Professor Lily Pereg

Professor, Molecular and Cellular Biology - Faculty of Science, Agriculture, Business and Law; School of Science and Technology

Lily Pereg

Phone: +61 02 6773 2708



Vale Lily Pereg

The University of New England extends deepest sympathy to the family, friends, colleagues and students of Dr Lily Pereg who tragically passed in January 2019.

Lily was a microbial ecologist with a 25-year research experience in plant, soil and benthos microbiology. She had been leading research on host-microbial interactions and their genetic regulations, microbial diversity and function in natural and agricultural settings, nitrogen cycle and, recently, soil and human health.  Lily obtained a PhD from the University of Sydney (1998) and gained postdoctoral experience from the Institute for Genetics, University of Cologne, Germany (1998-2001), before joining UNE in 2001.


BSc (BGU), MSc (TAU), PhD (USYD)



  • Chair of the Soil Biology, Microbiology and Biodiversity subdivision, EGU2017-18 (since April 2016)
  • Executive Editor of SOIL, an interactive open access journal of the European Geosciences Union (EGU) (since 2014)
  • Guest Editor of a special issue on Soil and Human Health, The European Journal of Soil Science (2017).
  • Guest Editor of a special issue on Plant-Microbe Interactions, Frontiers in Plant Science (2017-18).
  • Member of the International Advisory Committee of the Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation (since 2014).
  • Member of the International Advisory Committee of the International Symposium on Nitrogen Fixation with Non-Legumes (since 2015)
  • Vice Chair of the Soil System Science subdivision: Soil Biology, Microbiology and Biodiversity, EGU2015-16
  • Secretary of the Soil System Science subdivision: Soil Biology, Microbiology and Biodiversity, EGU2014 (2013–2014)
  • Member, Australian Society for Microbiology, Genetics Society of Australia, Australian Plant Pathology Society, Australian Coral Reef Society, Soil Science Society of America and International Society for Microbial Ecology (ongoing)
  • Referee for international scientific journals, for example AEM, EMI, Microbial Ecology, EEB, SBB, SDD, PlosOne, FEMSEC, LDD, Research in Microbiology (ongoing)

Academic positions

  • Chair, Research Group for Molecular Biology, School of Science and Technology, University of New England (2011-ongoing)
  • Discipline Convenor, Molecular and Cellular Biology, University of New England (2011- April2015)
  • Discipline representative on School Executive Committee (January 2011 – April 2015)
  • Leader, Research Centre for Molecular Microbiology, University of New England (2009-2011)
  • Discipline representative on School Research Committee (January 2008 – April 2015)
  • Member, Academic Board, University of New England(2002 – 2008)
  • Course Coordinator, Bachelor of Science, University of New England(2002 - 2003)
  • Chair, Bachelor of Science Award Advisory Committee, Faculty of the Sciences, UNE (2002 - 2003)
  • Member, Board of Studies in the Sciences, Faculty of the Sciences, UNE (2002 - 2003)
  • Member, Board of Examiners and Student Affair Committee, UNE (2002 - 2003)

Consultancy Interests

Soil microbiology; Plant pathology; Beneficial microbes; Inoculants; Biocontrol; Nitrogen cycle

Teaching Areas

During the last 20 years, Lily has been developing, teaching and coordinating units in biology, microbiology, biochemistry, molecular biology, biotechnology and genetics on all levels of undergraduate and postgraduate degrees.

Lily’s current teaching and coordinating includes the following units at UNE:

BCHM210/410 Introductory biochemistry and molecular biology
BTEC360/460/560 Biotechnology
MICR350/450/550 Infectious diseases of the human body
MICR220 Microbiology

Research Interests

Lily’s current research interests in microbial ecology are listed below. Lily is utilising a diverse range of methods, including molecular biology, biochemistry, microbiology and physiology, for investigating questions related to ecosystem health.

  • Plant interactions with pathogenic and beneficial soil microbes

  • Microbial nitrogen cycling in soil and the marine benthos

  • Soil biodiversity and human health

  • Agricultural management and soil health; Soil microbial function ; microbiomes

  • The impact of bushfire severity, tree community and management on the recovery of soil microbial function and diversity; forest soil microbiome

  • Detection and virulence of the pathogenic fungus Thielaviopsis basicola causing black root rot in agricultural soils

  • Biocontrol of crop soil-borne diseases

  • Gene regulation and signal transduction in root associated bacteria (Azospirillum spp.)

  • Microbial indicators of ecosystem health

  • Probiotics in lobster aquaculture

  • Coral microbial diversity and infectious disease
Selected competitive grants

  • Pereg, L. (April 2017-June 2017) 2017 Endeavour Executive Fellowship. Awarded to L Pereg for developing research collaboration and memorandum of understanding between Australian home university and a Spanish university. Approx. $11,000.
  • Jorge Mataix-Solera, Fuensnta Garcia-Orenesand a group of international collaborators, including L. Pereg (2017-2021) Post-fire management strategies oriented to preserve and improve soil quality. Led by University Miguel Hernández, Spain. 74,000 Euros.
  • Wilson B, Knox O, Heiko D, Pereg L, Griffith B, Hobley N and Nachimuthu G (July 2015 - July 2018) Soil System Research – physical, chemical and biological processes for plant growth and carbon capture down the whole soil profile. Awarded by the Cotton Research and Development Corporation. Approx. $550,000.
  • Pereg, L. (July 2012- July 2015) Microbial solutions for sustainable Cotton and soil health management. Awarded by the Cotton Research and Development Corporation for the isolation and application of microbial biocontrol agents and biofertilisers. $318,649.
  • Wilson, S., M Tighe and L Pereg (2015) Quantifying threats to Australian ecosystems from antimony contamination. Research Seed Grant, UNE. $19,826.
  • Pereg, L. (2013-2016) Microbial tools for advancing the management of soil and seedling health in cotton production systems. Cotton Research and Development Corporation. Scholarship and operational funds for supporting a PhD project under my supervision. $51,500
  • Pereg, L. (2013) Biological indicators for health and productivity in crop production soils. Research Seed Grant, UNE. $15,000.
  • Pereg, L. (Jan-March 2012) Scoping the potential uses of beneficial microorganisms for increasing the productivity of cropping systems. Desktop Review invited by Cotton Research and Development Corporation. $7000.
  • Pereg, L., Backhouse, D., Katz, M., Nehl, D and Driessen, S.  (2007-2011) Linking cotton-pathogen molecular interactions and black root rot management.  CCC-CRC/Cotton Research and Development Corporation. $476,405.
  • Pereg, L. (2006-2009) Bio-control agents for managing black root rot in Australian Cotton. Cotton Catchment Community CRC, Scholarship and operational funds for supporting a PhD project under my supervision. $96,000
  • Zhulin, I., (leader, Georgia Institute of Technology, Atlanta) and a group of international collaborators, including L. Pereg-Gerk (2005-2008) Sequencing the genome of the plant promoting bacterium Azospirillum brasilense. US Department of Agriculture (USDA)/National Science Foundation (NSF).
  • Pereg, L., Backhouse, D, Katz, M. and Nehl, D.  (2004-2007) Molecular Factors determining Thielaviopsis basicola-cotton interactions leading to Black Root Rot disease CCC-CRC/Cotton Research and Development Corp. $181,119.
  • Pereg, L., D. Backhouse, M. Katz, Cheetham, B. Entsch (2003-2006) Application of molecular methods for controlling microbial diseases of plants. VC-supported Postdoctoral Fellowship, UNE. $230,000.
  • Walkden-Brown, S.W., Le Jambre, L.F., Groves, P.J., Cheetham, B.F., Windon, R.G., Katz, M.E. McClure, S.J., Backhouse, D., Pereg, L., Islam, A.F. (2003) Quantitative PCR facility for New England Region.  ARC Linkage Infrastructure Equipment and Facilities Grant.  Partner Organisations: UNE, CSIRO, Baiada Poultry. $102,000
  • S.A. Glover, M.J. Gunter, J.R. McFarlane, P.R. Grave, T.C. Brown, D. Backhouse, D.J. Tucker, L. Pereg, D.J. Brunckhorst, k. Watson, D. Lamb, M. Choct, P.C. Gregg (2003) LC-MS system for Faculty of Sciences, UNE. ARC Linkage Infrastructure Equipment and Facilities Grant. $250,000.

Research Supervision Experience

Lily has supervised 21 PhD, 3 MSc and 10 Honours students in microbiology, most as Principal Supervisor. The student theses included research in the following areas:

  • Pathogenic and beneficial microbial-plant interactions,
  • Microbiomes,
  • Soil microbial function, in particular nitrogen cyclers,
  • Soil and human health,
  • Microbial diversity in agricultural and natural soils,
  • Microbial recovery after bushfire,
  • Molecular aspects of pathogen suppression by antagonistic bacteria,
  • Isolation, identification and application of soil beneficial & biocontrol microbes in crop production systems,
  • Probiotics in aquaculture for the control of larval microbial diseases,
  • Signalling pathways in plant growth promoting bacteria,
  • Ecological aspects and microbial populations of coral disease in subtropical waters and
  • Microbial protein biochemistry and genetic engineering.

Lily also co-supervised students at the University of Sydney, NSW, Australia, and at the K. University Leuven, Belgium, on plant interactions with soil beneficial bacteria.

Related Links

Dr Lily Pereg's Microbial Ecology Laboratory webpage, click here

Further Information


BCHM210 Introductory Molecular Biology and Biochemistry I
BCHM410 Introductory Molecular Biology and Biochemistry I
BTEC360/460/560 Biotechnology and Advanced Molecular Biology
MICR350/450/550 Clinical Microbiology and Virology
MICR220 Introduction Microbiology

Selected publications

  • F Garcia-Orenes, Mataix-Solera J, McMillan M and Pereg L (under revisions) The impact of post fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil. (Submitted to Science of the total Environment).
  • Pereg L, Morugán-Coronado A, McMillan M and García-Orenes F (under review) Restoration of nitrogen cycling community in grapevine soil under a decade of organic fertilization revealed by N-cycling gene abundance. (Submitted to Soil and Tillage Research).
  • MO Obiakor, SC Wilson, M Tighe, L Pereg (under review) Exposure to antimony induces a negative response in the soil functional bacterium Azospirillum brasilense Sp7. (submitted to Land Degradation and Development).
  • MO Obiakor, M Tighe, L Pereg, SC Wilson (under review) Bioaccumulation, trophodynamics and ecotoxicity of antimony in environmental freshwater food webs. (Submitted to Critical Reviews in Environmental Science and Technology).
  • MO Obiakor, M Tighe, Z Wang, CD Ezeonyejiaku, L Pereg, SC Wilson (under review) The relative sensitivity of freshwater species to antimony(III): Implications for water quality guidelines and ecological risk assessments. (Submitted to Environmental Science and Pollution Research).
  • Rabbi SMF, Daniel H, Lockwood PV, Macdonald C, Pereg L, Tighe M, Wilson B and I Young (2016) Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity. Scientific Reports 6:33012 | DOI: 10.1038/srep33012.
  • Pereg L, de-Bashan L and Bashan Y (2016) Assessment of affinity and specificity of Azospirillum for plants. Plant and Soil 399:389-414.
  • Pereg L and McMillan M (2015) Scoping the potential uses of beneficial microorganisms for increasing productivity in cotton cropping systems. Soil Biology and Biochemistry 80: 349-358 (available online since 04/11/2014 at doi:10.1016/j.soilbio.2014.10.020).
  • Quinton J,Mataix-Solera J, Brevik E, Cerdá A, Pereg L, Six J, van Oost K (2015) Soil: a journey through time and space. In: Blöschl G, Thybo H, Savenije H (eds.) A Voyage through scales. Edition Lammerhuber, ISBN: 978-3-901753-84-8. Pages 92-97.
  • Pereg L and McMillan M (2015) Molecular tools to study Azospirillum sp. and other related PGPRs. In: Okon Y, Cassan F and Creus C (eds.) Handbook for Azospirillum. Technical Issues and Protocols. Springer International Publishing. Pages 65-82.
  • Pereg L (2015) Azospirillum cell aggregation, attachment and plant interaction. In: Okon Y, Cassan F and Creus C (eds.) Handbook for Azospirillum. Technical Issues and Protocols. Springer International Publishing. Pages 181-197.
  • Brevik EC, Cerdá A, Mataix-Solera J, Pereg L, Quinton JN, Six J and Van Oost K (2014) The interdisciplinary nature of SOIL. SOIL 1: 117-129. (doi:10.5194/soil-1-117-2015).
  • Hou X, McMillan M, Coumans JVF, Poljak A, Raftery MJ and Pereg L (2014) Cellular Responses during Morphological Transformation in Azospirillum brasilense and Its flcA Knockout Mutant. PLoS ONE 9(12): e114435. doi:10.1371/journal.pone.0114435.
  • McMillan M and PeregL (2014)Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense. PLoS ONE 9(5): e98162. doi: 10.1371/journal.pone.0098162
  • Pereg LL (2013) Black root rot of cotton in Australia – the host, the pathogen and the disease. Crop and Pasture Science , 64:1112-1126.
  • Goulden EF, Hall MR, Pereg LL and Høj L (2013) Probiont niche specialization contributes to additive protection against Vibrio owensii in spiny lobster larvae. Environmental Microbiology Reports, 5(1):39-48.doi:10.1111/1758-2229.12007
  • Goulden EF, Hall MR, Pereg LL and Høj L (2012) Identification of an antagonistic probiotic combination protecting ornate spiny lobster (Panulirus ornatus) larvae against Vibrio owensii infection. PLoS ONE, 7(7): e39667. doi:10.1371/journal.pone.0039667
  • Goulden EF, Hall MR, Bourne DG, Pereg LL, Høj, L (2012) Pathogenicity and Infection Cycle of Vibrio owensii in Larviculture of the Ornate Spiny Lobster (Panulirus ornatus). Applied and Environmental Microbiology, 78(8): 2841-2849.
  • Godwin, S, Bent E, Borneman D and Pereg L (2012) The Role of Coral-Associated Bacterial Communities in Australian Subtropical White Syndrome of Turbinaria mesenterina. PLoS ONE, 7(9): e44243. doi:10.1371/journal.pone.0044243.
  • Amprayn K, Rose MT, Kecskés M, Pereg L, Nguyen HT and Kennedy IR (2012) Plant growth promoting characteristics of soil yeast (Candida tropicalis HY) and its effectiveness for promoting rice growth. Applied Soil Ecology, 61:295-299. (published on-line in advance of print in 2011, doi:10.1016/j.apsoil.2011.11.009 ).
  • Krishnen G, Kecskés ML, Rose MT, Geelan-Small P, Amprayn K, Pereg L and Kennedy IR (2011) Field monitoring of plant growth promoting rhizobacteria by colony immunoblotting. Canadian Journal of Microbiology, 51(11): 914-922.
  • Coumans JVF, Harvey J, Backhouse D, Poljak A, Raftery MJ, Nehl D, Katz ME, and Pereg L(2011) Proteomics assessment of host-associated microevolution in the fungus Thielaviopsis basicola isolates.  Environmental Microbiology, 13:3 576-588.