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Anderson MD, Taylor DL, Olson K, Ruess RW. Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska. Ecol Evol 2024; 14:e11458. [PMID: 38979008 PMCID: PMC11229434 DOI: 10.1002/ece3.11458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/10/2024] Open
Abstract
In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.
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Affiliation(s)
- M. D. Anderson
- Biology DepartmentMacalester CollegeSaint PaulMinnesotaUSA
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - D. L. Taylor
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - K. Olson
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - R. W. Ruess
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
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Berckx F, Wibberg D, Brachmann A, Morrison C, Obaid NB, Blom J, Kalinowski J, Wall LG, Pawlowski K. Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere. FEMS Microbiol Ecol 2024; 100:fiae042. [PMID: 38520167 DOI: 10.1093/femsec/fiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/19/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024] Open
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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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden
| | | | - Andreas Brachmann
- LMU München, Faculty of Biology, Genetics, 82152 Planegg-Martinsried, Germany
| | - Ciara Morrison
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Nadia B Obaid
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | | | - Luis G Wall
- CONICET, National Council for Scientific and Technical Research, Argentina
- Department of Science and Technology, National University of Quilmes, B12876BXD Bernal, Argentina
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Science, Stockholm University, 106 91 Stockholm, Sweden
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Nouioui I, Neumann-Schaal M, Pujic P, Fournier P, Normand P, Herrera-Belaroussi A, Vemulapally S, Guerra T, Hahn D. Frankia nepalensis sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Coriaria nepalensis Wall. Int J Syst Evol Microbiol 2023; 73. [PMID: 38098135 DOI: 10.1099/ijsem.0.006199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Strains CN4T, CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus. The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N2-fixing vesicles and do not fix nitrogen in vitro. The peptidoglycan of strain CN4T contains meso-diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H4) and MK-9(H6) are the predominant menaquinones (>15 %), and iso-C16 : 0 and C17 : 1ω8c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4T is most closely related to Frankia saprophytica CN 3T. An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3T , Frankia asymbiotica M16386T and Frankia inefficax EuI1cT with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4T, CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4T has a 10.76 Mb genome. CN4T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4T (=DSM 114740T = LMG 32595T) to a novel species, with CN4T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Aude Herrera-Belaroussi
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Pujic P, Carro L, Fournier P, Armengaud J, Miotello G, Dumont N, Bourgeois C, Saupin X, Jame P, Selak GV, Alloisio N, Normand P. Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles. Int J Mol Sci 2023; 24:ijms24119162. [PMID: 37298114 DOI: 10.3390/ijms24119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO2 levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO2 levels in N2-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH4+. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles' pH to prevent the escape of NH3 and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Lorena Carro
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
- Departamento de Microbiología y Genética, Facultad de CC Agrarias y Ambientales, Universidad de Salamanca, Plaza Doctores de la Reina, 37007 Salamanca, Spain
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | | | - Caroline Bourgeois
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Xavier Saupin
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Patrick Jame
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Gabriela Vuletin Selak
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, 21000 Split, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Nicole Alloisio
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
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Kim Tiam S, Boubakri H, Bethencourt L, Abrouk D, Fournier P, Herrera-Belaroussi A. Genomic Insights of Alnus-Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle. Genes (Basel) 2023; 14:530. [PMID: 36833457 PMCID: PMC9956245 DOI: 10.3390/genes14020530] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 02/23/2023] Open
Abstract
The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for "Alnus-infective strains" (i.e., Frankia strains belonging to Cluster Ia). Several genes were specifically found in these strains, including an agmatine deiminase which could possibly be involved in various functions as access to nitrogen sources, nodule organogenesis or plant defense. Within "Alnus-infective strains", Sp+ Frankia genomes were compared to Sp- genomes in order to elucidate the narrower host specificity of Sp+ strains (i.e., Sp+ strains being capable of in planta sporulation, unlike Sp- strains). A total of 88 protein families were lost in the Sp+ genomes. The lost genes were related to saprophytic life (transcriptional factors, transmembrane and secreted proteins), reinforcing the proposed status of Sp+ as obligatory symbiont. The Sp+ genomes were also characterized by a loss of genetic and functional paralogs, highlighting a reduction in functional redundancy (e.g., hup genes) or a possible loss of function related to a saprophytic lifestyle (e.g., genes involved in gas vesicle formation or recycling of nutrients).
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Affiliation(s)
- Sandra Kim Tiam
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
- UMR CNRS 5557 Ecologie Microbienne, INRA UMR 1418, Centre d’Etude des Substances Naturelles, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69361 Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR 1418, Ecologie Microbienne, F-69622 Villeurbanne, France
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Kucho KI, Asukai K, Nguyen TV. NAD + Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Microbes Environ 2023; 38. [PMID: 36858533 PMCID: PMC10037102 DOI: 10.1264/jsme2.me22093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Frankia spp. are multicellular actinobacteria that fix atmospheric dinitrogen (N2) not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species, called actinorhizal plants. To identify novel Frankia genes involved in N2 fixation, we previously isolated mutants of Frankia casuarinae that cannot fix N2. One of these genes, mutant N3H4, did not induce nodulation when inoculated into the host plant Casuarina glauca. Cell lineages that regained the ability to fix N2 as free-living cells were isolated from the mutant cell population. These restored strains also regained the ability to stimulate nodulation. A comparative ana-lysis of the genomes of mutant N3H4 and restored strains revealed that the mutant carried a mutation (Thr584Ile) in the glutamine-dependent NAD+ synthetase gene (Francci3_3146), while restored strains carried an additional suppressor mutation (Asp478Asn) in the same gene. Under nitrogen-depleted conditions, the concentration of NAD(H) was markedly lower in the mutant strain than in the wild type, whereas it was higher in restored strains. These results indicate that glutamine-dependent NAD+ synthetase plays critical roles in both free-living and symbiotic N2 fixation in Frankia.
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Affiliation(s)
- Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University
| | - Koya Asukai
- Graduate School of Science and Engineering, Kagoshima University
| | - Thanh Van Nguyen
- Graduate School of Science and Engineering, Kagoshima University
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7
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Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
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Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
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Normand P, Pujic P, Abrouk D, Vemulapally S, Guerra T, Carlos-Shanley C, Hahn D. Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions. J Genomics 2022; 10:61-68. [PMID: 35979511 PMCID: PMC9379372 DOI: 10.7150/jgen.75779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species. Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.
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Affiliation(s)
- Philippe Normand
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Petar Pujic
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Danis Abrouk
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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9
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Chetri SPK, Rahman Z, Thomas L, Lal R, Gour T, Agarwal LK, Vashishtha A, Kumar S, Kumar G, Kumar R, Sharma K. Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives. J Basic Microbiol 2022; 62:764-778. [PMID: 35638879 DOI: 10.1002/jobm.202200043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/17/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.
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Affiliation(s)
| | - Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, New Delhi, Delhi, India
| | - Ratan Lal
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Tripti Gour
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Akanksha Vashishtha
- Department of Plant Protection, CCS University, Meerut, Uttar Pradesh, India
| | - Sachin Kumar
- Department of Botany, Shri Venkateshwara College, University of Delhi, New Delhi, Delhi, India
| | - Gaurav Kumar
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Botany, Hindu College, University of Delhi, New Delhi, Delhi, India
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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10
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Carlos-Shanley C, Guerra T, Hahn D. Draft genomes of non-nitrogen-fixing Frankia strains. J Genomics 2021; 9:68-75. [PMID: 34703504 PMCID: PMC8542509 DOI: 10.7150/jgen.65429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa, genospecies CN and Ag, respectively. Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.
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Affiliation(s)
- Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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11
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Bustamante DE, Calderon MS, Leiva S, Mendoza JE, Arce M, Oliva M. Three new species of Trichoderma in the Harzianum and Longibrachiatum lineages from Peruvian cacao crop soils based on an integrative approach. Mycologia 2021; 113:1056-1072. [PMID: 34128770 DOI: 10.1080/00275514.2021.1917243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.
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Affiliation(s)
- Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru.,Facultad de Ingeniería Civil y Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Martha S Calderon
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru.,Facultad de Ingeniería Civil y Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Santos Leiva
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Jani E Mendoza
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Marielita Arce
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
| | - Manuel Oliva
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru
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12
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Herrera-Belaroussi A, Normand P, Pawlowski K, Fernandez MP, Wibberg D, Kalinowski J, Brachmann A, Berckx F, Lee N, Blom J, Pozzi AC, Fournier P, Bethencourt L, Dubost A, Abrouk D, Sellstedt A. Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta. Syst Appl Microbiol 2020; 43:126134. [PMID: 33059155 DOI: 10.1016/j.syapm.2020.126134] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022]
Abstract
We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A. incana, A. alnobetula), they form hyphae, vesicles and sporangia in the root nodule cortex but have resisted all attempts at isolation in pure culture. Their genomes have been sequenced, they are significantly smaller than those of other Alnus-infective species (5Mb instead of 7.5Mb) and are very closely related to one another (ANI of 100%). The name Candidatus Frankia nodulisporulans is proposed. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and draft genome sequences reported in this study for AgTrS, AgUmASt1 and AgUmASH1 are MT023539/LR778176/LR778180 and NZ_CADCWS000000000.1/CADDZU010000001/CADDZW010000001, respectively.
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Affiliation(s)
- Aude Herrera-Belaroussi
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France.
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Maria P Fernandez
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Wibberg
- The Center for Biotechnology CeBiTec, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- The Center for Biotechnology CeBiTec, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Andreas Brachmann
- Biocenter of the LMU Munich, Genetics Section, Grosshaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany
| | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Natuschka Lee
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University, 35392 Giessen, Hesse, Germany
| | - Adrien C Pozzi
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Anita Sellstedt
- Department of Plant Physiology, UPSC, Umeå University, 90187 Umeå, Sweden.
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13
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Pozzi ACM, Herrera-Belaroussi A, Schwob G, Bautista-Guerrero HH, Bethencourt L, Fournier P, Dubost A, Abrouk D, Normand P, Fernandez MP. Proposal of ' Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules. Int J Syst Evol Microbiol 2020; 70:5453-5459. [PMID: 32910750 DOI: 10.1099/ijsem.0.004433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The members of the genus Frankia are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on Alnus spp. (Betulaceae), Myrica spp., Morella spp. and Comptonia spp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'Candidatus Frankia alpina' species for some strains present in nodules of Alnus alnobetula and A. incana that grow in alpine environments at high altitudes or in subarctic environments at high latitudes.
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Affiliation(s)
- Adrien C Meynier Pozzi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Guillaume Schwob
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Hector H Bautista-Guerrero
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Lorine Bethencourt
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Danis Abrouk
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
| | - Maria P Fernandez
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France; INRA, UMR1418, Villeurbanne, France
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14
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Berckx F, Wibberg D, Kalinowski J, Pawlowski K. The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type. Genes (Basel) 2020; 11:genes11040432. [PMID: 32316316 PMCID: PMC7231273 DOI: 10.3390/genes11040432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Fede Berckx
- Department of Ecology, Environment, and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden;
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
| | - Katharina Pawlowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.W.); (J.K.)
- Correspondence: ; Tel.: +46-8-16-3772; Fax: +46-8-16-5525
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15
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Balkan MA, Stewart NU, Kauffman ES, Wolfe ER, Ballhorn DJ. Genotypic Diversity and Host-Specificity of Frankia Bacteria Associated with Sympatric Populations of Alnus rubra and Alnus rhombifolia in Oregon. NORTHWEST SCIENCE 2020. [DOI: 10.3955/046.093.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mehmet A. Balkan
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Nathan U. Stewart
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Emily S. Kauffman
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Emily R. Wolfe
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
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16
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Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, Kalinowski J, Brachmann A, Pawlowski K. Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams. Genome Biol Evol 2019; 11:2273-2291. [PMID: 31368478 PMCID: PMC6735867 DOI: 10.1093/gbe/evz153] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
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 perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American 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 New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes 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.
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Affiliation(s)
- Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | | | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Gießen, Germany
| | - Maria P Fernandez
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université Lyon I, Villeurbanne Cedex, France
| | | | - Alison M Berry
- Department of Plant Sciences, University of California, Davis
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Andreas Brachmann
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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17
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Nouioui I, Cortés-albayay C, Carro L, Castro JF, Gtari M, Ghodhbane-Gtari F, Klenk HP, Tisa LS, Sangal V, Goodfellow M. Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia. Front Microbiol 2019; 10:1457. [PMID: 31333602 PMCID: PMC6624747 DOI: 10.3389/fmicb.2019.01457] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carlos Cortés-albayay
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca, Spain
| | - Jean Franco Castro
- The Chilean Collection of Microbial Genetic Resources (CChRGM), Instituto de Investigaciones Agropecuarias (INIA) – Quilamapu, Chillán, Chile
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Institut National des Sciences Appliquées et de Technologie, Université de Carthage Centre Urbain Nord, Tunis, Tunisia
- Laboratoire Microorganismes et Biomolécules Actives, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Louis S. Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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18
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Deicke M, Mohr JF, Roy S, Herzsprung P, Bellenger JP, Wichard T. Metallophore profiling of nitrogen-fixingFrankiaspp. to understand metal management in the rhizosphere of actinorhizal plants. Metallomics 2019; 11:810-821. [DOI: 10.1039/c8mt00344k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Frankiaspp. are widespread nitrogen-fixing and metallophore releasing soil bacteria, which often live in symbiosis with a broad spectrum of hosts.
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Affiliation(s)
- Michael Deicke
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
| | - Jan Frieder Mohr
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
| | - Sébastien Roy
- Centre SÈVE
- Département de Biologie
- Faculté des Sciences
- Université de Sherbrooke
- Canada
| | - Peter Herzsprung
- UFZ – Helmholtz Centre for Environmental Research
- Department Lake Research
- 39114 Magdeburg
- Germany
| | | | - Thomas Wichard
- Friedrich Schiller University Jena
- Institute for Inorganic and Analytical Chemistry
- 07743 Jena
- Germany
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19
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In Planta Sporulation of Frankia spp. as a Determinant of Alder-Symbiont Interactions. Appl Environ Microbiol 2018; 84:AEM.01737-18. [PMID: 30217853 DOI: 10.1128/aem.01737-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
The Alnus genus forms symbiosis with the actinobacteria Frankia spp. and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta Spore-positive (Sp+) strains are predominant on Alnus incana and Alnus viridis in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, as well as the effect of the sporulation genotype on the ectomycorrhizal (ECM) communities. Trapping experiments were conducted using A. glutinosa, A. incana, and A. viridis plantlets on 6 soils, differing in the alder species and the frequency of Sp+ nodules in the field. Higher diversity of Frankia spp. and variation in Sp+ frequencies were observed in the trapping than in the fields. Both indigenous and trapping species shape Frankia community structure in trapped nodules. Nodulation impediments were observed under several trapping conditions in Sp+ soils, supporting a narrower host range of Sp+ Frankia species. A. incana and A. viridis were able to associate equally with compatible Sp+ and Sp- strains in the greenhouse. Additionally, no host shift was observed for Alnus-specific ECM, and the sporulation genotype of Frankia spp. defined the ECM communities on the host roots. The symbiotic association is likely determined by the host range, the soil history, and the type of in planta Frankia species. These results provide an insight into the biogeographical drivers of alder symbionts in the Holarctic region.IMPORTANCE Most Frankia-actinorhiza plant symbioses are capable of high rates of nitrogen fixation comparable to those found on legumes. Yet, our understanding of the ecology and distribution of Frankia spp. is still very limited. Several studies have focused on the distribution patterns of Frankia spp., demonstrating a combination of host and pedoclimatic parameters in their biogeography. However, very few have considered the in planta sporulation form of the strain, although it is a unique feature among all symbiotic plant-associated microbes. Compared with Sp- Frankia strains, Sp+ strains would be obligate symbionts that are highly dependent on the presence of a compatible host species and with lower efficiency in nitrogen fixation. Understanding the biogeographical drivers of Sp+ Frankia strains might help elucidate the ecological role of in planta sporulation and the extent to which this trait mediates host-partner interactions in the alder-Frankia-ECM fungal symbiosis.
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Normand P, Nouioui I, Pujic P, Fournier P, Dubost A, Schwob G, Klenk HP, Nguyen A, Abrouk D, Herrera-Belaroussi A, Pothier JF, Pflüger V, Fernandez MP. Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. Int J Syst Evol Microbiol 2018; 68:3001-3011. [PMID: 30059001 DOI: 10.1099/ijsem.0.002939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia. 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankiawith validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankiacluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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Affiliation(s)
- Philippe Normand
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Imen Nouioui
- 2Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia.,3School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Petar Pujic
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Pascale Fournier
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Audrey Dubost
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Guillaume Schwob
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Hans-Peter Klenk
- 3School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | | | - Danis Abrouk
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Aude Herrera-Belaroussi
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Joël F Pothier
- 5Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | | | - Maria P Fernandez
- 1Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
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