Permanent Draft Genome Sequences of Three
            <i>Frankia</i>
            sp. Strains That Are Atypical, Noninfective, Ineffective Isolates

Gueddou, Abdellatif; Swanson, Erik; Ktari, Amir; Nouioui, Imen; Hezbri, Karima; Ghodhbane‐Gtari, Faten; Simpson, Stephen D.; Morris, Krystalynne; Thomas, W. Kelley; Sen, Arnab; Gtari, Maher; Tisa, Louis S.

doi:10.1128/genomea.00174-17

Cited by 5 publications

(2 citation statements)

References 12 publications

(15 reference statements)

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“…Frankia cluster 2 dispersal outward from the Coriaria myrtifolia rhizosphere While the presence of Frankia cluster 2 (the host compatible microsymbionts) and cluster 4 (asymbiotic Frankia that are often isolated from Coriaria nodules; Mirza et al, 1992;Gueddou et al, 2017) was expected, the occurrence of cluster 1 and the superabundance of cluster 3 in C. myrtifolia nodule, root, and rhizosphere was surprising. As previously stated, clusters 1 and 3 are known to ubiquitously distributed in soils independent to the presence of compatible host-plants (Paschke and Dawson, 1992;Nalin et al, 1997;Gtari et al, 2004).…”

Section: Rhizocompartment Microbiomesmentioning

confidence: 99%

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Swanson

Sbissi²,

Ktari³

et al. 2022

Front. Microbiol.

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The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

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Section: Rhizocompartment Microbiomesmentioning

confidence: 99%

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Swanson

Sbissi²,

Ktari³

et al. 2022

Front. Microbiol.

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“…A better understanding of the Frankia cluster-2 symbiosis could improve the understanding of root nodule symbiosis as a whole. Unfortunately, the majority of Frankia cluster-2 strains cannot be cultured to this date, except for two strains: Frankia coriariae BMG5.1 (Gtari et al, 2015) and F. coriariae BMG5.30 (Gueddou et al, 2019). This implies that most analyses, such as gene expression studies via reverse transcription-quantitative polymerase chain reaction (RT-qPCR), must be conducted in planta.…”

Section: Introductionmentioning

confidence: 99%

Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities

Berckx

Nguyen

Hilker

et al. 2022

Preprint

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SummaryFrankia cluster-2 are diazotrophs that engage in root nodule symbiosis with host plants of the Cucurbitales and the Rosales. They are rarely found in the soil in the absence of their hosts. Previous studies have shown that an assimilated nitrogen source, presumable arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), but not in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported by cluster-2 strains, and which nitrogen source would then be exported to C. thyrsiflorus, gene expression levels, metabolite profiles and enzyme activities were analysed.We found that the export of assimilated nitrogen in symbiosis is a common feature for Frankia cluster-2 strains, but which source is host-plant dependent. We also identified several gene losses.The ammonium assimilation via the GS/GOGAT cycle for export to the host, entails a high demand of 2-oxoglutarate from the TCA cycle. This specialised metabolism seems to have led to genome reduction: we show that Frankia cluster-2 strains have lost the glyoxylate shunt and succinate semialdehyde dehydrogenase, leading to a linearization of the TCA cycle. This could explain the low saprotrophic potential of Frankia cluster-2.

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Frankia

Normand¹,

Fernández²

2019

Bergey's Manual of Systematics of Archaea and Bacteria

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Fran.ki.a. N.L. fem. n. Frankia named after Albert Bernhard Frank (1839–1900), a Swiss plant biologist, who studied extensively nitrogen nutrition in legumes and the microorganisms causing root nodulation from 1877 to 1892 and who coined the term “symbiosis.” Actinobacteria / Actinobacteria / Frankiales / Frankiaceae / Frankia A group of soil‐inhabiting mesophilic, mostly nitrogen‐fixing, organisms in symbiosis with pioneer plants collectively called “actinorhizal plants” in orders Cucurbitales, Fagales, and Rosales. Frankia isolates have branched septate hyphae, multilocular sporangia, and for the most part vesicles or diazo‐vesicles, specialized cells where nitrogen fixation takes place. All Frankia strains sporulate in culture, but only some genotypes maintain the capacity to form abundant sporangia within plant cells. Around 50% of endophytic Frankia have resisted isolation. Growth is slow, and it took a long time to obtain isolates after decades of unsuccessful attempts. Isolates are mostly white, sometimes pigmented, have mostly simple growth requirements, and can fix nitrogen in pure culture or in symbiotic nodules except for a small number of nonsymbiotic isolates. The genus comprises 11 species and 2 candidatus grouped into four phylogenetic clusters at the root of aerobic actinobacteria. DNA G + C content (mol % ) : 67.9–72.8. Type species : Frankia alni (Woronin 1866) Von Tubeuf 1895 AL .

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Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical, Noninfective, Ineffective Isolates

Abstract: Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that were isolated from root nodules but are unable to reinfect actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively.

Cited by 5 publications

References 12 publications

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities

Frankia

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