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.
Can supervise: YES
King, WL, Siboni, N, Kahlke, T, Dove, M, O'Connor, W, Mahbub, KR, Jenkins, C, Seymour, JR & Labbate, M 2020, 'Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community', FEMS MICROBIOLOGY ECOLOGY, vol. 96, no. 5.View/Download from: Publisher's site
Viet, KN, King, WL, Siboni, N, Mahbub, KR, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2020, 'The Sydney rock oyster microbiota is influenced by location, season and genetics', AQUACULTURE, vol. 527.View/Download from: Publisher's site
Commault, AS, Kaur Walia, N, Fabris, M, Barolo, L, Siboni, N, Adriaans, J, Ralph, PJ & Pernice, M 2020, 'Effect of biphasic temperature regime on therapeutic recombinant protein production in the green alga Chlamydomonas reinhardtii', Algal Research, vol. 50.View/Download from: Publisher's site
© 2020 Elsevier B.V. Microalgae are increasingly being considered for recombinant protein production because of low cultivation costs, absence of endotoxins and insusceptibility to human infectious agents. Despite these advantages, the yield of recombinant protein produced in microalgae is still low compared to more established expression systems and optimization at the genetic and cultivation levels is required for this new system to be economically viable. This study investigates the effect of biphasic temperature regimes on the yield of recombinant human interferon alpha 2a (IFN-α2a), a therapeutic protein known for its anti-cancer and anti-viral properties, produced by the model green alga Chlamydomonas reinhardtii (Cr.IFN-α2a). Biphasic growth is commonly employed to increase recombinant protein production in mammalian cell lines used for commercial production of therapeutic proteins, with a lowering of the temperature resulting in higher yields. In this study, lowering the temperature from 25 °C to 15 °C in mid-exponential growth phase increased the accumulation of Cr.IFN-α2a by 3.3-fold while it slowed down the growth of the three C. reinhardtii transgenic lines tested. In contrast, a rise of temperature from 25 °C to 35 °C accelerated cell growth, while negatively impacting the production of Cr.IFN-α2a. After a two-step chromatography purification, the Cr.IFN-α2a produced was estimated to be 53% pure with a yield of 90 μg/L of culture. The amino acid sequence of Cr.IFN-α2a was confirmed by mass spectrometry. However, the anti-viral activity of Cr.IFN-α2a was found to be 10 times lower than the human IFN-α2a standard produced using E. coli when challenged in a cytopathic effect (CPE) assay, likely due to the formation of aggregates. While the molecular mechanisms driving the accumulation of Cr.IFN-α2a at lower temperature remains unclear, our results support that reducing the temperature at the peak of expression is a valid strategy to increase the yield o...
Carney, RL, Brown, MV, Siboni, N, Raina, J-B, Kahlke, T, Mitrovic, SM & Seymour, JR 2020, 'Highly heterogeneous temporal dynamics in the abundance and diversity of the emerging pathogens Arcobacter at an urban beach', WATER RESEARCH, vol. 171.View/Download from: Publisher's site
Carney, RL, Labbate, M, Siboni, N, Tagg, KA, Mitrovic, SM & Seymour, JR 2019, 'Urban beaches are environmental hotspots for antibiotic resistance following rainfall.', Water research, vol. 167.View/Download from: Publisher's site
To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.
Green, TJ, Siboni, N, King, WL, Labbate, M, Seymour, JR & Raftos, D 2019, 'Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.', Microbial ecology, vol. 77, no. 3, pp. 736-747.View/Download from: Publisher's site
Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.
King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event.', Microbial Ecology, vol. 77, pp. 502-512.View/Download from: Publisher's site
The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.
King, WL, Siboni, N, Kahlke, T, Green, TJ, Labbate, M & Seymour, JR 2019, 'A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event.', Frontiers in Microbiology, vol. 10, pp. 2907-2907.View/Download from: Publisher's site
The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.
King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease.', Frontiers in microbiology, vol. 10, no. Mar.View/Download from: Publisher's site
Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.
Deschaseaux, E, O'Brien, J, Siboni, N, Petrou, K & Seymour, JR 2019, 'Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate Alexandrium minutum during a simulated marine heatwave', BIOGEOSCIENCES, vol. 16, no. 22, pp. 4377-4391.View/Download from: Publisher's site
Hewson, I, Sullivan, B, Jackson, EW, Xu, Q, Long, H, Lin, C, Carde, EMQ, Seymour, J, Siboni, N, Jones, MRL & Sewell, MA 2019, 'Perspective: Something Old, Something New? Review of Wasting and Other Mortality in Asteroidea (Echinodermata)', FRONTIERS IN MARINE SCIENCE, vol. 6.View/Download from: Publisher's site
Brodersen, KE, Siboni, N, Nielsen, DA, Pernice, M, Ralph, PJ, Seymour, J & Kühl, M 2018, 'Seagrass rhizosphere microenvironment alters plant-associated microbial community composition.', Environmental microbiology, vol. 20, no. 8, pp. 2854-2864.View/Download from: Publisher's site
The seagrass rhizosphere harbors dynamic microenvironments, where plant-driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass-mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2 S and pH occurred. Significantly higher relative abundances of sulphate-reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide-oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2 S re-oxidation here were similar to those observed in a pre-sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant-microbe interactions potentially affecting seagrass health.
Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, S & Seymour, J 2018, 'The microbiome of the cosmopolitan diatom Leptocylindrus reveals significant spatial and temporal variability', Frontiers in Microbiology, vol. 9.View/Download from: Publisher's site
Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative.', Scientific data, vol. 5, pp. 180130-180130.View/Download from: Publisher's site
Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Høj, L, Levy, N, Baillie, BK, Clode, PL, Strohmaier, RC, Siboni, N, Webster, NS, Uthicke, S & Bourne, DG 2018, 'Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction.', Applied and environmental microbiology, vol. 84, no. 13.View/Download from: Publisher's site
Outbreaks of coral-eating crown-of-thorns sea stars (CoTS; Acanthaster spp. complex) cause substantial coral loss, hence there is considerable interest in developing prevention and control strategies. We characterised the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, which were highly variable amongst individuals. Male gonads were dominated (>97% of reads) by a single Mollicutes-related OTU. Detailed phylogenetic and microscopy analysis demonstrated the presence of a novel Spiroplasma-related bacterium in the spermatogenic layer. Body wall samples had high relative abundance (43-64% of reads) of spirochetes, likely corresponding to subcuticular symbionts reported from many echinoderms. Tube feet were characterised by Hyphomonadaceae (24-55% of reads). Pyloric caeca microbiomes had high alpha diversity, comprising many taxa commonly found in gastro-intestinal systems. The order Oceanospirillales (genera Endozoicomonas and Kistimonas) was detected in all tissues. A microbiome shift occurred in diseased individuals, although differences between tissue types were retained. The relative abundance of spirochetes was significantly reduced in diseased individuals. Kistimonas was present in all diseased individuals and significantly associated with diseased tube feet, but its role in disease causation is unknown. While Arcobacter was significantly associated with diseased tissues and Vibrionaceae increased in diversity, no single OTUs were detected in all diseased individuals suggesting opportunistic proliferation of these taxa in this case. This study shows that CoTS have tissue-characteristic bacterial communities and identifies taxa that could play a role in reproduction and host health.IMPORTANCECoral-eating crown of thorns sea stars (CoTS; Acanthaster spp. complex) are native to the Indo-Pacific, but during periodic population out...
Tran, NAT, Seymour, JR, Siboni, N, Evenhuis, CR & Tamburic, B 2017, 'Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata', Algal Research, vol. 26, pp. 302-311.View/Download from: 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, AS, Laczka, O, Siboni, N, Tamburic, B, Crosswell, JR, Seymour, JR & Ralph, PJ 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: 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.
Lambert, BS, Raina, J-B, Fernandez, VI, Rinke, C, Siboni, N, Rubino, F, Hugenholtz, P, Tyson, GW, Seymour, JR & Stocker, R 2017, 'A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.', Nature microbiology, vol. 2, pp. 1344-1349.View/Download from: 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.
Siboni, N, Balaraju, V, Carney, R, Labbate, M & Seymour, JR 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7.View/Download from: Publisher's site
Siboni, N, Abrego, D, Evenhuis, C, Logan, M & Motti, CA 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: 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.
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: 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.
Tebben, J, Motti, CA, Siboni, N, Tapiolas, DM, Negri, AP, Schupp, PJ, Kitamura, M, Hatta, M, Steinberg, PD & Harder, T 2015, 'Chemical mediation of coral larval settlement by crustose coralline algae', SCIENTIFIC REPORTS, vol. 5.View/Download from: Publisher's site
Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 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: 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.
Tout, J, Siboni, N, Messer, LF, Garren, M, Stocker, R, Webster, NS, Ralph, PJ & Seymour, JR 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: 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: 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, CA, 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: 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, CA, Andreakis, N, Tebben, J, Blackall, LL & 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: 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: Publisher's site
Ben-Dov, E, Siboni, N, Shapiro, OH, 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: 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: 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: 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: 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: 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: 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.
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: 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: Publisher's site
Ben-Dov, E, Shapiro, OH, 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: 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: 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: 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: Publisher's site
Siboni, N, Fine, M, Bresler, V & Loya, Y 2004, 'Coastal coal pollution increases Cd concentrations in the predatory gastropod Hexaplex trunculus and is detrimental to its health', Marine Pollution Bulletin, vol. 49, no. 1-2, pp. 111-118.View/Download from: Publisher's site
Parameters of environmental health, including paracellular permeability of external epithelia, functional state of lysosomes and the level of metallothioneins (MTs), were examined using fluorescent markers and vital microfluorometry in different tissues of the marine gastropod, Hexaplex trunculus, from a coal-polluted and coal-free site. Vital microfluorometrical examinations exhibited enhanced paracellular permeability of external epithelia to the anionic marker, fluorescein (FLU), lower lysosomal accumulation of neutral red (NR) as well as higher levels of MTs, when compared with epithelia of gastropods from the coal-free site. Those differences were particularly marked in the foot epithelium, which is in direct contact with the substrate. In addition, cadmium was measured by ICP-AES in the hepatopancreas of gastropods sampled from the coal-polluted site and two coal-free sites. Significantly higher levels of Cd were found in gastropod hepatopancreas from the coal-polluted site. In addition, two months feeding experiments conducted in aquaria containing: (a) coal pieces covered by barnacles; (b) natural rocks covered by barnacles; and (c) natural rocks with barnacles+bare coal pieces, demonstrated significant increase of Cd concentration in the hepatopancreas of the gastropods exposed to coal. We suggest that coal in the marine environment has detrimental effects on marine gastropods, both directly through contact with the organisms and indirectly through the food web. © 2004 Elsevier Ltd. All rights reserved.
Siboni, N, Fine, M, Bresler, V & Loya, Y 2004, 'Coastal coal pollution increases Cd concentrations in the predatory gastropod Hexaplex trunculus and is detrimental to its health', MARINE POLLUTION BULLETIN, vol. 49, no. 1-2, pp. 111-118.View/Download from: Publisher's site
Deschaseaux, E, O'Brien, J, Siboni, N, Petrou, K & Seymour, JR, 'Shifts in organic sulfur cycling and microbiome composition in the red-tide causing dinoflagellate <i>Alexandrium minutum</i> during a simulated marine heat wave'.View/Download from: Publisher's site
Abstract. The biogenic sulfur compounds dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) are produced and transformed by diverse populations of marine microorganisms and have substantial physiological, ecological and biogeochemical importance spanning organism to global scales. Understanding the production and transformation dynamics of these compounds under shifting environmental conditions is important for predicting their roles in a changing ocean. Here, we report the physiological and biochemical response of Alexandrium minutum, a dinoflagellate with the highest reported intracellular DMSP content, exposed to a 6 day increase in temperature mimicking coastal marine heatwave conditions (+4 °C and +12 °C). Under mild temperature increases (+4 °C), A. minutum growth was enhanced, with no measurable physiological stress response. However, under an acute increase in temperature (+12 °C), A. minutum growth declined, photosynthetic efficiency (FV/FM) was impaired, and enhanced oxidative stress was observed. These physiological responses were accompanied by increased DMS and DMSO concentrations followed by decreased DMSP concentrations. At this higher temperature, we observed a cascading stress response in A. minutum, which was initiated 6 h after the start of the experiment by a spike in DMS and DMSO concentrations and a rapid decrease in FV/FM. This was followed by an increase in reactive oxygen species (ROS) and an abrupt decline in DMS and DMSO on day 2 of the experiment. A subsequent decrease in DMSP coupled with a decline in the growth rate of both A. minutum and its associated total bacterial assemblage coincided with a shift in the composition of the A. minutum microbiome. Specifically, an increase in the relative abundance of OTUs matching the genus Oceanicaulis (17.0 %), Phycisphaeraceae SM1A02 (8.8 %) and Balneola (4.9 %) as well as a decreased relative abundance of Maribacter (24.4 %), Marinoscillum (4.7 %) and...