PCR-amplified 16S rRNA sequence analysis to confirm nodulation of Datisca cannabina L. by the endophyte of Coriaria nepalensis Wall

Mirza, Muhammad Nadeem; Akkermans, W.; Akkermans, A.D.L.

doi:10.1007/bf00150356

Cited by 24 publications

(13 citation statements)

References 33 publications

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“…Additional fresh samples were obtained from various locations, including a river site, a grassland, a pine tree forest, a fruit tree garden, and a vegetable garden within Provinzende de Cima, Portugal, and from a vegetable garden in Sofia, Bulgaria. Air-dried samples originated from soil under Coriaria nepalensis plants from the Murree area of the Himalayan Mountains in Pakistan (collected in 1993) (20) and from the Russian tundra (collected in 2001). In addition, air-dried soil samples were used that had been collected from the top 0-to 25-cm layer of nonfertilized areas of an agricultural field in the Wieringermeer polder, The Netherlands.…”

Section: Methodsmentioning

confidence: 99%

Development and Application of a Selective PCR-Denaturing Gradient Gel Electrophoresis Approach To Detect a Recently Cultivated Bacillus Group Predominant in Soil

Tzeneva

Felske

et al. 2004

Appl Environ Microbiol

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The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance and cultivability of at least some of these microorganisms makes them an appropriate subject for studies on their biogeographical dissemination and diversity. Since cultivability can vary significantly with the physiological state and even between closely related strains, we developed a culture-independent 16S rRNA gene-targeted DGGE fingerprinting protocol for the detection of these bacteria from soil samples. The composition of the B. benzoevorans relatives in the soil samples from The Netherlands, Bulgaria, Russia, Pakistan, and Portugal showed remarkable differences between the different countries. Differences in the DGGE profiles of these communities in archived soil samples from the Dutch Wieringermeer polder were observed over time during which a shift from anaerobic to aerobic and from saline to freshwater conditions occurred. To complement the molecular methods, we additionally cultivated B. benzoevorans-related strains from all of the soil samples. The highest number of B. benzoevorans relatives was found in the soils from the northern part of The Netherlands. The present study contributes to our knowledge of the diversity and abundance of this interesting group of microbes in soils throughout the world.

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Section: Methodsmentioning

confidence: 99%

Development and Application of a Selective PCR-Denaturing Gradient Gel Electrophoresis Approach To Detect a Recently Cultivated Bacillus Group Predominant in Soil

Tzeneva

Felske

et al. 2004

Appl Environ Microbiol

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“…AG (14), CcI3 (29), Cc1.17 (18), CN3 (20), CpI1 succinate variant (CpI1-S) (5, 26), CpI1 propionate variant (CpI1-P) (5,26), DC12 (1), EI5c (17), EAN1pec (16), EuI1c (2), EUN1f (14), and QA3 (12) were grown and maintained in basal growth medium with NH 4 Cl as the nitrogen source, as described previously (26,27). For the heavy metal sensitivity assays, the basal growth medium contained 20 mM glucose and 20 mM succinate as the carbon and energy sources (glucose-succinate medium).…”

Section: Frankia Strains Acn1mentioning

confidence: 99%

Heavy Metal Resistance Patterns of Frankia Strains

Richards

Krumholz

Chval

et al. 2002

Appl Environ Microbiol

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The sensitivity of 12 Frankia strains to heavy metals was determined by a growth inhibition assay. In general, all of the strains were sensitive to low concentrations (<0.5 mM) of Ag 1؉ , AsO 2 1؊ , Cd 2؉ , SbO 2 1؊ , and Ni 2؉ , but most of the strains were less sensitive to Pb 2؉ (6 to 8 mM), CrO 4 2؊ (1.0 to 1.75 mM), AsO 4 3؊ (>50 mM), and SeO 2 2؊ (1.5 to 3.5 mM). While most strains were sensitive to 0.1 mM Cu 2؉ , four strains were resistant to elevated levels of Cu 2؉ (2 to 5 mM and concentrations as high as 20 mM). The mechanism of SeO 2 2؊ resistance seems to involve reduction of the selenite oxyanion to insoluble elemental selenium, whereas Pb 2؉ resistance and Cu 2؉ resistance may involve sequestration or binding mechanisms. Indications of the resistance mechanisms for the other heavy metals were not as clear.Frankia, a member of the order Actinomycetales, forms a symbiotic nitrogen-fixing association with a variety of woody dicotyledonous plants (for reviews see references 3 and 28). The members of this bacterial genus are known to be associated with over 200 species of plants representing eight plant families. These bacteria fix N 2 from the atmosphere and produce a significant amount of the fixed nitrogen on the planet. Actinorhizal plants are ecologically important as pioneer community plants and have economic value in land reclamation, reforestation, and soil stabilization.The lack of a well-established genetic system is a major obstacle in the elucidation of the mechanism of actinorhizal nitrogen fixation and plant-microbe interactions (for reviews see references 22, 23, and 25). There is a paucity of genetic markers for Frankia. Some of the most useful genetic markers include resistance to antibiotics, resistance to antimetabolites, and resistance to heavy metals. These directly selectable traits provide a mechanism for positive selection in genetic studies and are also useful in the development of cloning vectors. For example, metal resistance has been useful in the development of cloning vectors for Rhodococcus, another member of the Actinomycetales (8). Previously, we developed a growth inhibition assay that was used to screen several Frankia strains for resistance to antibiotics (27). Although several important antibiotic resistance markers were described in that study, we were interested in identifying other selectable genetic markers. Since actinorhizal plants have been used for land reclamation in strip-mined areas, we reasoned that it is possible that the bacteria are resistant to heavy metals. The purpose of this study was to extend the use of our growth inhibition assay to identify new selectable markers, resistance to heavy metals. Frankia strains ACN1AG (14), CcI3 (29), Cc1.17 (18), CN3 (20), CpI1 succinate variant (CpI1-S) (5, 26), CpI1 propionate variant (CpI1-P) (5, 26), DC12 (1), EI5c (17), EAN1pec (16), EuI1c (2), EUN1f (14), and QA3 (12) were grown and maintained in basal growth medium with NH 4 Cl as the nitrogen source, as described previously (26, 27). For the heavy metal s...

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“…The third microsymbiont infected Datisca plants that were not then known to be actinorhizal; these plants were later discovered to be nodulated by Frankia strains (9) and to have a unique morphology inside their nodules (round diazovesicles oriented toward the center of the host cell, with an excentric stele). The level of similarity of the sequences of these three organisms is high, and two of these organisms (the Coriana and Dutisca microsymbionts) can be cross-inoculated (34). On the other hand, it has been determined by rbcL sequence analysis that the Rosaceae (which includes the genus Dryas) is quite distant from the Datiscaceae and the Coriariaceae (2,10).…”

Section: Derrnatophilus-congolensismentioning

confidence: 99%

Molecular Phylogeny of the Genus Frankia and Related Genera and Emendation of the Family Frankiaceae

Normand

Orso

Cournoyer

et al. 1996

International Journal of Systematic Bacteriology

317

249

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The members of the actinomycete genus Frankia are nitrogen-fixing symbionts of many species of woody dicotyledonous plants belonging to eight families. Several strains isolated from diverse actinorhizal plants growing in different geographical areas were used in this study. The phylogenetic relationships of these organisms and uncharacterized microsymbionts that are recalcitrant to isolation in pure culture were determined by comparing complete 16s ribosomal DNA sequences. The resulting phylogenetic tree revealed that there was greater diversity among the Alnus-infective strains than among the strains that infect other host plants. The four main subdivisions of the genus Frankia revealed by this phylogenetic analysis are (i) a very large group comprising Frankia alni and related organisms (including Alnus rugosa Sp+ microsymbionts that are seldom isolated in pure culture), to which Casuarina-infective strains, a Myrica nagi microsymbiont, and other effective Alnus-infective strains are related; (ii) unisolated microsymbionts of Dryas, Coriaria, and Dutisca species; (iii) Elaeagnus-infective strains; and (iv) "atypical" strains (a group which includes an Anus-infective, non-nitrogen-fixing strain). Taxa that are related to this well-defined, coherent Frankia cluster are the genera Geodermatophilus, "Blastococcus," Sporichthya, Acidothermus, and Actinoplanes. However, the two genera whose members have multilocular sporangia (the genera Frankia and Geodermatophilus) did not form a coherent group. For this reason, we propose that the family Frankiaceae should be emended so that the genera Geodermatophilus and "Blastococcus" are excluded and only the genus Frankia is retained.The slowly growing members of the actinomycete genus Frankia are root symbionts that nodulate a wide range of perennial woody dicotyledonous plants. This nitrogen-fixing symbiosis is known to occur in more than 200 species of plants belonging to 24 genera and eight families that are called actinorhizal (6). The first Frankia strain was isolated in 1956 by Pommer (43), but this strain was subsequently lost. In 1978, Callaham et al. (8) isolated an infective Frankia strain from Comptonia peregrirza, and since then hundreds of isolates have been obtained from a number of plant species growing in many geographical areas.Becking (5) was unsuccessful in isolating the causative agent of actinorhizal nodules despite numerous attempts. He suggested that this organism was an "obligate symbiont" and devised a classification scheme based on cross-inoculation groups and on the morphology of the endosymbiont. This scheme was subsequently found to be erroneous when pure cultures became available (8). Nonetheless, Becking ( 5 ) correctly perceived the bacterial nature of the microsymbiont, named it Frankia sp., and classified it as the only member of the family Frankiaceae in the order Actinomycetales.The members of the genus Frankia can now be clearly distinguished from other bacterial genera on the basis of their host specificity, their morphology (hyphae, ...

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PCR-amplified 16S rRNA sequence analysis to confirm nodulation of Datisca cannabina L. by the endophyte of Coriaria nepalensis Wall

Cited by 24 publications

References 33 publications

Development and Application of a Selective PCR-Denaturing Gradient Gel Electrophoresis Approach To Detect a Recently Cultivated Bacillus Group Predominant in Soil

Development and Application of a Selective PCR-Denaturing Gradient Gel Electrophoresis Approach To Detect a Recently Cultivated Bacillus Group Predominant in Soil

Heavy Metal Resistance Patterns of Frankia Strains

Molecular Phylogeny of the Genus Frankia and Related Genera and Emendation of the Family Frankiaceae

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