scholarly journals Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria

2004 ◽  
Vol 54 (6) ◽  
pp. 2269-2273 ◽  
Author(s):  
Philippe Jourand ◽  
Eric Giraud ◽  
Gilles Béna ◽  
Abdoulaye Sy ◽  
Anne Willems ◽  
...  
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
Root Nodule ◽  
Root Nodules ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Protein Patterns ◽  
Gene Encoding

Data on 72 non-pigmented bacterial strains that specifically induce nitrogen-fixing root nodules on the legume species Crotalaria glaucoides, Crotalaria perrottetii and Crotalaria podocarpa are reviewed. By SDS-PAGE analysis of total protein patterns and by 16S rRNA PCR-RFLP, these strains form a homogeneous group that is separate from other legume root-nodule-forming bacteria. The 16S rRNA gene-based phylogeny indicates that these bacteria belong to the genus Methylobacterium. They can grow on C1 compounds such as methanol, formate and formaldehyde but not methylamine as sole carbon source, and carry an mxaF gene, encoding methanol dehydrogenase, which supports their methylotrophic metabolism. Presence of a nodA nodulation gene, and ability to nodulate plants of Crotalaria species and to fix nitrogen are features that separate the strains currently included in this group from other members of the genus Methylobacterium. The present study includes additional genotypic and phenotypic characterization of this novel Methylobacterium species, i.e. nifH gene sequence, morphology, physiology, enzymic and carbon source assimilation tests and antibiotic resistance. The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060T=CNCM I 2342T=LMG 21967T) is proposed for this group of root-nodule-forming bacteria.

Azospirillum melinis sp. nov., a group of diazotrophs isolated from tropical molasses grass

2006 ◽  
Vol 56 (6) ◽  
pp. 1263-1271 ◽  
Author(s):  
Guixiang Peng ◽  
Huarong Wang ◽  
Guoxia Zhang ◽  
Wei Hou ◽  
Yang Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pcr Amplification ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Azospirillum Lipoferum ◽  
Protein Patterns

Fifteen bacterial strains isolated from molasses grass (Melinis minutiflora Beauv.) were identified as nitrogen-fixers by using the acetylene-reduction assay and PCR amplification of nifH gene fragments. These strains were classified as a unique group by insertion sequence-PCR fingerprinting, SDS-PAGE protein patterns, DNA–DNA hybridization, 16S rRNA gene sequencing and morphological characterization. Phylogenetic analysis of the 16S rRNA gene indicated that these diazotrophic strains belonged to the genus Azospirillum and were closely related to Azospirillum lipoferum (with 97.5 % similarity). In all the analyses, including in addition phenotypic characterization using Biolog MicroPlates and comparison of cellular fatty acids, this novel group was found to be different from the most closely related species, Azospirillum lipoferum. Based on these data, a novel species, Azospirillum melinis sp. nov., is proposed for these endophytic diazotrophs of M. minutiflora, with TMCY 0552T (=CCBAU 5106001T=LMG 23364T=CGMCC 1.5340T) as the type strain.

scholarly journals Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

2011 ◽  
Vol 61 (11) ◽  
pp. 2582-2588 ◽  
Author(s):  
Fang Wang ◽  
En Tao Wang ◽  
Li Juan Wu ◽  
Xin Hua Sui ◽  
Ying Li ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7T (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570T (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA–DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T m). The type strain of R. vallis sp. nov. is CCBAU 65647T ( = LMG 25295T  = HAMBI 3073T), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

scholarly journals Effect of culture conditions on nitrogen-fixing activity of bacteria isolated from cassava cultivated soils of Vietnam

2021 ◽  
Vol 43 (3) ◽  
pp. 27-35
Author(s):  
Pham Viet Cuong ◽  
Nguyen Phuong Hoa
Keyword(s):  
Bacillus Subtilis ◽  
Carbon Source ◽  
16S Rrna ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Atmospheric Nitrogen ◽  
Bacillus Sp ◽  
Nitrogen Fixing ◽  
The 16S Rrna Gene ◽  
Cultivated Soils

The bacteria capable of fixing atmospheric nitrogen were isolated from cassava cultivated soils of Vietnam. The potential isolates were identified by analyzing the 16S rRNA gene and by morphological, biochemical, cultural characteristics. The selected isolates were assigned to the species Bacillus sp. DQT2 M17, Bacillus subtilis DTAN6 M17, and Bacillus megaterium DSHB I8. The effect of culture conditions on the nitrogen-fixing activity of three selected isolates were studied and the obtained results showed that the highest amount of accumulated ammonia was detected after 6 days of incubation at 35 oC, pH 7.0 with sucrose as a carbon source. The selected strains could be exploited as inoculants for microbial fertilizer production.

scholarly journals Bradyrhizobia isolated from root nodules of Parasponia (Ulmaceae) do not constitute a separate coherent lineage

2006 ◽  
Vol 56 (5) ◽  
pp. 1013-1018 ◽  
Author(s):  
Bénédicte Lafay ◽  
Erika Bullier ◽  
Jeremy J. Burdon
Keyword(s):  
16S Rrna ◽  
Host Range ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
Host Switch ◽  
Cultural Types ◽  
The Relationship

Rhizobial bacteria almost exclusively nodulate members of the families Fabaceae, Mimosaceae and Caesalpiniaceae, but are found on a single non-legume taxon, Parasponia (Ulmaceae). Based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from Parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. This hypothesis was investigated by focusing on four isolates that are representative of the morphological and cultural types of Parasponia-nodulating bradyrhizobia. Their evolutionary relationships with other rhizobia were analysed using 16S rRNA gene sequences and their nodulation properties were explored using the nodA gene as a proxy for host-range specificity. Phylogenetic analyses of the 16S rRNA and nodA gene sequences revealed that bacterial isolates from Parasponia species are embedded among other bradyrhizobia. They did not cluster together in topologies based on the 16S rRNA or nodA gene sequences, but were scattered among other bradyrhizobia belonging to either the Bradyrhizobium japonicum or the Bradyrhizobium elkanii lineages. These data suggest that the ability of some bradyrhizobia to nodulate species of the genus Parasponia does not represent a historical relationship that predates the relationship between rhizobia and legumes, but is probably a more recent host switch for some rhizobia.

scholarly journals Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs

2007 ◽  
Vol 57 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Yuchao Ma ◽  
Zhiqiang Xia ◽  
Xuming Liu ◽  
Sanfeng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Significant Feature ◽  
Rrna Gene ◽  
The Novel ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Rhizosphere Soils

Five novel endospore-forming, nitrogen-fixing bacterial strains were isolated from the rhizosphere soils of plants of the species Sabina squamata, Weigela florida and Zanthoxylum simulans. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. These novel strains showed the highest levels (96.2–98.2 %) of 16S rRNA gene sequence similarity with Paenibacillus azotofixans. However, the DNA–DNA relatedness between these novel strains and P. azotofixans was 12.9–29.5 %. The DNA G+C contents of the five strains were found to be 51.9–52.9 mol%. Phenotypic analyses showed that a significant feature of the novel strains (differentiating them from P. azotofixans and other Paenibacillus species) is that all of them were unable to produce acid and gas from various carbohydrates such as glucose, sucrose, lactose and fructose. Anteiso-branched C15 : 0 was the major fatty acid present in the novel type strain. On the basis of these data, the five novel strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sabinae sp. nov. is proposed. The type strain is T27T (=CCBAU 10202T=DSM 17841T).

scholarly journals Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere

2007 ◽  
Vol 57 (3) ◽  
pp. 620-624 ◽  
Author(s):  
Samina Mehnaz ◽  
Brian Weselowski ◽  
George Lazarovits
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Morphological Characterization ◽  
Major Fatty Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Closely Related Species ◽  
Gene Sequence Analysis ◽  
Biolog Analysis

A free-living diazotrophic strain, DS2T, was isolated from corn rhizosphere. Polyphasic taxonomy was performed including morphological characterization, Biolog analysis, and 16S rRNA, cpn60 and nifH gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain DS2T was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (DNA G+C content 67.9 mol%; Q-10 quinone system; major fatty acid 18 : 1ω7c) were also similar to those of the genus Azospirillum. In all the analyses, including phenotypic characterization using Biolog analysis and comparison of cellular fatty acids, this isolate was found to be different from the closely related species Azospirillum lipoferum, Azospirillum oryzae and Azospirillum brasilense. On the basis of these results, a novel species is proposed for this nitrogen-fixing strain. The name Azospirillum canadense sp. nov. is suggested with the type strain DS2T (=NCCB 100108T=LMG 23617T).

scholarly journals Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor

2005 ◽  
Vol 55 (6) ◽  
pp. 2543-2549 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Hee-Sung Bae ◽  
Jong-Hwan Baek ◽  
Wen-Feng Chen ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Encoding ◽  
Phenotypic Properties ◽  
Type Strains

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61T and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus Rhizobium comprising the type strains of Rhizobium giardinii, Rhizobium radiobacter, Rhizobium rubi, Rhizobium larrymoorei, Rhizobium vitis, Rhizobium undicola, Rhizobium loessense, Rhizobium galegae and Rhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0·6–0·7×1·1–1·3 μm), with peritrichous flagella. The DNA G+C content is 60·1–60·9 mol%. Cellular fatty acids are C16 : 0 (2·2–3·3 %), C18 : 0 (2·1–3·2 %), C19 : 0 cyclo ω8c (9·9–16·8 %), C20 : 3 ω6,9,12c (2·7–3·3 %), summed feature 3 (7·2–7·7 %) and summed feature 7 (67·8–73·7 %). The strains formed nodules on a legume plant, Medicago sativa. A nifH gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61T by PCR amplification by using a nifH-specific primer system. Strains L61T and L22 were distinguished from the type strains of recognized Rhizobium species in the same sublineage based on low DNA–DNA hybridization values (2–4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61T and L22 from Rhizobium species in the same sublineage. Based on the results obtained in this study, L61T and L22 are considered to be representatives of a novel species of Rhizobium, for which the name Rhizobium daejeonense sp. nov. is proposed. The type strain is L61T (=KCTC 12121T=IAM 15042T=CCBAU 10050T).

scholarly journals Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia

2011 ◽  
Vol 61 (2) ◽  
pp. 299-309 ◽  
Author(s):  
Mohammad S. Hoque ◽  
Linda M. Broadhurst ◽  
Peter H. Thrall
Keyword(s):  
Root Nodule ◽  
Root Nodules ◽  
Disease Suppression ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Symbiotic Relationships ◽  
South Eastern ◽  
Eastern Australia ◽  
Microbe Interactions ◽  
Ecological Importance

Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant–microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.

Diversity of Indigenous Symbiotic Nitrogen Fixing Bacteria from Blackgram [Vigna mungo (L.) Hepper] Cultivated in Rice Fallows

2020 ◽  
Author(s):  
T. Satyanandam ◽  
K. Babu ◽  
B. Yellamanda ◽  
K. Vijaya Kumar ◽  
G. Rosaiah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
High Genetic Diversity ◽  
Microbiological Methods

Background: Legume nodulating bacteria (LNB), also known as rhizobia produce root nodules on leguminous plants where in nitrogen fixation takes place. In agriculture, this symbiotic relationship is significant as it provides nitrogenous fertilizers to the leguminous crops. Traditionally rhizobia were exclusively members of the Rhizobiaceae family in the Alphaproteobacteria class of bacteria. Several reports revealed that large number of diazotrophs have the ability to nodulate and fix atmospheric N2 in legumes in addition to rhizobia which are outside the Alphaproteobacteria class. Relatively less information is available on the genetic diversity of indigenous rhizobia nodulating blackgram cultivated in rice fallows. Hence the present study was carried out to know the diversity of symbiotic native nitrogen fixing bacteria isolated from the root nodules of blackgram grown in rice fallows using partial 16S rRNA sequencing.Methods: Nitrogen fixing microsymbionts (Rhizobium strains) from root nodules of blackgram were isolated on yeast extract mannitol agar (YEMA) medium. The pure cultures were maintained at 28±2°C for 48 h. Identification of Rhizobium isolates was done by using various tests and Morphological characterization of isolates was also done by using standard microbiological methods. The PCR amplification and sequencing of 16S rRNA gene of isolates were carried out to identify the isolates.Result: In the present study four strains of Rhizobium designated as VM-2, VM-8, VM-9 and VM-15 were isolated. Morphologically colonies of all strains are round, transparent, entire, convex and smooth. They are Gram-ve and rod shaped. Mucilage production is noticed in VM-2, VM-8 and VM-9. The 16S rRNA gene sequences revealed that the strain VM-2 showed a close relation with Rhizobium, VM-8 and VM-9 with Bradyrhizobium where as VM-15 with Achromobater. It was concluded that the symbiotic nitrogen fixing bacteria isolated from the root nodules of blackgram cultivated in rice fallows exhibited high genetic diversity. 

scholarly journals Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

2006 ◽  
Vol 56 (4) ◽  
pp. 889-893 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and greater than 70 % DNA–DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99·5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68·0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA–DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T=IAM 15283T=CCTCC AB205007T).

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