Webster, Nicole

Dr Nicole Webster

Principle Research Scientist
A Healthy & Resilient Great Barrier Reef

Contact Information

Phone (07) 4753 4151
Int +61 7 4753 4151
Email n.webster@aims.gov.au

Other Profiles

Google Scholar
Research Gate


Nicole obtained her PhD in 2001 by researching the microbial ecology of Great Barrier Reef sponges and then undertook postdoctoral research between 2001-05 at the University of Canterbury / Gateway Antarctica where she investigated the utility of microbial symbionts as biomarkers for environmental stress in the Antarctic marine ecosystem. In 2005, Nicole commenced a research scientist position at AIMS to undertake research assessing the impact of environmental stress on model invertebrate symbioses and exploring the role of microorganisms as inducers for settlement and metamorphosis of coral reef invertebrates.

Nicole’s research group uses experimental and field based ecological research to explore multiple facets of coral reef microbiology.  Metagenomic, metatranscriptomic and advanced imaging approaches are employed to understand reef invertebrates as ‘metaorganisms’ and translate this research into strategic tools for coral reef management. Nicole also holds a joint appointment at the University of Queensland, where she leads inter-institutional research projects in the field of ecogenomics.


Tertiary education

James Cook University / Australian Institute of Marine Science, 2001 PhD

James Cook University, 1995 Bachelor of Science, Honours (Class I)

James Cook University, 1994 Bachelor of Science

Employment history

Australian Institute of Marine Science (2005-Present)

Australian Centre for Ecogenomics, University of Queensland (2017-Present)

University of Canterbury / Gateway Antarctica (2001-2005)


2012 Future Fellowship (Australian Research Council)

2010 Australian Academy of Science Dorothy Hill Award

2010 Australian Academy of Science Rod Rickards International Fellow

2010 Queensland International Fellowship (Qld Government)

Microbial Inducers of Coral Settlement

Many reef invertebrates settle and metamorphose in response to microbial biofilms. Microbial biofilms have a complex 3D structure comprised of many interacting microbial species encased in a hydrated matrix of extracellular polymeric substances. When invertebrate larvae are selecting a surface on which to settle and metamorphose, they can differentiate between biofilm characteristics including age, bacterial density, biochemical signals, and the overall community composition. However, in most instances, the specific microbial taxa, genes or pathways responsible for producing larval settlement cues are unknown. Work in this program aims to identify microbial inducers (taxa and/or functions) for coral settlement.  This research is expected to provide a novel suite of chemical / biological cues that can be used in coral aquaculture programs for reef restoration on the Great Barrier Reef.

Microbial Symbiosis & Environmental Stress

The vulnerability of marine invertebrates to environmental stress has traditionally been assessed by determining how animals respond to specific environmental factors.  However, over the past decade molecular science has highlighted the critical importance of microorganisms to invertebrate health, fitness and survival.  Research undertaken within this program explores the functional roles of microbial symbionts in coral reef invertebrates and uses multifactorial experiments to deliver stakeholders with knowledge about how temperature, ocean acidification, nutrients, sediments and contaminants affect the ‘metaorganism’ (host and associated microbial community).

Microbial Contributions to Reef Invertebrate Adaptation

Significant declines in coral reef health and biological diversity are predicted for the coming decades unless coral reef organisms adapt or acclimatise to increasing levels of environmental pressure. Research undertaken in this program uses the AIMS National Sea Simulator to explore the adaptive capacity of reef organisms to climate change.  Some organisms such as corals and sponges can rapidly alter their microbial symbionts in response to future climate change conditions. We explore whether these symbiotic shifts influence the ability of the host to acclimatise/adapt to new environmental conditions. Favorable symbiotic shifts that enhance the scope for growth or infer environmental tolerance to the host may be passed to subsequent generations, enabling long term acclimatisation.

Reef Viruses

Viruses are the most abundant entities in the oceans (if stretched end-to-end they would span farther than the nearest 60 galaxies).  Viruses are found in coral reef seawater, eukaryotic hosts and their associated eukaryotic and prokaryotic symbionts.  Despite this, our understanding of how viruses contribute to reef invertebrate health is limited. Our work on viruses that inhabit coral reef invertebrates is showing that they are host species-specific and have functional repertoires that are distinct from viruses in the surrounding seawater. We are also finding evidence for viral transfer of specific auxiliary genes involved in processes like heavy metal resistance, providing a mechanism for viral mediated acclimatisation of reef species to local environmental conditions.

Microbial Indicators

Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although microbes are a major contributor to the stability and functioning of coral reefs, there is uncertainty about how reef microbes respond to environmental perturbations and whether they are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. In this research we are establishing a comprehensive microbial genomic reference database for the Great Barrier Reef coupled with extensive environmental metadata to better assess the diagnostic value of free-living and host-associated microbes to infer the environmental state of the Reef.

Partnerships and collaborations

Prof. Gene Tyson, University of Queensland- Defining the functional role of the coral microbiome

Prof. Michael Wagner, University of Vienna- Unlocking the Ianthella basta symbiome

Prof. Thomas Rattei, University of Vienna- Revealing the structure, evolution and environmental sensitivity of symbioses in basal metazoan

Prof. Manuel Aranda, KAUST- Establishing Ircinia ramosa & A. loripes as model meta-organisms for climate change adaptation research

Prof. James Bell, Victoria University- Coral reefs of today: sponge reefs of the future?

Prof. Torsten Thomas, University of NSW- The global sponge microbiome project

Prof. Justin Seymour, University of Technology Sydney- The Australian microbiome project


Board Member of the International Society for Microbial Ecology

Director of the ISME International Ambassador Program

Member of the Australian Society of Microbiology

Member of the United Nations Pool of Experts for Assessment of the State of the Marine Environment

Senior Editor Environmental Microbiology

Senior Editor mSystems

Student supervision and teaching

Principal Research Fellow, University of Queensland

Adjunct Associate Professor at James Cook University

Graduated PhD students

Muhammad Abdul Wahab (AIMS@JCU - Sponge reproduction in a changing climate)

Heidi Luter (AIMS@JCU- Sponge disease)

Rachel Simister (Uni Auckland- Specificity of sponge symbiosis)

Chris Fan Lu (Uni NSW – Defining core functions in sponge symbiosis)

Raffaella Pantile (Uni Genoa- Defining environmental stress responses in marine sponges)

Jessica Tout (UTS- Structuring of coral reef microbial communities)

Holly Bennett (Victoria Uni - Modelling sponge community responses to climate change)

Carmen Astudillo (Uni Auckland- Biogeography and specificity of sponge symbionts)

Brian Strehlow (Uni WA- WAMSI Dredging effects on filter feeders)

Blake Ramsby (AIMS@JCU- Modelling changes in sponge bioerosion under climate change)

Currently enrolled PhD students

Cecilia Pascelli (AIMS@JCU- Sponge-virus interactions in a changing climate)

Florian Moeller (Uni Vienna- Sponge symbiotic function)

Bettina Glasl (AIMS@JCU- Microbial indicators for coral reef health)

Emma Marangon (AIMS@JCU- Microbial contributions to acclimatisation of reef species)

Paul O’Brien (AIMS@JCU- Co-evolution and phylosymbiosis in coral reef invertebrates)

Jose Montalvo Proano (AIMS@JCU- Acclimation responses of corals to future envionments)

Pam Engelberts (Uni Qld- Microbial symbiosis in the ecologically important Ianthella basta)


Over 150 scientific publications with over 8000 citations
Visit Google Scholar profile 

Most Recent 2019 Publications

  • Botté ES, Nielsen S, Webster J, Robbins S, Abdul-Wahab M, Thomas T, Webster NS (2019) Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nature Communications. In Press.
  • Zhang S, Song W-Z, Wemheuer B, Reveillaud J, Webster NS, Thomas T (2019) Evolutionary and ecological adaptation of Thaumarchaeota to the sponge environment. mSystems. In Press.
  • Laffy PW, Botté ES, Wood-Charlson EM, Weynberg KD, Rattei T, Webster NS (2019) Thermal stress modifies the marine sponge virome. Environmental Microbiology Reports. DOI.org/10.1111/1758-2229.12782.
  • Moeller FU, Webster NS et al. and Wagner M (2019) Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environmental Microbiology. DOI.org/10.1111/1462-2920.14732.
  • Cavicchioli R, et al. and Webster NS (2019) Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology. DOI.org/10.1038/s41579-019-0222-5.
  • Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS (2019) Microbial predictors of environmental perturbations in coral reef ecosystems.  Microbiome. 7:94 DOI.org/10.1186/s40168-019-0705-7.
  • Rovellini A, Dunn MR, Fulton EA, Webster NS, Smith DJ, Jompa J, Haris A, Berman J, Bell JJ (2019) Decadal variability in sponge abundance and biodiversity on an Indo-Pacific coral reef. Marine Ecology Progress Series. 620:63-76 DOI.org/10.3354/meps12968.
  • Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarria M, Stein L, McGenity TJ, Webster N, et al. and Harper L (2019) The urgent need for microbiology literacy in society. Environmental Microbiology 21:1513-1528 DOI.org/ 10.1111/1462-2920.14611.
  • Lurgi M, Thomas T, Wemheuer B, Webster NS, Montoya JM (2019) Modularity and functioning of the global sponge-microbiome network. Nature Communications 10:992 DOI.org/10.1038/s41467-019-08925-4.
  • Zhang W, et al., Webster NS, Qian P-Y  (2019) Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature Communications 10:517 DOI.org/10.1038/s41467-019-08463-z.
  • O’Brien PA, Webster NS, Miller DJ, Bourne DG (2019) Host-microbial co-evolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10: e02241-18 DOI.org/10.1128/mBio.02241-18.
  • Glasl B, Smith C, Bourne DG, Webster NS (2019) Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7:e6377 DOI.org/10.7717/peerj.6377.
  • Roux S, et al., Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton K, Yilmaz P, Yoshida T, Young MJ, Yutin N, Zeigler Allen L, Kyrpides NC, Eloe-Fadrosh EA (2019) Minimum Information about Uncultivated Virus Genomes (MIUViG): a Community Consensus on Standards and Best Practices for Describing Genome Sequences from Uncultivated Viruses. Nature Biotechnology 37(1):29-37 DOI.org/10.1038/nbt.4306.