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Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
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Number of Authors: 132019 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 11, no 8, p. 2273-2291Article in journal (Refereed) Published
Abstract [en]

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to performsymbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that NorthAmerican strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua NewGuinea, represents a novel species, postulated as Candidatus Frankiameridionalis. All Frankia-enrichedmetagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.

Place, publisher, year, edition, pages
2019. Vol. 11, no 8, p. 2273-2291
Keywords [en]
Frankia, metagenomes, transposases, genome instability, Nod factors, nodU
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-175125DOI: 10.1093/gbe/evz153ISI: 000484266300019PubMedID: 31368478OAI: oai:DiVA.org:su-175125DiVA, id: diva2:1360878
Available from: 2019-10-14 Created: 2019-10-14 Last updated: 2019-10-14Bibliographically approved

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Berckx, FedeDemchenko, Kirill N.Brachmann, AndreasPawlowski, Katharina
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