Ensifer melilotiis the preferred symbiont ofMedicago arboreain eastern Morocco soils

2013 ◽  
Vol 59 (8) ◽  
pp. 540-548 ◽  
Author(s):  
Kamal Guerrouj ◽  
Eduardo Pérez-Valera ◽  
Hanaa Abdelmoumen ◽  
Eulogio J. Bedmar ◽  
Mustapha Missbah El Idrissi
Keyword(s):  
Root Nodules ◽  
Rrna Gene ◽  
Local Conditions ◽  
Eastern Area ◽  
Physiological Diversity ◽  
Phylogenetic Affiliation ◽  
Nodc Gene ◽  
Polyphasic Characterization ◽  
Eastern Morocco

Polyphasic characterization of 61 bacteria isolated from root nodules of Medicago arborea (Medic tree) plants growing in 4 arid soils of the arid eastern area of Morocco was studied. All the isolates characterized were fast growers. The phenotypic, symbiotic, and cultural characteristics analyzed allowed the description of a broad physiological diversity among the isolates. The results obtained suggest that the phenotype of these rhizobia might have evolved to adapt to the local conditions. The genetic characterization consisted of an analysis of the rep-PCR (repetitive extragenic palindromic polymerase chain reaction) fingerprints and a PCR-based RFLP (restriction fragment length polymorphism) of the 16S rDNA patterns. The diversity of the isolates was investigated by rep-PCR, giving a similarity of 62%, delineated into 3 clusters, 4 groups, and 6 subclusters. This wide diversity was also observed by a phenotypic approach, where the carbohydrate assimilation test was the most discriminating. The results show a relationship between rep-PCR fingerprinting and sugar assimilation, which are complementary in diversity investigation. The nearly complete 16S rRNA gene sequence from representative strains of each soil showed they are closely related to members of the genus Ensifer of the family Rhizobiaceae within the Alphaproteobacteria and shows the highest similitude values (99.93%/100%) with Ensifer meliloti LMG 6133T(X67222). Sequencing of the symbiotic nodC gene from 7 representative strains revealed they had 94.89% identity with the nodC sequence of the type strain E. meliloti LMG 6133T(EF428922). Therefore, the 61 M. arborea isolates from the 4 different soils have the same phylogenetic affiliation, which proves the restricted host specificity among M. arborea species.

scholarly journals Mycobacterium celeriflavum sp. nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 510-515 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Cengiz Çavuşoğlu ◽  
Emanuele Borroni ◽  
Parvin Heidarieh ◽  
Orhan Kaya Koksalan ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).

scholarly journals Mycobacterium angelicum sp. nov., a non-chromogenic, slow-growing species isolated from fish and related to Mycobacterium szulgai

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4724-4729 ◽  
Author(s):  
Fazel Pourahmad ◽  
Mateja Pate ◽  
Matjaž Ocepek ◽  
Emanuele Borroni ◽  
Andrea M. Cabibbe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
The Status ◽  
Polyphasic Characterization

The name ‘Mycobacterium angelicum’ dates back to 2003 when it was suggested for a slowly growing mycobacterium isolated from freshwater angelfish. This name is revived here and the novel species is proposed on the basis of the polyphasic characterization of four strains including the original one. The four strains presented 100 % 16S rRNA gene sequence similarity with Mycobacterium szulgai but clearly differed from M. szulgai for the milky white aspect of the colonies. The sequence similarity with the type strain of M. szulgai ranged, in eight additionally investigated genetic targets, from 78.9 to 94.3 %, an evident contrast with the close relatedness that emerged at the level of 16S rRNA gene. The average nucleotide identity between the genomes of M. szulgai DSM 44166T and strain 126/5/03T (type strain of the novel species) was 92.92 %, and supported the status of independent species. The confirmation of the name Mycobacterium angelicum sp. nov. is proposed, with strain 126/5/03T ( = CIP 109313T = DSM 45057T) as the type strain.

scholarly journals Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

2016 ◽  
Vol 65 (3) ◽  
pp. 331-339 ◽  
Author(s):  
Mosbah Mahdhi ◽  
Nadia Houidheg ◽  
Neji Mahmoudi ◽  
Abdelhakim Msaadek ◽  
Mokhtar Rejili ◽  
...  
Keyword(s):  
Host Plants ◽  
Root Nodules ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Carbon And Nitrogen ◽  
16S Rdna Pcr ◽  
Pcr Rflp ◽  
Phenotypic Features ◽  
Rrna Gene Sequencing

Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole carbon and nitrogen source. The majority of isolate grew at pHs between 6 and 9, at temperatures up to 40°C and tolerated 3% NaCl concentrations. Phylogenetically, the new isolates were affiliated to four genera Sinorhizobium, Rhizobium, Mesorhizobium and Agrobacterium. About 73% of the isolates were species within the genera Sinorhizobium and Rhizobium. The isolates which failed to nodulate their host plants of origin were associated to Agrobacterium genus (three isolates).

scholarly journals Polyphasic characterization of Trichocoleus desertorum sp. nov. (Pseudanabaenales, Cyanobacteria) from desert soils and phylogenetic placement of the genus Trichocoleus

Phytotaxa ◽  
2014 ◽  
Vol 163 (5) ◽  
pp. 241 ◽  
Author(s):  
Radka Muhlsteinova ◽  
Jeffrey R. Johansen ◽  
Nicole Pietrasiak ◽  
Michael P. Martin ◽  
Karina Osorio-Santos ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Its Region ◽  
Taxonomic Diversity ◽  
Morphological Description ◽  
Rrna Gene ◽  
New Taxon ◽  
Desert Soils ◽  
Phylogenetic Placement ◽  
Polyphasic Characterization

Little is known about the taxonomic diversity of cyanobacteria in deserts, despite their important ecological roles in these ecosystems. In this study, cyanobacterial strains from the Atacama, Colorado, and Mojave Deserts were isolated and characterized using molecular, morphological, and ecological information. Phylogenetic placement of these strains was revealed through Bayesian and parsimony-based phylogenetic analyses utilizing sequences of the 16S rRNA gene and the associated 16S–23S ITS region. Based on the combined evidence of this polyphasic approach, a new species from desert soils morphologically corresponding to the genus Trichocoleus was described. Trichocoleus desertorum sp. nov. Mühlsteinová, Johansen et Pietrasiak was used to obtain a phylogenetic reference point for Trichocoleus, a genus so far characterized by morphological description only. Through characterization of this new taxon in desert soils we hope to contribute to the general understanding of cyanobacterial diversity in extreme arid habitats.

scholarly journals Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen. nov., comb. nov., and description of the Bacteriovorax–Peredibacter clade as Bacteriovoracaceae fam. nov.

2004 ◽  
Vol 54 (5) ◽  
pp. 1439-1452 ◽  
Author(s):  
Yaacov Davidov ◽  
Edouard Jurkevitch
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
New Family ◽  
Phylogenetic Affiliation

A phylogenetic analysis of Bdellovibrio-and-like organisms (BALOs) was performed. It was based on the characterization of 71 strains and on all consequent 16S rRNA gene sequences available in databases, including clones identified by data-mining, totalling 120 strains from very varied biotopes. Amplified rDNA restriction analysis (ARDRA) accurately reflected the diversity and phylogenetic affiliation of BALOs, thereby providing an efficient screening tool. Extensive phylogenetic analysis of the 16S rRNA gene sequences revealed great diversity within the Bdellovibrio (>14 % divergence) and Bacteriovorax (>16 %) clades, which comprised nine and eight clusters, respectively, exhibiting more than 3 % intra-cluster divergence. The clades diverged by more than 20 %. The analysis of conserved 16S rRNA secondary structures showed that Bdellovibrio contained motifs atypical of the δ-Proteobacteria, suggesting that it is ancestral to Bacteriovorax. While none of the Bdellovibrio strains were of marine origin, Bacteriovorax included separate soil/freshwater and marine-specific groups. On the basis of their extensive diversity and the large distance separating the groups, it is proposed that Bacteriovorax starrii be placed into a new genus, Peredibacter gen. nov., with Peredibacter starrii A3.12T (=ATCC 15145T=NCCB 72004T) as its type strain. Also proposed is a redefinition of the Bdellovibrio and the Bacteriovorax–Peredibacter lineages as two different families, i.e. ‘Bdellovibrionaceae’ and a new family, Bacteriovoracaceae. Also, a re-evaluation of oligonucleotides targeting BALOs is presented, and the implications of the large diversity of these organisms and of their distribution in very different environments are discussed.

scholarly journals Taxonomy and Polyphasic Characterization of Alkaline Amylase Producing Marine ActinomyceteStreptomyces rocheiBTSS 1001

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Aparna Acharyabhatta ◽  
Siva Kumar Kandula ◽  
Ramana Terli
Keyword(s):  
Bay Of Bengal ◽  
Aerial Mycelium ◽  
Amylolytic Activity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Marine Actinomycete ◽  
Streptomyces Plicatus ◽  
Alkaline Amylase ◽  
Polyphasic Characterization

Actinomycetes isolated from marine sediments along the southeast coast of Bay of Bengal were investigated for amylolytic activity. Marine actinomycete BTSS 1001 producing an alkaline amylase was identified from marine sediment of Diviseema coast, Bay of Bengal. The isolate produced alkaline amylase with maximum amylolytic activity at pH 9.5 at 50°C. The organism produced white to pale grey substrate mycelium and grayish aerial mycelium with pinkish brown pigmentation. A comprehensive study of morphological, physiological parameters, cultural characteristics, and biochemical studies was performed. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0as the major cellular fatty acids, LL-diaminopimelic acid as the characteristic cell wall component, and menaquinones MK-9H(6)and MK-9H(8)as the major isoprenoid quinones is attributed to the strain BTSS 1001 belonging to the genusStreptomyces. Comparison of 16S rRNA gene sequences showed that strain BTSS 1001 exhibited the highest similarities to the type strains ofStreptomyces rochei(99%),Streptomyces plicatus(99%), andStreptomyces enissocaesilis(99%). Using the polyphasic taxonomical approach and phenotypic characteristic studies, the isolate BTSS 1001 was characterized as marine actinomyceteStreptomyces rochei.

scholarly journals Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Konrad Egli ◽  
Anna Roditscheff ◽  
Ursula Flückiger ◽  
Martin Risch ◽  
Lorenz Risch ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
23S Rrna ◽  
Rrna Gene ◽  
Limited Information ◽  
Specific Pcr ◽  
Appropriate Treatment ◽  
23S Rrna Gene ◽  
Allele Type ◽  
Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

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