Bacterial community composition in different reef habitats of the Spermonde Archipelago, Indonesia.
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PROVIDER: PRJEB18641 | ENA |
REPOSITORIES: ENA
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Project description:Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.
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Project description:<p>Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina, Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used metabolic methods to quantify specific known metabolites of interest (targeted approach) and to survey trends in metabolite feature composition (untargeted approach) from surface and reef depth (6 – 14 m) seawater overlying forereefs in Jardines de la Reina. We found that untargeted metabolite feature composition was fairly similar between reef depth and surface seawater across the archipelago, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within Jardines de la Reina. Additionally, we quantified 32 of 53 detected metabolites, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and 5ʹ-methylthioadenosine (MTA), displayed interesting trends by depth and geographic location, respectively. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. 5ʹ-MTA concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.</p>
2020-11-30 | MTBLS1820 | MetaboLights
Project description:Bacterial communitiy compositions on natural and artificial substrates in the Spermonde Archipelago, Indonesia
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Project description:This study advances a topologically integrated genome archipelago model that undergoes extensive structural transformations through the formation of nFGFR1-associated Topologically Associated Domains (TADs), replacing CTCF TADs, during the development of the stem cells to neurons. The makeover of the TAD islands serves to recruit distinct ontogenic programs.
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Project description:Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3,112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.
2018-11-14 | GSE115448 | GEO
Project description:eDNA metabarcoding (marker: COI) of reef and mangrove habitats in Honduras and Kenya
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Project description:Understanding the drivers of species' geographic distribution has fundamental implications for the management of biodiversity. For coral reef fishes, mangroves have long been recognized as important nursery habitats sustaining biodiversity in the Western Atlantic but there is still debate about their role in the Indo-Pacific. Here, we combined LA-ICP-MS otolith microchemistry, underwater visual censuses (UVC) and mangrove cartography to estimate the importance of mangroves for the Indo-Pacific coral reef fish Lutjanus fulviflamma in the archipelago of New Caledonia. Otolith elemental compositions allowed high discrimination of mangroves and reefs with 83.8% and 98.7% correct classification, respectively. Reefs were characterized by higher concentrations of Rb and Sr and mangroves by higher concentrations of Ba, Cr, Mn and Sn. All adult L. fulviflamma collected on reefs presented a mangrove signature during their juvenile stage with 85% inhabiting mangrove for their entire juvenile life (about 1 year). The analysis of 2942 UVC revealed that the species was absent from isolated islands of the New Caledonian archipelago where mangroves were absent. Furthermore, strong positive correlations existed between the abundance of L. fulviflamma and the area of mangrove (r?=?0.84 for occurrence, 0.93 for density and 0.89 for biomass). These results indicate that mangrove forest is an obligatory juvenile habitat for L. fulviflamma in New Caledonia and emphasize the potential importance of mangroves for Indo-Pacific coral reef fishes.
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Project description:An adult P. rus colony was imported from Indonesia following the CITES protocols (Permit number 14846/IV/SATS-LN/2007) and kept in the Animal Facilities of the Justus Liebig University, Giessen. The colony was maintained in a circulating artificial seawater system at approximately 26 °C with 20-40 µmol photons m-2s-1 (T5 light) of photosynthetically active radiation on a 10:14 h light-dark cycle. A fragment of approx. 9 cm2 was separated from the colony and used as a source of tissue for hologenomic DNA/RNA isolation. Tissue was removed by scraping the fragment´s surface with a sterilized razor blade.
2018-05-25 | E-MTAB-6535 | biostudies-arrayexpress