Phylogenetic characterization of ineffective <i>Frankia</i> in <i>Alnus glutinosa</i> (L.) Gaertn. nodules from wetland soil inoculants

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

doi:10.1046/j.1365-294x.1997.00265.x

Cited by 35 publications

(14 citation statements)

References 25 publications

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“…If alder is able to select genotypes based on optimal physiological beneWt in a given environment, such host choice would be a strong contributing 'Wlter' on the genetic structure of the symbionts. Both positive and negative selection of symbionts have been observed in legume-rhizobia interactions (Simms et al 2006;Kiers et al 2003) and A. glutinosa appears to exert negative selection on ineVective (non-N-Wxing) Frankia genotypes (Wolters et al 1997;van Dijk and Sluimer 1994). Positive symbiont selection by Alnus does not appear to have been investigated.…”

Section: Discussionmentioning

confidence: 99%

Host species and habitat affect nodulation by specific Frankia genotypes in two species of Alnus in interior Alaska

et al. 2009

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Alders (Alnus spp.) are important components of northern ecosystems due to their ability to fix nitrogen (N) in symbiosis with Frankia bacteria. Availability of optimal Frankia may be a contributing factor in limiting the performance and ecological effects of Alnus, but the factors underlying distribution of Alnus-infective Frankia are not well understood. This study examined the genetic structure (nifD-K spacer RFLP haplotypes) of Frankia assemblages symbiotic with two species of Alnus (A. tenuifolia and A. viridis) in four successional habitats in interior Alaska. We used one habitat in which both hosts occurred to observe differences between host species independent of habitat, and we used replicate sites for each habitat and host to assess the consistency of symbiont structure related to both factors. We also measured leaf N content and specific N-fixation rate (SNF) of nodules ((15)N uptake) to determine whether either covaried with Frankia structure, and whether Frankia genotypes differed in SNF in situ. Frankia structure differed between sympatric hosts and among habitats, particularly for A. tenuifolia, and was largely consistent among replicate sites representing both factors. Leaf N differed between host species and among habitats for both hosts. SNF did not differ among habitats or host species, and little evidence for differences in SNF among Frankia genotypes was found, due largely to high variation in SNF. Consistency of Frankia structure among replicate sites suggests a consistent relationship between both host species and habitat among these sites. Correlations with specific environmental variables and possible underlying mechanisms are discussed.

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Section: Discussionmentioning

confidence: 99%

Host species and habitat affect nodulation by specific Frankia genotypes in two species of Alnus in interior Alaska

et al. 2009

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“…Actinorhizal plants are therefore found often on sandy and wet soils where low levels of available nitrogen may preclude the growth of other species, and thus usually occur as pioneer vegetation at early stages of plant succession [4]. The formation of root nodules is host plant-specific, with frankiae of clusters 1, 2, and 3 representing nitrogen-fixing frankiae of the Alnus, Dryas, and Elaeagnus host infection groups [5], and those of cluster 4 representing non-nitrogen-fixing strains [6].…”

Section: Introductionmentioning

confidence: 99%

Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees

et al. 2015

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Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations.

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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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Phylogenetic characterization of ineffective Frankia in Alnus glutinosa (L.) Gaertn. nodules from wetland soil inoculants

Cited by 35 publications

References 25 publications

Host species and habitat affect nodulation by specific Frankia genotypes in two species of Alnus in interior Alaska

Host species and habitat affect nodulation by specific Frankia genotypes in two species of Alnus in interior Alaska

Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees

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

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