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- Berckx, Fede, 1993-, et al.
(author)
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A tale of two lineages : how the strains of the earliest divergent symbiotic Frankia clade spread over the world
- 2022
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 23:1
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Journal article (peer-reviewed)abstract
- It is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first in Frankia cluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except for Frankia coriariae, and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related to Frankia cluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea.To unravel more biodiversity within Frankia cluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs of Frankia cluster-2 from Coriaria japonica and Coriaria intermedia growing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split within Frankia cluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana.Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.
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| 3. |
- Berckx, Fede
(author)
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Endosymbiosis of Frankia cluster-2
- 2019
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Licentiate thesis (other academic/artistic)abstract
- Actinobacteria of the genus Frankia engage in root endosymbiosis with actinorhizal plants belonging to the Fagales, Cucurbitales and Rosales. The genus Frankia consists of four different clades. Strains belonging to cluster-1, -2, and -3 exhibit host-specificity which plants they can nodulate, while cluster-4 strains do not engage in symbiosis. Cluster-2 is the earliest divergent clade, and most of its members could not be cultured thus far, with the exception of Frankia coriariae BMG5.1 and BMG5.30. Unlike other nodule symbioses where ammonia is the nitrogen source exported to the host, it has been shown in nodules of Datisca glomerata that an assimilated nitrogen metabolite, namely arginine, is exported to the host. In the study on bacterial transcription patterns during symbiosis presented here, it is suggested that in nodules of Ceanothus thyrsiflorus an assimilated nitrogen source, most likely asparagine, is delivered by Frankia cluster-2. Analysis of the carbon metabolism indicates that citrate could be the carboxylate delivered from the host to the bacteria. Analysis of the tricarboxylic acid cycle indicates that the glyoxylate shunt is missing in genomes of Frankia cluster-2. During symbiosis the pathway mostly works linear between input of carbon skeletons and the output of assimilated nitrogen metabolites. This feature could explain why Frankia cluster-2 strains have a low saprotrophic potential.Analysis of genomes of Frankia cluster-2 have shown that murC is present in two gene copies within the genome of cluster-2 and cluster-3 strains, but only present as one copy in cluster-1 and cluster-4. MurC plays a key role in biosynthesis of peptidoglycan, a polymer that makes up a thick layer as part of cell wall of Gram-positive bacteria. Phylogenetic analysis show one of the two copies encodes a protein highly similar to MurC protein of other actinobacteria, and therefore is considered the ancestral copy, murC1. The other copy, murC2, can be found in all Frankia clusters and encodes a protein showing more similarity to MurC from cyanobacteria and plants. This similarity could be explained through either horizontal gene transfer, which is not unlikely as Frankia can be found intracellularly in its host plants. The other possible scenario is that a gene duplication event was followed by convergent evolution, leading to similarity between MurC2 and the MurC proteins of cyanobacteria and plants. This would allow for plasticity in the structure of the peptidoglycan layer of the cell wall.The features of nitrogen and carbon metabolism, as well as the phylogeny of MurC, indicate Frankia cluster-2 has undergone several adaptations to intracellular endosymbiosis.
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| 4. |
- Berckx, Fede
(author)
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Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere
- 2024
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In: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 100
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Journal article (peer-reviewed)abstract
- Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
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| 5. |
- Berckx, Fede, 1993-, et al.
(author)
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Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere
- 2024
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In: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 100:5
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Journal article (peer-reviewed)abstract
- Coriariaceae are a small plant family of 14–17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
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| 7. |
- Berckx, Fede, et al.
(author)
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Harnessing plant–microbe interactions to promote nitrogen use efficiency in cereal crops
- 2024
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In: Plant and Soil. - 0032-079X .- 1573-5036. ; 494, s. 75-83
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Journal article (peer-reviewed)abstract
- Background: Increasing nitrogen (N) use efciency (NUE) can enhance cereal yields, improve grain quality and reduce agrochemical inputs. However, several challenges are associated with achieving enhanced NUE, e.g., a frequently poor synchronization between N supply and demand; low grain yields per unit of N input; and inherent trade-ofs between grain yield and quality. Scope: To address these challenges, we focus on the temporal perspective of NUE related processes at different growth stages, and propose the utilization of benefcial microbes, e.g. arbuscular mycorrhizal fungi (AMF) for their roles in afecting aspects of NUE particularly at the later development stages.Conclusion: Some evidence suggests that AMF can directly promote N uptake and use in cereals, by regulating N transporters, but the indirect efects of AMF on NUE related processes at diferent growth stages are poorly known. Here we explore AMF and their potential roles in promoting NUE related processes that enhance crop P and N uptake post-anthesis, when nutrient supply often is low. In order to fully exploit the opportunities for benefcial root-fungal symbiosis, we propose approaches for plant breeding and crop management, and consider the potential of plantmicrobe interactions post-anthesis to promote NUE and the sustainable production of especially cereals.
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| 10. |
- Berckx, Fede, 1993-, et al.
(author)
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Streptomyces coriariae sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia
- 2022
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In: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 72:12
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Journal article (peer-reviewed)abstract
- An actinobacterial strain, CMB-FB, was isolated from surface-sterilized root nodules of a Coriaria intermedia plant growing along Halsema Highway in the province of Benguet (Luzon, Philippines). The 16S rRNA gene sequence of CMB-FB showed high sequence similarity to those of the type strains of Streptomyces rishiriensis (99.4 %), Streptomyces humidus (99.1 %), Streptomyces cacaoi subsp. asoensis (99.0 %), and Streptomyces phaeofaciens (98.6 %). The major menaquinones of CMB-FB were composed of MK-9(H4), MK-9(H6) and MK-9(H8), and there was a minor contribution of MK-9(H10). The polar lipid profile consisted of phosphatidylethanolamine, unidentified aminolipids and phospholipids, a glycophospholipid and four unidentified lipids. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The results of physiological analysis indicated that CMB-FB was mesophilic. The results of phylogenetic, genome-genome distance calculation and average nucleotide identity analysis indicated that the isolated strain represents the type strain of a novel species. On the basis of these results, strain CMB-FB (=DSM 112754T=LMG 32457T) is proposed as the type strain of the novel species Streptomyces coriariae sp. nov.
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