Ineffective Frankia strains in wet stands of Alnus glutinosa L. Gaertn. in The Netherlands

Wolters, D.J.; Akkermans, A.D.L.; Dijk, C. Van

doi:10.1016/s0038-0717(97)00075-8

Cited by 28 publications

(19 citation statements)

References 18 publications

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“…The locations and soil characteristics of the fresh soils from The Netherlands were as follows: (i) Drentse A, where B. benzoevorans relatives were discovered, an agricultural research area (06°41ЈE, 53°03ЈN) with high bacterial diversity (10) representing a 1.5-km stretch of grasslands along the Anlooër Diepje river (11), 0-to 25-cm sampling depth; (ii) Hoeksma and Sikkema farms, Friesland, The Netherlands, 0-to 25-cm sampling depth; (iii) Wageningen University experimental field, sandy soil, 0-to 25-cm sampling depth; (iv) the shore of the river Rhine, Wageningen, The Netherlands, wet clay soil, 0-to 10-cm sampling depth; and (v) the root nodule surface of Alnus glutinosa and the surrounding bulk soil, 0-to 10-cm sampling depth (33). 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.…”

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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“…Studies on cluster 4 frankiae are scarce, even though they have been reported to form an important fraction of all frankiae in wet soils under A. glutinosa (33,34), with natural resistance to infection exhibited by different progenies of A. glutinosa (12,35). While these results were based on bioassays, we now also have the instruments to assess the importance of cluster 4 frankiae in different environments or to use different strains of the non-nitrogen-fixing frankiae in controlled inoculation studies to retrieve information on their ecology in soils.…”

Section: Discussionmentioning

confidence: 99%

Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils

Tekaya

Ganesan

Guerra

et al. 2017

Appl Environ Microbiol

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The nodule-forming actinobacterial genus Frankia can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of Frankia strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these Frankia clusters by either Sybr Green-or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 ϫ 10 5 to 15 ϫ 10 5 cells (g soil) Ϫ1 depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under Alnus glutinosa, a host plant for cluster 1 frankiae, or Betula nigra, a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees. IMPORTANCE Root nodule formation by the actinobacterium Frankia is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on Frankia have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus Frankia. Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.

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“…Trace elements were added according to Allen and Arnon (1955), and Fe-citrate (0.02 mM) was used as an iron source. The soil sample used for inoculation was collected at a the swamp-area Boezem van Brakel (Dutch State Survey Grid 0132.6 424.0) where high amounts of ineffective Frankia and low effective/ineffective nodulation ratio had been found (Wolters et at., 1996). Plants with a sufficiently large root system (at least 10 em of roots) were transfered to full strength Hoagland solution with reduced N-content, with addition of 80 ppm of Previcur N (Schering Aagrunol B.V., The Netherlands), according to Van Dijk and Sluimer (1994).…”

Section: Plant Growth Conditionsmentioning

confidence: 99%

Gene expression in ineffective actinorhizal nodules ofAlnus glutinosa

Guan¹,

Wolters²,

Dijk³

et al. 1996

Acta Botanica Gallica

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Summary.-Several Frankia strains have been shown to induce ineffective, i.e.non-nitrogen fixing nodules, sometimes in a host-plant dependent manner. Previous studies have demonstrated that the resistance to nodulation of Alnus glutinosa by ineffective Frankia strains is genetically determined. In this study, ineffective nodules induced on susceptible Alnus glutinosa clones by soil suspensions from a local swamp were analysed cytologically. Comparisons with effective nodules showed that ineffective nodules contain higher amounts of polyphenols than effective nodules, indicating a plant defense reaction. Polyphenols were found even in the infected cortical cells. In situ hybridization with a Frankia antisense 168 rRNA probe showed that Frankia is degraded at an early stage of development of infected cells. The mRNAs of two plant genes, ag12 and ag13, which had been found to be expressed in the infected cells of effective nodules, were localized in ineffective nodules. Their expression patterns seemed to be analogous in both types of nodules.Resume.-Plusieurs souches de Frankia induisent des nodules non-effectifs, c'est-a-dire non fixateurs d'azote, parfois sous Ia dependance de Ia plante-h6te. De precedentes etudes ont montre que Ia resistance d'Ainus glutinosa a l'infection par des souches de Frankia non-effectives repond a un determinisme genetique. Au cours de Ia presents etude, des nodules non-effectifs, induits sur des clones susceptibles d'Ainus glutinosa par des suspensions de sols locaux, ont fait l'objet d'une analyse cytologique. Une comparaison avec des nodules effectifs montre que les nodules non-effectifs contiennent plus de polyphenols, ce qui indique qu'une reaction de defense a lieu. Des polyphenols ont egalement ete observes dans les cellules infectees du cortex. Une hybridation in situ avec une sonde antisens pour I'ARNr 168 de Frankia montre que Frankia subit Ires tot une degradation lors du developpement des cellules infectees. La localisation des ARNm d'ag12 et ag13, deux genes de Ia plante qui sont exprimes dans les cellules infectees des nodules effectifs, a ete realises. Une expression analogue semble exister dans les deux types de nodules.

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Ineffective Frankia strains in wet stands of Alnus glutinosa L. Gaertn. in The Netherlands

Cited by 28 publications

References 18 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

Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils

Gene expression in ineffective actinorhizal nodules ofAlnus glutinosa

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