain, designated SgZ-5T, was isolated from a microbial fuel cell (MFC) and was characterized by means of a polyphasic approach. Growth occurred with 0–1 % (w/v) NaCl (optimum 1 %) and at pH 5.5–8.5 (optimum pH 7.2) and at 25–37 °C (optimum 30 °C) in nutrient broth (NB). The strain had the ability to grow under anaerobic conditions via the oxidation of various organic compounds coupled to the reduction of anthraquione-2,6-disulfonate (AQDS). Chemotaxonomic characteristics (main ubiquinone Q-10, major fatty acid C18 : 1ω7c/C18 : 1ω6c and DNA G+C content 67.7 mol%) were similar to those of members of the genus Azospirillum . According to the results of phylogenetic analyses, strain SgZ-5T belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria , and was related most closely to the type strains of Azospirillum lipoferum , Azospirillum thiophilum and Azospirillum oryzae (98.0, 97.6 and 97.1 % 16S rRNA gene sequence similarity, respectively). DNA–DNA pairing studies showed that the unidentified organism displayed reassociation values of 36.7±3.7, 24.1±2.2 and 22.3±2.4 % to the type strains of A. lipoferum , A. thiophilum and A. oryzae , respectively. Similarities between nifH gene sequences of strain SgZ-5T and members of the genus Azospirillum ranged from 94.0 to 97.0 %. A combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SgZ-5T represents a novel species, for which the name Azospirillum humicireducens sp. nov. is proposed. The type strain is SgZ-5T ( = CCTCC AB 2012021T = KACC 16605T).

scholarly journals Photosynthetic Bradyrhizobium sp. Strain ORS285 Is Capable of Forming Nitrogen-Fixing Root Nodules on Soybeans (Glycine max)

2013 ◽  
Vol 79 (7) ◽  
pp. 2459-2462 ◽  
Author(s):  
Eric Giraud ◽  
Lei Xu ◽  
Clémence Chaintreuil ◽  
Daniel Gargani ◽  
Djamel Gully ◽  
...  
Keyword(s):  
Glycine Max ◽  
Root Nodules ◽  
Culture Conditions ◽  
Nitrogen Fixing ◽  
Soybean Genotype ◽  
Content Type ◽  
Bradyrhizobium Sp ◽  
Soybean Roots

ABSTRACTThe ability of photosyntheticBradyrhizobiumstrains ORS285 and ORS278 to nodulate soybeans was investigated. While thenodgene-deficient ORS278 strain induced bumps only on soybean roots, thenodgene-containing ORS285 strain formed nitrogen-fixing nodules. However, symbiotic efficiencies differed drastically depending on both the soybean genotype used and the culture conditions tested.

Azoarcus olearius sp. nov., a nitrogen-fixing bacterium isolated from oil-contaminated soil

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3755-3761 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Euan K. James ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen
Keyword(s):  
Contaminated Soil ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Nitrogen Fixing ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A novel nitrogen-fixing strain, designated DQS-4T, was isolated from oil-contaminated soil in Taiwan and was characterized using a polyphasic taxonomic approach. Cells of strain DQS-4T stained Gram-negative, contained poly-β-hydroxybutyrate granules and were motile rods, surrounded by a thin capsule. Cells displayed a strictly aerobic type of metabolism and fixed nitrogen microaerobically. Growth occurred at 10–45 °C (optimum, 35–40 °C), at pH 7.0–8.0 (optimum, pH 7.0) and with 0–2 % NaCl (optimum, 0.5–1 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DQS-4T belonged to the genus Azoarcus , and its closest neighbours were Azoarcus indigens VB32T and Azoarcus communis SWub3T, with sequence similarities of 97.4 and 96.4 %, respectively. The major cellular fatty acids of strain DQS-4T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content was 64.5 mol%. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. The mean level of DNA–DNA relatedness between strain DQS-4T and A. indigens LMG 9092T was 27.4 %. On the basis of the genotypic and phenotypic data, strain DQS-4T represents a novel species in the genus Azoarcus , for which the name Azoarcus olearius sp. nov. is proposed. The type strain is DQS-4T ( = BCRC 80407T = KCTC 23918T = LMG 26893T).

scholarly journals Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1906-1912 ◽  
Author(s):  
Natasha R. Mavengere ◽  
Allan G. Ellis ◽  
Johannes J. Le Roux
Keyword(s):  
South African ◽  
Type Strain ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Associated Species

During a study to investigate the diversity of rhizobia associated with native legumes in South Africa’s Cape Floristic Region, a Gram-negative bacterium designated VG1CT was isolated from the root nodules of Aspalathus abietina Thunb. Based on phylogenetic analyses of the 16S rRNA and recA genes, VG1CT belongs to the genus Burkholderia , with the highest degree of sequence similarity to the type strain of Burkholderia sediminicola (98.5 % and 98 %, respectively). The DNA G+C content of strain VG1CT was 60.1 mol%, and DNA–DNA relatedness values to the type strain of closely related species were found to be substantially lower than 70 %. As evidenced by results of genotypic, phenotypic and chemotaxonomic tests provided here, we conclude that isolate VG1CT represents a novel rhizosphere-associated species in the genus Burkholderia , for which the name Burkholderia aspalathi sp. nov. is proposed, with the type strain VG1CT ( = DSM 27239T = LMG 27731T).

scholarly journals Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides inSinorhizobium meliloti

2017 ◽  
Vol 200 (3) ◽  
Author(s):  
Melanie J. Barnett ◽  
Sharon R. Long
Keyword(s):  
Cell Surface ◽  
Biofilm Formation ◽  
Sinorhizobium Meliloti ◽  
Developmental Process ◽  
Root Nodules ◽  
Critical Role ◽  
Nitrogen Fixing ◽  
Symbiotic Interaction ◽  
Content Type ◽  
Mutant Phenotypes

ABSTRACTSinorhizobium melilotiis a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn5-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene,emmD, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn5-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation inrpoAcorresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.IMPORTANCEThe alphaproteobacteriumSinorhizobium meliloticonverts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation ofS. melilotifrom a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, theS. meliloticell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterizedS. melilotimutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.

scholarly journals Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3202-3207 ◽  
Author(s):  
Xiumei Yu ◽  
Sylvie Cloutier ◽  
James T. Tambong ◽  
Eden S. P. Bromfield
Keyword(s):  
Glycine Max ◽  
Glycine Soja ◽  
Root Nodules ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Link Type ◽  
Macroptilium Atropurpureum

Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium . To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium . Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%.

Derxia lacustris sp. nov., a nitrogen-fixing bacterium isolated from a freshwater lake

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 965-970 ◽  
Author(s):  
Wen-Ming Chen ◽  
Wei-Cheng Huang ◽  
Shih-Yi Sheu
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Link Type

A novel nitrogen-fixing strain, designated HL-12T, was isolated from a freshwater lake in Taiwan. Cells of strain HL-12T were aerobic, Gram-negative, motile rods that were surrounded by a thick capsule, contained poly-β-hydroxybutyrate granules, and formed light-yellow to brownish-red colonies. Growth occurred at 15–40 °C (optimum 25–35 °C), at pH 6.0–7.0 (optimum pH 6.0) and with 0–4 % NaCl (optimum 0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HL-12T belonged to the genus Derxia and exhibited 99.1 and 98.8 % 16S rRNA gene sequence similarity, respectively, with Derxia gummosa IAM 14990 and D. gummosa IAM 13946T. The major fatty acids (>10 %) of strain HL-12T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The cellular hydroxy fatty acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The isoprenoid quinone was Q-8 and the DNA G+C content was 72.0 mol%. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unknown aminophospholipids and phospholipids. DNA–DNA relatedness between strain HL-12T and LMG 3975 and LMG 3977T was <70 %. On the basis of the genotypic and phenotypic data, strain HL-12T represents a novel species in the genus Derxia , for which the name Derxia lacustris sp. nov. is proposed. The type strain is HL-12T ( = BCRC 80208T  = KCTC 23311T).

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