Dr Marike Palmer



Postdoctoral Fellow

Department

Biochemistry, Genetics and Microbiology
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Research Profiles

As a bacterial systematist, I have always been interested in how bacteria adapt to diverse environments and what drives this adaptation. As part of my PhD research we utilised whole genome sequences to obtain a more holistic view of how bacteria evolve. Our main focus was on what processes make bacterial species intrinsically different from one another and how these processes influences our idea of bacterial species.

For my postdoctoral research I will continue to employ comparative and phylogenomic approaches to address a number of taxonomic questions in various bacterial groups. This research will broadly focus on our understanding of subspecies and whether this taxonomic rank can be biologically informative in bacteria, and genome-based species descriptions, particularly in a number of rhizobial groups.

The increased availability of genome sequences provide us with the unique opportunity to investigate divergence and cohesion within and between bacterial populations. This would thus entail identifying bacterial groups based on the evolutionary history of the taxa, followed by investigating the level of cohesion (genomic, phylogenetic and phenotypic) within the identified taxa. By employing this evolution-based approach for bacterial taxonomy we aim to obtain a more natural hierarchy reflective of the clusters of diversity observed in nature. 

Palmer M*, Steenkamp ET, Coetzee MPA, Venter SN. 2018. Bacterial species are sui generis evolutionary units. Fourth Meeting of Bergey’s International Society for Microbial Systematics, Muldersdrift, South Africa, 8-11 April. (oral presentation)


Palmer M*, Steenkamp ET, Coetzee MPA, van Wyk S, McTaggart AR, Avontuur JR, Beukes CW, Fourie G, Santana Q, van der Nest MA, Blom J, Venter SN. 2018. Phylogenomic analyses: the whole is greater than the sum of its parts. Fourth Meeting of Bergey’s International Society for Microbial Systematics, Muldersdrift, South Africa, 8-11 April. (oral presentation)


Palmer M*, Steenkamp ET, Coetzee MPA, Venter SN. 2018. Bacterial species are uniquely evolving entities. South African Society for Microbiology Conference, Muldersdrift, South Africa, 8-11 April. (oral presentation)

 

Avontuur JR*, Beukes CW, Chan WY, Coetzee MPA, Palmer M, Stępkowski T, Venter SN, Steenkamp ET 2018. Genome-informed Bradyrhizobium taxonomy: where to from here? Fourth Meeting of Bergey’s International Society for Microbial Systematics, Muldersdrift, South Africa, 8-11 April. (oral presentation)

 

Venter SN*, Palmer M, Steenkamp ET 2018. What exactly are bacterial subspecies? Fourth Meeting of Bergey’s International Society for Microbial Systematics, Muldersdrift, South Africa, 8-11 April. (oral presentation)


Palmer M*, Steenkamp ET, Coetzee MPA, Coutinho TA, Venter SN. 2016. Genome based phylogenetic analysis to investigate the relationships between the genera Erwinia, Pantoea and Tatumella. Third Meeting of Bergey’s International Society for Microbial Systematics, Pune, India, 12-15 September. (oral presentation)


Du Plessis M, Steenkamp ET, Coetzee MPA, Venter SN*. 2014. Phylo- and comparative genomics of the Pantoea core genome. Second Meeting of Bergey's International Society for Microbial Systematics, Edinburgh, Scotland, 7-10 April. (oral presentation)


Du Plessis M, Steenkamp ET, Coetzee MPA*, Venter SN. 2014.  Phylo- and comparative genomics of the Pantoea core genome. 11th Conference of the Southern African Society for Systematic Biology, Hogsback, South Africa, 6-10 April. (oral presentation)


Du Plessis M*, Steenkamp ET, Coetzee MPA, Coutinho TA, Venter SN. 2013. The evolution of the Pantoea core genome. 18th Biennial Congress of the South African Society for Microbiology, Bela-Bela, South Africa, 24-27 November. (poster presentation)


Du Plessis M*, Steenkamp ET, Coutinho TA, Venter SN. 2012. The validation of genomic approaches for the delineation of species in the genus Pantoea. 10th Meeting of the Southern African Society for Systematic Biology, Arniston, South Africa, 16-19 July. (oral presentation)


Phylo- and comparative genomics Workshop. 2016. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by A Kanzi, M Palmer and W-Y Chan.

Advanced PhylogeneticsWorkshop. 2016. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Phylogenomics Workshop. 2015. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by M Palmer and W-Y Chan.

Advanced PhylogeneticsWorkshop. 2015. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Phylogenomics Workshop. 2014. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by M Palmer and Dr. AJ Potts.

Advanced PhylogeneticsWorkshop. 2014. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Assistant)

Seeing the network for the trees: Phylogenetic Networks Workshop. 2013. Kirstenbosch Research Centre, Cape Town, South Africa. Presented by Dr. GW Grimm and Dr. AJ Potts. (Attendee)

Advanced Phylogenetics Workshop. 2012. Forestry and Agricultural Biotechnology Institute, Pretoria, South Africa. Presented by Dr. MPA Coetzee. (Attendee)

 


News

Fourth FABI Ph.D. success for 2018

FABI celebrated the fourth successful Ph. Marike’s supervisors were Proff Fanus Venter, Emma Steenkamp and Dr Martin Coetzee. The unique nature of bacterial species requires a pluralistic view of evolution.

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Publication
Palmer M, Venter SN, Coetzee MPA, Steenkamp ET. (2018) Prokaryotic species are sui generis evolutionary units. Systematic and Applied Microbiology 10.1016/j.syapm.2018.10.002
Estrada-de los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Bueno dos Reis F, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK. (2018) Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae. Genes 9(8):389. 10.3390/genes9080389
Palmer M, Steenkamp ET, Coetzee MPA, Avontuur JR, Chan WY, Van Zyl E, Blom J, Venter SN. (2018) Mixta gen. nov., a new genus in the Erwiniaceae. International Journal of Systematic and Evolutionary Microbiology 10.1099/ijsem.0.002540
Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. (2018) Genome-based characterization of biological processes that differentiate closely related bacteria. Frontiers in Microbiology 9:113. 10.3389/fmicb.2018.00113 PDF
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(1154) 10.3389/fmicb.2017.01154 PDF
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 110(10):1311-132. 10.1007/s10482-017-0869-8
Palmer M, Steenkamp ET, Coetzee MPA, Chan W-Y, Van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits THM, Duffy B, Venter SN. (2017) Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek 110(10):1287-1309. 10.1007/s10482-017-0852-4
Palmer M, De Maayer P, Poulsen M, Steenkamp ET, Van Zyl E, Coutinho TA, Venter SN. (2016) Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites. Standards in Genomic Sciences 11(23) 10.1186/s40793-016-0144-z PDF
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