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PhD student

Department

Microbiology and Plant Pathology
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Primary Supervisor
Emma Steenkamp

Co Supervisor
Fanus Venter

The focus of my research is to identify, characterise and study the evolution of a special group of soil bacteria. These bacteria (informally referred as rhizobia) can enter into a symbiotic interaction with legumes, where they fix atmospheric nitrogen for the plant and receive photosynthetic products in return. The most obvious result of the interaction is the formation of nodules on the roots of the plants and in some instances also on the stem.

 

In South Africa we have a large diversity of legumes, the most well-known of which is most probably rooibos tea (Aspalathus linearis). For the most part the identity of the rhizobia associated with our indigenous legumes are unknown, this could prove problematic as it has been discovered that it is possible for the rhizobia of invasive legumes to disrupt an indigenous interaction thereby providing the invasive legume with a competitive edge. If we ever needed to someday replace the indigenous rhizobia of 'our' legumes, we would of course need to know who they are and the conditions in which they function optimally. There is also always the possibility that these newly identified rhizobia could prove to be better inoculum for legume crops. My study therefore forms part of the scope of the DST/NRF Centre of Excellence in Tree Health Biotechnology.

 

Whereas my MSc study investigated the rhizobia associated with the tribes Hypocalypteae and Podalyrieae, my current study investigates the rhizobial partners of members of the tribes Crotalarieae and Genisteae. I also hope to include work on the association between nodulating members of the bacterial genera Bradyrhizobium, Methylobacterium and Burkholderia.    

 

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Publication
Beukes CW, Palmer M, Manyaka P, Chan W-Y, Avontuur JR, Van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers in Microbiology 8 10.3389/fmicb.2017.01154
Venter SN, Palmer M, Beukes CW, Chan W-Y, Shin G, Van Zyl E, Seale T, Coutinho TA, Steenkamp ET. (2017) Practically delineating bacterial species with genealogical concordance. Antonie van Leeuwenhoek 10.1007/s10482-017-0869-8
Beukes CW, Stepkowski T, Venter SN, Clapa T, Phalane FL, le Roux MM, Steenkamp ET. (2016) Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci. Molecular Phylogenetics and Evolution 100:206-218. 10.1016/j.ympev.2016.04.011
Steenkamp ET, van Zyl E, Beukes CW, Avontuur J, Chan W-Y, Palmer M, Mthombeni LS, Phalane FL, Sereme TK, Venter SN. (2015) Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa. Systematic and Applied Microbiology 38(8):545-554. 10.1016/j.syapm.2015.09.003
Beukes CW, Venter SN, Law IJ, Phalane FL, Steenkamp ET. (2013) South African papilionoid legumes are nodulated by diverse Burkholderia with unique nodulation and nitrogen-fixation loci. PLos ONE 8(7):e68406. 10.1371/journal.pone.0068406 PMCID: PMC3708930 PDF
Wingfield BD, Steenkamp ET, Santana QC, Coetzee MPA, Bam S, Barnes I, Beukes CW, Chane W-Y, de Vos L, Fourie G, Friend M, Gordon TR, Herron DA, Holt C, Korf I, Kvas M, Martin SH, Mlonyeni XO, Naidoo K, Phasha MM, Postma A, Reva O, Roos H, Simpson M, Slinski S, Slippers B, Sutherland R, van der Merwe NA, van der Nest MA, Venter SNV, Wilken PM, Yandell M, Zipfel R, Wingfield MJ. (2012) First fungal genome sequence from Africa: a preliminary analysis. South African Journal of Science 108:104-122. 10.4102/sajs.v108i1/2.537 PDF