Ana Cordeiro Pires

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

ABSTRACT 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.

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.

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.

Richness and composition of sediment bacterial assemblages in an Atlantic port environment

In the present study, we assessed the bacterial richness and composition of sediment samples collected in and around the port of Aveiro, on the Atlantic coast of mainland Portugal. Sediment samples were collected in five locations: two within the port harbor, two in port areas along a channel adjacent to the harbor and one in a relatively undisturbed reference location. These areas were characterized as under high, medium and no port activity, respectively. In-depth, barcoded-pyrosequencing analysis indicated that port activity affects the composition and abundance of bacterial communities colonizing surface sediments. Sampling sites under the influence of port activities (channel and harbor) were associated with higher relative abundances of Desulfobacterales and a marked decline in the abundance of Flavobacteriia. In addition, there was a pronounced prevalence of operational taxonomic units (OTUs) in the port area that were closely related to hydrocarbon-degrading bacteria (Desulfococcus spp.), antifouling paint (bacterium strain WH6-7) and copper rich sediments (bacterium strain CanalPD16A). Here we provide evidence that specific phylotypes detected have the potential to be used as biomarkers and should be evaluated in future studies as proxies for sediment disturbance associated with port activity.

Urban speleology applied to groundwater and geo-engineering studies: underground topographic surveying of the ancient Arca D'Água galleries catchworks (Porto, NW Portugal)

The Porto settlement (Northwest Portugal, Iberian Peninsula) was originally built in the twelfth century and has been developed on granitic hill slopes of the Douro riverside, being one of the oldest cities in Europe. In the urban area of Porto, the second most important city of the Portuguese mainland, there is a population of about 216,000 inhabitants. This study highlights the importance of urban speleological mapping applied to groundwater and geo-engineering studies. All the water that flows from the so-called Paranhos or Arca D’Agua springs is captured by catchwork galleries and their utilization date back around 1120 AD. Paranhos spring galleries catchworks (c. 3,3 km extension and a -21m below ground level) was one of the main water supplies to Porto City for more than six centuries and, nowadays, these waters are still appropriate for irrigation uses. Topographical, geological, geophysical and hydrogeological data were collected and interpreted, allowing the definition of a hydrogeotechnical zoning. All these features were mapped and overlaid using GIS mapping techniques. This multidisciplinary approach offers a good potential for reliable urban speleological and geo-engineering studies of Arca D’Agua site.

Assessing future climate change in the Iberian Upwelling System

ABSTRACT Cordeiro Pires, A., Nolasco, R., Rocha, A. and Dubert, J., 2013. Assessing future climate change in the Iberian Upwelling System The Western Iberian Margin is the northern limit of the Canary Upwelling System, a region of strong mesoscale activity, seasonal variability and thus very likely to be sensitive to climate change. Using a regional ocean model and data from several coupled global climate models (CGCM), climatological simulations were set up for present and for a future scenario. Forcing is obtained from averaging the outputs of an ensemble of CGCM provided by the Intergovernmental Panel for Climate Change (IPCC) A2 emission scenario. Results are focused on the continental shelf (~200 m). In general, the sea surface temperature (SST) seasonal evolution shows, for the future, an increase of about 1°C during the upwelling season (April to September) and 2°C in the rest of the year, while sea surface salinity (SSS) shows a freshening of about −0.2. These results agree with a general increase in air temperature and in fresh water input resulting from ice melting in the North Pole, which characterize this future scenario. However, differences depend on latitude and distance from the coast (higher differences to the south and more offshore, respectively). Also, SSS undergoes a shift of its minimum from July to May or September. Cross-shore sections show that SST and SSS differences are mainly observed in the upper 200 m. In winter, the typical upper slope poleward flow undergoes a slight weakening and shallowing. In summer, while the upwelling jet intensifies at the surface, it is also more restricted in both width and depth.

Coastal Geo-Engineering Techniques for the Assessment of Rock Armour Structures

This work deals with the problem of assessing armourstone structures focusing on strengthening the combination of geo-marine techniques and geotechnical properties. The research has two main purposes: (i) to establish an integrative coastal geo-engineering approach for better assessment of the hydraulic structures; and (ii) to draw attention to the importance of quarry evaluation in order to improve armourstone quality and durability. Several studies have demonstrated the relevance of a holistic approach to coastal design issues. The suggested approach couples GIS-based mapping with geo-engineering techniques assessment along five pilot sectors of the Espinho coastal system in Northwestern Portugal. This investigation allowed us to propose zoning a coastal structure according to its degree of deterioration, geomechanical properties and geomaterial status. Replacement of the primary armour layer in only selected sections or components of the structure will reduce the cost of maintenance, repair and reinforcement work. All the gathered data about the preservation status of the armour layer and the quarry inventory have been compiled in a powerful GIS geo-database. The paper argues for the wider use of combination of coastal geo-engineering and GIS analysis in planning the monitoring and/or maintenance of marine works using armourstone.

On the origin of summer upwelled waters on the Western Iberian Margin

ABSTRACT Cordeiro Pires, A., Nolasco, R. and Dubert, J., 2013. On the origin of summer upwelled waters in Western Iberian Peninsula As in most eastern boundary systems, on the Western Iberian Margin there is coastal upwelling during summer due to the alongshore northerly winds and the consequent offshore displacement of surface waters. This work addresses the origin of these upwelled waters. Using a regional ocean model, a climatological configuration and a lagrangian particle module that is run backward in time, we trace the trajectory of particles arriving at four coastal areas, delimited by the 200-m isobath, approximately, and at three depths: 20 m, 40 m and 60 m. Each point is traced backward for one month, with arrival dates of June 30, July 30 and August 30, the typical upwelling months. We find out where the particles were on June 1, July 1 and August 1, respectively, how deep they have reached and what distance they have traveled. In general, the points of origin were shallower (in the upper 100 m) for the particles that traveled the greatest distances (up to 500 km). These particles come mostly from the north and trace alongshore pathways at 20–40 km from the coast, i.e., within isobaths 100–200 m, the preferential path of the upwelling-associated equatorward jet. Conversely, particles that originate from deeper levels, down to 600 m, come from shorter distances, approximately 100 km. Some particles originate to the west of their point of upwelling, giving evidence of being dependent on meandering and other mesoscale features, such as offshore eddies and upwelling filaments.

Combining coastal geoscience mapping and photogrammetric surveying in maritime environments (Northwestern Iberian Peninsula): focus on methodology

Digital photogrammetry and GIS-based mapping are increasingly recognised as powerful tools in littoral issues. This paper considers the interoperability framework for high-resolution imagery acquisition and the development of coastal geoscience maps. The layered system architecture of the cartographic methodology is also explained. Moreover, it highlights a new approach to assessing heterogeneous geologic, geomorphological and maritime environments. The main goal of the present study was to test a new concept for photogrammetric images in order to assist modelling techniques, spatial analysis and coastal conceptual models. This approach proposes a methodological approach to coastal zone monitoring and to maritime forcing conditions evaluating. This approach will allow: (1) the acquisition of a large archive of high-resolution imagery; (2) the development of a coastal database including the entire data field and in situ assessments; (3) the study of coastal dynamics and shoreline evolution; (4) the assessment of the rock platforms and hydraulic structures; (5) the production of coastal geosciences maps. An integrated coastal geoscience and engineering methodology was outlined in NW of Iberian Peninsula (South Galicia and North/Central Portugal regions). This paper reports on the increased knowledge of the studied regions, providing essential data concerning coastal geo-morphodynamics. The overall assessment revealed additional evidence of erosion issues, which contributes to a better understanding of the hydraulic conditions. The main results are presented in regional coastal geoscience maps and local approach-outputs that could help government, local authorities and stakeholders to develop coastal management plans and to recommend strategies.