A Study of Sponge Symbionts from Different Light Habitats.

The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.

Recognizing megatsunamis in Mediterranean deep sea sediments based on the massive deposits of the 365 CE Crete event.

The Mediterranean Sea hosts two subduction systems along the convergent Africa-Eurasia plate boundary that have produced strong ground shaking and generated tsunamis. Based on historical descriptions and sedimentary records, one of these events, in 365 CE, impacted a broad geographical area, including tsunami evidence for distances of 700-800 km from the source event, qualifying it as a 'megatsunami'. Understanding how megatsunamis are produced, and where they are more likely, requires a better understanding of the different secondary processes linked to these events such as massive slope failures, multiple turbidity current generation, and basin seiching. Our sedimentary records from an extensive collection of cores located in distal and disconnected basins, identify turbidites which are analyzed using granulometry, elemental (XRF), micropaleontological, and geochemical data in order to reconstruct their coastal or marine source. The results show that the 365 CE basin floor sediments are a mixture of inner shelf and slope materials. The tsunami wave produced multiple far-field slope failures that resulted in stacked basal turbidites. It also caused transport of continent-derived organic carbon and deposition over basal turbidites and into isolated basins of the deep ocean. The composition of sediment in isolated basins suggests their deposition by large-scale sheet like flows similar to what has been caused by the Tohoku earthquake associated tsunamis. This is significant for rectifying and resolving where risk is greatest and how cross-basin tsunamis are generated. Based on these results, estimates of the underlying deposits from the same locations were interpreted as possible older megatsunamis.

Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea.

In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.

A comparison of prokaryote communities inhabiting sponges, bacterial mats, sediment and seawater in Southeast Asian coral reefs.

In the present study, we used Illumina sequencing to explore the prokaryote communities of 17 demosponge species and how they compare with bacterial mat, sediment and seawater samples (all sampled from coral reef habitat in Taiwan and Thailand). The studied sponge species formed three clusters. Operational taxonomic unit (OTU) richness and evenness were by far highest in the sediment and bacterial mat biotopes. There were pronounced differences in OTU richness and evenness among clusters and also considerable variation among certain host species within clusters. Additionally, the relative abundance of some prokaryotic taxa also differed among clusters with Poribacteria, e.g., being recorded in all sponge species, but with very low relative abundances in species of two of the three clusters. This sponge-associated phylum was, however, recorded at relatively high mean abundance in bacterial mat samples, which also housed relatively high abundances of actinobacterial and Chloroflexi members. Our results support high microbial abundance (HMA) status of the species Aaptos lobata, Hyrtios erectus, Pseudoceratina purpurea and Xestospongia testudinaria and low microbial abundance (LMA) status of the species Acanthella cavernosa, Echinodictyum asperum, Jaspis splendens, Ptilocaulis spiculifer, Stylissa carteri and Suberites diversicolor. Other species (Agelas cavernosa, Agelas nemoechinata, Acanthostylotella cornuta, Paratetilla sp., Hymeniacidon sp. and Haliclona cymaeformis) deviated somewhat from the typical HMA/LMA dichotomy and formed a strongly supported cluster.

Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes.

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.

Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems.

Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.

Lower plate serpentinite diapirism in the Calabrian Arc subduction complex.

Mantle-derived serpentinites have been detected at magma-poor rifted margins and above subduction zones, where they are usually produced by fluids released from the slab to the mantle wedge. Here we show evidence of a new class of serpentinite diapirs within the external subduction system of the Calabrian Arc, derived directly from the lower plate. Mantle serpentinites rise through lithospheric faults caused by incipient rifting and the collapse of the accretionary wedge. Mantle-derived diapirism is not linked directly to subduction processes. The serpentinites, formed probably during Mesozoic Tethyan rifting, were carried below the subduction system by plate convergence; lithospheric faults driving margin segmentation act as windows through which inherited serpentinites rise to the sub-seafloor. The discovery of deep-seated seismogenic features coupled with inherited lower plate serpentinite diapirs, provides constraints on mechanisms exposing altered products of mantle peridotite at the seafloor long time after their formation.

The impact of the 1999 Mw 7.4 event in the Izmit Bay (Turkey) on anthropogenic contaminant (PCBs, PAHs and PBDEs) concentrations recorded in a deep sediment core.

The 1999 Mw 7.4 earthquake triggered a tremendous human tragedy and had a great social impact over the population of the Izmit Bay, one of the most industrialized area of Turkey. Although the successive environmental disasters were well documented, information on its sedimentary record is lacking. The present research aims at filling this gap, through the analysis of organic contaminants (PCBs, PAHs, and PBDEs) in a dated sediment core collected in the depocenter of the Karamürsel Basin in 2005. Profiles of total PCBs and total PAHs overlap the timing of industrialization in the area (starting in the 1960s) with values increasing as the population and the number of industrial plants grew larger. Profiles for PBDEs are in accordance with increasing urban inputs but are probably affected by processes of natural formation and post-depositional mixing. The continuous sedimentary record is interrupted at a level dating back to 1980 due to the erosion caused by the 1999 earthquake, having removed a 5-7cm thick sediment layer. Contaminant concentrations in the deepest 10-15cm of a 30cm thick seismo-turbidite unit, triggered by the 1999 event, increase with the progressive fining up and evidence massive transport of sediments from coastal, more polluted sites of the north-eastern Karamürsel shelves and shores. Additional inputs of PAHs are also evident, originating from a fire at the oil refinery that followed the shaking. The effects of the earthquake generated tsunami, its backwash fluxes and the following seiches are not uniquely displayed by each class of contaminants, and they could probably reflect successive inputs deriving from different parts of the basin that are subject to anthropogenic impacts of different nature. Concentrations measured at the top of the core are consistent with an unvaried input of pollutants in the period 1980-2005.

EWSR1 rearrangement is a frequent event in papillary thyroid carcinoma and in carcinoma of the thyroid with Ewing family tumor elements (CEFTE).

Carcinomas of the thyroid with Ewing family tumor element (CEFTEs) are small-cell thyroid tumors with epithelial differentiation that disclose p63 expression and EWSR1-FLI1 rearrangement, carry a favorable prognosis and may co-exist with papillary thyroid carcinoma (PTC) foci. Two histogenetic hypotheses have been advanced regarding the origin of CEFTEs: arising in PTCs or in solid cell nests (SCN). A total of 3 CEFTEs, 54 PTCs, and 10 SCNs were reviewed, and fluorescence in situ hybridization (FISH) technique was performed in all cases to search for the presence of EWSR1 rearrangements. The three CEFTEs disclosed the EWSR1-FLI1 rearrangement both in the small cell and in the PTC component. Out of the 54 PTC cases, 28 (51.9%) were positive, 20 (37.0%) were negative, and 6 (11.1%) were inconclusive for EWSR1 rearrangement; in two of the positive PTC cases, the EWSR1-FLI1 rearrangement was detected. Classic PTC disclosed more often the EWSR1 rearrangement than other PTC variants (p = 0.031). PTCs with EWSR1 rearrangement disclosed a lower percentage of nuclei with EWSR1 polysomy than those without EWSR1 rearrangement (p = 0.001). Out of the 10 SCNs, 7 (70.0%) were negative and 3 (30.0%) were inconclusive for the EWSR1 rearrangement. Monosomic nuclei were more frequent (mean of 44.3%) in SCNs than in PTCs (p < 0.001). The presence of the EWSR1-FLI1 rearrangement in PTC component of all studied CEFTEs and the existence of the EWSR1 rearrangement in some PTCs favor the origin of CEFTE from PTC. The high frequency of EWSR1 rearrangements in PTC may represent a new diagnostic marker of these tumors.

Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex.

Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay-Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters.

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.

In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation.