I have completed my PhD (awarded on 2011) in Ben-Gurion University of the Negev, Faculty of Engineering, Department of Biotechnology Engineering, in Israel, focusing on the complex microbial populations on coral-biofilm surfaces and on initial biofilm formation on artificial reefs. Later on at The Australian Institute of Marine Science (AIMS), I investigated coral larval settlement and metamorphic processes focusing on coral gene regulation, and characterized microbial populations retrieved from crustose coralline algae (CCA) which induce different levels of coral larvae recruitment.
My current role at UTS is research assistant working within The Plant Functional Biology and Climate Change Cluster Aquatic Processes Group Ocean Microbiology Team, conducting molecular microbial ecology research on environmental aquatic samples. I specialize in utilizing and developing molecular tools to study environmental samples from the marine environment. My current project is investigated the dynamics of Vibrio spp., including human pathogen species, in Sydney Harbour estuary system using qPCR and next generation sequencing technique.
Lambert, B.S., Raina, J.-.B., Fernandez, V.I., Rinke, C., Siboni, N., Rubino, F., Hugenholtz, P., Tyson, G.W., Seymour, J.R. & Stocker, R. 2017, 'A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.', Nature microbiology.View/Download from: UTS OPUS or Publisher's site
Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be sampled by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.A microfluidics-based assay for in situ chemotaxis experiments.
Tran, N.A.T., Seymour, J.R., Siboni, N., Evenhuis, C.R. & Tamburic, B. 2017, 'Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata', Algal Research, vol. 26, pp. 302-311.View/Download from: UTS OPUS or Publisher's site
© 2017 Elsevier B.V. Microalgal biomass has been used to produce biofuels, aquaculture feed, high-value chemicals such as pigments and antioxidants, and even human food. This study addresses one of the key bottlenecks to the commercialisation of microalgal bioproducts: the high energy and environmental cost of harvesting microalgal cells out of suspension. An innovative and sustainable autoflocculation procedure was developed to pre-concentrate microalgal biomass for easier har vesting. Microalgal cell agglomeration by autoflocculation at high pH was induced for the first time, without the addition of a chemical flocculant, in the commercially-relevant microalga Nannochloropsis oculata. Photosynthetic inorganic carbon uptake, in the absence of carbon dioxide supply by mass transfer, was used to raise the culture pH. Autoflocculation started at pH 9.5 and reached a maximum flocculation efficiency of 90% at pH 10.4. Microalgal surface charge-neutralisation by calcium cations, and sweep flocculation by calcium carbonate and calcium phosphate precipitates were identified as the dominant flocculation mechanisms. This was also the first study to measure changes in bacterial community composition under autoflocculation. There was a clear shift from free-living bacteria in suspension to attached bacteria during autoflocculation, with Flavobacteriales becoming the dominant order of bacteria. This highlights the influential role of attached bacteria and bacteria-produced extracellular polymeric substances in microalgal flocculation. This study shows that regulating carbon dioxide supply is a promising green alternative to traditional microalgal flocculation processes as it alleviates the requirement for costly and harmful chemical flocculants and brings us closer to sustainable microalgal bioproducts.
Commault, A.S., Laczka, O., Siboni, N., Tamburic, B., Crosswell, J.R., Seymour, J.R. & Ralph, P.J. 2017, 'Electricity and biomass production in a bacteria-Chlorella based microbial fuel cell treating wastewater', Journal of Power Sources, vol. 356, pp. 299-309.View/Download from: UTS OPUS or Publisher's site
© 2017 Elsevier B.V. The chlorophyte microalga Chlorella vulgaris has been exploited within bioindustrial settings to treat wastewater and produce oxygen at the cathode of microbial fuel cells (MFCs), thereby accumulating algal biomass and producing electricity. We aimed to couple these capacities by growing C. vulgaris at the cathode of MFCs in wastewater previously treated by anodic bacteria. The bioelectrochemical performance of the MFCs was investigated with different catholytes including phosphate buffer and anode effluent, either in the presence or absence of C. vulgaris. The power output fluctuated diurnally in the presence of the alga. The maximum power when C. vulgaris was present reached 34.2 ± 10.0 mW m 2 , double that observed without the alga (15.6 ± 9.7 mW m 2 ), with a relaxation of 0.19 gL 1 d 1 chemical oxygen demand and 5 mg L 1 d 1 ammonium also removed. The microbial community associated with the algal biofilm included nitrogen-fixing (Rhizobiaceae), denitrifying (Pseudomonas stutzeri and Thauera sp., from Pseudomonadales and Rhodocyclales orders, respectively), and nitrate-reducing bacteria (Rheinheimera sp. from the Alteromonadales), all of which likely contributed to nitrogen cycling processes at the cathode. This paper highlights the importance of coupling microbial community screening to electrochemical and chemical analyses to better understand the processes involved in photo-cathode MFCs.
Siboni, N., Balaraju, V., Carney, R., Labbate, M. & Seymour, J.R. 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7.View/Download from: UTS OPUS or Publisher's site
Tout, J., Siboni, N., Messer, L.F., Garren, M., Stocker, R., Webster, N.S., Ralph, P.J. & Seymour, J.R. 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis', Frontiers in Microbiology, vol. 6, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
Arotsker, L., Kramarsky-Winter, E., Ben-Dov, E., Siboni, N. & Kushmaro, A. 2015, 'Changes in the bacterial community associated with black band disease in a Red Sea coral, Favia sp., in relation to disease phases', Diseases of Aquatic Organisms, vol. 116, no. 1, pp. 47-58.View/Download from: UTS OPUS or Publisher's site
Changes of the black band disease (BBD)-associated microbial consortium on the surface of a Favia sp. coral colony were assessed in relation to the different disease phases. A number of highly active bacterial groups changed in numbers as the BBD disease signs changed. These included Gamma- and Epsilonproteobacteria, Bacteroidetes and Firmicutes groups. One cyanobacterium strain, BGP10_4ST (FJ210722), was constantly present in the disease interface and adjacent tissues of the affected corals, regardless of disease phase. The dynamics of the operational taxonomic units (OTUs) of this BBD-specific strain provide a marker regarding the disease phase. The disease's active phase is characterized by a wide dark band progressing along the tissue-skeleton interface and by numerous bacterial OTUs. Cyanobacterial OTUs decreased in numbers as the disease signs waned, perhaps opening a niche for additional microorganisms. Even when black band signs disappeared there was a consistent though low abundance of the BBD-specific cyanobacteria (BGP10_4ST), and the microbial community of the disease-skeleton interface remained surprisingly similar to the original band community. These results provide an indication that the persistence of even low numbers of this BBD-specific cyanobacterium in coral tissues during the non-active (or subclinical) state could facilitate reinitiation of BBD signs during the following summer. This may indicate that this bacterium is major constituent of the disease and that its persistence and ability to infiltrate the coral tissues may act to facilitate the assembly of the other BBD-specific groups of bacteria.
Siboni, N., Abrego, D., Evenhuis, C., Logan, M. & Motti, C.A. 2015, 'Adaptation to local thermal regimes by crustose coralline algaedoes not affect rates of recruitment in coral larvae', Coral Reefs, vol. 34, pp. 1243-1253.View/Download from: UTS OPUS or Publisher's site
Crustose coralline algae (CCA) are well known for their ability to induce settlement in coral larvae. While their wide distribution spans reefs that differ substantially in temperature regimes, the extent of local adaptation to these regimes and the impact they have on CCA inductive ability are unknown. CCA Porolithon onkodes from Heron (southern) and Lizard (northern) islands on Australia's Great Barrier Reef (separated by 1181 km) were experimentally exposed to acute or prolonged thermal stress events and their thermal tolerance and recruitment capacity determined. A sudden onset bleaching model was developed to determine the health status of CCA based on the rate of change in the CCA live surface area (LSA). The interaction between location and temperature was significant (F (2,119) = 6.74, p = 0.0017), indicating that thermally driven local adaptation had occurred. The southern population remained healthy after prolonged exposure to 28 °C and exhibited growth compared to the northern population (p = 0.022), with its optimum temperature determined to be slightly below 28 °C. As expected, at the higher temperatures (30 and 32 °C) the Lizard Island population performed better that those from Heron Island, with an optimum temperature of 30 °C. Lizard Island CCA displayed the lowest bleaching rates at 30 °C, while levels consistently increased with temperature in their southern counterparts. The ability of those CCA deemed thermally tolerant (based on LSA) to induce Acropora millepora larval settlement was then assessed. While spatial differences influenced the health and bleaching levels of P. onkodes during prolonged and acute thermal exposure, thermally tolerant fragments, regardless of location, induced similar rates of coral larval settlement. This confirmed that recent thermal history does not influence the ability of CCA to induce settlement of A. millepora larvae.
Tebben, J., Motti, C.A., Siboni, N., Tapiolas, D.M., Negri, A.P., Schupp, P.J., Kitamura, M., Hatta, M., Steinberg, P.D. & Harder, T. 2015, 'Chemical mediation of coral larval settlement by crustose coralline algae', SCIENTIFIC REPORTS, vol. 5.View/Download from: UTS OPUS or Publisher's site
Tout, J., Siboni, N., Messer, L.F., Garren, M., Stocker, R., Webster, N.S., Ralph, P.J. & Seymour, J.R. 2015, 'Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis.', Frontiers in Microbiology, vol. 6, pp. 432-432.View/Download from: UTS OPUS or Publisher's site
Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
Kramarsky-Winter, E., Arotsker, L., Rasoulouniriana, D., Siboni, N., Loya, Y. & Kushmaro, A. 2014, 'The possible role of cyanobacterial filaments in coral black band disease pathology.', Microbial Ecology, vol. 67, no. 1, pp. 177-185.View/Download from: UTS OPUS or Publisher's site
Black band disease (BBD), characterized by a black mat or line that migrates across a coral colony leaving behind it a bare skeleton, is a persistent disease affecting massive corals worldwide. Previous microscopic and molecular examination of this disease in faviid corals from the Gulf of Eilat revealed a number of possible pathogens with the most prominent being a cyanobacterium identified as Pseudoscillatoria coralii. We examined diseased coral colonies using histopathological and molecular methods in order to further assess the possible role of this cyanobacterium, its mode of entry, and pathological effects on the coral host tissues. Affected areas of colonies with BBD were sampled for examination using both light and transmission electron microscopies. Results showed that this dominant cyanobacterium was found on the coral surface, at the coral-skeletal interface, and invading the polyp tissues and gastrovascular cavity. Although tissues surrounding the invasive cyanobacterial filaments did not show gross morphological alterations, microscopic examination revealed that the coral cells surrounding the lesion were dissociated, necrotic, and highly vacuolated. No amoebocytes were evident in the mesoglea of affected tissues suggesting a possible repression of the coral immune response. Morphological and molecular similarity of the previously isolated BBD-associated cyanobacterium P. coralii to the current samples strengthens the premise that this species is involved in the disease in this coral. These results indicate that the cyanobacteria may play a pivotal role in this disease and that the mode of entry may be via ingestion, penetrating the coral via the gastrodermis, as well as through the skeletal-tissue interface.
Siboni, N., Abrego, D., Motti, C.A., Tebben, J. & Harder, T. 2014, 'Gene expression patterns during the early stages of chemically induced larval metamorphosis and settlement of the coral Acropora millepora.', PLoS ONE, vol. 9, no. 3, pp. 1-9.View/Download from: UTS OPUS or Publisher's site
The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement.
Siboni, N., Abrego, D., Seneca, F., Motti, C.A., Andreakis, N., Tebben, J., Blackall, L.L. & Harder, T. 2012, 'Using Bacterial Extract along with Differential Gene Expression in Acropora millepora Larvae to Decouple the Processes of Attachment and Metamorphosis', PLOS ONE, vol. 7, no. 5.View/Download from: UTS OPUS or Publisher's site
Siboni, N., Ben-Dov, E., Sivan, A. & Kushmaro, A. 2012, 'Geographic Specific Coral-Associated Ammonia-Oxidizing Archaea in the Northern Gulf of Eilat (Red Sea)', MICROBIAL ECOLOGY, vol. 64, no. 1, pp. 18-24.View/Download from: UTS OPUS or Publisher's site
Ben-Dov, E., Siboni, N., Shapiro, O.H., Arotsker, L. & Kushmaro, A. 2011, 'Substitution by Inosine at the 3 '-Ultimate and Penultimate Positions of 16S rRNA Gene Universal Primers', MICROBIAL ECOLOGY, vol. 61, no. 1, pp. 1-6.View/Download from: UTS OPUS or Publisher's site
Siboni, N., Rasoulouniriana, D., Ben-Dov, E., Kramarsky-Winter, E., Sivan, A., Loya, Y., Hoegh-Guldberg, O. & Kushmaro, A. 2010, 'Stramenopile Microorganisms Associated with the Massive Coral Favia sp.', JOURNAL OF EUKARYOTIC MICROBIOLOGY, vol. 57, no. 3, pp. 236-244.View/Download from: UTS OPUS or Publisher's site
Arotsker, L., Siboni, N., Ben-Dov, E., Kramarsky-Winter, E., Loya, Y. & Kushmaro, A. 2009, 'Vibrio sp as a potentially important member of the Black Band Disease (BBD) consortium in Favia sp corals', FEMS MICROBIOLOGY ECOLOGY, vol. 70, no. 3, pp. 515-524.View/Download from: UTS OPUS or Publisher's site
Rasoulouniriana, D., Siboni, N., Ben-Dov, E., Kramarsky-Winter, E., Loya, Y. & Kushmaro, A. 2009, 'Pseudoscillatoria coralii gen. nov., sp nov., a cyanobacterium associated with coral black band disease (BBD)', DISEASES OF AQUATIC ORGANISMS, vol. 87, no. 1-2, pp. 91-96.View/Download from: UTS OPUS or Publisher's site
Siboni, N., Martinez, S., Abelson, A., Sivan, A. & Kushmaro, A. 2009, 'Conditioning film and initial biofilm formation on electrochemical CaCO3 deposition on a metallic net in the marine environment', BIOFOULING, vol. 25, no. 7, pp. 675-683.View/Download from: UTS OPUS or Publisher's site
Harel, M., Ben-Dov, E., Rasoulouniriana, D., Siboni, N., Kramarsky-Winter, E., Loya, Y., Barak, Z., Wiesman, Z. & Kushmaro, A. 2008, 'A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa', FEMS MICROBIOLOGY ECOLOGY, vol. 64, no. 3, pp. 378-387.View/Download from: UTS OPUS or Publisher's site
Siboni, N., Ben Dov E, Sivan A & Kushmaro A 2008, 'Coral-associated ammonium oxidizing crenarchaeota and their role in the coral holobiont nitrogen cycle', Coral Reef Symp, Ft. Lauderdale, Florida, 7-11 July, vol. Session number 8.View/Download from: UTS OPUS
Siboni, N., Ben-Dov, E., Sivan, A. & Kushmaro, A. 2008, 'Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle', ENVIRONMENTAL MICROBIOLOGY, vol. 10, no. 11, pp. 2979-2990.View/Download from: UTS OPUS or Publisher's site
Siboni, N., Lidor, M., Kramarsky-Winter, E. & Kushmaro, A. 2007, 'Conditioning film and initial biofilm formation on ceramics tiles in the marine environment', FEMS MICROBIOLOGY LETTERS, vol. 274, no. 1, pp. 24-29.View/Download from: UTS OPUS or Publisher's site
Ben-Dov, E., Shapiro, O.H., Siboni, N. & Kushmaro, A. 2006, 'Advantage of using inosine at the 3 ' termini of 16S rRNA gene universal primers for the study of microbial diversity', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 11, pp. 6902-6906.View/Download from: UTS OPUS or Publisher's site
Kramarsky-Winter, E., Harel, M., Siboni, N., Ben Dov, E., Brickner, I., Loya, Y. & Kushmaro, A. 2006, 'Identification of a protist-coral association and its possible ecological role', MARINE ECOLOGY PROGRESS SERIES, vol. 317, pp. 67-73.View/Download from: UTS OPUS or Publisher's site
Oren A, Pri-El N, Shapiro O & Siboni, N. 2006, 'Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds', Saline Systems, vol. 2.View/Download from: UTS OPUS or Publisher's site
Oren, A., Pri-El, N., Shapiro, O. & Siboni, N. 2005, 'Gas vesicles isolated from Halobacterium cells by lysis in hypotonic solution are structurally weakened', FEMS MICROBIOLOGY LETTERS, vol. 252, no. 2, pp. 337-341.View/Download from: UTS OPUS or Publisher's site