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Aims: A considerable amount of information is available on root nodule formation of the nitrogen fixing actinomycete Frankia and its host plants; however, studies on Frankia populations in soil, its second ecological niche, are generally hampered by the complexity of soil systems and the lack of adequate quantification methods for frankiae. The aim of this study was, using recently developed quantitative PCR methods, to follow population dynamics of introduced Frankia strains in soil microcosms under different edaphic conditions. Methods: Populations dynamics of four Frankia strains (ArI3, Ag45/Mut15, CcI3 and EAN1pec) representing frankiae of the Alnus host infection group (i.e. subgroups I and II infective on Alnus species, Casuarina-infective frankiae) and frankiae of the Elaeagnus host infection group, respectively, were analyzed by quantitative PCR ( qPCR) in a factorial design of microcosms with two plant species ( A. glutinosa, C. equisetifolia), two potential carbon resources (rhizosphere, leaf litter), and two matric potentials (wet, dry). Results: Introduction of frankiae into soil resulted in about 10-fold declines in abundance within the first 6 weeks of incubation in both bulk and rhizosphere soils, independently of plant species, leaf litter amendment and matric potential. While this decline continued in bulk soil during an additional 6 week period, numbers in the rhizosphere recovered and increased to values close to- or exceeding those of introduced frankiae. Independently of plant species, carbon resource or matric potential, cell numbers of strain EAN1pec recovered to inoculum values in nearly all treatment combinations, while those of strain ArI3 remained low. Strain Ag45/Mut15 recovered most prominently in the rhizosphere in leaf-litter-amended microcosms, regardless of plant species and matric potential, while cell numbers of Casuarina-infective Frankia strain CcI3 recovered only in the presence of C. equisetifolia, with higher numbers in the presence of leaf litter and under dry conditions. Conclusions: These results demonstrate differential effects of environmental conditions including plant species, carbon resources, and matric potentials on the fate of specific Frankia strains in soil, and identifies factors potentially affecting subpopulations of indigenous frankiae under natural conditions. [ABSTRACT FROM AUTHOR]

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 cells (g soil). 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. [ABSTRACT FROM AUTHOR]

The genetic diversity of Frankia populations in soil and in root nodules of sympatrically grown Alnus taxa was evaluated by rep-polymerase chain reaction (PCR) and nifH gene sequence analyses. Rep-PCR analyses of uncultured Frankia populations in root nodules of 12 Alnus taxa ( n = 10 nodules each) growing sympatrically in the Morton Arboretum near Chicago revealed identical patterns for nodules from each Alnus taxon, including replicate trees of the same host taxon, and low diversity overall with only three profiles retrieved. One profile was retrieved from all nodules of nine taxa ( Alnus incana subsp. incana, Alnus japonica, Alnus glutinosa, Alnus incana subsp. tenuifolia, Alnus incana subsp. rugosa, Alnus rhombifolia, Alnus mandshurica, Alnus maritima, and Alnus serrulata), the second was found in all nodules of two plant taxa ( A. incana subsp. hirsuta and A. glutinosa var. pyramidalis), and the third was unique for all Frankia populations in nodules of A. incana subsp. rugosa var . americana. Comparative sequence analyses of nifH gene fragments in nodules representing these three profiles assigned these frankiae to different subgroups within the Alnus host infection group. None of these sequences, however, represented frankiae detectable in soil as determined by sequence analysis of 73 clones from a Frankia-specific nifH gene clone library. Additional analyses of nodule populations from selected alders growing on different soils demonstrated the presence of different Frankia populations in nodules for each soil, with populations showing identical sequences in nodules from the same soil, but differences between plant taxa. These results suggest that soil environmental conditions and host plant genotype both have a role in the selection of Frankia strains by a host plant for root nodule formation, and that this selection is not merely a function of the abundance of a Frankia strain in soil. [ABSTRACT FROM AUTHOR]

Abstract: Bioassays with Morella pensylvanica as capture plant and comparative sequence analyses of nifH gene fragments of Frankia populations in nodules formed were used to investigate the diversity of Frankia in soils over a broad geographic range, i.e., from sites in five continents (Africa, Europe, Asia, North America, and South America). Phylogenetic analyses of 522-bp nifH gene fragments of 100 uncultured frankiae from root nodules of M. pensylvanica and of 58 Frankia strains resulted in a clear differentiation between frankiae of the Elaeagnus and the Alnus host infection groups, with sequences from each group found in all soils and the assignment of all sequences to four and five clusters within these groups, respectively. All clusters were formed or dominated by frankiae obtained from one or two soils with single sequences occasionally present from frankiae of other soils. Variation within a cluster was generally low for sequences representing frankiae in nodules induced by the same soil, but large between sequences of frankiae originating from different soils. Three clusters, one within the Elaeagnus and two within the Alnus host infection groups, were represented entirely by uncultured frankiae with no sequences from cultured relatives available. These results demonstrate large differences in nodule-forming frankiae in five soils from a broad geographic range, but low diversity of nodule-forming Frankia populations within any of these soils. [Copyright &y& Elsevier]

Investigates the effect of arbuscular mycorrhizae (AM) on soil microbial populations and on growth performance of the high salt marsh plant Spartina patens. AM suppression study on field-collected soil cores with S. patens; Reduction of AM suppression colonization on roots of S. patens; Increase in both microbial and bacterial population size and biomass.

Investigates the culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Use of molecular and activation techniques; Use of serial liquid dilution cultures to determine population sizes; Identification of microorganisms obtained from the terminal and subterminal positive dilution steps; RNA gene sequences of the isolates.

Actinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genus Frankia, and specific Frankia taxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms, we observed that some host species were nodulated (Alnus glutinosa, Alnus cordata, Shepherdia argentea, Casuarina equisetifolia) while others were not (Alnus viridis, Hippophaë rhamnoides). Nodule populations were represented by eight different sequences of nifH gene fragments. Two of these sequences characterized frankiae in S. argentea nodules, and three others characterized frankiae in A. glutinosa nodules. Frankiae in A. cordata nodules were represented by five sequences, one of which was also found in nodules from A. glutinosa and C. equisetifolia, while another was detected in nodules from A. glutinosa. Quantitative PCR assays showed that vegetation generally increased the abundance of frankiae in soil, independently of the target gene (i.e., nifH or the 23S rRNA gene). Targeted Illumina sequencing of Frankia-specific nifH gene fragments detected 24 unique sequences from rhizosphere soils, 4 of which were also found in nodules, while the remaining 4 sequences in nodules were not found in soils. Seven of the 24 sequences from soils represented >90% of the reads obtained in most samples; the 2 most abundant sequences from soils were not found in root nodules, and only 2 of the sequences from soils were detected in nodules. These results demonstrate large differences between detectable Frankia populations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specific Frankia populations in soils. [ABSTRACT FROM AUTHOR]

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 x 105 to 15 x 105 cells (g soil)-1 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. [ABSTRACT FROM AUTHOR]