Dr Lilia Costa Carvalhais
Senior Research Fellow
Centre for Horticultural Science
Researcher biography
I am driven by curiosity to understand the overwhelming complexity of the biological world and how we can use it to solve problems of our time. I find especially intriguing all the invisible interactions between plant and microbes. I investigate the drivers of these interactions and aim to address major societal challenges, like food security. Currently, I study the biology, distribution and epidemiology of banana diseases to: 1) develop molecular diagnostic assays to prevent new incursions and further spread, and 2) identify the best management strategies. Diseases include banana Fusarium wilt, banana wilt associated phytoplasma (BWAP), Black Sigatoka, Eumusae leaf spot, Moko (Bugtok), banana blood disease, Xanthomonas wilt and Freckle.
Book Chapters
Singh, Eugenie, Schenk, Peer M. and Carvalhais, Lilia C. (2021). Sample preparation for culture-independent profiling and isolation of phyllosphere bacteria to identify potential biopesticides. Methods in Molecular Biology. (pp. 193-208) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-1040-4_16
Liu, Hongwei, Mirzaee, Hooman, Rincon-Florez, Vivian, Moyle, Richard, Spohn, Marie, Carvalhais, Lilia C. and Schenk, Peer M. (2017). Emerging Culture-Independent Tools to Enhance Our Understanding of Soil Microbial Ecology. Microbial Biomass. (pp. 207-225) Hackensack, NJ United States: World Scientific Publishing. doi: 10.1142/9781786341310_0008
Fallath, Thorya, Rosli, Ahmad Bin, Kidd, Brendan, Carvalhais, Lilia C. and Schenk, Peer M. (2017). Toward plant defense mechanisms against root pathogens. Agriculturally Important Microbes for Sustainable Agriculture. (pp. 293-312) Gateway East, Singapore : Springer Singapore. doi: 10.1007/978-981-10-5343-6_10
Rincon-Florez, Vivian A., Carvalhais, Lilia C., Dang, Yash P. and Schenk, Peer M. (2016). Soil microbial community interactions under tillage systems in Australia. Plant, Soil and Microbes: Volume 1: Implications in Crop Science. (pp. 93-102) edited by Khalid Rehman Hakeem, Mohd Sayeed Akhtar and Siti Nor Akmar Abdullah. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-27455-3_5
Carvalhais, Lilia C., Rincon-Florez, Vivian and Schenk, Peer M. (2014). Soil functional gene microarrays and applications in plant-microbe interactions. Microarrays: current technology, innovations and applications. (pp. 169-180) edited by Zhili He. Norfolk, United Kingdom: Caister Academic Press.
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. Molecular Microbial Ecology of the Rhizosphere. (pp. 1137-1144) edited by Frans J. de Bruijn. Hoboken, NJ United States: Wiley-Blackwell. doi: 10.1002/9781118297674.ch109
Scotti, M. R., Sa, N., Marriel, I., Carvalhais, L. C., Matias, S. R., Correa, E. J., Freitas, N., Sugai, M. A. and Pagano, M. C. (2007). Effect of plant species and mycorrhizal inoculation on soil phosphate-solubilizing microorganisms in semi-arid Brazil: Growth promotion effect of rhizospheric phosphate-solubilizing microorganisms on Eucalyptus camaldulensis. First International Meeting on Microbial Phosphate Solubilization. (pp. 167-172) edited by E. Velazquez and C. Rodriguez-Barrueco. Dordrecht, The Netherlands: Springer.
Journal Articles
Ray, Jane, Subandiyah, Siti, Rincon-Florez, Vivian Andrea, Prakoso, Ady Bayu, Carvalhais, Lilia and Drenth, Andre (2022). Susceptibility of the banana inflorescence to Blood disease. Phytopathology®, 112 (4), 803-810. doi: 10.1094/phyto-07-21-0311-r
Syed-Ab-Rahman, Sharifah Farhana, Arkhipov, Alexander, Wass, Taylor J., Xiao, Yawen, Carvalhais, Lilia C. and Schenk, Peer M. (2022). Rhizosphere bacteria induce programmed cell death defence genes and signalling in chilli pepper. Journal of Applied Microbiology, 132 (4), 3111-3124. doi: 10.1111/jam.15456
Rincon-Florez, Vivian A, Ray, Jane D, Carvalhais, Lilia Costa, O'Dwyer, Cecilia A, Subandiyah, Siti, Zulperi, Dzarifah and Drenth, Andre (2022). Diagnostics of banana Blood disease. Plant Disease, 106 (3), 947-959. doi: 10.1094/pdis-07-21-1436-re
Ray, Jane D., Subandiyah, Siti, Rincon-Florez, Vivian A., Prakoso, Ady B., Mudita, I. W., Carvalhais, Lilia C., Markus, Jenny E. R., O’Dwyer, Cecilia A. and Drenth, André (2021). Geographic expansion of banana blood disease in Southeast Asia. Plant Disease, 105 (10), 2792-2800. doi: 10.1094/pdis-01-21-0149-re
Carvalhais, Lilia C., Dennis, Paul G., Poudel, Amrit, Birt, Henry W. G., Bhuiyan, Shamsul A., Card, Stuart D. and Joyce, Priya A. (2021). Simple solution to preserve plant samples for microbiome analyses. Molecular Ecology Resources, 22 (3), 1055-1064. doi: 10.1111/1755-0998.13538
Mirzaee, Hooman, Neira Peralta, Noelia L., Carvalhais, Lilia C., Dennis, Paul G. and Schenk, Peer M. (2021). Plant-produced bacteriocins inhibit plant pathogens and confer disease resistance in tomato. New Biotechnology, 63, 54-61. doi: 10.1016/j.nbt.2021.03.003
Liu, Hongwei, Li, Jiayu, Carvalhais, Lilia C., Percy, Cassandra D., Prakash Verma, Jay, Schenk, Peer M. and Singh, Brajesh K. (2021). Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens. New Phytologist, 229 (5), 2873-2885. doi: 10.1111/nph.17057
Carvalhais, Lilia C. and Dennis, Paul G. (2021). Preface. Methods in Molecular Biology, 2232, v-vi.
Akinsanmi, Olufemi A. and Carvalhais, Lilia C. (2020). Draft genome of the macadamia husk spot pathogen, Pseudocercospora macadamiae. Phytopathology®, 110 (9), PHYTO12190460A-12. doi: 10.1094/phyto-12-19-0460-a
Rincon-Florez, Vivian A., Carvalhais, Lilia C., Dang, Yash P., Crawford, Mark H., Schenk, Peer M. and Dennis, Paul G. (2020). Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management. Pedobiologia, 80 150640, 150640. doi: 10.1016/j.pedobi.2020.150640
Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Larsson, E., Angelini, C., Brandrud, T. E., Dearnaley, J. D.W., Dima, B., Dovana, F., Fechner, N., García, D., Gené, J., Halling, R. E., Houbraken, J., Leonard, P., Luangsa-Ard, J. J., Noisripoom, W., Rea-Ireland, A. E., Ševčíková, H., Smyth, C. W., Vizzini, A., Adam, J. D., Adams, G. C., Alexandrova, A. V., Alizadeh, A., Álvarez Duarte, E., Andjic, V., Antonín, V. ... Groenewald, J. Z. (2020). Fungal planet description sheets: 1112–1181. Persoonia: Molecular Phylogeny and Evolution of Fungi, 45, 251-409. doi: 10.3767/persoonia.2020.45.10
Syed-Ab-Rahman, Sharifah Farhana, Carvalhais, Lilia Costa and Omar, Dzolkhifli (2020). Development of plant-based emulsion formulations to control bacterial leaf blight and sheath brown rot of rice. Heliyon, 6 (1) e03151, e03151. doi: 10.1016/j.heliyon.2019.e03151
Syed-Ab-Rahman, Sharifah Farhana, Carvalhais, Lilia C., Chua, Elvis T., Chung, Fong Yi, Moyle, Peter M., Eltanahy, Eladl G. and Schenk, Peer M. (2019). Soil bacterial diffusible and volatile organic compounds inhibit Phytophthora capsici and promote plant growth. Science of the Total Environment, 692, 267-280. doi: 10.1016/j.scitotenv.2019.07.061
Carvalhais, Lilia C., Henderson, Juliane, Rincon-Florez, Vivian A., O'Dwyer, Cecilia, Czislowski, Elizabeth, Aitken, Elizabeth A. B. and Drenth, Andre (2019). Molecular diagnostics of banana Fusarium wilt targeting secreted-in-xylem genes. Frontiers in Plant Science, 10 547, 547. doi: 10.3389/fpls.2019.00547
Liu, Hongwei, Khan, Muhammad Yahya, Carvalhais, Lilia C., Delgado-Baquerizo, Manuel, Yan, Lijuan, Crawford, Mark, Dennis, Paul G., Singh, Brajesh and Schenk, Peer M. (2019). Soil amendments with ethylene precursor alleviate negative impacts of salinity on soil microbial properties and productivity. Scientific Reports, 9 (1) 6892, 6892. doi: 10.1038/s41598-019-43305-4
Wass, Taylor J., Syed-Ab-Rahman, Sharifah Farhana, Carvalhais, Lilia C., Ferguson, Brett J. and Schenk, Peer M. (2019). Complete genome sequence of Achromobacter spanius UQ283, a soilborne isolate exhibiting plant growth-promoting properties. Microbiology Resource Announcements, 8 (16) e00236-19. doi: 10.1128/mra.00236-19
Carvalhais, Lilia C., Rincon-Florez, Vivian A., Brewer, Philip B., Beveridge, Christine A., Dennis, Paul G. and Schenk, Peer M. (2019). The ability of plants to produce strigolactones affects rhizosphere community composition of fungi but not bacteria. Rhizosphere, 9, 18-26. doi: 10.1016/j.rhisph.2018.10.002
Syed-Ab-Rahman, Sharifah Farhana, Xiao, Yawen, Carvalhais, Lilia C., Ferguson, Brett J. and Schenk, Peer M. (2019). Suppression of Phytophthora capsici infection and promotion of tomato growth by soil bacteria. Rhizosphere, 9, 72-75. doi: 10.1016/j.rhisph.2018.11.007
Syed-Ab-Rahman, Sharifah Farhana, Carvalhais, Lilia C., Chua, Elvis, Xiao, Yawen, Wass, Taylor J. and Schenk, Peer M. (2018). Identification of soil bacterial isolates suppressing different Phytophthora spp. and promoting plant growth. Frontiers in Plant Science, 9 1502, 1502. doi: 10.3389/fpls.2018.01502
Liu, Hongwei, Carvalhais, Lilia C., Schenk, Peer M. and Dennis, Paul G. (2018). Activation of the salicylic acid signalling pathway in wheat had no significant short-term impact on the diversity of root-associated microbiomes. Pedobiologia, 70, 6-11. doi: 10.1016/j.pedobi.2018.08.001
Liu, Hongwei, Carvalhais, Lilia C., Crawford, Mark, Singh, Eugenie, Dennis, Paul G., Pieterse, Corné M.J. and Schenk, Peer M. (2017). Inner plant values: Diversity, colonization and benefits from endophytic bacteria. Frontiers in Microbiology, 8 (DEC) 2552, 2552. doi: 10.3389/fmicb.2017.02552
Moyle, Richard L, Pretorius, Lara, Carvalhais, Lilia C and Schenk, Peer M (2017). Complete Nucleotide Sequence of Australian Tomato spotted wilt virus Isolate TSWV-QLD2. Genome announcements, 5 (47) e01267-17, 1-2. doi: 10.1128/genomeA.01267-17
Moyle, Richard L., Carvalhais, Lilia C., Pretorius, Lara-Simone, Nowak, Ekaterina, Subramaniam, Gayathery, Dalton-Morgan, Jessica and Schenk, Peer M. (2017). An Optimized Transient Dual Luciferase Assay for Quantifying MicroRNA Directed Repression of Targeted Sequences. Frontiers in Plant Science, 8 1631, 1631. doi: 10.3389/fpls.2017.01631
Carvalhais, Lilia C., Schenk, Peer M. and Dennis, Paul G. (2017). Jasmonic acid signalling and the plant holobiont. Current Opinion in Microbiology, 37, 42-47. doi: 10.1016/j.mib.2017.03.009
Dang, Yash Pal, Balzer, Anna, Crawford, Mark, Rincon-Florez, Vivian, Liu, Hongwei, Melland, Alice Rowena, Antille, Diogenes, Kodur, Shreevatsa, Bell, Michael John, Whish, Jeremey Patrick Milroy, Lai, Yunru, Seymour, Nikki, Carvalhais, Lilia Costa and Schenk, Peer (2017). Strategic tillage in conservation agricultural systems of north-eastern Australia: why, where, when and how?. Environmental Science and Pollution Research, 25 (2), 1-16. doi: 10.1007/s11356-017-8937-1
Liu, Hongwei, Carvalhais, Lilia C., Schenk, Peer M. and Dennis, Paul G. (2017). Effects of jasmonic acid signalling on the wheat microbiome differ between body sites. Scientific Reports, 7 (1) srep41766, 41766. doi: 10.1038/srep41766
Liu, Hongwei, Carvalhais, Lilia C., Crawford, Mark, Dang, Yash P., Dennis, Paul G. and Schenk, Peer M. (2016). Strategic tillage increased the relative abundance of Acidobacteria but did not impact on overall soil microbial properties of a 19-year no-till Solonetz. Biology and Fertility of Soils, 52 (7), 1021-1035. doi: 10.1007/s00374-016-1138-0
Liu, Hongwei, Carvalhais, Lilia Costa, Kazan, Kemal and Schenk, Peer M. (2016). Development of marker genes for jasmonic acid signaling in shoots and roots of wheat. Plant Signaling and Behavior, 11 (5) e1176654, e1176654. doi: 10.1080/15592324.2016.1176654
Rincon-Florez, Vivian A., Ng, Clement, Dang, Yash P., Schenk, Peer M. and Carvalhais, Lilia C. (2016). Short-term impact of an occasional tillage on microbial communities in a Vertosol after 43 years of no-tillage or conventional tillage. European Journal of Soil Biology, 74, 32-38. doi: 10.1016/j.ejsobi.2016.03.001
Liu, Hongwei, Carvalhais, Lilia C., Rincon-Florez, Vivian, Crawford, Mark, Dang, Yash P., Dennis, Paul G. and Schenk, Peer M. (2016). One-time strategic tillage does not cause major impacts on soil microbial properties in a no-till Calcisol. Soil and Tillage Research, 158, 91-99. doi: 10.1016/j.still.2015.12.007
Liu, Hongwei, Crawford, Mark, Carvalhais, Lilia C., Dang, Yash P., Dennis, Paul G. and Schenk, Peer M. (2016). Strategic tillage on a Grey Vertosol after fifteen years of no-till management had no short-term impact on soil properties and agronomic productivity. Geoderma, 267, 146-155. doi: 10.1016/j.geoderma.2016.01.002
Newsham, Kevin K., Hopkins, David W., Carvalhais, Lilia C., Fretwell, Peter T., Rushton, Steven P., O'Donnell, Anthony G. and Dennis, Paul G. (2016). Relationship between soil fungal diversity and temperature in the maritime Antarctic. Nature Climate Change, 6 (2), 182-186. doi: 10.1038/nclimate2806
Rincon-Florez, Vivian A., Dang, Yash P., Crawford, Mark H., Schenk, Peer M. and Carvalhais, Lilia C. (2015). Occasional tillage has no effect on soil microbial biomass, activity and composition in Vertisols under long-term no-till. Biology and Fertility of Soils, 52 (2), 191-202. doi: 10.1007/s00374-015-1066-4
Correa, Eduardo, Carvalhais, Lilia, Utida, Mirian, Oliveira, Christiane Abreu and Scotti, Maria Rita (2015). Effect of plant species on P cycle-related microorganisms associated with litter decomposition and P soil availability: implications for agroforestry management. IForest, 9 (2), 294-302. doi: 10.3832/ifor1459-008
Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Kidd, Brendan N., Vivanco, Jorge M. and Schenk, Peer M. (2015). Linking jasmonic acid signaling, root exudates, and rhizosphere microbiomes. Molecular Plant-Microbe Interactions, 28 (9), 1049-1058. doi: 10.1094/MPMI-01-15-0016-R
Crawford, M. H., Rincon-Florez, V., Balzer, A., Dang, Y. P., Carvalhais, L. C., Liu, H. and Schenk, P. M. (2015). Changes in the soil quality attributes of continuous no-till farming systems following a strategic tillage. Soil Research, 53 (3), 263-273. doi: 10.1071/SR14216
Kierul, Kinga, Voigt, Birgit, Albrecht, Dirk, Chen, Xiao-Hua, Carvalhais, Lilia C. and Rainer Borriss (2015). Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology, 161 (1), 131-147. doi: 10.1099/mic.0.083576-0
Chen, Yi Chung, Kidd, Brendan N., Carvalhais, Lilia C. and Schenk, Peer M. (2014). Molecular defense responses in roots and the rhizosphere against Fusarium oxysporum. Plant Signaling and Behavior, 9 (12) e977710, e977710-1-e977710-3. doi: 10.4161/15592324.2014.977710
Carvalhais, Lilia C., Dennis, Paul G. and Schenk, Peer M. (2014). Plant defence inducers rapidly influence the diversity of bacterial communities in a potting mix. Applied Soil Ecology, 84, 1-5. doi: 10.1016/j.apsoil.2014.06.011
Carvalhais, Lilia C., Dennis, Paul G., Fedoseyenko, Dmitri, Hajirezaei, Mohammad-Reza, Borriss, Rainer and von Wirén, Nicolaus (2013). Erratum to Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency [J. Plant Nutr. Soil Sci 174 (2011) 311]. Journal of Plant Nutrition and Soil Science, 176 (4), 641-641. doi: 10.1002/jpln.201390025
Carvalhais, Lilia C., Dennis, Paul G., Fan, Ben, Fedoseyenko, Dmitri, Kierul, Kinga, Becker, Anke, von Wiren, Nicolaus and Borriss, Rainer (2013). Linking plant nutritional status to plant-microbe interactions. PLoS One, 8 (7) e68555, e68555.1-e68555.13. doi: 10.1371/journal.pone.0068555
Carvalhais, Lilia C., Muzzi, Frederico, Tan, Chin-Hong, Hsien-Choo, Jin and Schenk, Peer M. (2013). Plant growth in Arabidopsis is assisted by compost soil-derived microbial communities. Frontiers in Plant Science, 4 (JUL) 235, 235.1-235.15. doi: 10.3389/fpls.2013.00235
Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Tyson, Gene W., Vivanco, Jorge M. and Schenk, Peer M. (2013). Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE, 8 (2) e56457, e56457. doi: 10.1371/journal.pone.0056457
Carvalhais, Lilia C. and Schenk, Peer M. (2013). Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities. Methods in Enzymology, 531, 251-267. doi: 10.1016/B978-0-12-407863-5.00013-7
Rincon-Florez, Vivian A., Carvalhais, Lilia C. and Schenk, Peer M. (2013). Culture-independent molecular tools for soil and rhizosphere microbiology. Diversity, 5 (3), 581-612. doi: 10.3390/d5030581
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2012). Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91 (2), 246-251. doi: 10.1016/j.mimet.2012.08.011
Fan, Ben, Carvalhais, Lilia C., Becker, Anke, Fedoseyenko, Dmitri, von Wiren, Nicolaus and Borriss, Rainer (2012). Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates. BMC Microbiology, 12 (1) 116, 116.1-116.13. doi: 10.1186/1471-2180-12-116
Schenk, Peer M., Carvalhais, Lilia C. and Kazan, Kemal (2012). Unravelling plant-microbe interactions: Can multi-species transcriptomics help?. Trends in Biotechnology, 30 (3), 177-184. doi: 10.1016/j.tibtech.2011.11.002
Carvalhais, Lilia C., Dennis, Paul G., Fedoseyenko, Dmitri, Hajirezaei, Mohammad-Reza, Borriss, Rainer and von Wiren, Nicolaus (2011). Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency. Journal of Plant Nutrition and Soil Science, 174 (1), 3-11. doi: 10.1002/jpln.201000085
Raposeiras, Ruy, Marriel, Ivanildo Evodio, Muzzi, Maria Rita Scotti, Paiva, Edilson, Filho, Israel Alexandre Pereira, Carvalhais, Lilia Costa, Passos, Raul Vinicius Magalhaes, Pinto, Patricia Pereira and de Sa, Nadja Maria Horta (2006). Rhizobium strains competitiveness on bean nodulation in Cerrado soils. Pesquisa Agropecuaria Brasileira, 41 (3), 439-447. doi: 10.1590/S0100-204X2006000300010
Conference Papers
Liu, Hongwei, Rincon-Florez, Vivian, Dang, Yash, Crawford, Mark, Balzer, Anna, Bell, Mike, Ram, Dalal, Costa Carvalhais, Lilia and Schenk, Peer (2014). Strategic tillage impacts on biological attributes of long term no-till soils in northern grain region of Australia. Soil Science 2014: National Soil Science Conference, Melbourne, VIC, Australia, 23-27 November, 2014. Warragul, VIC, Australia: Australian Society of Soil Science.
Rincon-Florez, Vivian A., Carvalhais, Lilia C., Liu, Hongwei, Dang, Yash, Crawford, Mark, Balzer, Anna, Bell, Mike, Ram, Dalal and Schenk, Peer (2014). Strategic tillage did not affect soil microbial bioindicators in long-term no-till farming systems in vertosols from Queensland, Australia. Soil Science 2014: National Soil Science Conference, Melbourne, VIC, Australia, 23-27 November 2014. Warragul, VIC, Australia: Australian Society of Soil Science.