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Frankia
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Frankia
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This article is about the filamentous bacteria. For the Frankish empire, see Francia. For the plant, see Gymnarrhena.

Frankia
An alder root nodule.
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Bacillati
Phylum: Actinomycetota
Class: Actinomycetes
Order: Frankiales
Family: Frankiaceae
Becking 1970 (Approved Lists 1980)[2]
Genus: Frankia
Brunchorst 1886[1]
Type species
Frankia alni
(Woronin 1866) Von Tubeuf 1895 non Steud. 1840
Species[3]

See text

Synonyms
  • Frankiella Maire and Tison 1909 non von Speschnew 1900 non Racheboeuf 1983
  • Parafrankia Gtari 2023
  • Protofrankia Gtari 2023
  • Pseudofrankia Gtari 2023

Frankia is a genus of nitrogen-fixing bacteria that live in symbiosis with actinorhizal plants, similar to the Rhizobium bacteria found in the root nodules of legumes in the family Fabaceae. Frankia also initiate the forming of root nodules.

This genus was originally named by Jørgen Brunchorst, in 1886 to honor the German biologist Albert Bernhard Frank.[4] Brunchorst considered the organism he had identified to be a filamentous fungus. Becking [de; nl] redefined the genus in 1970 as containing prokaryotic actinomycetes and created the family Frankiaceae within the Actinomycetales. He retained the original name of Frankia for the genus.[5]

A section through an alder root nodule

Overview

[edit]

Most Frankia strains are specific to different plant species. The bacteria are filamentous and convert atmospheric nitrogen into ammonia via the enzyme nitrogenase, a process known as nitrogen fixation. They do this while living in root nodules on actinorhizal plants. The bacteria can supply most or all of the nitrogen requirements of the host plant. As a result, actinorhizal plants colonise and often thrive in soils that are low in plant nutrients.[6]

Several Frankia genomes are now available which may help clarify how the symbiosis between prokaryote and plant evolved, how the environmental and geographical adaptations occurred, the metabolic diversity, and the horizontal gene flow among the symbiotic prokaryotes.[6]

Frankia can resist low concentration of heavy metals such as, Cu, Co, and Zn.[7] Frankia may be an advantage for degraded soil. Degraded soil is known as soil that is heavy metal rich or nutrient depleted due to a drought. Frankia is a nitrogen-fixed organism, explaining why it is able to resist heavy metals.[8][clarification needed]

Frankia is a gram-positive Bacteria that is found on the roots of plants. The fact that Frankia is gram-positive means that the bacteria is made up of thick cell walls made out of protein called peptidologlycan. This helps with the resistance of the heavy metals that may be in the degraded soil.[9]

Frankia tolerates a narrow range of temperatures and soil pH levels. It grows best at around 30 degrees Celsius with an environment pH between 6.5 and 7.[10] These facts shows that Frankia is very sensitive to its environment. Though Frankia would not be suitable for all agriculture it does demonstrate possibilities in select areas, or in temperature controlled environments.[citation needed]

Symbiont plants

[edit]
Main article: Actinorhizal plant

Nodule Formation

[edit]
Longitudinal section of a Frankia nodule dyed with Toluidine Blue to highlight the vascular tissue in blue and purple.

Frankia forms nodules via two methods of root infection, intercellularly and intracellularly.[12] Intracellular infection is characterized by initial root-hair deformation which is then infected by the filamentous Frankia. The Frankia then moves within the root cells and forms a pre-nodule which is characterized by a bump on the root. This then gives rise to a Nodule primordium which feeds the bacteria via the vascular tissue of the plant allowing the nodule to mature.[12]

In contrast the intercellular infection does not have root hair deformation. Instead, the filamentous Frankia invades the roots in the space between cells on the root. After this invasion a Nodule primordium is created similarly to the intracellular mode of formation and the nodule matures.[12]

Phylogeny

[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[3] and National Center for Biotechnology Information (NCBI).[13]

16S rRNA based LTP_10_2024[14][15][16] 120 marker proteins based GTDB 09-RS220[17][18][19]
Frankia

F. coriariae Nouioui et al. 2017

F. casuarinae Nouioui et al. 2016

F. canadensis Normand et al. 2018[20]

F. umida Normand et al. 2023

F. alni (Woronin 1866) Von Tubeuf 1895

F. torreyi Nouioui et al. 2019

"F. gtarii" Nouioui et al. 2023

"F. tisai" Nouioui et al. 2023

F. inefficax Nouioui et al. 2017

F. asymbiotica Nouioui et al. 2017

F. saprophytica Nouioui et al. 2018

F. discariae Nouioui et al. 2017

F. soli Gtari et al. 2020

F. irregularis Nouioui et al. 2018

F. colletiae Nouioui et al. 2023

F. elaeagni (Schroeter 1886) Becking
1970 ex Nouioui et al. 2016

Protofrankia
Frankia s.s.
Pseudofrankia
Parafrankia
Protofrankia

"Ca. Frankia meridionalis" Nguyen et al. 2019

"Ca. Frankia californiensis" Normand et al. 2017[21]

P. coriariae [incl. "Ca. P. datiscae" (Persson et al. 2011) Gtari 2022]

Pseudofrankia

P. inefficax

P. asymbiotica

P. saprophytica

Parafrankia

P. discariae

P. soli

P. irregularis

P. colletiae

P. elaeagni

Frankia

F. casuarinae

F. canadensis

F. umida ["Ca. F. nodulisporulans" Herrera-Belaroussi et al. 2020]

F. alni

F. torreyi

"Ca. F. alpina" Pozzi et al. 2020 [incl. "F. subtilis" Brunchorst 1886]

"F. gtarii"

"F. tisai"

Species incertae sedis:

  • F. nepalensis Nouioui et al. 2023

See also

[edit]

References

[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Frankia

View on Grokipedia
from Grokipedia
Frankia is a of nitrogen-fixing, filamentous actinobacteria that form symbiotic associations with actinorhizal plants, enabling these woody to thrive in nitrogen-poor soils by converting atmospheric dinitrogen into bioavailable . Members of the genus Frankia are classified within the Frankiaceae of the order Frankiales, characterized as with mycelial growth, the production of nitrogen-fixing vesicles and sporangia, and a high G+C DNA content ranging from 66% to 72%. These slow-growing soil-dwelling microbes have generation times of 30–80 hours and sizes between 5 and 10.5 million base pairs, lacking canonical nodulation genes typical of rhizobial symbionts. Frankia establishes facultative symbioses with over 200 species across 25 genera in eight dicotyledonous plant families, including (Alnus spp.), (Casuarina spp.), and , primarily through infection leading to nodule formation. In these nodules, Frankia differentiates into vesicles that protect the oxygen-sensitive enzyme, facilitating under both aerobic and microaerobic conditions. Phylogenetically, Frankia strains are divided into four clusters based on 16S rRNA gene sequences and host infectivity, reflecting genotypic diversity with 8–12 genospecies in some host groups and adaptations to geographic and ecological variations. This diversity underscores their ecological significance, as actinorhizal plants hosting Frankia serve as in disturbed habitats like post-fire landscapes or landslides, enhancing and recovery. Notable species include Frankia alni, infective to Alnus hosts.

Taxonomy and Classification

History of Discovery

The discovery of Frankia began in the 1880s when Norwegian Jørgen Brunchorst observed root nodules on (Alnus) plants and identified the associated as a filamentous organism, initially misclassifying it as a due to its branching hyphae and lack of known bacterial characteristics. In 1886, Brunchorst formally named the genus Frankia in honor of the German Albert Bernhard Frank, designating Frankia alni as the based on its occurrence in nodules. Throughout the early , efforts to culture Frankia outside its host plants failed, leading to the view that it was an symbiont incapable of free-living growth, which hindered further characterization. This changed in the late with the successful isolation of axenic cultures; the first reported in by Callaham, Del Tredici, and Torrey, who obtained strain CpI1 from sweetfern (Comptonia peregrina) root nodules using enzymatic maceration and a medium, confirming Frankia as a cultivable actinomycete. Subsequent isolations from and other hosts followed in 1979, enabling morphological and physiological studies. In 1970, J.H. Becking redefined the genus Frankia as comprising prokaryotic within the order , establishing the family Frankiaceae based on initial cultural isolates and reclassifying it from its prior fungal association. The nitrogen-fixing capability of Frankia in with actinorhizal plants was definitively confirmed in the early 1980s through acetylene reduction assays on pure cultures, demonstrating activity in vesicle structures under nitrogen-limited conditions. These milestones shifted understanding of Frankia from an enigmatic to a key diazotrophic bacterium.

Current Species and Subgroups

Following a 2022 taxogenomic revision validly published in 2023, the genus Frankia (phylum Actinomycetota, family Frankiaceae) is now restricted to symbiotic, nitrogen-fixing (Nod+/Fix+) strains of phylogenetic Cluster 1, with Frankia alni as the type species (validly published 1984). The former broader genus has been split, with Clusters 2, 3, and 4 elevated to new genera: Protofrankia gen. nov. (Cluster 2), Parafrankia gen. nov. (Cluster 3), and Pseudofrankia gen. nov. (Cluster 4). These changes, now accepted in the literature, refine taxonomic boundaries based on phylogenomic coherence, while informal cluster designations continue for ecological and symbiotic studies. As of November 2025, the List of Prokaryotic names with Standing in Nomenclature (LPSN) records 17 validly published species across these genera. In the emended Frankia (Cluster 1), key species include F. alni (1984), F. casuarinae (1984), and F. canadensis (2009), isolated from hosts in Betulaceae, Casuarinaceae, and Myricaceae. Protofrankia (Cluster 2) includes species such as P. datiscae (formerly F. datiscae, 2009), P. torreyi (formerly F. torreyi, 2021), and P. irregularis (formerly F. irregularis, 2022), associated with Datiscaceae, Coriariaceae, and Rosaceae. Parafrankia (Cluster 3) encompasses P. elaeagni (formerly F. elaeagni, 2021), P. gtarii (formerly F. gtarii, 2022), P. tisai (formerly F. tisai, 2022), P. colletiae (formerly F. colletiae, 2023), and P. umida (formerly F. umida, 2023), from Elaeagnaceae and related families. Pseudofrankia (Cluster 4) includes non-nodulating, non-fixing species like Ps. asymbiotica (formerly F. asymbiotica, 2017). Additional species across genera, such as F. discariae (2015, now in Parafrankia), F. nepalensis (2023, in Pseudofrankia), and F. soli (2020, in Pseudofrankia), reflect ongoing discoveries. Strains are organized into the four phylogenetic clusters based on host infection patterns and molecular markers: Cluster 1 strains infect Alnus (Betulaceae), and (Casuarinaceae), and Comptonia and (Myricaceae); Cluster 2 strains infect Coriariaceae, Datisca (Datiscaceae), Dryadoideae (Rosaceae), and (Rhamnaceae); Cluster 3 strains infect (), Colletieae (Rhamnaceae), Morella (Myricaceae), and Gymnostoma (Casuarinaceae); Cluster 4 comprises asymbiotic, non-nitrogen-fixing strains isolated from nodules or soils. Species delineation employs polyphasic taxonomy integrating genotypic (16S rRNA similarity >98.7%, ANI >95-96%, dDDH >70%) and phenotypic data (e.g., sporangia size, filament morphology).

Phylogenetic Analysis

Phylogenetic analyses of Frankia have traditionally relied on 16S rRNA gene sequencing to delineate major evolutionary lineages, revealing a division into four distinct clusters that correlate with host infectivity groups and symbiotic traits. More refined resolutions have been achieved through multi-locus sequence analysis (MLSA) using housekeeping genes such as atpD, dnaA, ftsZ, pgk, and rpoB, which provide higher bootstrap support for intra-generic relationships compared to single-gene approaches. Whole-genome phylogenomics, incorporating conserved marker genes and average nucleotide identity (ANI) metrics, has further solidified these clusters, demonstrating robust monophyly within each. For instance, Cluster 1 comprises strains infecting Betulaceae (e.g., Alnus), Casuarinaceae (e.g., Casuarina), and Myricaceae (e.g., Myrica); Cluster 2 includes those associated with Coriariaceae, Datiscaceae, Dryadoideae (Rosaceae), and certain Rhamnaceae (e.g., Ceanothus); Cluster 3 targets Elaeagnaceae, Colletieae (Rhamnaceae), Morella (Myricaceae), and Gymnostoma (Casuarinaceae); while Cluster 4 consists of atypical, asymbiotic, non-nitrogen-fixing strains. Taxonomic classification integrates Genome Taxonomy Database (GTDB) criteria, emphasizing phylogenomic coherence and ANI thresholds above 95-96% for species boundaries, alongside LPSN for valid nomenclature. The 2022 revision elevated the clusters to genera—Frankia (Cluster 1), Protofrankia (Cluster 2), Parafrankia (Cluster 3), and Pseudofrankia (Cluster 4)—based on distinct genomic signatures and host ranges; these are now formally adopted. Candidate species such as Candidatus Frankia californiensis (now in Protofrankia) exemplify uncultured lineages within Cluster 2, identified through metagenomic reconstruction from nodules of western North American hosts like Ceanothus and defined by >99% 16S rRNA similarity to cultured relatives. Evidence of (HGT) has shaped symbiotic capabilities, particularly in nodulation-related genes. Some Cluster 2 strains harbor homologs of rhizobial nodABC genes, involved in synthesis, and nodH (sulfotransferase), suggesting acquisition from α-proteobacterial via HGT events that predate the divergence of actinorhizal symbioses. The nif cluster, encoding components, shows mosaic architectures indicative of ancient HGT, potentially from diazotrophic ancestors, though lacking the modular symbiotic islands typical of . These transfers likely facilitated host-specific adaptations, as nod homologs are expressed in nodules of Datisca glomerata despite the absence of canonical nodD regulators. Recent phylogenomic studies from 2022-2024 have elucidated intra-cluster diversity, revealing fine-scale host-specific adaptations through expanded sampling and metagenomic assemblies. For example, analyses of Alnus incana nodules and soils in Alaska identified four clades with varying abundances, where host proximity enriches symbiotic genotypes (e.g., AT clade dominance in early succession), indicating selective pressures for infection efficiency. Similarly, MLSA of introduced versus indigenous strains in alder systems demonstrated clade-specific competitive advantages, with nitrogen fertilization boosting symbiotic cluster representation by up to 84%, underscoring adaptive divergence within clusters tied to environmental and host cues.

Morphology and Physiology

Cellular Structure

Frankia exhibits filamentous growth characterized by hyphae-like structures that branch dichotomously, with diameters typically ranging from 0.5 to 2 μm. These hyphae are septate and form extensive mycelial networks in culture and symbiosis, serving as the primary vegetative form of the bacterium. The organism displays three main developmental stages: hyphae, vesicles, and sporangiospores. Hyphae represent the actively growing phase, while vesicles are specialized, spherical structures measuring 2-5 μm in diameter that develop terminally or on short lateral branches from hyphae. These vesicles feature a multi-lamellar envelope that protects from oxygen, as detailed in the process. Sporangiospores, which are endospores, form within multilocular sporangia that can reach up to 100 μm in diameter, providing a dormant stage. Frankia is Gram-positive and non-motile, consistent with its actinobacterial affiliation. Its cell wall consists of a thick layer typical of , along with an outer membranous component containing meso-diaminopimelic acid, but lacks mycolic acids. Cells contain intracellular lipid bodies and glycogen granules, which serve as energy storage reserves, particularly important during symbiotic associations with host plants. These inclusions accumulate in hyphae and vesicles, supporting metabolic demands under varying environmental conditions.

Growth and Reproduction

Frankia strains exhibit aerobic to microaerophilic respiration, employing a respiratory type of that requires oxygen for growth while tolerating reduced oxygen levels in some cases. Optimal growth conditions include temperatures of 25–30°C and a range of 6.8–7.2, with mesophilic strains showing no growth below 10°C or above 37°C. These bacteria are chemoorganotrophic and require complex media for cultivation, typically supplemented with carbon sources such as propionate, succinate, or , alongside nitrogen sources like , nitrate, or ; no external growth factors are necessary. Growth rates are characteristically slow, with doubling times of 24–48 hours in liquid cultures, reflecting their adaptation to nutrient-limited environments. Reproduction in Frankia is asexual and occurs via sporulation, during which vegetative hyphae differentiate into multilocular sporangia that contain hundreds of spores. Upon , these spores develop into new hyphal filaments, enabling and potentially initiating infections. In free-living states, sporulation is a prominent reproductive strategy under nutrient-rich or stress conditions, supporting dispersal in . However, within symbiotic root nodules, sporulation is often reduced or absent in certain strains, as Frankia shifts to relying on host-derived carbon compounds—such as sugars and organic acids—for sustained growth and metabolism. This adaptation prioritizes and biomass accumulation over spore production in the protected nodular environment.

Symbiotic Relationships

Actinorhizal Host Plants

Actinorhizal host plants comprise approximately 200 species belonging to eight families: , , Coriariaceae, Datiscaceae, , , , and . These angiosperms, mostly woody perennials such as trees and shrubs (with the exception of herbaceous genera like Datisca), form symbioses with Frankia bacteria, facilitating biological . The diversity spans about 25 genera, enabling these plants to colonize and stabilize marginal ecosystems. Prominent examples include alders (Alnus spp.) in the , which are fast-growing trees common in riparian and forest settings; sea buckthorn (Hippophae rhamnoides) in the , a hardy shrub valued for and production; and casuarinas (Casuarina and Allocasuarina spp.) in the , drought-tolerant trees widely used in . These representatives illustrate the ecological adaptability of actinorhizal plants, occurring across temperate, boreal, and tropical zones where soil is often limiting. Frankia strains exhibit varying degrees of host specificity linked to their phylogenetic clusters. For example, cluster 1 strains primarily form symbioses with and hosts, while cluster 2 strains associate primarily with , and some strains infect species. This specificity influences the distribution and compatibility of symbiotic partnerships, with some strains showing broader across related families. The symbiosis confers key advantages to host plants, notably improved growth and survival in nitrogen-deficient soils by providing fixed atmospheric nitrogen. In productive systems like red alder stands, nitrogen fixation rates can achieve up to 200 kg N ha⁻¹ year⁻¹, enhancing plant biomass accumulation and contributing to long-term soil fertility.

Infection Mechanisms

Frankia establishes symbiotic relationships with actinorhizal plants through specialized infection mechanisms that initiate nodule formation on host roots, differing from the rhizobial-legume symbiosis by lacking canonical Nod factors in most strains. The bacterium typically exists in soil as free-living hyphae that grow toward host roots in response to environmental cues, facilitating initial contact. Upon reaching the root surface, Frankia penetrates the host tissue via two primary pathways: intracellular infection, primarily observed in families like Betulaceae, where hyphae enter through deformed root hairs leading to intracellular infection threads; and intercellular infection, common in Casuarinaceae, involving direct penetration between cortical cells without root hair involvement. These pathways ensure efficient colonization tailored to host anatomy, with intracellular routes often resulting in infected cortical cells enclosed by plant-derived matrices. The infection process unfolds in distinct stages, beginning with pre-infection hyphal growth in the , where Frankia spores or hyphae sense root exudates and orient toward the host. contact triggers deformation of root hairs in susceptible hosts, followed by penetration facilitated by bacterial secretion of hydrolytic enzymes that degrade plant cell walls, such as pectinases and cellulases, allowing hyphal ingress without causing extensive tissue damage. Once inside, hyphae proliferate within the root cortex, inducing and forming prenodules—precursor structures that expand into mature nodules through continued hyphal branching and host cell infection. This cortical proliferation is tightly regulated to prevent over-infection, involving feedback mechanisms that limit bacterial entry after initial colonization. Signal exchange between Frankia and the host is crucial for infection specificity and progression, with root-secreted acting as primary plant signals that induce bacterial responses, including the production of deforming factors (RHDF) in compatible strains. These , such as quercetin derivatives in , enhance Frankia hyphal motility and signal molecule secretion, though Frankia lacks the full suite of rhizobial nod genes except in cluster II strains, which possess nodABC homologs for lipochitooligosaccharide-like signals. In turn, bacterial signals, including small hydrophilic factors like RHDF and NIN-inducing factors, trigger plant for and cortical reprogramming, activating symbiosis-related genes such as those encoding cytokinins and auxins within hours of contact. This bidirectional signaling ensures host specificity, with incompatible interactions failing at early deformation or penetration steps. Nodule morphogenesis varies by host family, reflecting infection pathway differences and leading to specialized structures for bacterial housing. In Betulaceae, such as Alnus species, nodules develop as modified lateral roots with a persistent , vascular core, and infected zone where hyphae differentiate into nitrogen-fixing vesicles. Myricaceae, like , form coralloid nodules—branched, coral-like aggregates of infected roots—arising from intracellular penetration and supporting diverse Frankia strains. These nodule types feature zonation: at the apex, fixation in the middle, and at the base, optimizing symbiotic efficiency while containing bacterial spread through plant-derived encapsulation.

Nitrogen Fixation Process

In Frankia, occurs within specialized vesicles that house the oxygen-sensitive enzyme complex, primarily the molybdenum-iron (MoFe) variant encoded by the nifHDK genes. This complex catalyzes the reduction of atmospheric dinitrogen (N₂) to (NH₃) through the reaction N₂ + 8H⁺ + 8e⁻ → 2NH₃ + H₂, requiring an investment of 16 ATP molecules per N₂ reduced. The vesicles provide from oxygen inactivation via multilayered envelopes rich in hopanoid , which limit O₂ , complemented by the host plant's low-oxygen nodule environment. Vesicle formation, detailed under cellular , is induced under nitrogen-limiting conditions to enable this process. The cluster in Frankia is organized into a compact ~20 kb region containing at least 12 core genes, including nifH (encoding the Fe protein), nifDK (encoding the MoFe protein), and accessory genes like nifEN (for cofactor ) and nifV (homocitrate ), arranged in operons such as nifHDK and nifENX. This organization mirrors that in but features actinobacterial-specific promoters, lacking the typical σ⁵⁴-RpoN dependency seen in Proteobacteria; instead, transcription is activated under starvation without homologs of nifA or nifL. involves the global response activator NtrC, which binds upstream of nif promoters to enhance expression in low- conditions, while two-component systems akin to FixL/FixJ in likely modulate oxygen-responsive fix genes supporting to . In , nitrogen fixation efficiency demands substantial host investment, with actinorhizal plants allocating 20-50% of photosynthate to support the process in nodules, covering the high ATP costs and maintenance of the diazotrophic state. Fixed is exported primarily as or incorporated into like , transported to the host via shared vascular tissues, sustaining plant growth in nutrient-poor soils. This allocation underscores the mutualistic balance, where Frankia provides up to 200-300 kg N ha⁻¹ year⁻¹ in optimal conditions.

Ecology and Distribution

Global Habitat Range

Frankia exhibits a broad global distribution, primarily in soils associated with actinorhizal host plants, where it forms symbiotic nitrogen-fixing relationships. In temperate forests of North America and Europe, it is commonly found in association with Alnus species, thriving in nitrogen-poor environments that support early successional stages. Similarly, in arid zones of central and western Asia, Frankia occurs with Elaeagnus species like Elaeagnus angustifolia, which colonize dry riparian and semi-desert habitats. On coastal dunes in Eurasia, it partners with Hippophae rhamnoides, stabilizing sandy substrates in maritime climates. The bacterium shows distinct preferences, favoring well-drained, sandy substrates with low content that enhance its symbiotic role in nutrient-poor settings. It tolerates a range of 5 to 8, with optimal growth around neutral levels, allowing adaptation to mildly acidic soils or neutral environments. Frankia achieves long-term persistence in these soils through formation, remaining viable and infective for many years even in the absence of host plants. Biogeographically, Frankia strains are native to all continents except , reflecting the cosmopolitan range of their actinorhizal hosts from subarctic to subtropical latitudes. Human-mediated introductions of host plants have expanded its presence, notably Casuarina species planted in tropical regions for reclamation, where compatible Frankia strains establish in non-native soils. Recent molecular studies from 2022 to 2024 using DNA cloning and metagenomic approaches have detected greater Frankia phylogenetic diversity in undisturbed, early-successional soils compared to those altered by agriculture or late-succession disturbances, highlighting sensitivity to land-use changes.

Ecological Roles and Interactions

Frankia plays a pivotal role in global nitrogen cycling, particularly as a primary nitrogen fixer in pioneer ecosystems such as early successional forests and disturbed sites, where it enhances soil fertility through symbiotic associations with actinorhizal plants. In alder stands, for example, these symbioses can contribute 50-100 kg of nitrogen per hectare annually, supporting plant growth and facilitating succession by increasing available nitrogen for subsequent vegetation. This process is especially vital in nutrient-poor environments, where Frankia-mediated fixation helps restore soil nitrogen levels and promotes ecosystem recovery. Beyond symbiosis, certain Frankia strains exhibit free-living capabilities, functioning as saprophytes capable of decomposing in . Non-symbiotic strains, particularly those in Cluster 3, possess comparatively large genomes that suggest enhanced saprotrophic potential, allowing them to break down complex organic compounds and contribute to nutrient recycling in the independently of host plants. Frankia engages in various microbial interactions that influence ecosystem dynamics, often co-occurring with mycorrhizal fungi and in the root zones of actinorhizal plants. Dual inoculations with vesicular-arbuscular mycorrhizae and Frankia have been shown to synergistically boost plant growth and , with mycorrhizae enhancing uptake that complements Frankia's provision. In nodules, Frankia may compete with or facilitate other , such as Parafrankia strains; recent studies indicate that effective nitrogen-fixing Parafrankia outcompetes non-fixing relatives like Pseudofrankia under nitrogen-limited conditions, dominating nodule occupancy and potentially excluding less efficient symbionts through resource partitioning. Environmentally, Frankia-inoculated actinorhizal plants are valuable for land reclamation, particularly at mine sites, where they improve soil stability, biomass production, and nitrogen content while tolerating heavy metals and poor substrates. However, the symbiosis can exacerbate ecological risks when associated with non-native actinorhizal species, such as the invasive shrub Elaeagnus umbellata (autumn olive), which uses Frankia-mediated nitrogen fixation to thrive in disturbed habitats, alter soil nitrogen levels, and displace native vegetation.

Genomics and Evolution

Genome Characteristics

The genomes of Frankia species typically range in size from 5 to 10.5 Mb, exhibit a high of 66–72%, and encode between approximately 4,500 and 8,000 protein-coding genes, reflecting their to diverse environmental and symbiotic niches. For instance, the of Frankia alni strain ACN14a measures 7.5 Mb and contains 6,786 protein-coding genes, while Frankia sp. strain HFPCcI3 has a more compact 5.43 Mb with 4,499 genes, and Frankia sp. strain EAN1pec spans 9.04 Mb with 7,976 genes. These genomes consist of a single circular with no evidence of independently replicating plasmids in most sequenced strains, though plasmids have been detected in a minority of isolates (about 10% of tested strains). Prominent genomic features include symbiosis-related regions containing nod and nif genes, which facilitate host infection and ; in certain strains, such as those in cluster II, these genes are clustered in genomic segments of 100–200 kb, though canonical nod homologs are absent in many lineages. Frankia genomes devote a substantial portion to functional gene categories supporting and environmental resilience. Secondary metabolite biosynthesis is particularly enriched, with up to 65 clusters identified across representative strains, including numerous polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) for compounds like and siderophores, which aid in acquisition and microbial competition. Genes involved in stress responses are also prevalent, enabling survival in harsh conditions such as heavy metal contamination and ; for example, hundreds of iron-related genes and operons like cadCA and cadB/DX confer tolerance to metals including and lead, while proteins mitigating are upregulated under symbiotic or environmental pressures. sequencing efforts began with the first complete assemblies of Frankia alni strain ACN14a in 2007, marking a in understanding actinorhizal symbionts, followed by over 30 strains sequenced by 2024, encompassing diverse host specificities and enhancing insights into genomic architecture.

Genetic Diversity and Evolution

Genetic diversity within Frankia is substantial, reflecting its to diverse actinorhizal host plants and environmental conditions. Average identity (ANI) values among strains range from approximately 77% to 100%, with values often exceeding 95% within defined clusters, indicating both species-level delineation and intraspecific variation. For instance, in cluster Ia strains infective to Alnus , ANI comparisons reveal close relatedness among geographically proximate isolates, such as 98% between strains from Italian alder (Alnus cordata). A analysis of 33 Alnus-infective cluster Ia strains identifies a core of about 1,404 genes, comprising roughly 45% of the average per-genome content of 3,112 genes. Evolutionary dynamics in Frankia are driven by host-specific selection pressures and (HGT), which facilitate adaptation to symbiotic lifestyles. Host-specific selection is evident in the diversification of genes involved in nitrogen metabolism and nodule formation, such as the agmatine deiminase pathway (e.g., FRAAL0164 orthologs), which aids in accessing host-derived nitrogen compounds and modulating defenses. Nodulation-related genes (nod) exhibit significant variation, with diversification and occasional presence in cluster II strains (e.g., nodABC in Frankia datiscae Dg1), but absence in most cluster Ia and IV genomes, suggesting evolutionary loss in non-nodulating lineages. HGT events, particularly surrounding nod operons and transposon-flanked symbiosis gene clusters, contribute to this plasticity, enabling rapid acquisition of symbiotic capabilities across actinobacterial lineages. Recent comparative genomic studies from 2023–2024 highlight biogeographic structuring and ongoing evolutionary processes. Analysis of 33 Alnus-infective strains demonstrates clustering aligned with host plant phylogeny and geography, where strains like AcoPra associate specifically with A. cordata in Mediterranean regions, indicating localized . In free-living or strains (e.g., cluster IV), complete loss of nod genes has been documented, potentially reflecting a return to saprophytic lifestyles post-symbiosis. Biogeographic patterns in the earliest divergent cluster-2 strains, isolated from and , show divergence times of 82–36 million years ago, with ANI values of 98–99.9% within regional groups but lower across continents, underscoring vicariance-driven . These findings imply ecological sorting of Frankia strains by environmental factors like (optimal ranges 5.0–7.5 varying by cluster) and host phylogeny, which select compatible endophytes from soil pools for nodulation. Such mechanisms promote isolation and potential , as seen in genome-reduced spore-positive (Sp+) strains evolving toward obligate symbiosis, with losses of up to 88 protein families enhancing host restriction.

References

  1. https://www.sciencedirect.com/topics/immunology-and-microbiology/frankia
  2. https://www.tandfonline.com/doi/full/10.1080/13416979.2022.2036417
  3. https://lpsn.dsmz.de/genus/frankia
  4. https://link.springer.com/chapter/10.1007/7171_2008_121
  5. https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.12962
  6. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1041425/full
  7. https://journals.asm.org/doi/10.1128/aem.00288-24
  8. https://doi.org/10.1099/ijsem.0.006199
  9. https://doi.org/10.3389/fmicb.2022.1041425
  10. https://link.springer.com/article/10.1007/s10482-018-1165-y
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