This research programme focuses on bacterial diseases of trees, both plantation and native tree species and to a lesser extent, fruit trees. We have two major research focuses – one on taxonomy and the other on pathogenicity factors exhibited by a select group of pathogens. The taxonomic research involves identifying new species using modern approaches, mainly in the Enterobacteriaceae. The majority of bacteria we have identified thus far have been opportunistic plant pathogens whilst others have been associated with plants as endophytes. This has led to a number of studies where we have attempted to understand how these opportunists can function as successful plant pathogens despite the fact that they occur in other ecological niches which are often diverse, such as in diesel fuel.

Our interest has primarily been on Pantoea ananatis and related Pantoea species, although we do have research projects on Xanthomonas spp. and Ralstonia solanacearum. P. ananatis is responsible for bacterial blight and die-back of Eucalyptus, brown stalk rot of maize and occurs on onion seed in South Africa. Our studies have centred on taxonomy and on developing rapid and reliable methods of distinguishing between the species of Pantoea. We are now expanding this research and are using a phylogenomic approach to examine this genus. Other elements currently under investigation include understanding the epidemiology and biology of primarily P. ananatis, but this has been expanded to include the other pathogens mentioned above as well. We have identified a number of pathogenicity factors in P. ananatis and this has given us some insight into its life as a phytopathogen. The approach we have used has involved both comparative and functional genomics. The pathogenicity factors investigated have included motility, Type VI secretion system, quorum sensing and exopolysaccharide production.

New Publications

Siphathele Sibanda, Stanford Kwenda, Collins K. Tanui, Divine Shyntum, Teresa Coutinho, Lucy Moleleki. (2018) Transcriptome profiling reveals the EanI/R quorum sensing regulon in Pantoea ananatis LMG 2665T. Genes 9(3):148. 10.3390/genes9030148
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 68:1396-1407. 10.1099/ijsem.0.002540
Siphathele Sibanda, Lucy Moleleki, Divine Shyntum, Teresa Coutinho. 2018. Quorum Sensing in Gram-Negative Plant Pathogenic Bacteria. In: Advances in Plant Pathology. Intechopen., London SE1 9SG, United Kingdom, pp 67-89.
Otto M, Petersen Y, Roux J, Wright J, Courtinho. (2018) Bacterial canker of cherry trees, Prunus avium, in South Africa. European Journal of Plant Pathology 151:427-438. 10.1007/s10658-017-1384-5
De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. (2017) Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers in Microbiology 8(1755) 10.3389/fmicb.2017.01755
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
Weller-Stuart T, De Maayer P, Coutinho T. (2017) Pantoea ananatis: genomic insights into a versatile pathogen. Molecular Plant Pathology 18(9):1191-1198. 10.1111/mpp.12517
Nesamari R, Coutinho TA, Roux J. (2017) Investigations into Encephalartos insect pests and diseases in South Africa identifies Phytophthora cinnamomi as a pathogen of the Modjadji cycad. Plant Pathology 66(4):612-622. 10.1111/ppa.12619
Weller-Stuart T, Toth I, De Maayer P, Coutinho T. (2017) Swimming and twitching motility are essential for attachment and virulence of Pantoea ananatis in onion seedlings. Molecular Plant Pathology 18(5):734-745. 10.1111/mpp.12432
Breedt G, Coutinho TA, Labuschagne N. (2017) Seed treatment with selected plant growth promoting rhizobacteria increases maize yield in the field. Annals of Applied Biology 171:229-236.
Moloto V, Goszczynska T, du Toit L, Coutinho TA. (2017) A new pathovar of Pseudomonas syringae, pathovar allii, isolated from onion plants exhibiting symptoms of blight. European Journal of Plant Pathology 147:591-603.
Zimudzi J, Coutinho TA, van der Waals J. (2017) Pathogenicity of fungi isolated from atypical skin blemishes on potatoes in South Africa and Zimbabwe. Potato Research 60:119-144.
Kwenda S, Motlolometsi TV, Birch PRJ, Moleleki LN. (2016) RNA-seq profiling reveals defense responses in a tolerant potato cultivar to stem infection by Pectobacterium carotovorum ssp. brasiliense. Frontiers in Plant Science 7(1905) 10.3389/fpls.2016.01905
Kwenda S, Birch PRJ, Moleleki LN. (2016) Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC Genomics 17(614) 10.1186/s12864-016-2967-9
Carstensen GD, Venter SN, Wingfield MJ, Coutinho TA. (2016) Two Ralstonia species associated with bacterial wilt of Eucalyptus. Plant Pathology 66:393-403. 10.1111/ppa.12577
Sibanda S, Theron J, Shyntum DY, Moleleki LN, Coutinho TA. (2016) Characterization of two LuxI/R homologs in Pantoea ananatis LMG 2665 T. Canadian Journal of Microbiology 62(11):893-903. 10.1139/cjm-2016-0143
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
Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PRJ, Moleleki LN. (2016) Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum. BMC Genomics 17(1) 10.1186/s12864-016-2376-0
du Raan S, Coutinho TA, van der Waals JE. (2015) Cardinal temperature differences, determined in vitro, between closely related species and subspecies of pectinolytic bacteria responsible for blackleg and soft rot on potatoes. European Journal of Plant Pathology 144(2):361-369. 10.1007/s10658-015-0773-x
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
De Maayer P, Chan W-Y, Martin DAJ , Blom J, Venter SN, Duffy B, Cowan DA, Smits THM, Coutinho TA. (2015) Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Frontiers in Microbiology 6:576. 10.3389/fmicb.2015.00576
Nesamari R, Millar IM, Coutinho TA, Roux J. (2015) South African cycads at risk: Aulacaspis yasumatsui (Hemiptera: Coccoidea: Diaspididae) in South Africa. African Entomology 23(1):198-206.
Shyntum D, Theron J, Moleleki L, Toth I, Venter SN, Coutinho TA. (2015) Pantoea ananatis utilizes a type VI secretion system for pathogenesis and bacterial competition. Molecular Plant-Microbe Interactions 28(4):420-431. 10.1094/MPMI-07-14-0219-R
Coutinho TA, van der Westhuizen L, Roux J, McFarlane SA, Venter SN. (2015) Significant host jump of Xanthomonas vasicola from sugarcane to a Eucalyptus grandis clone in South Africa. Plant Pathology 64(3):576-581. 10.1111/ppa.12298
Weller-Stuart T, Chan W-Y, Coutinho TA, Venter SN, Smits THM, Duffy B, Goszczynska T, Cowan DA, de Maayer P. (2014) Draft genome sequences of the onion center rot pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442. Genome Announcements 2(4) e00750-14
De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PR, Coutinho TA. (2014) Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genomics 15:404. 10.1186/1471-2164-15-404 PDF
Ngadze E, Coutinho TA, Icishahayo D, van der Waals JE. (2014) Effect of calcium soil amendments on phenolic compounds and soft rot resistance in potato tubers. Crop Protection 62:40-45. 10.1016/j.cropro.2014.04.009
Mitchell RG, Wingfield MJ, Steenkamp ET, Roux J, Verryn S, Coutinho TA. (2014) Comparison of the tolerance of Pinus patula seedlings and established trees to infection by Fusarium circinatum. Southern Forests 76(3):151-159. 10.2989/20702620.2014.899061 PDF
Shyntum DY, Venter SN, Moleleki LN, Toth I, Coutinho TA. (2014) Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments. BMC Genomics 15:163. 10.1186/1471-2164-15-163
Steenkamp ET, Makhari OM, Coutinho TA, Wingfield BD, Wingfield MJ. (2014) Evidence for a new introduction of the pitch canker fungus Fusarium circinatum in South Africa. Plant Pathology 63(3):530-538. 10.1111/ppa.12136 PDF
Bull CT, Coutinho TA, Denny TP, Firrao G, Fischer-Le Saux M, Li X, Saddler GS, Scortichini M, Stead DE, Takikawa Y. (2014) List of new names of plant pathogenic bacteria (2011-2012). Journal of Plant Pathology 96(2):223-226. 10.4454/JPP.V96I2.026 PDF
Reva ON, Chan WY, Benzuidt OKI, Lapa SV, Safronova LA, Avdeeva LV, Borriss R. 2014. Genetic barcoding of bacteria and its microbiological and biotechnological applications. In: Bioinformatics and Data Analysis in Microbiology. Bishop OT. (eds). Caister Academic Press, Norfolk, pp 231-245.
Roux J, Greyling I, Coutinho TA, Verleur M, Wingfield MJ. (2013) The Myrtle rust pathogen, Puccinia psidii, discovered in Africa. IMA Fungus 4:155-159. 10.5598/imafungus.2013.04.01.14 PDF
Chan WY, Dietel K, Lapa SV, Avdeeva LV, Borriss R, Reva ON. (2013) Draft genome sequence of Bacillus atrophaeus UCMB-5137, a plant-growth-promoting rhizobacterium. Genome Announcements 1(3):1-2. 10.1128/genomeA.00233-13 PDF
Kubheka GC, Coutinho T, Moleleki N, Moleleki LN. (2013) Colonisation patterns of a mCherry-tagged Pectobacterium carotovorum subsp. brasiliense in potato. Phytopathology 103(12):1269-1279. 10.1094/PHYTO-02-13-0049-R
Le Roux WJ, Chan WY, De Maayer P, De Maayer P, Venter SN. (2013) Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate. Genome Announcements 1(2):1-2. 10.1128/genomeA.00040-13 PDF
Mitchell RG, Wingfield MJ, Hodge GR, Dvorak WS, Coutinho TA. (2013) Susceptibility of provenances and families of Pinus maximinoi and Pinus tecunumanii to frost in South Africa. New Forests 44:135-146. 10.1007/s11056-012-9306-z PDF
Mitchell RG, Wingfield MJ, Hodge GR, Steenkamp ET, Coutinho TA. (2013) The tolerance of Pinus patula × Pinus tecunumanii, and other pine hybrids, to Fusarium circinatum in greenhouse trials. New Forests 44:443-456. 10.1007/s11056-012-9355-3 PDF
Amy Charkowski, Sylvie Reverchon, Pablo Rodr´ıguez Palenzuela, Michael San Francisco, Ian Toth, Shinji Tsuyumu, Jacquie van der Waals, Jan van der Wolf, Fr´ed´erique Van Gijsegem, Ching-Hong Yang, Nicole Perna, Andrew Pitman, Minna Pirhonen, Carlos Blanco, Guy Condemine, Dominique Expert, Thierry Franza, Christopher Hayes, Nicole Hugouvieux-Cotte-Pattat, Emilia L´ opez Solanilla, David Low, Lucy Moleleki, Iris Yedidia. (2012) The role of secretion systems and small molecules in soft rot Enterobacteriaceae pathogenicity. Annual Review of Phyotopathology 50:425-49. 10.1146/annurev-phyto-081211-173013
De Maayer P, Chan WY, Blom J, Venter SN, Duffy B, Smits THM, Coutinho TA. (2012) The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. BMC Genomics 13(625):1-12. 10.1186/1471-2164-13-625 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
De Maayer P, Chan WY, Rezzonico F, Buhlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits THM, Duffy B, Coutinho TA. (2012) Complete Genome Sequence of Clinical Isolate Pantoea ananatis LMG 5342. Journal of Bacteriology 194(6):1615-1616. 10.1128/JB.06715-11 PDF
Mitchell RG, Wingfield MJ, Hodge GR, Steenkamp ET, Coutinho TA. (2012) Selection of Pinus spp. in South Africa for tolerance to infection by the pitch canker fungus. New Forests 43:473-489. 10.1007/s11056-011-9293-5 PDF
Mitchell RG, Coutinho TA, Steenkamp E, Herbert M, Wingfield MJ. (2012) Future outlook for Pinus patula in South Africa in the presence of the pitch canker fungus (Fusarium circinatum). Southern Forests 74:203-210. 10.2989/20702620.2012.741792 PDF
Mitchell RG, Wingfield MJ, Steenkamp ET, Coutinho TA. (2012) Tolerance of Pinus patula full-sib families to Fusarium circinatum in a greenhouse study. Southern Forests 74:247-252. 10.2989/20702620.2012.741788 PDF
Coutinho TA, Brady CL, Vaart MVD, Venter SN, Telechea N, Rolfo M, Perez C, Wingfield MJ. (2011) A new shoot and stem disease of Eucalyptus species caused by Erwinia psidii. Australasian Plant Pathology 40(1):55-60. 10.1007/s13313-010-0013-y PDF
Mitchell RG, Steenkamp ET, Coutinho TA, Wingfield MJ. (2011) The pitch canker fungus, Fusarium circinatum: Implications for South African forestry. Southern Forests 73(1):1-13. 10.2989/20702620.2011.574828 PDF
De Maayer P, Chan WY, Venter SN, Toth IK, Birch PRJ, Joubert F, Coutinho TA. (2010) Genome Sequence of Pantoea ananatis LMG20103, the Causative Agent of Eucalyptus Blight and Dieback. Journal of Bacteriology 192(11):2936-2937. 10.1128/JB.00060-10 PDF