Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed

Self-similar community structure in a network of human interactions

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.

Impact of community structure on information transfer

The observation that real complex networks have internal structure has important implication for dynamic processes occurring on such topologies. Here we investigate the impact of community structure on a model of information transfer able to deal with both search and congestion simultaneously. We show that networks with fuzzy community structure are more efficient in terms of packet delivery than those with pronounced community structure. We also propose an alternative packet routing algorithm which takes advantage of the knowledge of communities to improve information transfer and show that in the context of the model an intermediate level of community structure is optimal. Finally, we show that in a hierarchical network setting, providing knowledge of communities at the level of highest modularity will improve network capacity by the largest amount.

Community structure in mediterranean shallow lentic ecosystems: size-based vs. taxon-based approaches

The main environmental variables determining the community structure and the functioning of Mediterranean shallow lentic ecosystems are described. These ecosystems are characterized by the unpredictability of their water inputs and the high variability in their water level and physical and chemical composition. Variations in flooding, salinity, and water turnover are determinant in species composition and nutrient dynamics. Taxon-based and size-based approaches to the study of the community structure of aquatic organisms that colonise these ecosystems are also compared. The conventional taxonomic approach, based on the determination of species composition, has been used for the identification of patterns in species richness, distribution and temporal dynamics, and for ecological requirements of species and their potential use as ecological indicators. This taxonbased approach has been compared with a size-based approach, where individuals are classified by their size. Size-based approach gives complementary information about community structure and dynamics, especially when communities are dominated by a single species. The use of size diversity combined with species diversity is suggested for a more complete understanding of community structuring in this type of ecosystem. Detailed examples of two Mediterranean shallow lentic ecosystems, the salt marshes of the Empordà wetlands and the Espolla temporary karstic pond, which differ in hydrology and water origin, are used to discuss the suitability of these different approaches

Self-similar community structure in a network of human interactions

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.

Community structure and water quality in Mediterranean streams of a Natural Park (Sant Llorenç del Munt, NE Spain)

Se estudian las comunidades de macroinvertebrados de los ríos del Parque Natural de Sant Llorenç del Munt i la Serra de l'Obac (Barcelona, NE España) y su relación con las condiciones de flujo de los ríos. Hasta 78 localidades se visitaron en dos ocasiones (invierno y verano de 1996) y en 26 de ellas se tomaron muestras de macroinvertebrados. Mientras en invierno el 63 % de los kilÛmetros investigados tenía flujo continuo y menos del 1% estaba seco, en verano solo el 26% tenía flujo continuo, un 20% estaba totalmente seco y el resto presentaba pozas en su lecho. A pesar de ello el número de familias de macroinvertebrados fue de 54 en invierno y 94 en verano, siendo dominantes en este último caso los heterópteros, coleópteros, odonatos y dípteros, mientras que en invierno los tricópteros y plecópteros eran más diversos. En general, la comunidad presentó una estrategia trófica recolectora aunque la proporción de los ramoneadores y depredadores aumentó en verano. El estudio de las comunidades mediante el análisis de su abundancia en los dos perÌodos, mostró que las variables temporales (flujo, temperatura) o las relacionadas con el incremento de la producciÛn primaria (oxÌgeno, pH) explicaban la mayor parte de la variabilidad con los elementos mas reófilos propios de invierno y los leníticos de verano, mientras que otros factores fisicoquímicos no eran relevantes. Calculado el índice biológico BMWP' se demostró que los valores en verano eran superiores o similares a los de invierno lo que se explica por la mayor diversidad aunque la calificaciÛn individual de cada una de las familias encontradas en verano fuera menor que las halladas en invierno.

Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis

A cultivation-independent approach based on polymerase chain reaction (PCR)-amplified partial small subunit rRNA genes was used to characterize bacterial populations in the surface soil of a commercial pear orchard consisting of different pear cultivars during two consecutive growing seasons. Pyrus communis L. cvs Blanquilla, Conference, and Williams are among the most widely cultivated cultivars in Europe and account for the majority of pear production in Northeastern Spain. To assess the heterogeneity of the community structure in response to environmental variables and tree phenology, bacterial populations were examined using PCR-denaturing gradient gel electrophoresis (DGGE) followed by cluster analysis of the 16S ribosomal DNA profiles by means of the unweighted pair group method with arithmetic means. Similarity analysis of the band patterns failed to identify characteristic fingerprints associated with the pear cultivars. Both environmentally and biologically based principal-component analyses showed that the microbial communities changed significantly throughout the year depending on temperature and, to a lesser extent, on tree phenology and rainfall. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant bacterial populations. Most DGGE band sequences were related to bacterial phyla, such as Bacteroidetes, Cyanobacteria, Acidobacteria, Proteobacteria, Nitrospirae, and Gemmatimonadetes, previously associated with typical agronomic crop environments

Habitat selection by grey mullets (Osteichthyes: Mugilidae) in Mediterranean estuaries: the role of salinity.

A stratified study of microhabitat use by grey mullet on the island of Minorca (Balearic archipelago, western Mediterranean) showed that the distribution of all the species was dramatically affected by salinity. Sites with a salinity level under 15 were positively selected in spring and summer by those species whose growth performance was the best in oligomesohaline water (Liza ramado and Mugil cephalus) but also by a species whose growth was not affected by salinity (Chelon labrosus). Liza aurata concentrated in polyhaline and euhaline sites, where growth was improved, a pattern also exhibited by Liza saliens. Both species avoided fresh water sites all year round. As a consequence, community structure was correlated with salinity. The above reported electivity patterns often disappeared in autumn, when most grey mullets migrate off-shore.

The dynamics of biofilm bacterial communities is driven by flow wax and wane in a temporary stream

Biofilm communities are exposed to long periods of desiccation in temporary streams. We investigated how water flow intermittency affected the bacterial community structure colonizing three different streambed compartments in a Mediterranean stream. Massive parallel sequencing revealed different bacterial communities in biofilms from sand sediments and cobbles. Bacterial communities were similar (62% of shared operational taxonomic units) in the epipsammic and hyporheic biofilms, and more diverse than those in the epilithic biofilms. The non-flow phase caused a decrease of bacterial diversity in the biofilms, when communities included only bacterial taxa assumed to be adapted to water stress. The most sensitive bacterial communities to flow intermittency were in the epilithic, where the exposure to physical stress was the highest. In sand sediments a wide group of bacterial taxa was tolerant to desiccation. During non-flow the proliferation of opportunistic taxa in the superficial compartments evidenced the biological link with the terrestrial environment. Bacterial communities better tolerate rewetting than desiccation, since a major number of taxa tolerant to rewetting occurred in all biofilms. Overall, bacterial communities in sandy compartments showed higher resistance to flow intermittency than those in epilithic biofilms

Dinámica del heleoplancton en relación a las fluctuaciones hidrológicas en aiguamolls de l’Empordà (NE de la península Ibérica). Propuesta de un método sencillo de monitorización basado en la abundancia de grupos taxonómicos

Monitoring of the 'ecological water quality' in 'Aiguamolls de l’Empordà' Natural Park was carried out between September 1996 and August 1997 . The aim of this sampling programme was to design a simple method for rapid detect changes in water quality due to human activity. These include flow regulation by the Park management, nutrient entries from effluents of a nearby wastewater treatment plant or agricultural fertilising. The proposed method is based on the analysis of the abundance of characteristic taxonomic groups of aquatic invertebrates (heleoplankton). The simplicity of the method is ensured by the use of large taxa which are easier to recognise than species. The functioning of aquatic systems has been modelled by means of correspondence analysis between samples and taxa. Results can be summerized in five environmental conditions with a regular community structure. Dominated by one taxon: cladocerans, ostracods, calanoids, cyclopoids and harpacticoids. The dynamics of both freshwater and brackish lagoons can be modelled as displacements between these five groups of environmental conditions. Nevertheless, the “calanoids situation” and the “harpacticoids situation” occur mainly in brackish lagoons, whereas the “cladocerans situation” occurs mainly in freshwater. The four principal axes of data variation have been respectively identified as nutrient turnover rate, hypertrophy, degree of mineralization of the organic matter and eutrophy. The use of these taxa has been validated by comparison with a model obtained from the species. We conclude that in a highly fluctuating system such as the one here, only persistent situations of eutrophy or hypertrophy must be equated to low 'ecological water quality'

Effects of Temperature, Salinity and Fish in Structuring the Macroinvertebrate Community in Shallow Lakes: Implications for Effects of Climate Change

Climate warming may lead to changes in the trophic structure and diversity of shallow lakes as a combined effect of increased temperature and salinity and likely increased strength of trophic interactions. We investigated the potential effects of temperature, salinity and fish on the plant-associated macroinvertebrate community by introducing artificial plants in eight comparable shallow brackish lakes located in two climatic regions of contrasting temperature: cold-temperate and Mediterranean. In both regions, lakes covered a salinity gradient from freshwater to oligohaline waters. We undertook day and night-time sampling of macroinvertebrates associated with the artificial plants and fish and free-swimming macroinvertebrate predators within artificial plants and in pelagic areas. Our results showed marked differences in the trophic structure between cold and warm shallow lakes. Plant-associated macroinvertebrates and free-swimming macroinvertebrate predators were more abundant and the communities richer in species in the cold compared to the warm climate, most probably as a result of differences in fish predation pressure. Submerged plants in warm brackish lakes did not seem to counteract the effect of fish predation on macroinvertebrates to the same extent as in temperate freshwater lakes, since small fish were abundant and tended to aggregate within the macrophytes. The richness and abundance of most plant-associated macroinvertebrate taxa decreased with salinity. Despite the lower densities of plant-associated macroinvertebrates in the Mediterranean lakes, periphyton biomass was lower than in cold temperate systems, a fact that was mainly attributed to grazing and disturbance by fish. Our results suggest that, if the current process of warming entails higher chances of shallow lakes becoming warmer and more saline, climatic change may result in a decrease in macroinvertebrate species richness and abundance in shallow lakes

The structure of Mediterranean rocky reef ecosystems across environmental and human gradients, and conservation implications

Historical exploitation of the Mediterranean Sea and the absence of rigorous baselines makes it difficult to evaluate the current health of the marine ecosystems and the efficacy of conservation actions at the ecosystem level. Here we establish the first current baseline and gradient of ecosystem structure of nearshore rocky reefs at the Mediterranean scale. We conducted underwater surveys in 14 marine protected areas and 18 open access sites across the Mediterranean, and across a 31-fold range of fish biomass (from 3.8 to 118 g m22). Our data showed remarkable variation in the structure of rocky reef ecosystems. Multivariate analysis showed three alternative community states: (1) large fish biomass and reefs dominated by non-canopy algae, (2) lower fish biomass but abundant native algal canopies and suspension feeders, and (3) low fish biomass and extensive barrens, with areas covered by turf algae. Our results suggest that the healthiest shallow rocky reef ecosystems in the Mediterranean have both large fish and algal biomass. Protection level and primary production were the only variables significantly correlated to community biomass structure. Fish biomass was significantly larger in well-enforced no-take marine reserves, but there were no significant differences between multi-use marine protected areas (which allow some fishing) and open access areas at the regional scale. The gradients reported here represent a trajectory of degradation that can be used to assess the health of any similar habitat in the Mediterranean, and to evaluate the efficacy of marine protected areas.

Small but powerful: Top predator local extinction affects ecosystem structure and function in an intermittent stream.

Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators' extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a 'mesopredator release', affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the topdown effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire.We found that top predator absence led to 'mesopredator release', and also to 'prey release' despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem's structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers' extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore ecosystem structure and function.

Effects of the sewage pollution in the structure and dynamics of the community of Cystoseira mediterranea (Fucales, Phaeophyceae)

We performed a study on the specific composition, structure, and dynamics of two Cystoseira mediterranea communities from the north-western Mediterranean submitted to different degrees of pollution. The structural complexity (species richness, specific distribution, and species and pattern diversity) and biomass production were lower in the polluted site. In this station, opportunistic algae (mainly Ulva rigida) loomed, and Mesophyllum lichenoides and some encrusting brown algae increased their cover. Other species (Jania rubens, and some Ceramiales) decreased their abundance when compared with the polluted site