Dr Emmanuelle Botte

Dr Emmanuelle Botte

Administrative Officer
  • PADI Rescue Diver
  • PADI Scientific Diver
  • First Aid training
  • Oxygen provider training
Medicine & Health
Education & Student Experience

Marine microbial ecologist, more precisely specialised in the characterisation of the microbiomes of marine invertebrates in an ecological context.

I was born and raised in France, including in the Overseas French Territories of Guadeloupe (Caribbean) and Reunion island (West Indian Ocean). 

Passionate about the environmental cause (especially threats on tropical marine ecosystems) and all things molecular, I graduated from a Bachelor of biochemistry from the University of Pau and Adour countries (France) in 2004, with my last semester conducted at the University of Wollongong (NSW). I then studied at the University Paul Sabatier in Toulouse (France) for my Master's first year (Functional analysis of genomes) and then at the University of Perpignan via domitia (France) for the 2nd year, where I further specialised in Functional molecular ecology.

I obtained a PhD in Tropical marine ecotoxicology from James Cook University in Townsville (Qld). In 2010, I became a Technical Officer, and later on an Experimental Scientist in Marine molecular biology and microbiology within the Australian Institute of Marine Science (AIMS, Qld), under the supervision of Prof Nicole Webster (as well as Lone Hoj and David Bourne until 2013).

In 2021 I resigned from AIMS and took a position as a Research officer in the Centre for Marine Science and Innovation at UNSW under the supervision of Prof Torsten Thomas, on a project funded by the Gordon and Betty Moore Foundation (GBMF).  

Biological Scien​ces building D26, Level 5 East,Office 501
  • Journal articles | 2023
    Botté ES; Bennett H; Engelberts JP; Thomas T; Bell JJ; Webster NS; Luter HM, 2023, 'Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis.', ISME Commun, 3, pp. 53, http://dx.doi.org/10.1038/s43705-023-00247-3
    Journal articles | 2023
    Turnlund AC; Vanwonterghem I; Botté ES; Randall CJ; Giuliano C; Kam L; Bell S; O'Brien P; Negri AP; Webster NS; Lurgi M, 2023, 'Linking differences in microbial network structure with changes in coral larval settlement.', ISME Commun, 3, pp. 114, http://dx.doi.org/10.1038/s43705-023-00320-x
    Journal articles | 2022
    Botté ES; Cantin NE; Mocellin VJL; O’Brien PA; Rocker MM; Frade PR; Webster NS, 2022, 'Reef location has a greater impact than coral bleaching severity on the microbiome of Pocillopora acuta', Coral Reefs, 41, pp. 63 - 79, http://dx.doi.org/10.1007/s00338-021-02201-y
    Journal articles | 2021
    Evensen NR; Vanwonterghem I; Doropoulos C; Gouezo M; Botté ES; Webster NS; Mumby PJ, 2021, 'Benthic micro- and macro-community succession and coral recruitment under overfishing and nutrient enrichment', Ecology, 102, http://dx.doi.org/10.1002/ecy.3536
    Journal articles | 2021
    Robbins SJ; Song W; Engelberts JP; Glasl B; Slaby BM; Boyd J; Marangon E; Botté ES; Laffy P; Thomas T; Webster NS, 2021, 'A genomic view of the microbiome of coral reef demosponges', ISME Journal, 15, pp. 1641 - 1654, http://dx.doi.org/10.1038/s41396-020-00876-9
    Journal articles | 2020
    Botté ES; Luter HM; Marangon E; Patel F; Uthicke S; Webster NS, 2020, 'Simulated future conditions of ocean warming and acidification disrupt the microbiome of the calcifying foraminifera Marginopora vertebralis across life stages', Environmental Microbiology Reports, 12, pp. 693 - 701, http://dx.doi.org/10.1111/1758-2229.12900
    Journal articles | 2019
    Botté ES; Nielsen S; Abdul Wahab MA; Webster J; Robbins S; Thomas T; Webster NS, 2019, 'Changes in the metabolic potential of the sponge microbiome under ocean acidification', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-12156-y
    Journal articles | 2019
    Laffy PW; Botté ES; Wood-Charlson EM; Weynberg KD; Rattei T; Webster NS, 2019, 'Thermal stress modifies the marine sponge virome', Environmental Microbiology Reports, 11, pp. 690 - 698, http://dx.doi.org/10.1111/1758-2229.12782
    Journal articles | 2019
    Luter HM; Whalan S; Andreakis N; Wahab MA; Botté ES; Negri AP; Webster NS, 2019, 'The effects of crude oil and dispersant on the larval sponge holobiont', mSystems, 4, http://dx.doi.org/10.1128/mSystems.00743-19
    Journal articles | 2018
    Laffy PW; Wood-Charlson EM; Turaev D; Jutz S; Pascelli C; Botté ES; Bell SC; Peirce TE; Weynberg KD; van Oppen MJH; Rattei T; Webster NS, 2018, 'Reef invertebrate viromics: diversity, host specificity and functional capacity', Environmental Microbiology, 20, pp. 2125 - 2141, http://dx.doi.org/10.1111/1462-2920.14110
    Journal articles | 2016
    Laffy PW; Wood-Charlson EM; Turaev D; Weynberg KD; Botté ES; Van Oppen MJH; Webster NS; Rattei T, 2016, 'HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts', Frontiers in Microbiology, 7, http://dx.doi.org/10.3389/fmicb.2016.00822
    Journal articles | 2016
    Negri AP; Brinkman DL; Flores F; Botte ES; Jones RJ; Webster NS, 2016, 'Acute ecotoxicology of natural oil and gas condensate to coral reef larvae', Scientific Reports, 6, http://dx.doi.org/10.1038/srep21153
    Journal articles | 2016
    Webster NS; Negri AP; Botté ES; Laffy PW; Flores F; Noonan S; Schmidt C; Uthicke S, 2016, 'Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification', Scientific Reports, 6, http://dx.doi.org/10.1038/srep19324
    Journal articles | 2015
    Morrow KM; Bourne DG; Humphrey C; Botté ES; Laffy P; Zaneveld J; Uthicke S; Fabricius KE; Webster NS, 2015, 'Natural volcanic CO2 seeps reveal future trajectories for host-microbial associations in corals and sponges', ISME Journal, 9, pp. 894 - 908, http://dx.doi.org/10.1038/ismej.2014.188
    Journal articles | 2013
    Botté ES; Smith-Keune C; Jerry DR, 2013, 'Temperature: A prolonged confounding factor on cholinesterase activity in the tropical reef fish Acanthochromis polyacanthus', Aquatic Toxicology, 140-141, pp. 337 - 339, http://dx.doi.org/10.1016/j.aquatox.2013.06.021
    Journal articles | 2013
    Bourne DG; van der Zee MJJ; Botté ES; Sato Y, 2013, 'Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions', Environmental Microbiology Reports, 5, pp. 518 - 524, http://dx.doi.org/10.1111/1758-2229.12055
    Journal articles | 2013
    Taylor MW; Tsai P; Simister RL; Deines P; Botte E; Ericson G; Schmitt S; Webster NS, 2013, 'Sponge-specific bacteria are widespread (but rare) in diverse marine environments', ISME Journal, 7, pp. 438 - 443, http://dx.doi.org/10.1038/ismej.2012.111
    Journal articles | 2013
    Webster N; Pantile R; Botté E; Abdo D; Andreakis N; Whalan S, 2013, 'A complex life cycle in a warming planet: Gene expression in thermally stressed sponges', Molecular Ecology, 22, pp. 1854 - 1868, http://dx.doi.org/10.1111/mec.12213
    Journal articles | 2013
    Webster NS; Negri AP; Flores F; Humphrey C; Soo R; Botté ES; Vogel N; Uthicke S, 2013, 'Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa', Environmental Microbiology Reports, 5, pp. 243 - 251, http://dx.doi.org/10.1111/1758-2229.12006
    Journal articles | 2013
    Webster NS; Uthicke S; Botté ES; Flores F; Negri AP, 2013, 'Ocean acidification reduces induction of coral settlement by crustose coralline algae', Global Change Biology, 19, pp. 303 - 315, http://dx.doi.org/10.1111/gcb.12008
    Journal articles | 2012
    Botté ES; Jerry DR; Codi King S; Smith-Keune C; Negri AP, 2012, 'Effects of chlorpyrifos on cholinesterase activity and stress markers in the tropical reef fish Acanthochromis polyacanthus', Marine Pollution Bulletin, 65, pp. 384 - 393, http://dx.doi.org/10.1016/j.marpolbul.2011.08.020
    Journal articles | 2012
    Simister RL; Deines P; Botté ES; Webster NS; Taylor MW, 2012, 'Sponge-specific clusters revisited: A comprehensive phylogeny of sponge-associated microorganisms', Environmental Microbiology, 14, pp. 517 - 524, http://dx.doi.org/10.1111/j.1462-2920.2011.02664.x
    Journal articles | 2012
    Webster NS; Luter HM; Soo RM; Botté ES; Simister RL; Abdo D; Whalan S, 2012, 'Same, same but different: Symbiotic bacterial associations in GBR sponges', Frontiers in Microbiology, 3, http://dx.doi.org/10.3389/fmicb.2012.00444
    Journal articles | 2011
    Webster NS; Botté ES; Soo RM; Whalan S, 2011, 'The larval sponge holobiont exhibits high thermal tolerance', Environmental Microbiology Reports, 3, pp. 756 - 762, http://dx.doi.org/10.1111/j.1758-2229.2011.00296.x

My current research involves:

  • a Gordon and Betty Moore Foundation project: the testing and validation of a new microfluidic device (Symbio-chip) for the in-situ cultivation of sponge-associated microbes.
  • an AIMS/UNSW collaboration: the characterisation of the microbiome of the marine sponge Stylissa flabelliformis under future ocean conditions.

More broadly, I enjoy:

  • answering current questions in marine microbial ecology by conducting experimental & laboratory work (aquarium, research vessels & research stations) as well as data & statistical analysis (high-performance computing, R, etc…).
  • communicating scientific findings via publications & conference attendance.
  • supporting students by providing advice and mentoring throughout their internships or degree.