Pedro Gomes

Role of fungi, bacteria, and invertebrates in leaf litter breakdown in a polluted river

Abstract The effects of water-quality degradation caused by urbanization, agricultural, and industrial activities on leaf litter breakdown and associated communities of invertebrates and microorganisms were examined at 1 reference and 2 downstream polluted sites in the Ave River (northwestern Portugal). Conductivity, concentrations of NH4+-N, NO3−-N, and PO43−-P, and density of culturable microorganisms were high at the polluted sites. Rates of leaf breakdown also were high, and the highest value was found at the most-downstream, nutrient-enriched polluted site. However, the other polluted site had low current velocity and sedimentation, and nutrient enrichment did not lead to rapid leaf breakdown. Shredders were scarce or absent at all sampling sites, and low shredder density probably explained the lack of differences in leaf breakdown rates between fine-mesh and coarse-mesh bags. High fungal and bacterial production on leaves supported high leaf breakdown rates. Bacterial production was greater at both polluted sites than at the reference site, but it did not exceed 11% of the total microbial production. Fungal biomass and production were markedly different between polluted sites, with the highest values corresponding to the fastest leaf breakdown. Our findings indicate that fungi were the major decomposers in this polluted river. We encourage further research on the effects of multiple stressors on the activity of fungal decomposers to help us better understand the mechanisms underlying leaf litter breakdown in streams under stress.

Leaf breakdown rates : a measure of water quality?

The breakdown rates of Alnus glutinosa leaves and the structure of macroinvertebrate communities were used to evaluate the impact of the village of Montalegre (Portugal) on the water quality of the Cavado river. Chemical and microbial analyses of stream water indicated a high organic load in the vicinity of the village. The abundance of macroinvertebrates associated with leaves increased along the pollution gradient, whereas richness of the community decreased. Biotic indices and multivariate analysis applied to aquatic macroinvertebrate communities discriminated polluted from non-polluted sites. Exponential breakdown rates of alder leaves were high (0.014 to 0.060 day -1 ) and the differences observed among sites suggested that nutrient enrichment stimulated leaf breakdown significantly. Leaf breakdown rates have not reflected improved biotic conditions as assessed by biotic indices at the most downstream site. These results suggest that both data from the structure and function of a stream are important for assessing water quality.

Biogeographic patterns of spiders in coastal dunes along a gradient of mediterraneity

The Iberian Peninsula is recognized for its high levels of species richness, rarity and endemicity. Our main aim was to study biogeographic patterns of spiders in coastal dunes along a gradient of mediterraneity. Distance-decay of similarity, nestedness and co-occurrence metrics were used to explore spider’ distribution patterns. A similarity analysis was performed in order to obtain a hierarchical classification of sites. Indicator species analysis was conducted to identify indicator species for the various clustering levels of the site typology. The differentiation among assemblages was further explored by non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM). Assemblages’ similarity among sites decreased with climatic/geographic distance. The observed values of nestedness metrics (T and NODF) were not significant, while the co-occurrence metrics (C-score and Checkerboard units) were higher than expected by chance. Cluster analysis showed that spider’ assemblages were structured along a gradient from North to South, forming four geographically distinct clusters. ANOSIM tests and NMDS supported the biogeographic patterns identified by cluster analysis. Several indicator species were found for the different levels of the hierarchic site typology. Spider assemblages revealed a high degree of biogeographical structure along the Atlantic coast of the Iberian Peninsula. The coast is a “biogeographic crossroad”, encompassing faunistic elements of different origins. The hierarchic typology of sites is generally consistent with the major biogeographic regions and the thermoclimatic belts recognized for the region. Our results indicate that the climatic gradient and historic factors played a key role in the current spiders’ biogeographic patterns.

Influence of herbaceous cover, shelter and land cover structure on wild rabbit abundance in NW Portugal

The European wild rabbitOryctolagus cuniculus (Linnaeus, 1758) populations in the Iberian Peninsula has suffered a serious decline. Therefore, the knowledge about the factors that influence rabbit distribution and abundance is of major interest for conservation and management programmes. Rabbit relative abundance was evaluated by pellet counting in relation to herbaceous ground cover, shelter availability (tall scrub cover and gaps in rocks) and land cover structure in the Peneda-Gerês National Park (PGNP), NW Portugal. Rabbit abundance was higher at intermediate levels of herbaceous cover, but no significant statistical differences were detected. A strong association between the abundance index and tall scrub cover was verified, and when this cover was rare, an association with gaps in rocks was observed. At the land cover level, rabbit abundance was associated with high interspersion sites of rocks with matorral and high interspersion sites of tall scrubland. Evidence from this study highlighted the importance of shelter and the interspersion of open/shelter habitats for rabbits. This pattern could be interpreted as an anti-predator strategy. Therefore, management actions should favour the growing and establishing of tall scrub patches and the selective cutting in highly continuous areas of tall scrub vegetation.

Assessing NoSQL Databases for Telecom Applications

The constant evolution of access technologies are turning Internet access more ubiquitous, faster, better and cheaper. In connection with the proliferation of Internet access, Cloud Computing is changing the way users look at data, moving from local applications and installations to remote services, accessible from any device. This new paradigm presents numerous opportunities that even traditional businesses like telecoms cannot ignore, in particular, enabling new and more cost effective solutions to old problems. The work presented in this paper provides a detailed description of how a telecom application can be migrated to a NoSQL database. Particularly, by pointing out the necessary change of how we reason about data as well as the data structures that support it, in order to take full advantage of Cloud Computing. In addition, we also present a preliminary evaluation of different data persistency paradigms based on a fully tunable simulation platform that mimics the operation of a telecom business.

Determinants of spider species richness in coastal dunes along a gradient of mediterraneity

Abstract.  1. The Iberian Peninsula is one of the most relevant areas in terms of species richness, rarity and endemism in the Mediterranean Basin. Using spiders as a model, we studied the relative importance of environmental and non‐environmental spatial variation along a gradient of mediterraneity on the western coast of the Iberian Peninsula.

Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast

In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences (<2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%-22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.

Evaluating Cassandra as a manager of large file sets

All companies developing their business on the Web, not only giants like Google or Facebook but also small companies focused on niche markets, face scalability issues in data management. The case study of this paper is the content management systems for classified or commercial advertisements on the Web. The data involved has a very significant growth rate and a read-intensive access pattern with a reduced update rate. Typically, data is stored in traditional file systems hosted on dedicated servers or Storage Area Network devices due to the generalization and ease of use of file systems. However, this ease in implementation and usage has a disadvantage: the centralized nature of these systems leads to availability, elasticity and scalability problems. The scenario under study, undemanding in terms of the systems consistency and with a simple interaction model, is suitable to a distributed database, such as Cassandra, conceived precisely to dynamically handle large volumes of data. In this paper, we analyze the suitability of Cassandra as a substitute for file systems in content management systems. The evaluation, conducted using real data from a production system, shows that when using Cassandra, one can easily get horizontal scalability of storage, redundancy across multiple independent nodes and load distribution imposed by the periodic activities of safeguarding data, while ensuring a comparable performance to that of a file system.

A technology cocktail for a 3D photo-realistic model of a i century Roman fountain: range scanning, RTI and physically based rendering

Archaeology is a science that uses multiple disciplines to ensure the validity of archaeological data and to accurately support theoretical foundations. Archaeology uses computer graphics to create credible virtual representations of archaeological sites and artifacts, which are used for interpretation, research purposes and archiving. Accurate virtual representations of an archaeological site rely on a balanced mixture of techniques, and some are discussed in this communication aplied to a I century roman fountain. Different imaging techniques were integrated - point cloud from a total station, 3D mid-range laser scanning and reflectance transformation imaging (RTI) - where their best features are extracted and combined to get the most accurate data in different scales. A point cloud enables a fair representation of the entire site (macro-scale), including the surrounding environment features. A 3D mid-range scanning captures the surface detail (medium-scale), but it may not be reliable to capture microstructure elements. An RTI technique (such as polynomial texture mapping, PTM) may overcome this limitation, since it can capture the microstructure elements through the surface reflectance properties. A physically based rendering technique (such as the one used by PBRT) can contribute to produce an improved view of an archaeological site, from a virtual 3D model. A collection of open-source software tools is under development to efficiently merge these techniques. This integrated set aims to provide a smooth integration of data gathered on the field, while adequately documenting all processing steps for archival purposes. Obtained results so far are promising and suggest some paths for improvements.

Invasive plants induce the taxonomic and functional replacement of dune spiders

Understanding the impacts caused by invasive plants on higher trophic levels is fundamental to predict future changes to native communities. Invasive plants like Acacia longifolia can change habitat structure and thereby alter the taxonomic and functional diversity and composition of predator communities. This work aims to evaluate the effect of this invasive plant species on spider assemblages, at both taxonomic and functional levels, in grey dunes. Spiders were sampled in six native and six invaded sites, in northwestern Portugal. Individuals were identified to species level and their functional features were quantified. Generalized Linear Models (GLM) were used to compare differences of species richness, abundance, functional diversity (FDQ) and trait proportions between native and invaded dunes. We also assessed the relative contribution of replacement and richness differences to overall taxonomic and functional dissimilarity between native and invaded dunes. GLMs showed that there was no change in species richness between dune types, but there was a significant increase in FDQ in invaded dunes. Significant shifts in the proportion of trait categories were observed. Native dunes favoured ambush hunters and myrmecophagous species. On the contrary, invaded dunes favoured species that inhabit leaf litter, web builders and crustaceophagous species. The proportion of diurnal species was higher in native dunes, contrary to invaded dunes, where both diurnal and nocturnal species dominated. Taxonomic and functional dissimilarity was mainly determined by the replacement, not the net loss, of species and traits. These results showed that functionally different spider species were favoured by the invasion of Acacia longifolia. The invasion of Acacia longifolia certainly attenuated the extreme habitat conditions normally found in grey dunes, allowing the immigration of more generalist species from neighbouring habitat types into invaded dunes. Thus, it can be concluded that there was no homogenization, taxonomic or functional, but changes in the composition of spider assemblages and the replacement of functions after dune invasion.