Biosurfactant production in sub-oxic conditions detected in hydrocarbon-degrading isolates from marine and estuarine sediments

Hydrocarbon bioremediation in anoxic sediment layers is still challenging not only because it involves metabolic pathways with lower energy yields but also because the production of biosurfactants that contribute to the dispersion of the pollutant is limited by oxygen availability. This work aims at screening populations of culturable hydrocarbonoclastic and biosurfactant (BSF) producing bacteria from deep sub-seafloor sediments (mud volcanos from Gulf of Cadiz) and estuarine sub-surface sediments (Ria de Aveiro) for strains with potential to operate in sub-oxic conditions. Isolates were retrieved from anaerobic selective cultures in which crude oil was provided as sole carbon source and different supplements were provided as electron acceptors. Twelve representative isolates were obtained from selective cultures with deep-sea and estuary sediments, six from each. These were identified by sequencing of 16S rRNA gene fragments belonging to Pseudomonas, Bacillus, Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera. BSF production by the isolates was tested by atomized oil assay, surface tension measurement and determination of the emulsification index. All isolates were able to produce BSFs under aerobic and anaerobic conditions, except for isolate DS27 which only produced BSF under aerobic conditions. These isolates presented potential to be applied in bioremediation or microbial enhanced oil recovery strategies under conditions of oxygen limitation. For the first time, members of Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera are described as anaerobic producers of BSFs.publishe

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation

Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.Portuguese Foundation for Science and Technology [EXPL/MAR-EST/1664/2013, SFRH/BPD/34282/2006]German Volkswagen (VW) foundation [Az. 81 040-2]info:eu-repo/semantics/publishedVersio

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants.A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment.In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments

Incidence of Rotavirus and Adenovirus: detection by molecular and immunological methods in human faeces

Rotaviruses and Adenoviruses are reported worldwide among the main agents of gastroenteritis and, consequently, the development and validation of sensitive and cost effective methods of detection is necessary. In this study, two approaches for detection of Rotavirus A and Adenovirus in samples of human faeces were compared: the immunological kit VIKIA Rota-Adeno and the nested-polymerase chain reaction (nested-PCR for Adenovirus) and Reverse Transcriptase-PCR (RT-PCR for Rotavirus) molecular methods. From January 2006 to July 2009, 467 samples of faeces from individuals with gastroenteritis symptoms assisted at the Hospital Infant D. Pedro (Aveiro, Portugal) were analysed for Rotavirus and Adenovirus, using the VIKIA kit. From the 467 samples, 59 (12.6%) were positive for Rotavirus and 5 (1.1%) for Adenovirus. Between December 2008 to July 2009, 18 samples were analysed by both immunologic and molecular methods. From the 18 samples, 10 were positive for Rotavirus (55.5%) and 16 for Adenovirus (88.9%) when analysed by RT-PCR and nested-PCR, respectively With VIKIA kit, 11 samples were positive for Rotavirus (61.1%) and only one was positive for Adenovirus (5.5%). Sequencing of PCR products confirmed the presence of Rotavirus in 1 sample and Adenovirus in the 10 samples that were classified as negative with VIKIA Kit. The results of VIKIA kit suggest that from the both viruses studied Rotavirus are the most incident viruses in gastroenteritis, however, molecular analysis results suggest that Adenovirus could be the most responsible for the viral gastroenteritis studied.The authors would like to thank University of Aveiro and Centre for Environmental and Marine Studies (CESAM, project Pest-C/MAR/LA0017/2011) for funding the study and to Hospital Infant D. Pedro of Aveiro for providing the faeces amples and to Dr. Albert Bosch from Barcelona University for the donation of Rotavirus and Adenovirus suspension.publishe

An ecotoxicological analysis of the sediment quality in a European Atlantic harbor emphasizes the current limitations of the Water Framework Directive

The "PortoNovo" project was developed to standardize the methodologies for water quality management in the port areas of coastal Atlantic regions to improve the Water Frame Directive (WFD) for these specific water bodies. Under this scope, water and sediment samples were collected from five sites within the Port of Aveiro, Portugal. According to the physical and chemical parameters that were analyzed (i.e., metals, total organic carbon, polychlorinated biphenyls and polycyclic aromatic hydrocarbons), the sediments were not considered at risk based on European sediment quality laws. However, the bioassays that were performed on the sediment samples (Microtox®) and the standardized acute toxicity test using the marine rotifer, Brachionus plicatilis, on sediment elutriates revealed higher toxicity levels. The use of bioassays to assess sediment quality clearly complements more conservative approaches and highlights current gaps within the WFD. The approach presented here can be easily transferred to other port areas for more reliable water quality management

Bacterioplankton Community Shifts during a Spring Bloom of Aphanizomenon gracile and Sphaerospermopsis aphanizomenoides at a Temperate Shallow Lake

Climate change is enhancing the frequency of cyanobacterial blooms not only during summer but also in spring and autumn, leading to increased ecological impacts. The bacterioplankton community composition (BCC), in particular, is deeply affected by these blooms, although at the same time BCC can also play important roles in blooms’ dynamics. However, more information is still needed regarding BCC during species-specific cyanobacterial blooms. The goal of this study was to assess BCC succession in a hypereutrophic shallow lake (Vela Lake, Portugal) during a warm spring using a metagenomic approach to provide a glimpse of the changes these communities experience during the dominance of Aphanizomenon-like bloom-forming species. BCC shifts were studied using 16S rRNA gene metabarcoding and multivariate analyses. A total of 875 operational taxonomic units (OTUs) were retrieved from samples. In early spring, the dominant taxa belonged to Proteobacteria (mainly Alphaproteobacteria—Rickettsiales) and Bacteroidetes (Saprospirales, Flavobacteriales and Sphingobacteriales). However, at the end of May, a bloom co-dominated by cyanobacterial populations of Aphanizomenon gracile, Sphaerospermopsis aphanizomenoides and Synechococcus sp. developed and persisted until the end of spring. This led to a major BCC shift favouring the prevalence of Alphaproteobacteria (Rickettsiales and also Rhizobiales, Caulobacteriales and Rhodospirillales) and Bacteroidetes (Saprospirales, followed by Flavobacteriales and Sphingobacteriales). These results contribute to the knowledge of BCC dynamics during species-specific cyanobacterial blooms, showing that BCC is strongly affected (directly or indirectly) by Aphanizomenon-Sphaerospermopsis blooms.publishe

Fusion versus Breakup: Observation of Large Fusion Suppression for ^9Be + ^{208}Pb

Complete fusion excitation functions for $^{9}$Be + $^{208}$Pb have been measured to high precision at near barrier energies. The experimental fusion barrier distribution extracted from these data allows reliable prediction of the expected complete fusion cross-sections. However, the measured cross-sections are only 68% of those predicted. The large cross-sections observed for incomplete fusion products support the interpretation that this suppression of fusion is caused by $^{9}$Be breaking up into charged fragments before reaching the fusion barrier. Implications for the fusion of radioactive nuclei are discussed.Comment: RevTex, 11 pages, 2 postscript figures, to appear in PR

Marine sponge and octocoral-associated bacteria show versatile secondary metabolite biosynthesis potential and antimicrobial activities against human pathogens

Marine microbiomes are prolific sources of bioactive natural products of potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-far unclassified lineages to identify isolates with potentially rich secondary metabolism and antimicrobial activities. Seventy representative isolates had their genomes mined for secondary metabolite biosynthetic gene clusters (SM-BGCs) and were screened for antimicrobial activities against four pathogenic bacteria and five pathogenic Candida strains. In total, 466 SM-BGCs were identified, with antimicrobial peptide- and polyketide synthase-related SM-BGCs being frequently detected. Only 38 SM-BGCs had similarities greater than 70% to SM-BGCs encoding known compounds, highlighting the potential biosynthetic novelty encoded by these genomes. Cross-streak assays showed that 33 of the 70 genome-sequenced isolates were active against at least one Candida species, while 44 isolates showed activity against at least one bacterial pathogen. Taxon-specific differences in antimicrobial activity among isolates suggested distinct molecules involved in antagonism against bacterial versus Candida pathogens. The here reported culture collections and genome-sequenced isolates constitute a valuable resource of understudied marine bacteria displaying antimicrobial activities and potential for the biosynthesis of novel secondary metabolites, holding promise for a future sustainable production of marine drug leads.info:eu-repo/semantics/publishedVersio

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.Patricia Martins benefited from a PhD grant (SFRH/BD/73889/2010) provided by the Portuguese FCT (Fundação para a Ciência e Tecnologia). This study has been carried out with the financial support of project AQUASAFE - Development of new technologies to anticipate and diagnose disease outbreaks in aquaculture (PROMAR 31-03-05-FEP-0016) (PROMAR, a Portuguese instrument for the sectors of fisheries and aquaculture funded by the European Fisheries Fund). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.publishe

Influence of environmental variables in the efficiency of phage therapy in aquaculture

Aquaculture facilities worldwide continue to experi-ence significant economic losses because of disease caused by pathogenic bacteria, including multidrug-resistant strains. This scenario drives the search for alternative methods to inactivate pathogenic bacteria. Phage therapy is currently considered as a viable alternative to antibiotics for inactivation of bacterial pathogens in aquaculture systems. While phage therapy appears to represent a useful and flexible tool for microbiological decontamination of aquaculture effluents, the effect of physical and chemical proper-ties of culture waters on the efficiency of this tech-nology has never been reported. The present study aimed to evaluate the effect of physical and chemical properties of aquaculture waters (e.g. pH, tempera-ture, salinity and organic matter content) on the efficiency of phage therapy under controlled experi-mental conditions in order to provide a basis for the selection of the most suitable protocol for subse-quent experiments. A bioluminescent genetically transformed Escherichia coli was selected as a model microorganism to monitor real-time phage therapy kinetics through the measurement of bioluminescence, thus avoiding the laborious and time-consuming conventional method of counting colony-forming units (CFU). For all experiments, a bacterial concentration of ≈ 10 5 CFU ml −1 and a phage concentration of ≈ 10 6–8 plaque forming unit ml −1 were used. Phage survival was not significantly affected by the natural variability of pH (6.5–7.4), temperature (10–25°C), salinity (0–30 g NaCl l −1) and organic matter concentration of aquaculture waters in a tem-perate climate. Nonetheless, the efficiency of phage therapy was mostly affected by the variation of salin-ity and organic matter content. As the effectiveness of phage therapy increases with water salt content, this approach appears to be a suitable choice for marine aquaculture systems. The success of phage therapy may also be enhanced in non-marine systems through the addition of salt, whenever this option is feasible and does not affect the survival of aquatic species being cultured