BOOK CHAPTERS
1. Cowan, DA, Ah Tow, L, Smith, JJ, Cary, C, Moodley, K. (2005) Microbial molecular ecology of Antarctic mineral soil biotopes. In Antarctica; Global Laboratory for Scientific and International Collaboration, A. Tan, Z Yasin, M Mansor, eds., Academy of Sciences Malaysia, Kuala Lumpur, pp. 113-118.
2. Sjöling, S. Stafford, W, Cowan, DA (2006) Soil metagenomics: Exploring and exploiting the soil microbial gene pool. Ch. 16 in Modern Soil Microbiology, 2nd Edn. van Elsas, JD, Jansson, J, Trevors, JT, Eds., CRC Press, Taylor & Francis, pp. 241 – 266.
3. Russell, NR and Cowan, DA. (2006) Methods for the handling of psychrophiles microorganisms. Ch. in Methods in Microbiology. Vol. 35, Oren, A, & Rainey, F, eds. 838pp. [ISBN 978-0-12-521537-4].
4. Cowan, DA, Casanueva, A, Stafford, W. (2007) Ecology and biodiversity of cold-adapted organisms. Ch. 9 in Physiology and Biochemistry of Extremophiles. Gerday, C., Glansdorff, N., eds. ASM Press, Washington DC, pp. 119-133.
5. Cowan, DA and Stafford, W. (2007) Metagenomic methods for determining active microorganisms and genes in bioremediation and biotransformation processes. Ch. 58 in ASM Manual of Environmental Microbiology, 3rd Edition. Editors: CJ Hurst, RL. Crawford, JL. Garland, DA Lipson, AL Mills, LD Stetzenbach. Eds., 1310 pp. ISBN: 978-1-55581-379-6
6. Daniel, R.M., Danson, M.J., Hough, D.W., Lee, C.K., Peterson, M.E. and Cowan, D.A. (2007) Enzyme stability and activity at high temperatures. Ch. 17 in Anatomy & Physiology of Extremophilic Proteins, Pub Nova Science, Eds. Thomas, T, Sidiqui, S. In Press
7. Sjoling, S, Cowan, DA. (2008) Metagenomics – microbial community genomes revealed. Ch. 20 in Psychrophiles: from Biodiversity to Biotechnology. Margesin, R.; Schinner, F.; Marx, J.-C.; Gerday, C. (Eds.) 462 pp. ISBN: 978-3-540-74334-7
8. Berjak, P, Cowan, DA, Cowling, R, Pammenter N, Scholes, R. (2009) Biological Sciences. Ch. 5 in Research in South Africa. TWAS Publication.
9. Kirby, BM, Vengadajellum, CJ, Burton, SG, Cowan, DA. (2010) Anthropogenically-created habitats – coal, coal mines and spoil heaps. In: Timmis, Kenneth N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology, Springer Heidelberg, Vol 3, pp. 2277-2292
10. Cowan, DA, Tuffin, IM, Robb, F. (2010) ‘‘Sequence First, Ask Questions Later’’: The Impact of Next Generation-Omics on the Discovery of Novel Microbial and Lipid Hydrocarbon Metabolism. In: Timmis, Kenneth N. (Ed.) Handbook of Hydrocarbon and Lipid Microbiology, Springer Heidelberg, Vol 4, pp. 3367-3374
11. Cowan, DA, Khan, N*, Heath, C, Mutondo, M. (2010) Microbiology of Antarctic terrestrial soils and rocks. Ch. 1 in Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments. Atlas, R, Aislabie, J, Bej, A, Eds. CRC Press, pp. 1-30
12. Bauer, R, Mutondo, M, Huddy, RJ, Tuffin, IM, Cowan, DA. (2011) Metagenomic gene discovery. Ch. 15 in Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies. RW Li, Ed. Nova Science Publ. pp. 287-320.
13. Meiring, TL, Bauer, R, Scheepers, I, Ohloff, C, Tuffin, IM, Cowan, DA. (2011) Metagenomics and beyond: current approaches and integration with complementary technologies. Ch. 1 in Metagenomics: Current Innovations and Future Trends. Marco, D., Ed., Horizon Press, pp. 1 – 19.
14. Taylor, MP, Van Zyl, L, Tuffin, M, Cowan, DA. (2011) Extremophiles and biotechnology: How far have we come? Ch. 1. In Extremophiles: Microbiology and Biotechnology. Anitori, RP, ed. Caister Academic Press, Norwich, pp. 1-23
15. Grant, WD, Pagaling, E, Marquez, C, Gutierrez, C, Cowan, DA, Ma, Y, Jones, BE, Ventosa, A, Heaphy, S. (2011) The Hypersaline Lakes of Inner Mongolia. Ch. 4 in Halophiles and Hypersaline Environments, A. Ventosa et al. (eds.), Springer-Verlag Berlin, pp. 65-107.
16. Kirby, BM, Le Roes-Hill, M, Cary, SC, Burton, SG, Tuffin, IM, Cowan, DA. (2011) Actinobacterial diversity associated with Antarctic Dry Valley mineral soils. Ch. 13 in Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, Frans J. de Bruijn, Ed., John Wiley & Sons, New Jersey. ISBN 978-0-470-64719-6
18. Taylor, MT, Ramond, J-B, Tuffin, IM, Burton, SG, Eley, K, Cowan, DA. (2011) Mechanisms and Applications of Microbial Solvent Tolerance. Ch. 6 in Microbial stress tolerance for biofuels: systems biology. L. Liu, Ed., Springer, London. pp. 177-208
19. Kirby, BM, Barnard, D, Tuffin, IM, Cowan, DA. (2011) Ecological distribution of microorganisms in terrestrial, psychrophilic habitats. In: Extremophiles Handbook., Horikoshi, K.; Antranikian, G.; Bull, A.T.; Robb, F.T.; Stetter, K.O. (Eds.) pp. 839-859.
20. Kirby, BM, Easton, S, Tuffin, IM, Cowan, DA. (2012) Bacterial Diversity in Polar Habitats. Ch. in Polar Microbiology: Life in a deep freeze. Miller, RV, Whyte, LG., Eds. ASM Press. ISBN 978-1-55581-604-9. 312pp.
21. Cowan, D., Tuffin, M., Mulako, I., Cass, J. (2012) Life in Terrestrial Hydrothermal Environments. Ch. in Life in Extremes, Bell, E., Ed., CABI Press. 576 pp. ISBN 978 1 84593 814 7
22. Taylor, MP, Bauer, R, Mackay, S, Tuffin, IM, Cowan, DA. (2012) Extremophiles and their application to biofuel research. In: Sustainable Resources and Biotechnological Implications. OV Singh, Ed, Wiley.
23. Smart M, Huddy RJ, Cowan DA, Trindade M (2017) Liquid Phase Multiplex High-Throughput Screening of Metagenomic Libraries Using p-Nitrophenyl-Linked Substrates for Accessory Lignocellulosic Enzymes. In: Metagenomics: Methods and Protocols, Methods in Molecular Biology. Wolfgang R. Streit and Rolf Daniel (eds.), doi: 10.1007/978-1-4939-6691-2_13
24. Williams W, Trindade M (2017) Metagenomics for the discovery of novel biosurfactants. In: Functional Metagenomics: Tools and Applications. T. Charles (Ed.). Springer. doi: 10.1007/978-3-319-61510-3
25. Mhlongo J, Beukes D, Trindade M (2017) Endosymbiotic Bacteria Isolated from Algoa and Kalk Bay, South Africa, as Source of Antimicrobial Compounds. Ch 20 In Proceedings of The International Conference on Pure and Applied Chemistry 2016. Ramasami P. et al (eds). Springer
26. Cowan DA, Adriaenssens E, Pieter De Maayer P, Lebre P, Makhalanyane TP, Ramond J-B, Trindade IM, Valverde A, Vikram S. (2019) Metagenomics of Extreme Environments: Methods and Applications. Chapter 5, In: Advanced Techniques for Studying Microorganisms in Extreme Environments, E Yergeau, Ed. De Gruyter. Pp.93-116. ISBN 978-3-11-052578-6
27. Trindade M, Sithole N, Kubicki S, Thies S, Burger A (2021) Screening Strategies for Biosurfactant Discovery. Adv. Biochem. Eng. Biotechnol. doi: 10.1007/10_2021_174
28. van Zyl, L.J., Alvarez, L.M., Trindade, M. (2022) Journey of a Thousand Miles: The Evolution of Our Understanding of Viruses in Hot Deserts. In: Ramond, JB., Cowan, D.A. (eds) Microbiology of Hot Deserts. Ecological Studies, vol 244. Springer, Cham. https://doi.org/10.1007/978-3-030-98415-1_6
PAPERS
1. Meyer, QC, Burton, SB, Cowan, DA (2007) Subtractive hybridization magnetic bead capture: A new technique for the recovery of full length ORFs from the metagenome. Biotechnol. J. 2:36-40
2. Makhongela, HS, Glowacka, A, Agarkar, VB, Sewell, BT, Weber, B, Cameron, RA, Cowan, DA and Burton, SG. (2007) A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity. Appl. Microbiol. Biotechnol. 75:801-811.
3. Márquez, C, Carrasco, IJ, Xue, Y, Ma, Y, Cowan, DA, Jones, BE, Grant WD, Ventosa, A. (2007) Aquisalimonas asiatica gen. nov., sp. nov., a moderately halophilic bacterium isolated from an alkaline, saline lake in Inner Mongolia, China. Int. J. System. Evol. Microbiol. 57:1137-1142.
4. Castillo, AM, Gutierrez, MC, Kamekura, K, Ma, Y, Cowan, DA, Jones, BE, Grant WD, Ventosa, A. (2007) Halovivax ruber sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China. Int. J. System. Evol. Microbiol. 57:1024-1027.
5. Olaniran, AO, Stafford, WHL, Cowan, DA, Pillay, D, Pillay, B. (2007) Microbial community profiling in cis- and trans-dichloroethene enrichment systems using denaturing gradient gel electrophoresis. J. Microb. Biotechnol. 17:560-570.
6. Rashamuse, KJ, Burton, SG, Stafford, W, Cowan, DA. (2007) Molecular characterization of a novel family VIII esterase from Burkholdaria multivorans UWC10. J. Mol. Microbiol. Biotechnol. 13:181-188
7. Gutiérrez, MC, Castillo, AM, Kamekura, M, Xue, Y, Ma, Y, Cowan, DA, Jones, BE, Grant, WD, Ventosa, A. (2007) Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake in Inner Mongolia, China. Int. J. System. Evol. Microbiol. 57:1402-1407.
8. Silva-Stenico, E, Vengadajellum, CJ, Janjua, HJ, Harrison, STL, Burton,SG, Cowan, DA. (2007) Degradation of low rank coal by Trichoderma atroviride ES11. J. Indust. Microbiol. Biotechnol. 34:625-631.
9. Pagaling, E., Haigh, R., Grant, WD, Cowan, DA, Jones, B., Ma, Y., Ventosa A., Shaun Heaphy. (2007) Sequence analysis of an archaeal virus isolated from a hypersaline lake in Inner Mongolia, China. BMC Genomics, 8:410-416
10. Carrasco, IJ, Márquez, MC, Xue, Y, Ma, Y, Cowan, DA, Jones, BE, Grant, WD, Ventosa, A. (2007) Bacillus chagannorensis sp. nov., a moderate halophile from a soda lake in Inner Mongolia, China. Int. J. System. Evol. Microbiol. 57:2084-2088.
11. Carrasco, IJ, Márquez, MC, Xue, Y, Ma, Y, Cowan, DA, Jones, BE, Grant, WD, Ventosa, A. (2007) Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda lake sediment. Int. J. System. Evol. Microbiol. 57: 2381-2386.
12. Rashamuse, KJ, Burton, SG, Cowan, DA. (2007) A novel recombinant ethyl ferulate esterase from Burkholdaria multivorans. J Appl. Microbiol. 103:1610-1620.
13. Carrasco, IJ, Márquez, MC, Xue, Y, Ma, Y, Cowan, DA, Jones, BE, Grant, WD, Ventosa, A. (2007) Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China. Int. J. System. Evol. Microbiol. 57:2538-2542.
14. Kimani, SW, Agarkar, VB, Cowan, DA, Sayed, MF-R, Sewell, BT. (2007) The crystal structure of an aliphatic amidase from Geobacillus pallidus RAPc8: evidence for a fourth nitrilase catalytic residue. Acta Cryst. D. 63:1048-1058.
15. Cowan, DA, Casanueva, A. (2007) Stability of ATP in Antarctic desert soils. Polar Biology, 30:1599-1603.
16. Porter, D., Roychoudhury, AN, Cowan, DA. (2007) Dissimilatory sulphate reduction in hypersaline coastal pans: Part 1. Activity across a salinity gradient. Geochim Cosmochim. Acta. 71:5102-5116
17. Wood SA, Rueckert A, Cowan DA, Cary SC. (2008) Aquatic cyanobacteria, important contributors to edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica? ISME J. 2:308-320
18. Oboirien, BO, Burton, SG, Cowan, DA, Harrison, STL. (2008) The effect of the particulate phase on coal biosolubilisation mediated by Trichoderma atroviride in a slurry bioreactor. Fuel Processing Technology. 89:123-130.
19. Babalola, OO, Kirby, BM, Le Roes-Hill, M, Cook, AE, Cary, SC, Burton, SG, Cowan, DA. (2009) Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils. Envir. Microbiol. 11:566-576
20. le Roes-Hill, M, Rohland, J, Meyers, PR, Cowan, DA, Burton, SG. (2009) Streptomyces hypolithicus sp. nov., a novel streptomycete isolated from a hypolith community, Antarctica. Int. J. System. Evol. Microbiol. 59:2033-2036
21. Taylor, M, Eley, K, Martin, S, Tuffin, IM, Burton, SG, Cowan DA (2009) Thermophilic ethanologenesis. Future prospects for second generation ethanol production. Trends Biotechnol. 27:398-405
22. Ruiz Sebastián, C, Sink, KJ, McClanahan, TR, Cowan, DA (2009) Bleaching response of corals and their Symbiodinium communities in southern Africa. Marine Biology doi: 10.1007/s00227-009-1236-8
23. Heath, C, Hu*, XP, Cary, SC, Cowan, DA. (2009) Isolation and characterisation of a novel, low-temperature-active alkaliphilic esterase from an Antarctic desert soil metagenome. Appl. Environ. Microbiol. 75:4657-4659
24. Pagaling, E, Wang, H, Venables, M, Wallace, A, Grant, WD, Cowan, DA, Jones, BE, Ma, Y, Ventosa, A, Heaphy, S. (2009) Microbial biogeography of six salt lakes in Inner Mongolia and one salt lake in Argentina. Appl. Environ. Microbiol. 75:5750-5760
25. Tuffin, IM, Anderson*, D, Heath, C, Cowan, DA (2009) Metagenomic gene discovery: How far have we moved in sequence space? Biotechnol. J. 4:1671-1683.
26. Cowan, DA (2009) Cryptic microbial communities in Antarctic deserts. Proc. Natl. Acad. Sci, USA. 106:19749-19750
27. Cowan, DA, Tuffin, IM (2009) Capturing global metabolism. Nature Biotechnol. 27:1132-1133
28. Wong FK, Lau MC, Lacap DC, Aitchison JC, Cowan DA, Pointing SB (2009) Endolithic Microbial Colonization of Limestone in a High-altitude Arid Environment. Microb. Ecol. 59: 689-99. doi: 10.1007/s00248-009-9607-8
29. Cary, SC, McDonald, I, Barrett, JE and Cowan, DA. (2010) On the rocks: Microbial ecology of Antarctic cold desert soils. Nature Rev. Microbiol. 8:129-138.
30. Wong FK, Lau MC, Lacap DC, Aitchison JC, Cowan DA, Pointing SB (2010) Endolithic microbial colonization of limestone in a high-altitude arid environment. Microb. Ecol. 59:689-699
31. Wong, FKY, Lacap, DC, Lau, MCY, Aitchison, JC, Cowan, DA, Pointing, SB. (2010) Hypolithic microbial community of quartz pavement in the high-altitude tundra of central Tibet. Microb. Ecol. 60:730-739
32. Musingarimi, W., Tuffin, M., Cowan, D. (2010) Characterisation of the Arsenic Resistance Genes in Bacillus sp. UWC Isolated from Maturing Fly Ash-Acid Mine Drainage Neutralized Solids. S.A. J. Sci. 106:59-63.
33. Staniland, S., Coppock, M., Tuffin, M., van Zyl, L., Roychoudhury, A. N., Cowan, D. (2010) Cobalt uptake and resistance to trace metals in Comamonas testosteroni isolated from a heavy-metal contaminated site in the Zambian Copperbelt. Geomicrobiol. J. 27:656-662
34. Bauer, R, Cowan, DA, Crouch, A. (2010) Acrolein in wine: Importance of 3-hydroxypropionaldehyde and derivatives in production and detection. J. Agric. Food Chem. 58:3243-3250.
35. Barnard, D, Casanueva, A, Tuffin, IM, Cowan DA. (2010) Extremophiles in biofuels production. Environ. Technol. 31:871-888.
36. Cowan, DA, Khan, N, Pointing, S, Cary, SC. (2010) Diverse hypolithic refuge communities in Antarctic Dry Valleys, Antarct. Sci. 22:714-720
37. Casanueva, A., Tuffin, IM, Cary, SC and Cowan, DA. (2010) Molecular adaptations to psychrophily: The impact of ‘omic’ technologies. Trends Microbiol. 18:374-381.
38. Williamson, DS, Dent, KC, Weber, BW, Varsani, A, Frederick, J, Thuku, RN, Cameron, RA, van Heerden, JH, Cowan, DA, Sewell, BT. (2010) Structural and biochemical characterization of a nitrilase from the thermophilic bacterium, Geobacillus pallidus RAPc8. Appl. Microbiol. Biotechnol. 88:143-153.
39. Velankar H, Clarke KG, du Preez R, Cowan DA, Burton SG. (2010) Developments in nitrile and amide biotransformation processes. Trends Biotechnol. 28:561-569
40. Meiring, T, Mulako, I, Tuffin, MI, Meyer, Q, Cowan, DA. (2010) Retrieval of full-length functional genes using subtractive hybridization magnetic bead capture. Methods Mol. Biol. 668:287-297.
41. Olaofe, OA, Burton, SG, Cowan, DA, Harrison, STL (2010) Improving the production of a thermostable amidase through optimising IPTG induction in a highly dense culture of recombinant Escherichia coli. Biochem. Engineer. J. 52:19-24
42. Chiyanzu, I, Cowan, DA, Burton, SG (2010) Immobilization of a nitrile hydratase (NHase) from Geobacillus pallidus RAPc8 overcomes substrate inhibition and enhances stability. J. Mol. Catal. B, Enzymatic. 63:109-115.
43. Cowan DA, Pointing SB, Stevens MI, Cary SC, Stomeo F, Tuffin IM. (2011) Distribution and abiotic influences on hypolithic microbial communities in an Antarctic Dry Valley. Polar Biol. 34:307–311.
44. Taylor, MP, van Zyl, L, Tuffin, IM, Leak, DJ, Cowan, DA. (2011) Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts. Microb. Biotechnol. 4:438-448.
45. Welz, PJ, Ramond, J-B, Cowan, DA, Prins, A, Burton SG. (2011) Ethanol degradation and the benefits of incremental priming in pilot-scale constructed wetlands. Ecol. Engineer. 37:1453-1459.
46. Nel, AJM, Tuffin, IM, Sewell, BT, Cowan, DA. (2011) A unique aliphatic amidase from a psychrotrophic and haloalkaliphilic Nesterenkonia isolate. Appl. Environ. Microbiol. 77:3696-3702.
47. Rohr, LM, Mashaphu, N, Sheridan, C, Burton, SG, and Cowan, DA. (2011) Seasonal shifts of the microbial community structure in a winery waste-impacted wetland soil. Trans. Roy. Soc. S.A. 66:41-53.
48. Cowan, DA, Sohm, JA, Makhalanyane, T, Capone, DG, Green, TGA and Cary, SC. (2011) Hypolithic communities: important nitrogen sources in Antarctic desert soils. Envir. Microbiol. Rep. 3:581-586
49. Cowan, DA, Fernendez-Lafuente, R (2011) Enhancement of thermophilic enzymes by chemical modification and immobilization. A review. Enz. Microb. Technol. 49: 326-346
50. Cowan, DA, Chown, SL, Convey, P, Tuffin, IM, Hughes, K, Pointing, SB, Vincent, WF. (2011) Non-indigenous microorganisms in the Antarctic – assessing the risks. Trends Microbiol. 19:540-548
51. Ramond J-B, Welz P.J., Cowan D.A., Burton S.G. (2012) Microbial community structure stability, a key parameter in monitoring the development of constructed wetland mesocosms during start-up. Res. Microbiol. 163:28-35
52. Hu, XP, Heath, C, Taylor, MP, Tuffin, IM, Cowan, DA (2012). A novel, extremely alkaliphilic and cold active esterase from Antarctic desert soil. Extremophiles. 16: 79-86
53. Basson, CE, J.-H. Groenewald, J. Kossmann, C. Cronje, R. Bauer. (2011) Upregulation of pyrophosphate:D-fructose-6-phosphate 1-phosphotransferase activity in strawberry. Transgenic Research. 20:925-931.
54. Cronje, C, GM George, AR Fernie, J Kossmann, R Bauer. (2011) Manipulation of L-Ascorbic acid biosynthesis pathways in Solanum lycopersicum: Elevated GDP-mannose pyrophosphorylase activity enhances L-ascorbate levels in red fruit. PLANTA, doi: 10.1007/s00425-011-1525-6.
55. Tiao, G, Lee, CK, McDonald, IR, Cowan, DA, Cary, SC. (2012) Rapid microbial response to removal of the presence of an ancient relic in the Antarctic Dry Valleys. Nature Comms. 3: 360
56. Taylor, MP, Mulako, I, Tuffin, IM, Cowan, DA (2012). Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations. Biotechnol. J. 7: 1169-81
57. George, GM, R Bauer, A Blennow, J Kossmann, JR Lloyd. (2012) Virus induced multiple gene silencing to study metabolic pathways. Biotechnol. J. doi: 10.1002/biot.201100469.
58. Sanyika, WT, Stafford, W, Tuffin, IM, Cowan, DA. (2012) Phylogenetic analysis of actinobacterial diversity associated with three Marion Island terrestrial habitats (Sub-Antarctica) and the culturability of actinomycetes from eleven habitats: a comparative study. Polar Biol. 35: 1129-1141
59. Szekera, K, Zhou, X, Schwab, T, Casanueva, A, Cowan, D, Mikhailopulo, IA, Neubauer, P. (2012) Comparative investigations on thermostable pyrimidine nucleoside phosphorylases from Geobacillus thermoglucosidasius and Thermus thermophilus. J. Mol. Cat. B: Enzymatic. 84:27-34
60. Stomeo, F, Makhalanyane, T, Valverde, A, Pointing, S, Stevens, M, Cary, SC, Tuffin, Cowan, DA (2012) Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. FEMS Microb. Ecol. DOI 10.1111/j.1574-6941.2012.01360
61. Pagaling E, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy, S. (2012) Bacterial and Archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China. Extremophiles. 16: 607-618
62. Chown,SL, Lee, JE, Hughes, KA, Barnes, J, Barrett, PJ, Bergstrom, DM, Convey, P, Cowan, DA, Crosbie, K, Dyer, G, Frenot,Y, Grant, SM, Herr, D, Kennicutt, MC, Lamers, M, Murray, A, Possingham, HP, Reid, K, Riddle, MJ, Ryan, PG, Sanson, L, Shaw, JD, Sparrow, MD, Summerhayes, C, Terauds, A, Wall, DH. (2012) Challenges to the Future Conservation of the Antarctic. Science. 337: 158-159.
63. Valverde, A, Tuffin, IM, Cowan, DA. (2012) Biogeography of bacterial communities in hot springs: a focus on the actinobacteria. Extremophiles. 16: 669-679
64. Welz, PJ, Ramond, J-B, Cowan, DA, Burton, SG (2012) Phenolic removal processes in biological sand filters, sand columns and microcosms. Biores. Technol. 119: 262-269.
65. Meiring, T, Tuffin, IM, Cowan, DA. (2012) Genome sequence of temperate bacteriophage Psymv2 from Antarctic Dry Valley soil isolate Psychrobacter sp. MV2. Extremophiles. 16: 715-726.
66. Loftie-Eaton, W, Taylor, M, Horne, K, Tuffin, IM, Burton, SG, Cowan, DA. (2012) Balancing redox cofactor generation and ATP synthesis: Key microaerobic responses in thermophilic fermentations. Biotechnol. Bioeng. 110:1057-65
67. Makhalanyane, TP, Valverde, A, Lacap, D, Pointing, SB, Tuffin, IM, Cowan, DA. (2012) Evidence of species recruitment and development of hot desert hypolithic communities. Environ. Microb. Rep. 5: 219-224
68. Chan, Y, Lacap, DC, Lau, MCY, Warren-Rhodes, KA, Cockell, CC, Cowan, DA, McKay, CP, Pointing, SB. 2012. Hypolithic microbial communities: Between a rock and a hard place. Environ. Microbiol. 14: 2272-2282.
69. di Prisco, G, Convey, P, Gutt, J, Cowan, DA, Conlan, K, Verde, C. 2012. Understanding and Protecting the World’s Biodiversity: the Role and Legacy of the SCAR Programme “Evolution and Biodiversity in the Antarctic”. Marine Genomics. 8:3-8
70. Stomeo, F., Valverde, A., Pointing, S., McKay, C., Warren-Rhodes, K., Tuffin, M., Seely, M., Cowan, D. 2013. Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert. Extremophiles. 17: 329-337.
71. Gokul, J., Valverde, A., Tuffin, M., Cowan, D. 2013. Micro-eukaryotic diversity in hypolithons from Miers Valley, Antarctica. Biology. 2: 331-340. doi:10.3390/biology2010331.
72. Ramond, JB., Welz, P., Tuffin, M., Burton, S., Cowan, D. 2013. Assessment of temporal and spatial evolution of bacterial communities in a biological sand filter mesocosm treating winery wastewater. Journal of Applied Microbiology. 115:91-101
73. Ramond, J-B., Tshabuse, F., Bopda, C., Cowan, D., Tuffin, M. 2013. Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacteria communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench). Plant and Soil. DOI 10.1007/s11104-013-1737-6.
74. Ramond, JB., Welz, P., Tuffin, M., Burton, S., Cowan, D. 2013. Selection of diazotrophic bacterial communities in biological sand filter mesocosms used for the treatment of phenolic-laden wastewater. Microbial Ecology. DOI 10.1007/s00248-013-0258-4.
75. Makhalanyane, TP., Valverde, A., Birkeland, N-K., Cary, SC., Tuffin, IM., Cowan, DA. 2013. Evidence for successional development in Antarctic hypolithic bacterial communities. ISME J. 7: 2080–2090
76. Cowan, D., Rybicki, E., Tuffin, M., Valverde, A., Wingfield, M. 2013. Biodiversity: So Much More than Legs and Leaves. South African Journal of Science. DOI 10.1590/sajs.2013/a0037
77. Ramond, J-B., Welz, P., Le Roes-Hill, M., Tuffin, M., Burton, S., Cowan, D. 2014. Selection of Clostridium spp. in biological sand filters neutralizing synthetic acid mine drainage. FEMS Microbiol. Ecol. 87:678-90
78. van Zyl, LJ, Taylor, MP, Eley, K, Tuffin, M, Cowan, D. 2014. Engineering pyruvate decarboxylase-mediated ethanol production in the thermophilic host Geobacillus thermoglucosidasius. Appl. Micro. Biotechnol. 98:1247-1259
79. Aliyu, H., De Maayer, P., Rees, J., Tuffin, M., Cowan, DA. 2014. Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain AN1. Genome Announce. DOI 10.1128/genomeA.00197-14
80. Adriaenssens, EM., van Zyl, L., De Maayer, P., Rubagotti, E., Rybicki, E., Tuffin, M., Cowan, DA. 2014. Metagenomic analysis of the viral community in Namib Desert hypoliths. Environ. Microbiol. DOI 10.1111/1462-2920.12528
81. Zablocki, O., van Zyl, L., Adriaenssens, EM., Rubagotti, E., Tuffin, M., Cary, Craig., Cowan, D. 2014. High diversity of tailed phages, eukaryotic viruses and virophage-like elements in the metaviromes of Antarctic soil. Appl. Environ. Microbiol. doi: 10.1128/AEM.01525-14
82. van Zyl, LJ., Schubert, W-D., Tuffin, IM., Cowan, D. 2014. Structure and Functional Characterization of Pyruvate decarboxylase from Gluconacetobacter diazotrophicus. BMC Struct. Biol. doi: 10.1186/s12900-014-0021-1
83. Zablocki, O., van Zyl, L., Adriaenssens, EM., Rubagotti, E., Tuffin, M., Craig, C., Cowan, D. 2014. Niche-depe
84. Welz PJ, Palmer Z, Isaacs S, Kirby B, le Roes-Hill M. 2014. Analysis of substrate degradation, metabolite formation and microbial community responses in sand bioreactors treating winery wastewater: A comparative study. J. Environ. Man. 145:147-156
85. Ramond J-B, Makhalanyane TP, Tuffin MI, Cowan DA. 2014. Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members. Lett. Appl. Microbiol. DOI: 10.1111/lam.12380
86. Prins A, Kleinsmidt L, Khan N, Kirby B, Kudanga T, Vollmer J, Pleiss J, Burton S, le Roes-Hill M. 2015. The effect of mutations near the T1 copper site on the biochemical characteristics of the small laccase from Streptomyces coelicolor A3(2). Enzyme Microb. Technol. 68: 23–32
87. Olonade I, van Zyl LJ, Trindade MI. 2015. Draft genome sequence of marine isolates Thalassomonas viridans and Thalassomonas actiniarum. Genome A. doi: 10.1128/genomeA.00297-15
88. Maropola MKA, Ramond J-B, Trindade M. 2015. Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). J. Microbiol. Met. 112:104-117
89. Ohlhoff CW, Kirby BM, van Zyl LJ, Mutepfa DLR, Casanueva A, Huddy RJ, Bauer R, Cowan DA, Tuffin M. 2015. An unusual feruloyl esterase belonging to family VIII esterases and displaying a broad substrate range. J. Mol. Cat. B: Enzymatic. 118: 79-88
90. van Zyl LJ, Sunda F, Taylor MP, Cowan DA, Trindade MI. 2015. Identification and characterization of a novel Geobacillus thermoglucosidasius bacteriophage, GVE3. Arch. Virol. doi:10.?1007/?s00705-015-2497-9
91. Ramond J-B., Lako J., Stafford W., Tuffin M., Cowan D. 2015. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils. Journal of Basic Microbiology. doi: 10.1002/jobm.201400933.
92. Anderson D, Ferreras E, Tuffin M, Cowan D. 2015. A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage. FEMS Microbiol. Lett. doi: 10.1093/femsle/fnv110
93. Albakosh M, Naidoo R, Kirby B, Bauer R. 2015. Identification of epiphytic bacterial communities associated with brown alga Splachnidium rugosum. Journal of Applied Phycology. doi:10.1007/s10811-015-0725-z
94. Trindade M, van Zyl L, Navarro-Fernández J, Abd Elrazak A. 2015. Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Frontiers in Microbiology. 6:890. doi: 10.3389/fmicb.2015.00890
95. Missengue M, Musyoka N, Madzivire G, Babajide O, Fatoba O, Tuffin M, Petrik L. 2015. Leaching and antimicrobial properties of silver nanoparticles loaded onto natural zeolite clinoptilolite by ion exchange and wet impregnation. Journal of Environmental Science and Health, Part A. doi:10.1080/10934529.2015.1087731
96. van Zyl LJ, Taylor MP, Trindade M. 2015. Engineering resistance to phage GVE3 in Geobacillus thermoglucosidasius. Appl. Microbiol. Biotechnol. doi: 10.1007/s00253-015-7109-9
97. Le Roes-Hill M, Palmer Z*, Rohland J, Kirby B, Burton SG. 2015. Partial purification and characterisation of two actinomycete tyrosinases and their application in cross-linking reactions. J. Mol. Cat. B: Enzymatic 122:353-364
98.Fisher RG, Smith DM, Murrell B, Slabbbert R, Kirby BM, Edson C, Cotton MF, Haubrich RH, Pond SLK, Van Zyl G. 2015. MiSeq and Ion PGM sequencing improves detection of drug resistance mutations in infants after HIV PMTCT failure. J. Clin. Virol. 62: 48-53
99. Adriaenssens EM, van Zyl LJ, Cowan DA, Trindade M. 2016. Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses. Viruses. doi:10.3390/v8010014
100. van Zyl LJ, Matobole R, Biteghe FAN, Klein T, Kirby B, Trindade M. 2016. Draft Genome Sequences of Three Bacillus Species from South African Marine Sponges. Genome A. doi:10.1128/genomeA.00143-16
101. Wilcox DA, Cowan DA. 2016. Diversity of Frankia in root nodules of six Morella sp. from the Cape flora of South Africa. Plant Soil doi: 10.1007/s11104-016-2881-6
102. van Zyl LJ, Nemavhulani S, Cass J, Cowan DA, Trindade M. 2016. Three novel bacteriophages isolated from the East African Rift Valley soda lakes. Virol. J. doi: 10.1186/s12985-016-0656-6
103. Armstrong A, Valverde A, Ramond J-B, Makhalanyane TP, Jansson JK, Hopkins DW, Aspray TJ, Seely M, Trindade MI, Cowan DA. 2016. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci. Rep. 6: doi: 10.1038/srep34434
104. Missengue RNM, Musyoka NM, Madzivire G, Babajide O, Fatoba OO, Tuffin M, Petrik LF. 2016. Leaching and antimicrobial properties of silver nanoparticles loaded onto natural zeolite clinoptilolite by ion exchange and wet impregnation. J. Environ. Sci . Health. 0: 1-8 doi: 10.1080/10934529.2015.1087731
105. Zablocki O, Adriaenssens EM, Frossard A, Seely M, Ramond J-B, Cowan D. 2017. Metaviromes of extracellular soil viruses along a Namib Desert aridity gradient. Genome Announc 5:e01470-16 doi: 10.1128/ genomeA.01470-16
106. Zablocki O, van Zyl LJ, Kirby B, Trindade M. 2017. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses. doi: 10.3390/v9110348.
107. Hesse U, van Heusden P, Kirby BM, Olonade I, van Zyl LJ, Trindade M. 2017. Virome assembly and annotation: a surprise in the Namib Desert. Front. Microbiol. doi: 10.3389/fmicb.2017.00013
108. Matobole RM, Van Zyl LJ, Parker-Nance S, Davies-Coleman MT, Trindade M. 2017. Antibacterial activities of bacteria isolated from the marine sponges Isodictya compressa and Higginsia bidentifera collected from Algoa Bay, South Africa. Marine Drugs. doi: 10.3390/md15020047
109. Wani Lako JD, Yengkopiong JP, Stafford WHL, Tuffin M, Cowan DA. 2018. Cloning, expression and characterization of thermostable YdaP from Bacillus licheniformis 9A. Acta. Biochim. Pol. 65:59-66.
110. van Zyl LJ, Abrahams Y, Stander EA, Kirby-McCollough B, Jourdain R, Clavaud C, Breton L, Trindade M. 2018. Novel phages of healthy skin metaviromes from South Africa. Sci. Rep. 8: 12265
111. Zablocki O, van Zyl L, Trindade M. 2018. Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages. Extremophiles. doi.org/10.1007/s00792-018-1052-5
112. Adriaenssens EM, Wittmann J, Kuhn JH. et al. 2018. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch. Virol. 163: 1125. doi.org/10.1007/s00705-018-3723-z
113. Harris L, van Zyl LJ, Kirby-McCullough BM, Damelin LH, Tiemessen CT, Trindade M. 2018. Identification and sequence analysis of two novel cryptic plasmids isolated from the vaginal mucosa of South African women. Plasmid. 98: 56-62. doi: 10.1016/j.plasmid.2018.09.008.
114. Silva-Castro GA, Moyo AC, Khumalo L, van Zyl LJ, Petrik LF, Trindade M. 2018. Factors influencing pigment production by halophilic bacteria and its effect on brine evaporation rates. Microb. Biotechnol. doi.org/10.1111/1751-7915.13319
115. Williams W, Kunorozva L, Klaiber I, Henkel M, Pfannstiel J, Günther J, Conrad J, Van Zyl LJ, Hausmann R, Burger A, Trindade M. 2019. Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants. Appl Microbiol Biotechnol. 103:4429-4441. doi: 10.1007/s00253-019-09768-1.
116. Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M. 2019. Characterisation of three novel a-L-arabinofuranosidases from a compost metagenome. BMC Biotechnology 19:22
117. Katusiime MC, Halvas EK, Wright I, Joseph K, Bale MJ, Kirby-McCullough B, Engelbrecht S, Shao W, Hu W-S, Cotton MF, Mellors JW, Kearney MF, van Zyl GU. 2019. Intact HIV Proviruses Persist in Children Seven to Nine Years after Initiation of Antiretroviral Therapy in the First Year of Life. J Virol 94:e01519-19. https://doi.org/10.1128/JVI.01519-19.
118. January GG, Naidoo RK, Kirby-McCullough B, Bauer R. 2019. Assessing methodologies for fucoidan extraction from South African brown algae. Algal Research 40: 101517
119. Oosthuizen L, Charimba G, Hitzeroth A, Nde AL, Steyn L, Newman J, Hugo C. 2019. Chryseobacterium pennipullorum sp. nov., isolated from poultry feather waste. Int J Syst Evol Microbiol 69:2380–2387
120. Stander EA, Williams W, Rautenbach F, Le Roes-Hill M, Mgwatyu Y, Marnewick J, Hesse U. 2019. Visualization of Aspalathin in Rooibos (Aspalathus linearis) Plant and Herbal Tea Extracts Using Thin-Layer Chromatography. Molecules 24: 938
121. Adriaenssens, E.M., Sullivan, M.B., Knezevic, P. et al. 2020. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol https://doi.org/10.1007/s00705-020-04577-8
122. Tang Y, Ma Q, Du Y, Ren Lu, Van Zyl LJ, Long X. 2020. Efficient purification of sophorolipids via chemical modifications coupled with extractions and their potential applications as antibacterial agents. Separ. Purif. Technol. 245: 116897
123. Dell’Anno F, Brunet C, van Zyl LJ, Trindade M, Golyshin PN, Dell’Anno A, Ianora A, Sansone C. 2020. Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments. Microorganisms 8: 1402.
124. Stander EA, Williams W, Mgwatyu Y, Heusden PV, Rautenbach F, Marnewick J, Roes-Hill ML, Hesse U. 2020. Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex. BioTech 9: 19
125. Du Preez A, Van Zyl WF, Trindade M, Dicks LMT, Smith C. 2021. Therapeutic applications of lantibiotics and other lanthipeptides: Old and new findings. Applied and Environmental Microbiology: Antimicrobial Chemotherapy doi.org/10.1128/AEM.00186-21
126. Tedesco P, Palma Esposito F, Masino A, Vitale GA, Tortorella E, Poli A, Nicolaus B, van Zyl LJ, Trindade M, de Pascale D. 2021. Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. Microorganisms 9: 890. doi.org/10.3390/microorganisms9050890
127. Dell’Anno F, van Zyl LJ, Trindade M, Brunet C, Dell’Anno A, Ianora A, Sansone C. 2021. Genome Sequence of an Alkaliphilus Species Isolated from Historically Contaminated Sediments of the Gulf of Naples (Mediterranean Sea). Microbiol. Resour. Announc. 10:e00060-21
128. Krupovic M, Turner D, Morozova V. et al. 2021. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Arch. Virol. doi.org/10.1007/s00705-021-05205-9
129. Nde AL, Charimba G, Hitzeroth A, Oosthuizen L, Steyn L, Newman JD, Hugo C. 2021. Chryseobacterium pennae sp. nov., isolated from poultry feather waste. IJSEM 71: 004912
130. Freitag A, Cluff MD, Hitzeroth AC, van Wyngaardt L, Hugo A, Hugo CJ. 2021. Community level physiological profiling of reduced or replaced salt fresh sausage inoculated with Escherichia coli ATCC 25922. LWT – Food Science and Technology 148: 111786
131. Olonade I, van Zyl LJ, Trindade M. 2021. Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring. Microorganisms 9: 2043. doi.org/10.3390/microorganisms9102043
132. Ndata K, Nevondo W, Cekuse B, van Zyl LJ, Trindade M. 2021. Characterization of a highly xylose tolerant ß-xylosidase isolated from high temperature horse manure compost. BMC Biotechnol 21: 61 doi.org/10.1186/s12896-021-00722-6
133. G3 Genes|Genomes|Genetics 11: 9 doi.org/10.1093/g3journal/jkab210
134. Di Costanzo F, Di Dato V, van Zyl LJ, Cutignano A, Esposito F, Trindade M, Romano G. 2021. Three Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoi. Int. J. Mol. Sci. 22: 13199 doi.org/10.3390/ijms222413199
135. Moyo AC, Dufossé L, Giuffrida D, van Zyl LJ, Trindade M. 2022. Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. Microbial Cell Factories 21: 43 doi.org/10.1186/s12934-022-01752-1
136. Vermeulen R, Du Preez Van Staden A, van Zyl LJ, Dicks LMT and Trindade M. 2022. Unusual Class I Lanthipeptides from the Marine Bacteria Thalassomonas viridans. ACS Synth. Biol. 11: 3608–3616 https://doi.org/10.1021/acssynbio.2c00480
137. Aaron J, van Zyl LJ, Dicks LMT. 2022. Isolation and Characterization of Lytic Proteus Virus 309. Viruses. 14: 1309. doi: 10.3390/v14061309.
138. Boumehira AZ , Kirby B, Trindade M, Hacène H, Park EY and El Enshasy EA. 2022. Streptomyces sp. ADR1, Strain Producing ?- and ?-Rubromycin Antibiotics, Isolated from Algerian Sahara Desert. Fermentation. 8: 473 https://doi.org/10.3390/ fermentation8100473
139. Fisher S, De Villers D, Du Plessis M, Hattingh K, Saulse C, Basson G, Barker A, Daniel AI, Al-Hashimi A, Hitzeroth A, Makhalanyane T, Mavumengwana V, Gokul A, Keyster M, Klein A. 2022. Draft Whole-Genome Sequence of Penicillium simplicissimum A4, a Putative Endophyte from Echium plantagineum. Microbiol. Resour. Announc. 11: e0085422. doi: 10.1128/mra.00854-22
140. Dell’Anno F, van Zyl LJ, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell’Anno A, Rastelli E. 2023. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. Environmental Pollution. 317: 120772 https://doi.org/10.1016/j.envpol.2022.120772.
141. Pheiffer F, Schneider YK-H, Hansen EH, Andersen JH, Isaksson J, Busche T, Rückert C, Kalinowski J, Zyl Lv, Trindade M. 2023. Bioassay-Guided Fractionation Leads to the Detection of Cholic Acid Generated by the Rare Thalassomonas sp. Marine Drugs. 21 :2 https://doi.org/10.3390/md21010002
142. Jimoh AA, Booysen E, van Zyl L, Trindade M. 2023. Do biosurfactants as anti-biofilm agents have a future in industrial water systems? Front Bioeng Biotechnol. 15: 11:1244595. doi: 10.3389/fbioe.2023.1244595.
143. Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, R?mnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM. 2023. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol. 23: 168(2):74. doi: 10.1007/s00705-022-05694-2.
144. Van Zyl WF, Van Staden AD, Dicks LMT, Trindade M. 2023. Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli. Microb Cell Fact. 22: 149. doi: 10.1186/s12934-023-02162-7.
145. Cowan DA, Babenko D, Bird R, Botha A, Breecker DO, Clarke CE, Francis ML, Gallagher T, Lebre PH, Nel T, Potts AJ, Trindade M, Van Zyl L. 2024. Oxalate and oxalotrophy: an environmental perspective. Sustainable Microbiology. qvad004, https://doi.org/10.1093/sumbio/qvad004