BULLETIN 3.04 Crop Production & Biosecurity 2015 RESEARCH FINDINGS in the School of VETERINARY & LIFE SCIENCES WAYNE REEVE, JULIE ARDLEY & RUI TIAN Gene profi ling bugs: A project to sequence 100 bacterial genomes itrogen is needed by all forms of life available form of ammonia within a Creek, California, have spearheaded a Nas it is an essential building block of specialised organ, the nodule (Figure 1). global effort, coordinated by Dr Wayne DNA, RNA and proteins. SNF agricultural inputs are both cheaper Reeve (CRS), to sequence the genomes and more environmentally sustainable. In of over 100 root nodule bacteria strains. Nitrogen is a critical element in plant Australia, the nitrogen fi xed by RNB in The ultimate goal will be to extend this growth, and since the 1950s, the fi ve-fold symbiosis with pasture and pulse legumes symbiosis to other agricultural crops, increase in the input of chemical nitrogen is worth approximately $4 billion annually. including cereals. fertilizers has allowed rapid increases in agricultural production. However, this To meet the challenge of providing Methods and results use of chemical nitrogen has come at a environmentally sustainable increases in The Genomic Encyclopedia of Bacteria and high and environmentally unsustainable food production for the growing world Archaea — Root Nodule Bacteria (GEBA- cost: increased fossil fuel use, emission of population, we need to maximise the RNB) joint venture is the largest-ever root greenhouse gases, environmental pollution, nitrogen-fi xing potential of the legume- nodule bacterial genome sequencing and loss of biodiversity. rhizobia symbiosis, as this can vary project. This joint venture has been signifi cantly (Figure 2). To understand Nitrogen can also be supplied by symbiotic established between the CRS and the JGI, the genetic basis of RNB symbiotic nitrogen fi xation (SNF), where root nodule along with thirty scientists from fi fteen compatibility, researchers at Murdoch bacteria (RNB), in association with their countries across the globe. University’s Centre for Rhizobium Studies legume hosts, take inert atmospheric (CRS) and the Department of Energy nitrogen and reduce it to the biologically Joint Genome Institute (JGI) in Walnut FIGURE 1 Nodules on the pasture legume FIGURE 2 An illustration of the difference in nitrogen-fi xing capacity of three Rhizobium Medicago polymorpha inoculated with the leguminosarum bv. trifolii strains (WU95, WSM409 and WSM1325) on four annual clover species sequenced root nodule bacterial strain WSM419 (Trifolium vesiculosum, T. dasyurum, T. isthmocarpum and T. spumosum) A series of bulletins outlining key research in the School of Veterinary & Life Sciences | 2015 The sequenced bacterial strains belong novel species that have been named and Conclusions and recommendations to nine of the 16 validly described RNB described by the CRS team (Figure 4). In This sequencing data is being used genera and have been isolated from 69 total the GEBA-RNB Project has generated to identify genes and gene products different legume species, growing in twice the amount of sequence information that are required for i) nodulation and diverse countries and environments across as the human genome sequencing project, nitrogen fi xation with host legumes; ii) the globe (Figure 3). The sequenced and has resulted in the publication of over survival in a range of different soils and RNB include elite inoculant strains of 40 papers in the last two years. climates; iii) diagnostic tests to identify high commercial importance as well as and type different RNB strains in the fi eld. Signifi cantly, this work has identifi ed various protein signatures that are uniquely found within the RNB and not within related non-symbiotic bacteria. In a major research project, we are identifying the symbiotic role of these proteins. I More information Contact Wayne Reeve E: [email protected] Acknowledgements This work was performed under the auspices of the US Department of Energy Offi ce of Science, Biological and FIGURE 3 Map showing the location of isolation of root nodule bacteria strains in the GEBA- Environmental Research Program, and RNB sequencing project. Color codes are as follows: Alphaproteobacteria (tags); Azorhizobium by the University of California, Lawrence (yellow), Bradyrhizobium (green), Ensifer (red), Mesorhizobium (light blue), Methylobacterium Berkeley National Laboratory under (purple), Microvirga (orange), Rhizobium (blue) and Betaproteobacteria (circles); Burkholderia (yellow), Cupriavidus (blue) contract No. DE-AC02-05CH11231. References 1 Reeve, W.G., Ardley, J.K., Tian, R., Eshragi, L., Yoon, J.W., Ngamwisetkun, P., Seshadri, R., Ivanova, N.N., and Kyrpides, N.C. (2015) A genomic encyclopedia of the root nodule bacteria: Assessing genetic diversity through a systematic biogeographic survey. Standards in Genomic Sciences 10–14. 2 Ziegler, D., Pothier, J., Ardley, J., Fossou, R.K., Pfl üger, V., De Meyer, S., Vogel, G., Tonolla, M., Howieson, J., Reeve, W., and Perret, X. (2015) Ribosomal protein biomarkers provide root nodule bacterial identifi cation by MALDI-TOF MS. Applied Microbiology and Biotechnology 99 (13) 5547–62. 3 Ardley, J.K., Parker, M.A., De Meyer, S.E., Trengove, R.D., O’Hara, G.W., Reeve, W.G., Yates, R.J., Dilworth, M.J., Willems, A., and Howieson, J.G. (2012). Microvirga lupini sp. nov., Microvirga lotononidis sp. nov., and Microvirga zambiensis sp. nov. are Alphaproteobacterial root nodule bacteria that specifi cally nodulate and fi x nitrogen with geographically and taxonomically separate legume hosts. International Journal of Systematic and Evolutionary FIGURE 4 Fotofl exer-edited transmission electron microscope micrograph of the sequenced novel Microbiology 62 (11) 2579–2588. rhizobial strain Microvirga lotononidis WSM3557 If you are interested in our research and would like to know more, then please contact us on [email protected] Our research bulletins can be downloaded from www.murdoch.edu.au/School-of-Veterinary-and-Life-Sciences/Our-research/Our-Bulletins/ Undergraduate or postgraduate degrees, please see www.murdoch.edu.au/School-of-Veterinary-and-Life-Sciences/Our-courses/ CRICOS Code: 00125J A series of bulletins outlining key research in the School of Veterinary & Life Sciences | 2015.