Figure S3. Dendrogram for three technical replicates each of roundworm (C), fruit fly (D), human ... more Figure S3. Dendrogram for three technical replicates each of roundworm (C), fruit fly (D), human (H), mouse (M) and yeast (Y) using average linkage hierarchical clustering based on all pairwise distances of 15 MS/MS runs. Computed via method DB.a. (PDF 4 kb)
Materials and Methods. This file provides detailed information about the sample preparation and L... more Materials and Methods. This file provides detailed information about the sample preparation and LC-MS/MS analyses. (PDF 145 kb)
<p>(a) Map of the Florida Keys, USA, indicating the sampling site at Tennessee Reef in 18 m... more <p>(a) Map of the Florida Keys, USA, indicating the sampling site at Tennessee Reef in 18 m depth and the Florida Keys National Marine Sanctuary (FNKMS) station in 5 m depth where the bottom water temperature was continuously measured from 2004 to 2006; (b) Bottom water temperature at FKNMS station Tennessee Reef shows temperature fluctuations from 20°C in winter to above 30°C in summer [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0179753#pone.0179753.ref034" target="_blank">34</a>].</p
Additional file 3. Sequence of diatoms identified using Sanger sequencing (primer set SymSF1-1528... more Additional file 3. Sequence of diatoms identified using Sanger sequencing (primer set SymSF1-1528R) that were utilised to generate figures 5 and 6.
The proliferation of key marine ecological engineers and carbonate producers often relies on thei... more The proliferation of key marine ecological engineers and carbonate producers often relies on their association with photosymbiotic algae. Evaluating stress responses of these organisms is important to predict their fate under future climate projections. Physiological approaches are limited in their ability to resolve the involved molecular mechanisms and attribute stress effects to the host or symbiont, while probing and partitioning of proteins cannot be applied in organisms where the host and symbiont are small and cannot be physically separated. Here we apply a label-free quantitative proteomics approach to detect changes of proteome composition in the diatom-bearing benthic foraminifera Amphistegina gibbosa experimentally exposed to three thermal-stress scenarios. We developed a workflow for protein extraction from less than ten specimens and simultaneously analysed host and symbiont proteomes. Despite little genomic data for the host, 1,618 proteins could be partially assembled...
Abstract Tropical coastal ecosystems provide a unique complex marine habitat with a high diversit... more Abstract Tropical coastal ecosystems provide a unique complex marine habitat with a high diversity of algal species, Vietnam being a particular hotspot. These algae may host a variety of potential unknown or underestimated bioactive algal compounds. In parallel the worldwide rising interest in macroalgae-based products lead to increasing activities in seaweed natural harvest and mariculture within coastal waters With this growing interest, the present work provides baseline data for a systematic and science-based macroalgal monitoring program in Nha Trang Bay, Vietnam, to keep track of potentially interesting taxa and to identify driving environmental factors which may also naturally influence biodiversity and species abundance. The present study investigated macrophyte diversity and abundance by combining a qualitative and quantitative macroalgal survey approach with environmental sampling (e.g. physicochemical properties of water column, underwater light regime, and sediment characteristics). Surveys were performed in the dry season (May/June) 2019 in different water depths (3, 6 and 10 m) at seven sites within Nha Trang Bay. The study revealed a coastal patchwork of diverse habitats inhabited by complex macrophyte communities, including estuarine dense Sargassum forests and Turbinaria meadows, sheltered sandy seagrass (Halodule spp.) beds with upcoming Lyngbya blooms, low diverse Padina deserts and highly turbid aquaculture (lobster and fish farms) impacted sites with surprisingly high macroalgal diversity. During our study a total of 86 macrophyte species were encountered in the subtidal (>1 m water depth), whereas only 6 species (Padina australis, Sargassum mcclurei, Turbinaria ornata, Halimeda discoidea, Amphiroa fragilissima, Tricleocarpa cylindrical) were frequently found at every survey site. The observed high patchiness and presence of economically important (e.g. Sargassum spp., Gracilaria spp., Caulerpa spp., Gelidiella acerosa, Acanthophora spicifera) and potentially economically interesting (e.g. Padina australis, Turbinaria ornata, Stypopodium zonale, Chondria armata) taxa during the survey underlines the high potential of the present macrophytic bio-resource, which apparently is strongly structured and will be altered by the changing heterogenic environment.
Studies on the effects of global marine plastic pollution have largely focused on physiological r... more Studies on the effects of global marine plastic pollution have largely focused on physiological responses of few organism groups (e.g., corals, fishes). Here, we report the first observation of polymer nanoparticles being incorporated into the calcite skeleton of a large benthic foraminifera (LBF), a significant contributor to global carbonate production. While previous work on LBF has documented selectivity in feeding behaviour and a high degree of specialization regarding skeletal formation, in this study, abundant cases of nanoplastic encrustation into the calcite tests were observed. Nanoplastic incorporation was associated with formation of new chambers, in conjunction with rapid nanoplastic ingestion and subsequent incomplete egestion. Microalgae presence in nanoplastic treatments significantly increased the initial feeding response after 1 day, but regardless of microalgae presence, nanoplastic ingestion was similar after 6 weeks of chronic exposure. While ~ 40% of ingesting ...
Ocean acidification and ocean warming compromise the capacity of calcifying marine organisms to g... more Ocean acidification and ocean warming compromise the capacity of calcifying marine organisms to generate and maintain their skeletons. While many marine calcifying organisms precipitate low-Mg calcite or aragonite, the skeleton of echinoderms consists of more soluble Mg-calcite. To assess the impact of exposure to elevated temperature and increased pCO2 on the skeleton of echinoderms, in particular the mineralogy and microstructure, the starfish Aquilonastra yairi (Echinodermata: Asteroidea) was exposed for 90 days to simulated ocean warming (27 °C and 32 °C) and ocean acidification (455 µatm, 1052 µatm, 2066 µatm) conditions. The results indicate that temperature is the major factor controlling the skeletal Mg (Mg/Ca ratio and Mgnorm ratio), but not for skeletal Sr (Sr/Ca ratio and Srnorm ratio) and skeletal Ca (Canorm ratio) in A. yairi. Nevertheless, inter-individual variability in skeletal Sr and Ca ratios increased with higher temperature. Elevated pCO2 did not induce any stati...
&amp;lt;p&amp;gt;Larger benthic foraminifera (LBF) are important carbonate producers in t... more &amp;lt;p&amp;gt;Larger benthic foraminifera (LBF) are important carbonate producers in tropical and subtropical settings and play a large role in the carbon cycle. They suffer from bleaching (the expulsion/loss of the photosymbiotic microalgae) under increased sea surface temperature due to climate change. For artificial bleaching experiments, we used the diatom-bearing foraminiferan &amp;lt;em&amp;gt;Amphistegina lobifera, &amp;lt;/em&amp;gt;because of its robustness in the laboratory for symbiosis investigations, and also the more sensitive &amp;lt;em&amp;gt;Sorites orbiculus&amp;lt;/em&amp;gt; which hosts endosymbiotic dinoflagellates. In order to induce bleaching, the LBF were exposed to menthol at non-lethal concentrations. Additionally, DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) was applied as a photosynthetic inhibitor. After the 6 week experiment, foraminifera were &amp;gt;95% bleached, visible with the flourescence microscope. Survival rate of protists was high, as pseudopodial movement was still visible. The foraminifer in this bleached state was able to move and extend its pseudopodial network. The next step will be to test symbiont-uptake of those bleached foraminifera, and measure survival time and ecophysiological features of re-infected foraminifera.&amp;lt;/p&amp;gt;
Additional file 4 : Supplementary Fig. S1. Heatmap of relative abundance of ASVs grouped by phylu... more Additional file 4 : Supplementary Fig. S1. Heatmap of relative abundance of ASVs grouped by phylum for each species collected from different sites. Scale was log-10 transformed. Supplementary Fig. S2. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lobifera collected from different sites. Supplementary Fig. S3. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lessonii collected from different sites. Supplementary Fig. S4. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. radiata collected from different sites.
Figure S3. Dendrogram for three technical replicates each of roundworm (C), fruit fly (D), human ... more Figure S3. Dendrogram for three technical replicates each of roundworm (C), fruit fly (D), human (H), mouse (M) and yeast (Y) using average linkage hierarchical clustering based on all pairwise distances of 15 MS/MS runs. Computed via method DB.a. (PDF 4 kb)
Materials and Methods. This file provides detailed information about the sample preparation and L... more Materials and Methods. This file provides detailed information about the sample preparation and LC-MS/MS analyses. (PDF 145 kb)
<p>(a) Map of the Florida Keys, USA, indicating the sampling site at Tennessee Reef in 18 m... more <p>(a) Map of the Florida Keys, USA, indicating the sampling site at Tennessee Reef in 18 m depth and the Florida Keys National Marine Sanctuary (FNKMS) station in 5 m depth where the bottom water temperature was continuously measured from 2004 to 2006; (b) Bottom water temperature at FKNMS station Tennessee Reef shows temperature fluctuations from 20°C in winter to above 30°C in summer [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0179753#pone.0179753.ref034" target="_blank">34</a>].</p
Additional file 3. Sequence of diatoms identified using Sanger sequencing (primer set SymSF1-1528... more Additional file 3. Sequence of diatoms identified using Sanger sequencing (primer set SymSF1-1528R) that were utilised to generate figures 5 and 6.
The proliferation of key marine ecological engineers and carbonate producers often relies on thei... more The proliferation of key marine ecological engineers and carbonate producers often relies on their association with photosymbiotic algae. Evaluating stress responses of these organisms is important to predict their fate under future climate projections. Physiological approaches are limited in their ability to resolve the involved molecular mechanisms and attribute stress effects to the host or symbiont, while probing and partitioning of proteins cannot be applied in organisms where the host and symbiont are small and cannot be physically separated. Here we apply a label-free quantitative proteomics approach to detect changes of proteome composition in the diatom-bearing benthic foraminifera Amphistegina gibbosa experimentally exposed to three thermal-stress scenarios. We developed a workflow for protein extraction from less than ten specimens and simultaneously analysed host and symbiont proteomes. Despite little genomic data for the host, 1,618 proteins could be partially assembled...
Abstract Tropical coastal ecosystems provide a unique complex marine habitat with a high diversit... more Abstract Tropical coastal ecosystems provide a unique complex marine habitat with a high diversity of algal species, Vietnam being a particular hotspot. These algae may host a variety of potential unknown or underestimated bioactive algal compounds. In parallel the worldwide rising interest in macroalgae-based products lead to increasing activities in seaweed natural harvest and mariculture within coastal waters With this growing interest, the present work provides baseline data for a systematic and science-based macroalgal monitoring program in Nha Trang Bay, Vietnam, to keep track of potentially interesting taxa and to identify driving environmental factors which may also naturally influence biodiversity and species abundance. The present study investigated macrophyte diversity and abundance by combining a qualitative and quantitative macroalgal survey approach with environmental sampling (e.g. physicochemical properties of water column, underwater light regime, and sediment characteristics). Surveys were performed in the dry season (May/June) 2019 in different water depths (3, 6 and 10 m) at seven sites within Nha Trang Bay. The study revealed a coastal patchwork of diverse habitats inhabited by complex macrophyte communities, including estuarine dense Sargassum forests and Turbinaria meadows, sheltered sandy seagrass (Halodule spp.) beds with upcoming Lyngbya blooms, low diverse Padina deserts and highly turbid aquaculture (lobster and fish farms) impacted sites with surprisingly high macroalgal diversity. During our study a total of 86 macrophyte species were encountered in the subtidal (>1 m water depth), whereas only 6 species (Padina australis, Sargassum mcclurei, Turbinaria ornata, Halimeda discoidea, Amphiroa fragilissima, Tricleocarpa cylindrical) were frequently found at every survey site. The observed high patchiness and presence of economically important (e.g. Sargassum spp., Gracilaria spp., Caulerpa spp., Gelidiella acerosa, Acanthophora spicifera) and potentially economically interesting (e.g. Padina australis, Turbinaria ornata, Stypopodium zonale, Chondria armata) taxa during the survey underlines the high potential of the present macrophytic bio-resource, which apparently is strongly structured and will be altered by the changing heterogenic environment.
Studies on the effects of global marine plastic pollution have largely focused on physiological r... more Studies on the effects of global marine plastic pollution have largely focused on physiological responses of few organism groups (e.g., corals, fishes). Here, we report the first observation of polymer nanoparticles being incorporated into the calcite skeleton of a large benthic foraminifera (LBF), a significant contributor to global carbonate production. While previous work on LBF has documented selectivity in feeding behaviour and a high degree of specialization regarding skeletal formation, in this study, abundant cases of nanoplastic encrustation into the calcite tests were observed. Nanoplastic incorporation was associated with formation of new chambers, in conjunction with rapid nanoplastic ingestion and subsequent incomplete egestion. Microalgae presence in nanoplastic treatments significantly increased the initial feeding response after 1 day, but regardless of microalgae presence, nanoplastic ingestion was similar after 6 weeks of chronic exposure. While ~ 40% of ingesting ...
Ocean acidification and ocean warming compromise the capacity of calcifying marine organisms to g... more Ocean acidification and ocean warming compromise the capacity of calcifying marine organisms to generate and maintain their skeletons. While many marine calcifying organisms precipitate low-Mg calcite or aragonite, the skeleton of echinoderms consists of more soluble Mg-calcite. To assess the impact of exposure to elevated temperature and increased pCO2 on the skeleton of echinoderms, in particular the mineralogy and microstructure, the starfish Aquilonastra yairi (Echinodermata: Asteroidea) was exposed for 90 days to simulated ocean warming (27 °C and 32 °C) and ocean acidification (455 µatm, 1052 µatm, 2066 µatm) conditions. The results indicate that temperature is the major factor controlling the skeletal Mg (Mg/Ca ratio and Mgnorm ratio), but not for skeletal Sr (Sr/Ca ratio and Srnorm ratio) and skeletal Ca (Canorm ratio) in A. yairi. Nevertheless, inter-individual variability in skeletal Sr and Ca ratios increased with higher temperature. Elevated pCO2 did not induce any stati...
&amp;lt;p&amp;gt;Larger benthic foraminifera (LBF) are important carbonate producers in t... more &amp;lt;p&amp;gt;Larger benthic foraminifera (LBF) are important carbonate producers in tropical and subtropical settings and play a large role in the carbon cycle. They suffer from bleaching (the expulsion/loss of the photosymbiotic microalgae) under increased sea surface temperature due to climate change. For artificial bleaching experiments, we used the diatom-bearing foraminiferan &amp;lt;em&amp;gt;Amphistegina lobifera, &amp;lt;/em&amp;gt;because of its robustness in the laboratory for symbiosis investigations, and also the more sensitive &amp;lt;em&amp;gt;Sorites orbiculus&amp;lt;/em&amp;gt; which hosts endosymbiotic dinoflagellates. In order to induce bleaching, the LBF were exposed to menthol at non-lethal concentrations. Additionally, DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) was applied as a photosynthetic inhibitor. After the 6 week experiment, foraminifera were &amp;gt;95% bleached, visible with the flourescence microscope. Survival rate of protists was high, as pseudopodial movement was still visible. The foraminifer in this bleached state was able to move and extend its pseudopodial network. The next step will be to test symbiont-uptake of those bleached foraminifera, and measure survival time and ecophysiological features of re-infected foraminifera.&amp;lt;/p&amp;gt;
Additional file 4 : Supplementary Fig. S1. Heatmap of relative abundance of ASVs grouped by phylu... more Additional file 4 : Supplementary Fig. S1. Heatmap of relative abundance of ASVs grouped by phylum for each species collected from different sites. Scale was log-10 transformed. Supplementary Fig. S2. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lobifera collected from different sites. Supplementary Fig. S3. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lessonii collected from different sites. Supplementary Fig. S4. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. radiata collected from different sites.
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