An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis
A meeting was held from the 24th to the 27th of August 2015 in Montpellier, France, on Frankia-actinorhizal plants relations. This meeting was the 18th of the series that began in 1978 at Harvard Forest, USA. The initial meeting was sparked by the first isolation of a microbe from a Comptonia peregrina root nodule in pure culture, which had morphological features similar to those of the Frankia symbiont in nodules and was capable of forming nodules on its host (Callaham et al. 1978). This effectively boosted research on the symbiosis. The 2015 meeting was the opportunity to have 80 scientists from 17 different countries, present 34 oral presentations and 51 posters. The object was to exchange ideas on a range of subjects, initiate projects and discuss various controversies. The Montpellier meeting was opened by Jean-Marc Chataîgner, the IRD deputy managing director who outlined the opportunities and challenges facing scientists working on actinorhizal plants. Then there was an invited presentation by Allan Downie, Emeritus fellow at the John Innes Centre, Norwich, UK, who outlined the positive and negative aspects of the actinorhizal symbiosis research in comparison with the Legumes-rhizobia symbiosis.
Among the various recent developments, that have occurred since the previous meeting held in Shillong, India in 2013, are the cost reduction and ensuing generalization of genome sequencing techniques. Since 2013, there have been 18 genomes published representing all major lineages (Tisa et al. 2016). This mass of data, in turn, permits other “omics” approaches such as transcriptomics (Alloisio et al. 2010; Bickhart and Benson 2011), metabolomics (Brooks and Benson 2016) and proteomics (Mastronunzio and Benson 2010; Udwary et al. 2011) to analyze various physiological aspects.
The resultant databases permit more precise phylogenetic analyses to be performed.
A study has been completed on the conserved genomic core proteins within actinobacteria and this positioned Frankia at the root of aerobic actinobacteria (Sen et al. 2014). The datasets can also be used to generate and characterize mutants (Kakoi et al. 2014), identify cytosine methylations (Kucho and Kamiharai 2016), or follow the expression of genes involved in a given function such as the hup genes coding for hydrogenase (Richau et al. 2013). Metabolic profiling has also been undertaken to discern how PAS domains have evolved (Sarkar et al. 2016) or to compare globally metabolic machineries (Thakur and Sen 2016).
Besides Frankia, other bacteria have been isolated from actinorhizal nodules and sequencing them has become a convenient approach to gain knowledge on their function and physiology (Bose et al. 2016; Ghodhbane-Gtari et al. 2014).
A review of stress-responses in Frankia has shown the extent of its physiological adaptability (Ngom et al. 2016a). Most Frankia lineages have a representative that was isolated many years ago. The exception is cluster2, that resisted numerous isolation attempts and for which a representative genome was determined (Persson et al. 2015). However last year, this obstacle was overcome using an approach combining massive direct phenotypic characterization and growth medium fine tuning (Gtari et al. 2015).
On the plant-side, the sequencing of the first genomes for the actinorhizal plants, Casuarina glauca and Datisca glomerata, was announced and will be initiated. Other approaches based on ESTs and transcriptomics were also reported (Hocher et al. 2011; Demina et al. 2013; Diedhiou et al. 2014). In addition, metabolomics have been used to analyse globally nitrogen and carbon metabolism in (Carro et al. 2016a) and in Datisca (Persson et al. 2016).
Signalling between partners in particular was much discussed. Transgenic C. glauca expressing a transcriptional fusion between the promoter from the Nodule Inception (NIN) gene and the GFP reporter gene was used to develop a bioassay for the purification of the biologically active molecules in the supernatant of Frankia sp. CcI3 (Chabaud et al. 2016). This confirmed a previous study on a factor from Frankia ACoN24d (Ceremonie et al. 1999). Interestingly, such diffusible active molecules were found to induce calcium spiking in C. glauca (Chabaud et al. 2016) and in A. glutinosa (Granqvist et al. 2015). The existence of defense peptides in several lineages was also discussed as well as their effects on symbiotic Frankia (Carro et al. 2015; Carro et al. 2016b). The role of auxins and auxin transporters was studied (Imanishi et al. 2014) and a gene coding for a chitinase was investigated (Graça et al. 2016).
The phytometabolomic fingerprinting of consumed actinorhizal plants permitted the identification of a large diversity of the compounds present (Kar et al. 2016). Other focused studies also permitted the screen of molecules found in actinorhizal leaves and fruits of Myrica nagi that have analgesic, cyclooxygenase inhibiting (Middha et al. 2016b) or anti-inflammatory properties (Middha et al. 2016a).
The ecology of actinorhizal plants was another topic and information was presented on these plants and their associated microbes. Besides the global contribution of filaos for the rehabilitation of poor sites in various areas of the world such as China and India (Zhang et al. 2016) and of alder for the same purpose in Canada (Callender et al. 2016), a major focus is the search for salinity-resistant casuarina lineages (Ribeiro-Barros et al. 2016). The underlying mechanisms are also being studied (Mansour et al. 2016; Selvakesavan et al. 2016). As pioneer species, actinorhizal plants are exposed to a wide array of stresses (Ngom et al. 2016b) which have been reviewed along with approches to transform Casuarina genetically (Froussart et al. 2016). The ecology and diversity of strains and Morella hosts in South Africa (Wilcox and Cowan 2016) or Betulaceae hosts in North America (Samant et al. 2016) and Europe (Cotin-Galvan et al. 2016) have been studied in relation to soils. The impact of climate change on alder has also been examined (Tobita et al. 2016).
The participants at the meeting had the opportunity to visit an Agroforestry site managed by INRA colleagues in Restinclières where trees (mostly high-return walnuts, and black alders) are grown in association with cereal crops (Cardinael et al. 2015). This excursion was followed by a visit to the medieval village of St-Guilhem-le-Désert.
We acknowledge the receipt of grants from the Institute of Research for Development (IRD), the Centre National de la Recherche Scientifique (CNRS), the University of Montpellier (UM), the French Ministry of Foreign and European Affairs, the Conseil Régional Languedoc-Roussillon and the Agropolis Foundation for the organization of the 18th Frankia and actinorhizal plants meeting.
- Bose D, Sarkar I, Labar R, Oshone R, Ghazal S, Morris K, Abebe-Akele F, Kelley Thomas W, Tisa LS, Sen A (2016) Comparative genomics of Prauserella sp. Am3, an actinobacterium isolated from root nodules of Alnus nepalensis in India. Symbiosis 70:49–58Google Scholar
- Brooks JM, Benson DR (2016) Comparative metabolomics of root nodules infected with Frankia sp. strains and uninfected roots from Alnus glutinosa and Casuarina cunninghamiana reflects physiological integration. Symbiosis 70:87–96Google Scholar
- Callender KL, Roy S, Khasa DP, Whyte LG, Greer CW (2016) Actinorhizal alder phytostabilization alters microbial community dynamics in gold mine waste rock from Northern Quebec: a greenhouse study. PLoS One 11:e0150181Google Scholar
- Carro L, Pujic P, Alloisio N, Fournier P, Boubakri H, Hay AE, Poly F, Francois P, Hocher V, Mergaert P, Balmand S, Rey M, Heddi A, Normand P (2015) Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia. The ISME journal 9:1723–1733CrossRefPubMedPubMedCentralGoogle Scholar
- Carro L, Persson T, Pujic P, Alloisio N, Fournier P, Boubakri H, Pawlowski K, Normand P (2016a) Organic acids metabolism in Frankia alni. Symbiosis 70:37–48Google Scholar
- Ceremonie H, Debelle F, Fernandez MP (1999) Structural and functional comparison of Frankia root hair deforming factor and rhizobia nod factor. Can J Bot 77:1293–1301Google Scholar
- Chabaud M, Gherbi H, Pirolles E, Vaissayre V, Fournier J, Moukouanga D, Franche C, Bogusz D, Tisa LS, Barker DG, Svistoonoff S (2016) Chitinase-resistant hydrophilic symbiotic factors secreted by Frankia activate both Ca(2+) spiking and NIN gene expression in the actinorhizal plant Casuarina glauca. New Phytol 209:86–93CrossRefPubMedGoogle Scholar
- Diedhiou I, Tromas A, Cissoko M, Gray K, Parizot B, Crabos A, Alloisio N, Fournier P, Carro L, Svistoonoff S, Gherbi H, Hocher V, Diouf D, Laplaze L, Champion A (2014) Identification of potential transcriptional regulators of actinorhizal symbioses in Casuarina glauca and Alnus glutinosa. BMC Plant Biol 14:342CrossRefPubMedPubMedCentralGoogle Scholar
- Froussart E, Zhong C, Jiang Q, Bonneau J, Bogusz D, Franche C (2016) Biotechnological strategies for studying actinorhizal symbiosis in Casuarinaceae: transgenesis and beyond. Symbiosis 70:101–109Google Scholar
- Graça I, Liang J, Guilherme M, Tavares P, Ferreira-Pinto MM, Melo AMP, Ribeiro-Barros AI, Pereira AS (2016) Cloning, overexpression and functional characterization of a class III chitinase from Casuarina glauca nodules. Symbiosis 70:139–148Google Scholar
- Hocher V, Alloisio N, Auguy F, Fournier P, Doumas P, Pujic P, Gherbi H, Queiroux C, Da Silva C, Wincker P, Normand P, Bogusz D. (2011) Transcriptomics of actinorhizal symbioses reveals homologs of the whole common symbiotic signaling cascade. Plant Physiol 156: 700–711Google Scholar
- Kakoi K, Yamaura M, Kamiharai T, Tamari D, Abe M, Uchiumi T, Kucho K (2014) Isolation of mutants of the nitrogen-fixing actinomycete Frankia. Microbes Environ 29:31–37Google Scholar
- Kar P, Dey P, Misra AK, Chaudhuri TK, Sen A (2016) Phytometabolomic fingerprinting of selected actinorhizal fruits popularly consumed in North-East India. Symbiosis 70:159–168Google Scholar
- Kucho K-i, Kamiharai T (2016) Comprehensive identification of 5-methylcytosines in Frankia genomes. Symbiosis 70:31–36Google Scholar
- Mansour SR, Abdel-lateif K, Bogusz D, Franche C (2016) Influence of salt stress on inoculated Casuarina glauca seedlings. Symbiosis 70:129–138Google Scholar
- Mastronunzio JE, Benson DR (2010) Wild nodules can be broken: proteomics of Frankia in field-collected root nodules. Symbiosis 50:13–26Google Scholar
- Middha SK, Usha T, Babu D, Misra AK, Lokesh P, Goyal AK (2016a) Evaluation of antioxidative, analgesic and anti-inflammatory activities of methanolic extract of Myrica nagi leaves - an animal model approach. Symbiosis 70:179–184Google Scholar
- Middha SK, Goyal AK, Bhardwaj A, Kamal R, Lokesh P, Prashanth HP, Wadhwa W, Usha T (2016b) In silico exploration of cyclooxygenase inhibitory activity of natural compounds found in Myrica nagi using GC–MS. Symbiosis 70:169–178Google Scholar
- Ngom M, Diagne N, Laplaze L, Champion A, Sy MO (2016a) Symbiotic ability of diverse Frankia strains on Casuarina glauca plants in hydroponic conditions. Symbiosis 70:79–86Google Scholar
- Ngom M, Oshone R, Diagne N, Cissoko M, Svistoonoff S, Tisa LS, Laplaze L, Sy MO, Champion A (2016b) Tolerance to environmental stress by the nitrogen-fixing actinobacterium Frankia and its role in actinorhizal plants adaptation. Symbiosis 70:17–29Google Scholar
- Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Vanden Heuvel B, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Cruz Hernandez MA, Mendoza Herrera A, Medigue C, Normand P, Pawlowski K, Berry AM (2015) Candidatus Frankia Datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, expresses the canonical nod genes nodABC in Symbiosis with its host plant. PLoS One 10:e0127630CrossRefPubMedPubMedCentralGoogle Scholar
- Persson T, Van Nguyen T, Alloisio N, Pujic P, Berry AM, Normand P, Pawlowski K (2016) The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated? Symbiosis 70:149–157Google Scholar
- Ribeiro-Barros AI, da Costa M, Duro N, Graça I, Batista-Santos P, Jorge TF, Lidon FC, Pawlowski K, António C, Ramalho JC (2016) An integrated approach to understand the mechanisms underlying salt stress tolerance in Casuarina glauca and its relation with nitrogen-fixing Frankia Thr. Symbiosis 70:111–116Google Scholar
- Sarkar I, Normand P, Tisa LS, Gtari M, Bothra A, Sen A (2016) Characterization of PAS domains in Frankia and selected actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis 70:69–78Google Scholar
- Selvakesavan RK, Nair DN, Thushara P, Abraham SM, Jayaraj RSC, Balasubramanian A, Deeparaj B, Sudha S, K. S. Sowmiya Rani, Bachpai VKW, Ganesh D, Diagne N, Laplaze L, Gherbi H, Svistoonoff S, Hocher V, Franche C, Bogusz D, Nambiar-Veetil M (2016) Intraspecies variation in sodium partitioning, potassium and proline accumulation under salt stress in Casuarina equisetifolia Forst. Symbiosis 70:117–127Google Scholar
- Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832Google Scholar
- Thakur S, Sen A (2016) Comparative analysis of metabolic machinery of Frankia along with other selected actinobacteria. Symbiosis 70:59–68Google Scholar
- Tisa LS, Oshone R, Sarkar I, Ktari A, Sen A, Gtari M (2016) Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of Frankia genomes. Symbiosis 70:5–16Google Scholar
- Udwary DW, Gontang EA, Jones AC, Jones CS, Schultz AW, Winter JM, Yang JY, Beauchemin N, Capson TL, Clark BR, Esquenazi E, Eustaquio AS, Freel K, Gerwick L, Gerwick WH, Gonzalez D, Liu WT, Malloy KL, Maloney KN, Nett M, Nunnery JK, Penn K, Prieto-Davo A, Simmons TL, Weitz S, Wilson MC, Tisa LS, Dorrestein PC, Moore BS (2011) Significant natural product biosynthetic potential of actinorhizal symbionts of the genus Frankia, as revealed by comparative genomic and proteomic analyses. Appl Environ Microbiol 77:3617–3625CrossRefPubMedPubMedCentralGoogle Scholar
- Wilcox D, Cowan D (2016) Diversity of Frankia in root nodules of six Morella sp. from the cape flora of South Africa. Plant & Soil 400:123-132Google Scholar