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

Abstract

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.

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

“…Previous analyses of soils ABA, BAHF, LWRB, and RBW revealed cell densities of about 10 6 cells (g soil) Ϫ1 , with cluster 1b representing the most prominent Frankia population, while cluster 3 frankiae were present in small numbers and clusters 1a, 1d, and 1c were usually absent (17). These results were largely confirmed in our current analyses, where specific analyses retrieved frankiae of cluster 1b only (soils ABA and BAHF), while soils LWRB and RBW harbored small numbers of cluster 3 frankiae as well (Fig.…”

“…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).…”

“…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.…”

“…Information on the ecology of cluster 2 and 4 frankiae therefore is quite limited. We have recently developed Sybr Green-based quantitative PCR (qPCR) methods that used nifH or 23S rRNA genes as a target to quantify uncultured Frankia populations in different soils (15)(16)(17). nifH as a target only detected the combination of members of clusters 1 and 3 but not those of clusters 2 and 4, while 23S rRNA genes as targets covered all frankiae on the genus level, i.e., clusters 1, 2, 3, and 4 together.…”

An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis

“…As pioneer species, actinorhizal plants are exposed to a wide array of stresses (Ngom et al 2016b) which have been reviewed along with approches to transform Casuarina genetically (Froussart et al 2016). The ecology and diversity of strains and Morella hosts in South Africa (Wilcox and Cowan 2016) or Betulaceae hosts in North America (Samant et al 2016) and Europe (Cotin-Galvan et al 2016) have been studied in relation to soils. The impact of climate change on alder has also been examined (Tobita et al 2016).…”