The plant-growth-promoting actinobacteria of the genus Nocardia induces root nodule formation in Casuarina glauca
Actinorhizal plants form a symbiotic association with the nitrogen-fixing actinobacteria Frankia. These plants have important economic and ecological benefits including land reclamation, soil stabilization, and reforestation. Recently, many non-Frankia actinobacteria have been isolated from actinorhizal root nodules suggesting that they might contribute to nodulation. Two Nocardia strains, BMG51109 and BMG111209, were isolated from Casuarina glauca nodules, and they induced root nodule-like structures in original host plant promoting seedling growth. The formed root nodule-like structures lacked a nodular root at the apex, were not capable of reducing nitrogen and had their cortical cells occupied with rod-shaped Nocardiae cells. Both Nocardia strains induced root hair deformation on the host plant. BMG111209 strain induced the expression of the ProCgNin:Gus gene, a plant gene involved in the early steps of the infection process and nodulation development. Nocardia strain BMG51109 produced three types of auxins (Indole-3-acetic acid [IAA], Indole-3-Byturic Acid [IBA] and Phenyl Acetic Acid [PAA]), while Nocardia BMG111209 only produced IAA. Analysis of the Nocardia genomes identified several important predicted biosynthetic gene clusters for plant phytohormones, secondary metabolites, and novel natural products. Co-infection studies showed that Nocardia strain BMG51109 plays a role as a “helper bacteria” promoting an earlier onset of nodulation. This study raises many questions on the ecological significance and functionality of Nocardia bacteria in actinorhizal symbioses.
KeywordsNon-Frankia actinobacteria Nocardia Plant infectivity Auxins Actinorhizal symbiosis Plant-growth-promotion
This work was supported in part by CMCU (Comité Mixte Tuniso-Français pour la Coopération inter-Universitaire no 09G0916 to MG and LL) and the Agence Nationale de la Recherche (Grant ANR-08-JCJC-0070-01 to LL). FG-G was supported in part by the Visiting Scientist and Postdoctoral Scientist Program administered by the NH AES at the University of New Hampshire. This work was also supported by the USDA National Institute of Food and Agriculture Hatch 022821 (LST), Agriculture and Food Research Initiative Grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture (LST), and the College of Life Science and Agriculture at the University of New Hampshire-Durham. A Summer Undergraduate Research Fellowship (SURF) from the University of New Hampshire-Durham supported EL. Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2786.
FGG, LL, AB and LST conceived the study. FGG, IN, EL, TD, ZM, HK, VV, and HG performed the research. EL, TD, IN, FGG, and LST analysed the data. FGG, and LST wrote the manuscript. All the authors approved the paper.
Compliance with ethical standards
Conflict of interest
The authors have declared that they have no competing interest exists.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
- Benson DR, Silvester WB (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev 57:293–319Google Scholar
- Blin K, Wolf T, Chevrette MG, Lu XW, Schwalen CJ, Kautsar SA, Duran HGS, Santos ELCDL, Kim Hu, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH (2017) antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41. https://doi.org/10.1093/nar/gkx319 CrossRefGoogle Scholar
- Champion A, Lucas M, Tromas A, Vaissayre V, Crabos A, Diedhiou I, Prodjinoto H, Moukouanga D, Pirolles E, Cissoko M, Bonneau J, Gherbi H, Franche C, Hocher V, Svistoonoff S, Laplaze L (2015) Inhibition of auxin signaling in Frankia species-infected cells in Casuarina glauca nodules leads to increased nodulation. Plant Physiol 167(3):1149–1157. https://doi.org/10.1104/pp.114.255307 CrossRefGoogle Scholar
- Clavijo F, Diedhiou I, Vaissayre V, Acolatse J, Moukouanga D, Crabos A, Auguy F, Franche C, Gherbi H, Champion A, Hocher V, Bogusz D, Tisa LS, Svistoonhoff S (2015) The Casuarina NIN gene is a transcriptionally activated throughout Frankia root infection as well as in response to bacterial diffusible signals. New Phytol 208:887–903. https://doi.org/10.1111/nph.13506 CrossRefGoogle Scholar
- Diagne N, Diouf D, Svistoonoff S, Kane A, Noba K, Franche C, Bogusz D, Duponnois R (2013b) Casuarina in Africa: distribution, role and importance of arbuscular mycorrhizal, ectomycorrhizal fungi and Frankia on plant development. J Environ Manag 128:204–209. https://doi.org/10.1016/j.jenvman.2013.05.009 CrossRefGoogle Scholar
- Ghodhbane-Gtari F, Beauchemin N, Gueddou A, Hezbri K, Ktari A, Louati M, Nouioui I, Chen A, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS (2016a) Permanent improved high quality draft genome sequence of Nocardia casuarinae strain BMG51109 an endophyte of actinorhizal root nodules of Casuarina glauca. Genome Announc 4(4):e00799-16. https://doi.org/10.1128/genomeA.00799-16 CrossRefGoogle Scholar
- Ghodhbane-Gtari F, Beauchemin N, Gueddou A, Hezbri K, Ktari A, Louati M, Nouioui I, Chen A, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Pagani I, Sen A, Wall L, Woyke T, Gtari M, Tisa LS (2016b) Permanent draft genome sequence of Nocardia sp. BMG111209, an actinobacterium isolated from nodules of Casuarina glauca. Genome Announc 4(4):e00770-16. https://doi.org/10.1128/genomea.00770-16 CrossRefGoogle Scholar
- Hirsch AM, Alvarado J, Bruce D, Chertkov O, De Hoff PL, Detter JC, Fujishigea NA, Goodwind LA, Hand J, Hanc S, Ivanovac N, Lande ML, Luma MR, Milani-Nejada N, Nolane M, Patic A, Pitluckd S, Trana SS, Woyke T, Valdés M (2013) Complete genome sequence of Micromonospora strain L5, a potential plant-growth-regulating actinomycete, originally isolated from Casuarina equisetifolia root nodules. Genome Announc 1(5):e00759-13CrossRefGoogle Scholar
- Jukes TH, Cantor CR (1969) Evolution of protein molecules. Academic Press, New York, pp 21–132Google Scholar
- Ngom M, Oshone R, Diagne N, Cissoko M, Svistoonoff S, Tisa LS, Laplaze L, Sy MO, Champion A (2016) Tolerance to environmental stress by the nitrogen-fixing actinobacterium Frankia and its role in actinorhizal plants adaptation. Symbiosis 70:17–29. https://doi.org/10.1007/s13199-016-0396-9 CrossRefGoogle Scholar
- Niner BM, Brandt JP, Villegas MC, Marshall CR, Hirsch AM, Valdes M (1996) Analysis of partial sequences of genes coding for 16S rRNA of actinomycetes isolated from Casuarina equisetifolia nodules in Mexico. Appl Environ Microbiol 62:3034–3036Google Scholar
- Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz NC, Göker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk H-P, Gtari M (2016) Proposal of a type strain for Frankia alni (Woronin 1866), and recognition Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Int J Syst Evol Microbiol 66:5201–5210. https://doi.org/10.1099/ijsem.0.001496 CrossRefGoogle Scholar
- Perrine-Walker F, Doumas P, Lucas M, Vaissayre V, Beauchemin N, Band L, Chopard J, Crabos A, Conejero G, Peret B, Verdeil J-L, Hocher V, Franche C, Bennett MJ, Tisa LS, Lalpaze L (2010) Specific auxin carriers localization direct auxin accumulation in plants cells infected by Frankia in Casuarina glauca actinorhizal nodules. Plant Physiol 154:1372–1380. www.plantphysiol.org/cgi/doi/10.1104/pp.110.163394
- Ritchie NJ, Myrold DD (1999) Geographic distribution and genetic diversity of Ceanothus-infective Frankia strains. Appl Environ Microb 65(4):1378–1383Google Scholar
- Sambrook J, Fritsh EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
- Solans M, Vobis G (2003) Actinomycetes saprofiticos asociados a la rizosfera rizoplano de Discaria trinervis. Ecologia Austral 13:97–107Google Scholar
- Svistoonoff S, Laplaze L, Auguy F, Runions J, Duponnois R, Haseloff J, Franche C, Bogusz D (2003) cg12 expression is specifically linked to infection of root hairs and cortical cells during Casuarina glauca and Allocasuarina verticillata actinorhizal nodule development. Mol Plant Microbe Interact 16:600–607CrossRefGoogle Scholar
- Tisa LS, Chval MS, Krumholz GD, Richards J (1999) Antibiotic resistance patterns of Frankia strains. Can J Bot 77:1257–1260Google Scholar
- Tsukamura M (1982) Numerical analysis of the taxonomy of nocardiae and rhodococci. Division of Nocardia asteroides sensu stricto into two species and descriptions of Nocardia paratuberculosis sp. nov. Tsukamura (formerly the Kyoto-I group of Tsukamura), Nocardia nova sp. nov. Tsukamura, Rhodococcus aichiensis sp. nov., Tsukamura, Rhodococcus chubuensis sp. nov., Tsukamura, and Rhodococcus obuensis sp. nov. Tsukamura. Microbiol Immunol 26:1101–1119CrossRefGoogle Scholar
- Valdés D, Huss-Danell K, Lavire C, Normand P, Wall L (2006) Further characterization of new symbiotic nitrogen fixing non-Frankia actiomycetes isolated from nodules of Alnus acuminata. In: The 14th international meeting on Frankia and actinorhizal plants. Department of Plant Physiology, UPSC, Umea University, UmeaGoogle Scholar
- Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M (1992) Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36:1251–1275CrossRefGoogle Scholar