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To be together or not to be together: Ca. 100 million years of evolutionary history of the earliest divergent Frankia clade
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
2022 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Root nodule symbiosis evolved ca. 100 Mya between a nitrogen-fixing bacterium and the common ancestor to the Fabales, Fagales, Rosales, and Cucurbitales plant orders. Over time the majority of the lineages derived from this ancestor lost their symbiotic capability. While extant symbiotic members found in the Fabales order (legumes) all engage in symbiosis with rhizobia, extant symbiotic members of the latter three plant orders are referred to as actinorhizal plants. These engage in symbiosis with Frankia.

Frankia is a genus of soil actinobacteria, which can be split into four phylogenetically distinct clades. The earliest divergent symbiotic clade, Frankia cluster-2, encompasses strains that have a broad host range and could not be cultured in vitro thus far with two exceptions. Based on Frankia enriched meta-genomes from whole nodules collected at different locations across the globe, it is clear there is very little diversity of Frankia cluster-2 in continental Eurasia, spanning from France to Japan. These strains are also closely related to strains found in North America. However, very little is known about strains occurring in the islands in the Pacific Ocean and the southern hemisphere.

In short, this thesis aimed to investigate the biodiversity of the earliest divergent symbiotic Frankia clade and to understand how Frankia spread across the globe (Study 1 and Study 2). From nodules collected in study 1, a novel Streptomyces species was identified and declared (Study 3). The thesis also aimed to study genetic changes within Frankia cluster-2 which might be associated with their endosymbiotic lifestyle and low saprotrophic potential (Study 4 and Study 5).

Place, publisher, year, edition, pages
Stockholm: Department of Ecology, Environment and Plant Sciences, Stockholm University , 2022. , p. 84
Keywords [en]
root nodule symbiosis, Frankia, actinorhizal symbiosis
National Category
Evolutionary Biology Other Biological Topics
Research subject
Plant Physiology
Identifiers
URN: urn:nbn:se:su:diva-199308ISBN: 978-91-7911-734-4 (print)ISBN: 978-91-7911-735-1 (electronic)OAI: oai:DiVA.org:su-199308DiVA, id: diva2:1617118
Public defence
2022-02-04, Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20 and online via Zoom, Stockholm, 13:00 (English)
Opponent
Supervisors
Available from: 2022-01-12 Created: 2021-12-06 Last updated: 2021-12-16Bibliographically approved
List of papers
1. A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world
Open this publication in new window or tab >>A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:su:diva-199266 (URN)
Available from: 2021-11-30 Created: 2021-11-30 Last updated: 2021-12-06
2. The earliest divergent Frankia from the Gondwana continent
Open this publication in new window or tab >>The earliest divergent Frankia from the Gondwana continent
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:su:diva-199269 (URN)
Available from: 2021-11-30 Created: 2021-11-30 Last updated: 2021-12-06
3. Streptomyces benguetensis sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia
Open this publication in new window or tab >>Streptomyces benguetensis sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia
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(English)Manuscript (preprint) (Other academic)
National Category
Microbiology
Identifiers
urn:nbn:se:su:diva-199306 (URN)
Available from: 2021-12-01 Created: 2021-12-01 Last updated: 2021-12-06
4. Genome reduction in the earliest divergent Frankia clade is responsible for its low saprotrophic capabilities
Open this publication in new window or tab >>Genome reduction in the earliest divergent Frankia clade is responsible for its low saprotrophic capabilities
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:su:diva-199307 (URN)
Available from: 2021-12-01 Created: 2021-12-01 Last updated: 2021-12-06
5. The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type
Open this publication in new window or tab >>The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type
2020 (English)In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 11, no 4, article id 432Article in journal (Refereed) Published
Abstract [en]

Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases, MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.

Keywords
Peptidoglycan, MurC, Frankia, nitrogen fixation, actinorhizal symbiosis, root nodules
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-183160 (URN)10.3390/genes11040432 (DOI)000537224600033 ()32316316 (PubMedID)
Available from: 2020-07-01 Created: 2020-07-01 Last updated: 2022-03-23Bibliographically approved

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Berckx, Fede

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