Exploring Prokaryotic Communities in the Guts and Mucus of Nudibranchs, and Their Similarity to Sediment and Seawater Microbiomes.

In the present study, we compared mucus and gut-associated prokaryotic communities from seven nudibranch species with sediment and seawater from Thai coral reefs using high-throughput 16S rRNA gene sequencing. The nudibranch species were identified as Doriprismatica atromarginata (family Chromodorididae), Jorunna funebris (family Discodorididae), Phyllidiella nigra, Phyllidiella pustulosa, Phyllidia carlsonhoffi, Phyllidia elegans, and Phyllidia picta (all family Phyllidiidae). The most abundant bacterial phyla in the dataset were Proteobacteria, Tenericutes, Chloroflexi, Thaumarchaeota, and Cyanobacteria. Mucus and gut-associated communities differed from one another and from sediment and seawater communities. Host phylogeny was, furthermore, a significant predictor of differences in mucus and gut-associated prokaryotic community composition. With respect to higher taxon abundance, the order Rhizobiales (Proteobacteria) was more abundant in Phyllidia species (mucus and gut), whereas the order Mycoplasmatales (Tenericutes) was more abundant in D. atromarginata and J. funebris. Mucus samples were, furthermore, associated with greater abundances of certain phyla including Chloroflexi, Poribacteria, and Gemmatimonadetes, taxa considered to be indicators for high microbial abundance (HMA) sponge species. Overall, our results indicated that nudibranch microbiomes consisted of a number of abundant prokaryotic members with high sequence similarities to organisms previously detected in sponges.

Molecular analysis of bacterial communities and detection of potential pathogens in a recirculating aquaculture system for Scophthalmus maximus and Solea senegalensis.

The present study combined a DGGE and barcoded 16S rRNA pyrosequencing approach to assess bacterial composition in the water of a recirculating aquaculture system (RAS) with a shallow raceway system (SRS) for turbot (Scophthalmus maximus) and sole (Solea senegalensis). Barcoded pyrosequencing results were also used to determine the potential pathogen load in the RAS studied. Samples were collected from the water supply pipeline (Sup), fish production tanks (Pro), sedimentation filter (Sed), biofilter tank (Bio), and protein skimmer (Ozo; also used as an ozone reaction chamber) of twin RAS operating in parallel (one for each fish species). Our results revealed pronounced differences in bacterial community composition between turbot and sole RAS, suggesting that in the systems studied there is a strong species-specific effect on water bacterial communities. Proteobacteria was the most abundant phylum in the water supply and all RAS compartments. Other important taxonomic groups included the phylum Bacteriodetes. The saltwater supplied displayed a markedly lower richness and appeared to have very little influence on bacterial composition. The following potentially pathogenic species were detected: Photobacterium damselae in turbot (all compartments), Tenacibaculum discolor in turbot and sole (all compartments), Tenacibaculum soleae in turbot (all compartments) and sole (Pro, Sed and Bio), and Serratia marcescens in turbot (Sup, Sed, Bio and Ozo) and sole (only Sed) RAS. Despite the presence of these pathogens, no symptomatic fish were observed. Although we were able to identify potential pathogens, this approach should be employed with caution when monitoring aquaculture systems, as the required phylogenetic resolution for reliable identification of pathogens may not always be possible to achieve when employing 16S rRNA gene fragments.

Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters.

Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.

Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities.

An experimental life support system (ELSS) was constructed to study the interactive effects of multiple stressors on coastal and estuarine benthic communities, specifically perturbations driven by global climate change and anthropogenic environmental contamination. The ELSS allows researchers to control salinity, pH, temperature, ultraviolet radiation (UVR), tidal rhythms and exposure to selected contaminants. Unlike most microcosms previously described, our system enables true independent replication (including randomization). In addition to this, it can be assembled using commercially available materials and equipment, thereby facilitating the replication of identical experimental setups in different geographical locations. Here, we validate the reproducibility and environmental quality of the system by comparing chemical and biological parameters recorded in our ELSS with those prevalent in the natural environment. Water, sediment microbial community and ragworm (the polychaete Hediste diversicolor) samples were obtained from four microcosms after 57 days of operation. In general, average concentrations of dissolved inorganic nutrients (NO3 (-) ; NH4 (+) and PO4 (-3) ) in the water column of the ELSS experimental control units were within the range of concentrations recorded in the natural environment. While some shifts in bacterial community composition were observed between in situ and ELSS sediment samples, the relative abundance of most metabolically active bacterial taxa appeared to be stable. In addition, ELSS operation did not significantly affect survival, oxidative stress and neurological biomarkers of the model organism Hediste diversicolor. The validation data indicate that this system can be used to assess independent or interactive effects of climate change and environmental contamination on benthic communities. Researchers will be able to simulate the effects of these stressors on processes driven by microbial communities, sediment and seawater chemistry and to evaluate potential consequences to sediment toxicity using model organisms such as Hediste diversicolor.

Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.