Dr Sofie De Meyer
Bsc. MSc. PhD

Post doctoral fellow

About me

After completing my Master of Science degree in Biology (speciality Botany) at Ghent University (Belgium) in 2007, I commenced a PhD study in the Laboratory of Microbiology at Ghent University, investigating the bacterial diversity in Belgium legume root nodules. I completed my PhD in 2011 and took up a Postdoctoral research position at the Centre for Rhizobium Studies in 2012. Pursuing international collaboration and expanding my rhizobia expertise, I took up a Postdoctoral research position at the Botany department of the University of Cape Town (South Africa) in 2013.

My research focuses on the identification and characterisation of root nodule bacteria associated with legume plants. The family of leguminous plants is one of the major plant families in the world and the symbiosis between these plants and rhizobia, is well known since the 19th century. The plant supplies nutrition and a safe shelter for the bacteria. In return the bacteria fix nitrogen and deliver this to the plant, enabling it to grow in nitrogen-limited conditions. My latest research focuses on the implementation of Lebeckia species as perennial pasture plants in Australian agriculture. These plants associate with Burkholderia bacteria, of which several novel species have been described and two promising strains for potential inocula production have been found.

My expertise further lead to the commercialisation of a novel technology for rhizobia identification directly from root nodules and in 2017 MALDI-ID Pty Ltd was established. More information can be found on www.maldiid.com

Research areas

My specific research areas include:

  • Novel legume symbiosis suitable for changing environments: Lebeckia as a novel agricultural pasture in Mediterranean climates
  • Quick and reliable bacterial identification for the future
  • Rhizobia diversity in endemic and invasive legume species

Current projects

* 2016 – 2019: Turning sand into sheep feed – Lebeckia ambigua an agricultural perennial! – ARC Linkage project LP150100848 – Chief Investigator: Prof John Howieson (J.Howieson@murdoch.edu.au)

Nitrogen fixation from legumes is worth $3 billion to the Australian agricultural economy, but changing rainfall patterns threatens much of this. One solution is to transition pasture growth to a reliance on perennial plants, which are less affected by unseasonal rain. Lebeckia ambigua is an outstanding perennial legume to begin this change, but its nitrogen fixation is severely compromised by nodulation failure, caused by death of its symbiotic rhizobia. This research will focus on improving the survival in acid and infertile soils of the unique rhizobial symbionts we have discovered for Lebeckia ambigua in South Africa. If we succeed we can build an agriculture based upon legumes adapted to our future climate.

* 2013 – 2017: Investigating pasture legumes in the mixed farming zones of WA and NSW. – Meat and Livestock Australia/Australian Wool Innovation Project B.PSP.0013 – Chief Investigator: Prof John Howieson (J.Howieson@murdoch.edu.au)

This research aims to increase the productivity of annual pastures in mixed farming systems (primarily in NSW and WA) through the ease and reliability of establishment of several newer, more productive legume species and cultivars, and through developing grazing strategies that optimise the persistence and benefits of thees newer legumes.

Awards and grants

Awards and grants for research:

Awards and grants for MALDI-ID:

Events and speaking engagements

Conference presentations

  • De Meyer SE. New microbes for Nitrogen fixation with agricultural legumes. Murdoch Agricultural research symposium, Murdoch (Australia), Sept. 2016
  • De Meyer SE, Ziegler D, Hackney B, Pflüger V, Vogel G and Howieson J. A new tool for direct identification of rhizobia strains in nodules: A sub-clover case study. 19th International congress on Nitrogen fixation California (USA), Oct. 2015
  • De Meyer SE, Ivanova N, Kyrpides N and Reeve W. Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB). 14th European Nitrogen Fixation Conference, genomics satellite meeting presentation. Tenerife (Spain), Sept. 2014

Science communication and outreach

  • The Innovators Tea Party mentor in 2017
  • Nannup South West Food Bowl Festival 17 October 2016: Trade stall on legume agricultural research
  • The Innovators Tea Party mentor in 2016
  • Science café mentor in 2016
  • Perth Science Festival 2016
  • Muresk Open Day 28 May 2016
  • Geraldton Science festival 30-31 March 2016
  • Point Walter Concert 06 March 2016
  • Fresh science WA finalist 2015: Greener pastures for Australian sheep industry. (http://freshscience.org.au/2015/greener-pastures-for-sheep)
  • Perth science festival 2015
  • Master class on science communication with Dr Chris Smith from The Naked Scientist August 2015
  • Famelab: NSW state heat finalist 2015 https://www.youtube.com/watch?v=ZhLYgqOyC-s

Farmer field days

  • MLA Pasture day Brookton (05/10/17)
  • NSW Farmer workshops (14/06/16 – 17/06/16, 19/03/17 – 24/03/17, 20/02/18 – 22/02/18): Getting legumes to work harder
  • Brookton summer sowing field day (28/04/16)
  • Esperance pasture updates (11/08/15): Free nitrogen it’s yours for the taking!
  • Lebeckia field walk (30/03/2015)
  • Summer sowing field day (23/09/2014)

Doctoral and masters supervisions

PhD students

  • Talitha Rogers (Current) – “The physiology and energetics of respiratory systems in Burkholderia species”

Honours students

  • Robert Harrison (2017)  – “Enhancing the survival of Burkholderia species for the inoculation of the South African legume, Lebeckia ambigua

Independent study contract (ISC) students

  • Georgina Stagg (2017) – “Characterising symbiotic performance of Lebeckia spp. isolates”
  • Mitchel McDonnell (2016) – “Identifying Lebeckia sp. root-nodule symbionts and N2-fixing efficiency”

Work experience students

  • Chloé de Malézieux (2018) – “work experience on effectiveness and desiccation tolerance of Burkholderia symbionts with L. ambigua”
  • Katharina Bruhl  (2015) – “Work experience in Christmas Island National Park, investigating rhizobia diversity”

Master students

  • Ntwai Abram Moiloa (2013) –  “Is Wiborgia (Fabaceae) biogeography determined by available soil rhizobia in the Greater Cape Floristic Region?”
  • Jolien Vermeulen (2011) – “Characterisation of rhizobia associated with indigenous legumes in Flanders (Belgium)”
  • Tamara Braeckman (2010) –  “Genetic characterisation of rhizobia associated with indigenous legumes in the province of Antwerp (Belgium)”
  • Bram Veckeman (2009) – “Diversity of rhizobia associated with legumes from the area around Brakel (Belgium): a molecular inventory”

Publications

Chapters

  • Reeve, W., Tiwari, R., Melino, V., De Meyer, S., (2016),Specialised genetic techniques for rhizobia,In: Working with rhizobia, Australian Centre for International Agricultural Research (ACIAR), pages 245 to 282.

Journals

  • Mwenda, G., O'Hara, G., De Meyer, S., Howieson, J., Terpolilli, J., (2018), Genetic diversity and symbiotic effectiveness of Phaseolus vulgaris-nodulating rhizobia in Kenya, Systematic and Applied Microbiology, 41, 4, pages 291 - 299.
  • Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D., da Costa, M., Rooney, A., Yi, H., Xu, X., De Meyer, S., Trujillo, M., (2018), Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes, International Journal of Systematic and Evolutionary Microbiology, 68, 1, pages 461 - 466.
  • Nguyen, T., Heenan, P., De Meyer, S., James, E., Chen, W., Morton, J., Andrews, M., (2017), Genetic diversity and nitrogen fixation ofmesorhizobia symbionts of New Zealand endemicSophora species, New Zealand Journal of Botany, 55, 4, pages 466 - 478.
  • De Meyer, S., Nguyen, T., Wang, P., Andrews, M., (2017), Complete genome sequence of Mesorhizobium sophorae ICMP 19535T, a highly specific, nitrogen-fixing symbiont of New Zealand endemic Sophora spp, Genome Announcements, 5, 43, pages Article number e00958-17 -.
  • Michel, D., Passos, S., Simoes-Araujo, J., Barauna, A., da Silva, K., Parma, M., Melo, I., De Meyer, S., O'Hara, G., Zilli, J., (2017), Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil, Archives of Microbiology, 199, , pages 657 - 664.
  • De Meyer, S., Parker, M., Van Berkum, P., Tian, R., Seshadri, R., Reddy, T., Markowitz, V., Ivanova, N., Pati, A., Woyke, T., Kyrpides, N., Howieson, J., Reeve, W., (2016), High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp strain AMP6, Standards in Genomic Sciences, 10, 1, pages DOI: 10.1186/s40793-015-0074-1 -.
  • De Meyer, S., Wee Tan, H., Andrews, M., Heenan, P., Willems, A., (2016), Mesorhizobium calcicola sp nov., Mesorhizobium waitakense sp nov., Mesorhizobium sophorae sp nov., Mesorhizobium newzealandense sp nov and Mesorhizobium kowhaii sp nov isolated from Sophora root nodules, International Journal of Systematic and Evolutionary Microbiology, 66, 0, pages 786 - 795.
  • De Meyer, S., Briscoe, L., Martinez-Hidalgo, P., Agapakis, C., de-los Santos, P., Seshadri, R., Reeve, W., Weinstock, G., O'Hara, G., Howieson, J., Hirsch, A., (2016), Symbiotic burkholderia species show diverse arrangements of nif/fix and nod genes and lack typical High-Affinity cytochrome cbb3 Oxidase genes, Molecular Plant - Microbe Interactions, 29, 8, pages 609 - 619.
  • De Meyer, S., Tian, R., Seshadri, R., Ivanova, N., Pati, A., Markowitz, V., Woyke, T., Yates, R., Howieson, J., Kyrpides, N., Reeve, W., (2016), High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T), Standards in Genomic Sciences, 10, doi: 10.1186/s40793-015-0048-3, pages -.
  • De Meyer, S., Tian, R., Seshadri, R., Reddy, T., Markowitz, V., Ivanova, N., Pati, A., Woyke, T., Kyrpides, N., Yates, R., Howieson, J., Reeve, W., (2016), High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp strain WSM4176, Standards in Genomic Sciences, 10, 1, pages DOI: 10.1186/s40793-015-0072-3 -.
  • De Meyer, S., Fabiano, E., Tian, R., Berkum, P., Seshadri, R., Markowitz, V., Ivanova, N., Pati, A., Woyke, T., Howieson, J., Kyrpides, N., Reeve, W., (2015), High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp strain UYPR2.512, Standards in Genomic Sciences, 10, 0, pages 0 - 0.
  • Yates, R., Howieson, J., De Meyer, S., Tian, R., Seshadri, R., Pati, A., Woyke, T., Markowitz, V., Ivanova, N., Kyrpides, N., Loi, A., Nutt, B., Garau, G., Sulas, L., Reeve, W., (2015), High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy, Standards in Genomic Sciences, 10, 7, pages 1 - 6.
  • Mazur, A., De Meyer, S., Tian, R., Wielbo, J., Zerbracki, K., Seshadri, R., Reddy, T., Markowitz, V., Ivanova, N., Pati, A., Woyke, T., Kyrpides, N., Reeve, W., (2015), High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland, Standards in Genomic Sciences, 10, 7, pages 1 - 7.
  • De Meyer, S., Fabiano, E., Tian, R., Van Berkum, P., Seshadri, R., Reddy, T., Markowitz, V., Ivanova, N., Pati, A., Woyke, T., Howieson, J., Kyrpides, N., Reeve, W., (2015), High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp strain UYPR1.413, Standards in Genomic Sciences, 10, 1, pages 1 - 8.
  • Eshraghi, L., De Meyer, S., Tian, R., Seshadri, R., Ivanova, N., Pati, A., Markowitz, V., Woyke, T., Kyrpides, N., Tiwari, R., Yates, R., Howieson, J., Reeve, W., (2015), High-quality permanent draft genome sequence of Bradyrhizobium sp strain WSM1743-an effective microsymbiont of an Indigofera sp growing in Australia, Standards in Genomic Sciences, 10, 87, pages 1 - 8.
  • De Meyer, S., De Beuf, K., Vekeman, B., Willems, A., (2015), A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium), Soil Biology & Biochemistry, 83, , pages 1 - 11.
  • Ziegler, D., Pothier, J., Ardley, J., Fossou, R., Pfluger, V., De Meyer, S., Vogel, G., Tonolla, M., Howieson, J., Reeve, W., Perret, X., (2015), Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS, Applied Microbiology and Biotechnology, 99, 13, pages 5547 - 5562.
  • Wee Tan, H., Heenan, P., De Meyer, S., Willems, A., Andrews, M., (2015), Diverse novel mesorhizobia nodulate New Zealand native Sophora species, Systematic and Applied Microbiology, 38, 2, pages 91 - 98.
  • Sheu, S., Chen, M., Liu, W., Andrews, M., James, E., Ardley, J., De Meyer, S., James, T., Howieson, J., Coutinho, B., Chen, W., (2015), Burkholderia dipogonis sp nov., isolated from root nodules of Dipogon lignosus in New Zealand and Western Australia, International Journal of Systematic and Evolutionary Microbiology, 65, 0, pages 4716 - 4723.
  • De Meyer, S., Wee Tan, H., Heenan, P., Andrews, M., Willems, A., (2015), Mesorhizobium waimense sp nov isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp nov isolated from Sophora microphylla root nodules, International Journal of Systematic and Evolutionary Microbiology, 65, 0, pages 3419 - 3426.
  • Silva, F., De Meyer, S., Simoes-Araujo, J., Barbe, T., Xavier, G., O'Hara, G., Ardley, J., Rumjanek, N., Willems, A., Zilli, J., (2014), Bradyrhizobium manausense sp nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils, International Journal of Systematic and Evolutionary Microbiology, 64, 0, pages 2358 - 2363.
  • da Silva, K., De Meyer, S., Rouws, L., Farias, E., dos Santos, M., O'Hara, G., Ardley, J., Willems, A., Pitard, R., Zilli, J., (2014), Bradyrhizobium ingae sp nov., isolated from effective nodules of Inga laurina grown in Cerrado soil, International Journal of Systematic and Evolutionary Microbiology, 64, , pages 3395 - 3401.
  • Zilli, J., Barauna, A., da Silva, K., De Meyer, S., Farias, E., Kaminski, P., da Costa, I., Ardley, J., Willems, A., Camacho, N., Dourado, F., O'Hara, G., (2014), Bradyrhizobium neotropicale sp nov., isolated from effective nodules of Centrolobium paraense, International Journal of Systematic and Evolutionary Microbiology, 64, 0, pages 3950 - 3957.
  • De Meyer, S., Cnockaert, M., Ardley, J., van Wyk, B., Vandamme, P., Howieson, J., (2014), Burkholderia dilworthii sp nov., isolated from Lebeckia ambigua root nodules, International Journal of Systematic and Evolutionary Microbiology, 64, 0, pages 1090 - 1095.
  • Reeve, W., Ardley, J., Tian, R., De Meyer, S., Terpolilli, J., Melino, V., Tiwari, R., Yates, R., O'Hara, G., Howieson, J., Ninawi, M., Zhang, X., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Szeto, E., Ivanova, N., Pagani, I., Pati, A., Goodwin, L., Woyke, T., Kyrpides, N., (2014), Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T), Standards in Genomic Sciences, 9, 3, pages 540 - 550.
  • Howieson, J., De Meyer, S., Vivas Marfisi, A., Ratnayake, S., Ardley, J., Yates, R., (2013), Novel Burkholderia bacteria isolated from Lebeckia ambigua - a perennial suffrutescent legume of the fynbos, Soil Biology & Biochemistry, 60, , pages 55 - 64.
  • Reeve, W., Terpolilli, J., Melino, V., Ardley, J., Tian, R., De Meyer, S., Tiwari, R., Yates, R., O'Hara, G., Howieson, J., Ninawi, M., Teshima, H., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavrommatis, K., Markowitz, V., Ivanova, N., Ovchinnikova, G., Pagani, I., Pati, A., Goodwin, L., Peters, L., Woyke, T., Kyrpides, N., (2013), Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417, Standards in Genomic Sciences, 9, 2, pages 273 - 282.
  • Reeve, W., Drew, E., Ballard, R., Melino, V., Tian, R., De Meyer, S., Brau, L., Ninawi, M., Teshima, H., Goodwin, L., Chain, P., Liolios, K., Pati, A., Mavromatis, K., Ivanova, N., Markowitz, V., Woyke, T., Kyrpides, N., (2013), Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565, Standards in Genomic Sciences, 9, 2, pages 220 - 231.
  • De Meyer, S., Cnockaert, M., Ardley, J., Maker, G., Yates, R., Howieson, J., Vandamme, P., (2013), Burkholderia sprentiae sp nov., isolated from Lebeckia ambigua root nodules, International Journal of Systematic and Evolutionary Microbiology, 63, 0, pages 3950 - 3957.
  • De Meyer, S., Cnockaert, M., Ardley, J., Trengove, R., Garau, G., Howieson, J., Vandamme, P., (2013), Burkholderia rhynchosiae sp nov., isolated from Rhynchosia ferulifolia root nodules, International Journal of Systematic and Evolutionary Microbiology, 63, , pages 3944 - 3949.
  • Reeve, W., Drew, E., Ballard, R., Melino, V., Tian, R., De Meyer, S., Brau, L., Ninawi, M., Daligault, H., Davenport, K., Erkkila, T., Goodwin, L., Gu, W., Munk, C., Teshima, H., Xu, Y., Chain, P., Kyrpides, N., (2013), Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943, Standards in Genomic Sciences, 9, 2, pages 232 - 242.
  • Reeve, W., Tian, R., De Meyer, S., Melino, V., Terpolilli, J., Ardley, J., Tiwari, R., Howieson, J., Yates, R., O'Hara, G., Ninawi, M., Teshima, H., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Ivanova, N., Ovchinnikova, G., Pagani, I., Pati, A., Goodwin, L., Pitluck, S., Woyke, T., Kyrpides, N., (2013), Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1, Standards in Genomic Sciences, 9, 2, pages 243 - 253.
  • Reeve, W., Terpolilli, J., Melino, V., Ardley, J., Tian, R., De Meyer, S., Tiwari, R., Yates, R., O'Hara, G., Howieson, J., Ninawi, M., Held, B., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Ivanova, N., Ovchinnikova, G., Pagani, I., Pati, A., Goodwin, L., Woyke, T., Kyrpides, N., (2013), Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597, Standards in Genomic Sciences, 9, 2, pages 264 - 272.
  • Reeve, W., De Meyer, S., Terpolilli, J., Melino, V., Ardley, J., Tian, R., Tiwari, R., Howieson, J., Yates, R., O'Hara, G., Ninawi, M., Lu, M., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Ivanova, N., Pagani, I., Pati, A., Goodwin, L., Woyke, T., Kyrpides, N., (2013), Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471, Standards in Genomic Sciences, 9, 2, pages 254 - 263.
  • Reeve, W., De Meyer, S., Terpolilli, J., Melino, V., Ardley, J., Tian, R., Tiwari, R., Howieson, J., Yates, R., O'Hara, G., Lu, M., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Szeto, E., Ivanova, N., Mikhailova, N., Ovchinnikova, G., Pagani, I., Pati, A., Goodwin, L., Peters, L., Pitluck, S., Woyke, T., Kyrpides, N., (2013), Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005, Standards in Genomic Sciences, 9, 2, pages 385 - 394.
  • Reeve, W., Melino, V., Ardley, J., Tian, R., De Meyer, S., Terpolilli, J., Tiwari, R., Yates, R., O'Hara, G., Howieson, J., Ninawi, M., Held, B., Bruce, D., Detter, C., Tapia, R., Han, C., Wei, C., Huntemann, M., Han, J., Chen, I., Mavromatis, K., Markowitz, V., Szeto, E., Ivanova, N., Mikhailova, N., Pagani, I., Pati, A., Goodwin, L., Woyke, T., Kyrpides, N., (2013), Genome sequence of the Trifolium rueppellianum - nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012, Standards in Genomic Sciences, 9, 2, pages 283 - 293.