Assessing Frankia populations in plants and soil using molecular methods

In recent years, molecular approaches have increasingly supplemented nodula tion-dependent detection methods for studying Frankia populations in nature . The new methods are revealing much about the genetic diversity and distri bution of Frankia, as well as refining and expanding knowledge about endoph yte-host specificities. PCR-based approaches have been used to unravel the phylogenetic relationships of isolates, as well as of uncultured endophytes in root nodules of many actinorhizal plants from which no isolates have be en obtained. A comparative sequence analysis of PCR-amplified 16S ribosomal DNA led to the emendation of the family Frankiaceae to contain only the ge nus Frankia with four main subdivisions: (i) a large group mainly comprisin g Frankia alni and other typical nitrogen-fixing strains belonging to the A lnus and the Casuarina host infection groups, respectively, (ii) uncultured endophytes of Dryas, Coriaria and Datisca species, (iii) strains of the El aeagnus host infection group and (iv) atypical non-nitrogen-fixing strains. A considerable diversity among both cultured Frankia strains and unculture d endophytes in nodules was indicated using RFLP analyses of PCR-amplified fragments of the 16S rRNA gene, the glutamine synthetase II (glnII) gene, t he intergenic spacer of the 16S-23S rRNA operon or the intergenic spacer be tween the nitrogenase nifH and nifD (nifH-D) or the nifD and nifK (nifD-K) genes. The growing database of discriminative target sequences for frankiae is increasingly exploited for studies on the distribution of specific Fran kia populations in the environment using PCR or in situ hybridization. Unti l recently, most studies have focused on the analysis of Frankia population s in root nodules, the natural locale of enrichment for this organism. Thes e populations, however, represent only the fraction of physiologically acti ve, infecting frankiae in soils rather than the total Frankia population. F uture approaches to studies of Frankia populations should therefore incorpo rate the many opportunities for more than just phylogenetic analyses, the d escription of diversity and studies of Frankia populations in nodules. The molecular approaches open the door to more sophisticated studies of environ mental influences on the dynamics of indigenous or introduced Frankia popul ations in plants and soil. These studies may lead to advancements in the ma nagement of actinorhizal plants and Frankia, provided specific Frankia popu lations can be attributed with silviculturally beneficial features. Such fe atures include persistence and the growth in soil, competition with less ef ficient Frankia populations for nodule formation, prompt and efficient nodu le formation and an ultimately superior nitrogen-fixing capacity. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Sci ence B.V. All rights reserved.