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Green TJ, Siboni N, King WL, Labbate M, Seymour JR, Raftos D. Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event. MICROBIAL ECOLOGY 2019; 77:736-747. [PMID: 30097682 DOI: 10.1007/s00248-018-1242-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
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.
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King WL, Siboni N, Williams NLR, Kahlke T, Nguyen KV, Jenkins C, Dove M, O'Connor W, Seymour JR, Labbate M. Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease. Front Microbiol 2019; 10:473. [PMID: 30915058 PMCID: PMC6421512 DOI: 10.3389/fmicb.2019.00473] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/22/2019] [Indexed: 11/13/2022] Open
Abstract
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.
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King WL, Jenkins C, Go J, Siboni N, Seymour JR, Labbate M. Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event. MICROBIAL ECOLOGY 2019; 77:502-512. [PMID: 29987529 DOI: 10.1007/s00248-018-1226-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
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.
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Ajani PA, Kahlke T, Siboni N, Carney R, Murray SA, Seymour JR. The Microbiome of the Cosmopolitan Diatom Leptocylindrus Reveals Significant Spatial and Temporal Variability. Front Microbiol 2018; 9:2758. [PMID: 30498485 PMCID: PMC6249420 DOI: 10.3389/fmicb.2018.02758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
The ecological interactions between phytoplankton and marine bacteria have important implications for the productivity and biogeochemistry of ocean ecosystems. In this study we characterized the microbial assemblages associated with multiple isolates of the ecologically important diatom Leptocylindrus using amplicon sequencing of the 16S rRNA gene, to examine levels of conservation of the microbiome across closely related species or strains. We also assessed if the microbiome structure of a given diatom strain was dependent on the location from which it was isolated and if the microbiome of cultured isolates significantly changed overtime from the seawater in which they were isolated. The bacterial assemblages from 36 strains belonging to three species (Leptocylindrusdanicus, Leptocylindrus convexus, and Leptocylindrus aporus) isolated from six locations spanning > 1000 km of south east Australian coastline over 1 year, were dominated by the Rhodobacteraceae (∼60%) and the Flavobacteriaceae (∼10%). Across all strains, only one ‘core OTU’ (Roseovarius sp.) was identified across all samples. We observed no significant differences in bacterial community composition between diatom species. Significant differences in microbiome structure were, however, observed between diatom strains collected at different sampling times and from differing locations, albeit these two factors were coupled. Moreover, while bacterial communities under domestication varied from the seawater in which they were isolated, they remained specific to the location/month of origin, i.e., different regions and time points harbored distinct bacterial communities. Our study delivers new knowledge in relation to diatom-bacterial associations, revealing that the location/time from which a diatom is isolated plays an important role in shaping its microbiome.
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Brodersen KE, Siboni N, Nielsen DA, Pernice M, Ralph PJ, Seymour J, Kühl M. Seagrass rhizosphere microenvironment alters plant-associated microbial community composition. Environ Microbiol 2018; 20:2854-2864. [PMID: 29687545 DOI: 10.1111/1462-2920.14245] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 11/26/2022]
Abstract
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.
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Tran NAT, Seymour JR, Siboni N, Evenhuis CR, Tamburic B. Photosynthetic carbon uptake induces autoflocculation of the marine microalga Nannochloropsis oculata. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Lambert BS, Raina JB, Fernandez VI, Rinke C, Siboni N, Rubino F, Hugenholtz P, Tyson GW, Seymour JR, Stocker R. A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nat Microbiol 2017; 2:1344-1349. [DOI: 10.1038/s41564-017-0010-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 07/19/2017] [Indexed: 11/09/2022]
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Siboni N, Balaraju V, Carney R, Labbate M, Seymour JR. Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary. Front Microbiol 2016; 7:460. [PMID: 27148171 PMCID: PMC4829023 DOI: 10.3389/fmicb.2016.00460] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/21/2016] [Indexed: 01/22/2023] Open
Abstract
Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region.
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Arotsker L, Kramarsky-Winter E, Ben-Dov E, Siboni N, Kushmaro A. 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 2015; 116:47-58. [PMID: 26378407 DOI: 10.3354/dao02911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
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.
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Tout J, Siboni N, Messer LF, Garren M, Stocker R, Webster NS, Ralph PJ, Seymour JR. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis. Front Microbiol 2015; 6:432. [PMID: 26042096 PMCID: PMC4435422 DOI: 10.3389/fmicb.2015.00432] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/22/2015] [Indexed: 12/22/2022] Open
Abstract
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.
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Siboni N, Abrego D, Motti CA, Tebben J, Harder T. Gene expression patterns during the early stages of chemically induced larval metamorphosis and settlement of the coral Acropora millepora. PLoS One 2014; 9:e91082. [PMID: 24632854 PMCID: PMC3954620 DOI: 10.1371/journal.pone.0091082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
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.
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Kramarsky-Winter E, Arotsker L, Rasoulouniriana D, Siboni N, Loya Y, Kushmaro A. The possible role of cyanobacterial filaments in coral black band disease pathology. MICROBIAL ECOLOGY 2014; 67:177-185. [PMID: 24141943 DOI: 10.1007/s00248-013-0309-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
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.
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Siboni N, Ben-Dov E, Sivan A, Kushmaro A. Geographic specific coral-associated ammonia-oxidizing archaea in the northern Gulf of Eilat (Red Sea). MICROBIAL ECOLOGY 2012; 64:18-24. [PMID: 22286497 DOI: 10.1007/s00248-011-0006-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 12/27/2011] [Indexed: 05/31/2023]
Abstract
Coral holobionts are densely populated with microorganisms that are essential for their well-being. Here we compared the diversity of the archaeal ammonia monooxygenase alpha subunit (amoA) gene from three coral genera, Acanthastrea sp., Favia sp., and Fungia granulosa, from the Gulf of Eilat, Red Sea. At 99% similarity, archaeal amoA from the three coral genera shared 71% of their cloned sequences, while the Favia and Acanthastrea presented a few genus-specific clones. In addition, the sequences retrieved in our samples displayed lower similarity to amoA sequences previously found in association with other coral species from different geographic regions. This finding suggests that the populations of ammonia-oxidizing archaea are less host-specific and more geographically dependent.
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Siboni N, Abrego D, Seneca F, Motti CA, Andreakis N, Tebben J, Blackall LL, Harder T. Using bacterial extract along with differential gene expression in Acropora millepora larvae to decouple the processes of attachment and metamorphosis. PLoS One 2012; 7:e37774. [PMID: 22655067 PMCID: PMC3359992 DOI: 10.1371/journal.pone.0037774] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 04/24/2012] [Indexed: 02/06/2023] Open
Abstract
Biofilms of the bacterium Pseudoalteromonas induce metamorphosis of acroporid coral larvae. The bacterial metabolite tetrabromopyrrole (TBP), isolated from an extract of Pseudoalteromonas sp. associated with the crustose coralline alga (CCA) Neogoniolithon fosliei, induced coral larval metamorphosis (100%) with little or no attachment (0–2%). To better understand the molecular events and mechanisms underpinning the induction of Acropora millepora larval metamorphosis, including cell proliferation, apoptosis, differentiation, migration, adhesion and biomineralisation, two novel coral gene expression assays were implemented. These involved the use of reverse-transcriptase quantitative PCR (RT-qPCR) and employed 47 genes of interest (GOI), selected based on putative roles in the processes of settlement and metamorphosis. Substantial differences in transcriptomic responses of GOI were detected following incubation of A. millepora larvae with a threshold concentration and 10-fold elevated concentration of TBP-containing extracts of Pseudoalteromonas sp. The notable and relatively abrupt changes of the larval body structure during metamorphosis correlated, at the molecular level, with significant differences (p<0.05) in gene expression profiles of 24 GOI, 12 hours post exposure. Fourteen of those GOI also presented differences in expression (p<0.05) following exposure to the threshold concentration of bacterial TBP-containing extract. The specificity of the bacterial TBP-containing extract to induce the metamorphic stage in A. millepora larvae without attachment, using a robust, low cost, accurate, ecologically relevant and highly reproducible RT-qPCR assay, allowed partially decoupling of the transcriptomic processes of attachment and metamorphosis. The bacterial TBP-containing extract provided a unique opportunity to monitor the regulation of genes exclusively involved in the process of metamorphosis, contrasting previous gene expression studies that utilized cues, such as crustose coralline algae, biofilms or with GLW-amide neuropeptides that stimulate the entire onset of larval metamorphosis and attachment.
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Ben-Dov E, Siboni N, Shapiro OH, Arotsker L, Kushmaro A. Substitution by inosine at the 3'-ultimate and penultimate positions of 16S rRNA gene universal primers. MICROBIAL ECOLOGY 2011; 61:1-6. [PMID: 20614115 DOI: 10.1007/s00248-010-9718-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 06/23/2010] [Indexed: 05/29/2023]
Abstract
Universal 16S rRNA gene primers (8F and 518R) bearing inosine substitutions at either the 3'-ultimate or the 3'-ultimate and penultimate base positions were exploited for the first time to study the bacterial community associated with coral polymicrobial Black Band Disease (BBD). Inosine-modified universal primer pairs display some shifting in the composition of 16S rRNA gene libraries, as well as expanding the observed diversity of a BBD bacterial community at the family/class level. Possible explanations for the observed shifts are discussed. These results thus point to the need for adopting multiple approaches in designing 16S rRNA universal primers for PCR amplification and subsequent construction of 16S rRNA gene libraries or pyrosequencing in the exploration of complex microbial communities.
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Siboni N, Rasoulouniriana D, Ben-Dov E, Kramarsky-Winter E, Sivan A, Loya Y, Hoegh-Guldberg O, Kushmaro A. Stramenopile microorganisms associated with the massive coral Favia sp. J Eukaryot Microbiol 2010; 57:236-44. [PMID: 20236189 DOI: 10.1111/j.1550-7408.2010.00469.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The surfaces of massive corals of the genus Favia from Eilat, Red Sea, and from Heron Island, Great Barrier Reef, are covered by a layer of eukaryotic microorganisms. These microorganisms are embedded in the coral mucus and tissue. In the Gulf of Eilat, the prevalence of corals covered by patches of eukaryotic microorganisms was positively correlated with a decrease in water temperatures (from 25-28 degrees C in the summer to 20-23 degrees C in winter). Comparisons carried out using transmission and scanning electron microscopy showed morphological similarities between the microorganisms from the two geographically distant reefs. The microorganisms found on and in the tissues were approximately 5-15 microm in diameter, surrounded by scales in their cell wall, contained a nucleus, and included unique auto-florescent coccoid bodies of approximately 1 mum. Such morphological characters suggested that these microorganisms are stramenopile protists and in particular thraustochytrids. Molecular analysis, carried out using specific primers for stramenopile 18S rRNA genes, revealed that 90% (111/123) of the clones in the gene libraries were from the Thraustochytriidae. The dominant genera in this family were Aplanochytrium sp., Thraustochytrium sp., and Labyrinthuloides sp. Ten stramenopile strains were isolated and cultured from the corals. Some strains showed > or =97% similarity to clones derived from libraries of mucus-associated microorganisms retrieved directly from these corals. Fatty acid characterization of one of the prevalent strains revealed a high percentage of polyunsaturated fatty acids, including omega-3. The possible association of these stramenopiles in the coral holobiont appeared to be a positive one.
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Arotsker L, Siboni N, Ben-Dov E, Kramarsky-Winter E, Loya Y, Kushmaro A. Vibriosp. as a potentially important member of the Black Band Disease (BBD) consortium inFaviasp. corals. FEMS Microbiol Ecol 2009; 70:515-24. [DOI: 10.1111/j.1574-6941.2009.00770.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Rasoulouniriana D, Siboni N, Ben-Dov E, Kramarsky-Winter E, Loya Y, Kushmaro A. Pseudoscillatoria coralii gen. nov., sp. nov., a cyanobacterium associated with coral black band disease (BBD). DISEASES OF AQUATIC ORGANISMS 2009; 87:91-96. [PMID: 20095244 DOI: 10.3354/dao02089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Black band disease (BBD) is a widespread coral disease which mainly infects massive framework-building corals. BBD is believed to be caused by a consortium of microorganisms and may not result from the actions of a primary pathogen. The BBD microbial community is dominated, in terms of biomass, by filamentous cyanobacteria. Here we describe a cyanobacterial strain, designated BgP10_4S(T), cultured from a BBD-affected Favia sp. 25 degreesoal from the northern Red Sea (Gulf of Eilat, Israel). This dark-green pigmented cyanobacterium showed optimal growth at salinities of 5.0 to 5.5% (w/v), pH of 7 to 8 and cultivation temperatures of 25 0C. Morphological examination revealed cylindrical, unbranched trichomes with tapering and blunt cells at the ends which leave a thin mucilaginous trail as they glide. No sheath was evident under these conditions. Inclusion bodies and straight thylakoids were clearly discerned by transmission electron microscopy. Pigment analysis revealed absorption spectra for phycocyanin, carotenoid and chlorophyll a. The sequence of the 16S rRNA gene in this cyanobac(t)erium isolate showed high similarity (99%) to cyanobacterial sequences retrieved from BBD-affected corals from different geographical sites (i.e. the Caribbean Sea, Palau and the Red Sea). The BgP10_4ST strain is observed to be a persisten(t) component of the BBD mat of Faviid corals and may thus be an important agent in the disease etiology. On the basis (of its morphological, physiological and phylogenetic distinctiveness, strain BgP10_4ST represents a novel genus and species of Subsection III (formerly Oscillatoriales), for which the name Pseudoscillatoria coralii gen. nov., sp. nov. is proposed.
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Siboni N, Martinez S, Abelson A, Sivan A, Kushmaro A. Conditioning film and initial biofilm formation on electrochemical CaCO3 deposition on a metallic net in the marine environment. BIOFOULING 2009; 25:675-683. [PMID: 20183126 DOI: 10.1080/08927010903097204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Electrochemical deposition of minerals is a unique technology for artificial reef constructions, relying on calcium carbonate (CaCO3) build-up over metallic structures through electrolysis of seawater. The present study traces the first 72 h following electric current termination on bacterial biofilm build-up on a metallic net covered with CaCO3. 16S rRNA clone libraries indicated a dynamic succession. Proteobacteria and Bacteroidetes were evident at all sampling times while Cyanobacteria appeared only within the first 8 h. A significant increase in total organic carbon (TOC) and total protein was observed after 48 h with a significant correlation (R(2) = 0.74), indicating TOC is a good tool for characterizing initial biofilm formation. 18S rRNA gene sequences obtained 72 h following current termination indicated a significant presence of Cnidarians (51%). Understanding the dynamics among primary bacterial settlers is important because they play a crucial role in driving the colonization of sessile invertebrate communities on artificial, as well as natural surfaces.
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Siboni N, Ben-Dov E, Sivan A, Kushmaro A. Global distribution and diversity of coral-associatedArchaeaand their possible role in the coral holobiont nitrogen cycle. Environ Microbiol 2008; 10:2979-90. [DOI: 10.1111/j.1462-2920.2008.01718.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Harel M, Ben-Dov E, Rasoulouniriana D, Siboni N, Kramarsky-Winter E, Loya Y, Barak Z, Wiesman Z, Kushmaro A. A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa. FEMS Microbiol Ecol 2008; 64:378-87. [DOI: 10.1111/j.1574-6941.2008.00464.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Siboni N, Lidor M, Kramarsky-Winter E, Kushmaro A. Conditioning film and initial biofilm formation on ceramics tiles in the marine environment. FEMS Microbiol Lett 2007; 274:24-9. [PMID: 17578524 DOI: 10.1111/j.1574-6968.2007.00809.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The formation of biofilm on surfaces in the marine environment is believed to be an important factor driving colonization and recruitment of some sessile invertebrate communities. The present study follows the process of biofilm buildup on unglazed ceramic tiles deployed into the marine environment in the northern Gulf of Eilat. PCR-DGGE of film eluted from the tile surface indicated the presence of bacteria as early as 2 h after deployment. The makeup of the biofilm bacterial community was dynamic. Bacterial presence was apparent microscopically 6 h after deployment, though a developed biofilm was not observed until 24 h following deployment. Total organic carbon (TOC) data suggest that a conditioning film was built within the first four hours following deployment. During this time period TOC reached the highest level possibly due to adhesion of organics (e.g., sugars, proteins and humic substances) from the water column. We suggest that the primary adhering bacteria, whilst still in the reversible stage of adhesion, utilize the conditioning film as food causing the decrease in TOC. Understanding the dynamics between these primary bacterial settlers is of importance, since they may play a role on the succession of invertebrate species settlement onto artificial surfaces.
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Ben-Dov E, Shapiro OH, Siboni N, Kushmaro A. Advantage of using inosine at the 3' termini of 16S rRNA gene universal primers for the study of microbial diversity. Appl Environ Microbiol 2006; 72:6902-6. [PMID: 16950904 PMCID: PMC1636166 DOI: 10.1128/aem.00849-06] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3' termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54 degrees C, while Proteobacteria sequences were more frequent (62.7%) in a library obtained at 50 degrees C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3' termini in studying the microbial diversity of environmental samples.
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Oren A, Pri-El N, Shapiro O, Siboni N. Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds. SALINE SYSTEMS 2006; 2:4. [PMID: 16613609 PMCID: PMC1459177 DOI: 10.1186/1746-1448-2-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 04/14/2006] [Indexed: 01/10/2023]
Abstract
Background Possession of gas vesicles is generally considered to be advantageous to halophilic archaea: the vesicles are assumed to enable the cells to float, and thus reach high oxygen concentrations at the surface of the brine. Results We studied the possible ecological advantage of gas vesicles in a dense community of flat square extremely halophilic archaea in the saltern crystallizer ponds of Eilat, Israel. We found that in this environment, the cells' content of gas vesicles was insufficient to provide positive buoyancy. Instead, sinking/floating velocities were too low to permit vertical redistribution. Conclusion The hypothesis that the gas vesicles enable the square archaea to float to the surface of the brines in which they live was not supported by experimental evidence. Presence of the vesicles, which are mainly located close to the cell periphery, may provide an advantage as they may aid the cells to position themselves parallel to the surface, thereby increasing the efficiency of light harvesting by the retinal pigments in the membrane.
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Oren A, Pri-El N, Shapiro O, Siboni N. Gas vesicles isolated fromHalobacteriumcells by lysis in hypotonic solution are structurally weakened. FEMS Microbiol Lett 2006; 252:337-41. [PMID: 16213677 DOI: 10.1016/j.femsle.2005.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2005] [Revised: 09/06/2005] [Accepted: 09/09/2005] [Indexed: 11/17/2022] Open
Abstract
Analysis of pressure-collapse curves of Halobacterium cells containing gas vesicles and of gas vesicles released from such cells by hypotonic lysis shows that the isolated gas vesicles are considerably weaker than those present within the cells: their mean critical collapse pressure was around 0.049-0.058 MPa, as compared to 0.082-0.095 MPa for intact cells. The hypotonic lysis procedure, which is widely used for the isolation of gas vesicles from members of the Halobacteriaceae, thus damages the mechanical properties of the vesicles. The phenomenon can possibly be attributed to the loss of one or more structural gas vesicle proteins such as GvpC, the protein that strengthens the vesicles built of GvpA subunits: Halobacterium GvpC is a highly acidic, typically "halophilic" protein, expected to denature in the absence of molar concentrations of salt.
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