Molecular diversity of Frankia in root nodules of Alnus incana grown with inoculum from polluted urban soils

ABSTRACT

The establishment and growth of trees can be compromised by soil contamination which can reduce populations of key microbial symbionts. We describe the colonisation of grey alder (Alnus incana) by Frankia from 10 urban soils with varying degrees of organic and inorganic pollution. Principal components analysis (PCA) of soil chemical profiles showed a separation of remediated and unremediated soils. A. incana seedlings were used as trap plants to capture the microsymbiont from soil. After 6 months growth, nodulation was lowest on trees grown with the most contaminated soils. Plant biomass was positively correlated with root nodule biomass and negatively correlated with PAH concentration. DNA was isolated from nodules for the analysis of Frankia genetic diversity. The polymerase chain reaction (PCR) was used to amplify the 16S–23S intergenic spacer (IGS) of Frankia ribosomal DNA. PCR products were subject to restriction digestion yielding 10 restriction fragment length polymorphism (RFLP) types from 72 nodules analysed. Our results demonstrate that each soil supports a distinct nodulating Frankia community. Partial 16S sequencing placed most strains in Frankia clusters 1a and 1b, which are typically Alnus-infecting, but sequences from several nodules obtained from a gasworks soil belonged to cluster 3, normally associated with Elaeagnus. These results show for the first time that polluted soils can be an effective source of Alnus-infective Frankia. Inoculation with site-adapted Frankia under greenhouse conditions could thus be an appropriate strategy to increase the symbiotic capacity of A. incana and to improve its chances of survival and growth when planted on polluted soils.