Growth responses of indigenous Frankia populations to edaphic factors in actinorhizal rhizospheres

Samant, Suvidha; Dawson, Jeffrey O.; Hahn, Dittmar

doi:10.1016/j.syapm.2015.07.005

Cited by 15 publications

(17 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Host and nonhost rhizospheres were recently compared with respect to cluster I Frankia strains in one location (34), showing no significant host rhizosphere effect. Cluster III Frankia strains were shown to have a distribution independent of the host rhizophere, implying a broad physiological adaptation in soil (37). The current report is the first comprehensive study showing a significant host plant influence on cluster II Frankia strains in natural soil environments, an effect that is distinct from that of other ecological parameters.…”

Section: Discussionmentioning

confidence: 62%

“…in the microbiome was significantly higher in the host-plant-present site, it is still clear that this group of OTUs is quite rare in the microbiome, representing only Ͻ0.05‰ in any sample. This suggests that the host factor is not a source of energy to sustain a large population; i.e., it is not promoting the proliferation of cluster II Frankia outside the host, in contrast to some strains within the cluster I Frankia that can utilize a host-derived soil carbon source (37).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

Battenberg

Wren

Hillman³

et al. 2017

Appl Environ Microbiol

View full text Add to dashboard Cite

The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the ␣-diversity or in the microbiome composition between the host-plantpresent or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growthpromoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere.IMPORTANCE Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp.

show abstract

Section: Discussionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 99%

The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

Battenberg

Wren

Hillman³

et al. 2017

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Frankiae of clusters 2 and 4 remained undetected, indicating that these populations are either absent or present in numbers below the detection limit. Cluster 1b frankiae have been detected as major populations in several studies, with absolute numbers depending on the sampling depth, physicochemical conditions, and vegetation (15,17,18). These results demonstrated differential effects of environmental conditions, including plant species, carbon resources, and matric potentials on the fate of specific Frankia strains in soil.…”

Section: Discussionmentioning

confidence: 84%

“…1) that, however, could not be distinguished from subgroup 1a with the primer combinations used in our study (Table 1). Using sequences of the insertion in domain III of the 23S rRNA gene as the target for specific detection and quantification of these subgroups, subgroup 1b was found to be most prominent in many soils from temperate regions (15,17,18).…”

Section: Discussionmentioning

confidence: 99%

“…Targeting the 23S rRNA gene also allowed us to distinguish between cluster 1 and 3 frankiae and subgroups within cluster 1 (i.e., clusters 1a, 1b, and 1c) (15). The sum of individual detections generally equaled those on the genus level with both nifH and 23S rRNA genes as targets, indicating that members of clusters 2 and 4 were not present at all or not in detectable numbers in the soils analyzed (15,17,18). However, this statement is highly speculative, since direct proof of the presence or absence of cluster 2 and 4 frankiae in these soils has not been provided due to the lack of adequate detection and quantification procedures.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska

Anderson,

Taylor,

Olson

et al. 2024

Ecology and Evolution

View full text Add to dashboard Cite

In root nodule symbioses (RNS) between nitrogen (N)‐fixing bacteria and plants, bacterial symbionts cycle between nodule‐inhabiting and soil‐inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil‐dwelling assemblages of the actinorhizal symbiont Frankia in sites with long‐term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long‐term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil‐dwelling than nodule‐dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non‐symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

show abstract

Growth responses of indigenous Frankia populations to edaphic factors in actinorhizal rhizospheres

Cited by 15 publications

References 38 publications

The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

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

Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska

Contact Info

Product

Resources

About