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

Diversitat bacteriana a les esponges marines

L’objectiu principal del projecte era aprofundir en el coneixement de les malalties de les esponges, centrant-nos en la diversitat bacteriana que acullen. Als estius 2008 i 2009 va haver episodis d’elevades temperatures de l’aigua de mar que van suposar importants mortalitats massives d’esponges a la Mediterrània. Contra tot pronòstic, els estius del projecte, el 2010 i el 2011, no van resultar especialment calorosos i no hi va haver episodis de mortalitat. És un fet molt positiu per les comunitats bentòniques però algun dels objectius específics de la meva proposta no es va poder dur a terme com havien estat platejats inicialment. Disposàvem de diferents mostres d’esponges malaltes de l’espècie Ircinia fasciculata, sanes i aigua circumdant recollides l’estiu 2009 i fixades per DNA, per això s’han pogut identificar i caracteritzar els canvis en la comunitat microbiològica de les esponges malaltes respecte de les sanes. Hem constatat que més que una infecció per un o pocs patògens puntuals, com havien proposat alguns autors, hi ha un canvi dràstic en la comunitat microbiològica associada a les esponges. Les esponges malaltes, on dominen els bacteris heterotròfics, presenten una major diversitat bacteriana que les sanes, on dominen els autòtrofs. Tot i que no es va poder realitzar un nou mostreig d’individus malalts, i algun objectiu específic no es va poder desenvolupar, vaig aprofitar l’estada en un centre de referència en estudis de la diversitat microbiana, per ampliar el coneixement general de les comunitats bacterianes associades a esponges. Es van realitzar nous estudis en què vam testar si totes les esponges (bacteriosponges i no) presenten simbionts reals o si les no-bacteriosponges presenten un enriquiment de les comunitats de l’aigua de mar però no una flora específica. El resultat és que totes les esponges presenten associacions molt específiques malgrat hi ha fortes diferències entre les comunitats microbianes associades a bacteriosponges i a no-bacteriosponges.

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

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

Multifunctionality and Diversity in Bacterial Biofilms

Bacteria are highly diverse and drive a bulk of ecosystem processes. Analysis of relationships between diversity and single specific ecosystem processes neglects the possibility that different species perform multiple functions at the same time. The degradation of dissolved organic carbon (DOC) followed by respiration is a key bacterial function that is modulated by the availability of DOC and the capability to produce extracellular enzymes. In freshwater ecosystems, biofilms are metabolic hotspots and major sites of DOC degradation. We manipulated the diversity of biofilm forming communities which were fed with DOC differing in availability. We characterized community composition using molecular fingerprinting (T-RFLP) and measured functioning as oxygen consumption rates, the conversion of DOC in the medium, bacterial abundance and the activities of five specific enzymes. Based on assays of the extracellular enzyme activity, we calculated how the likelihood of sustaining multiple functions was affected by reduced diversity. Carbon source and biofilm age were strong drivers of community functioning, and we demonstrate how the likelihood of sustaining multifunctionality decreases with decreasing diversity

Individual-based modelling of bacterial cultures to study the lag ohase

Els bacteris són la forma dominant de vida del planeta: poden sobreviure en medis molt adversos, i en alguns casos poden generar substàncies que quan les ingerim ens són tòxiques. La seva presència en els aliments fa que la microbiologia predictiva sigui un camp imprescindible en la microbiologia dels aliments per garantir la seguretat alimentària. Un cultiu bacterià pot passar per quatre fases de creixement: latència, exponencial, estacionària i de mort. En aquest treball s’ha avançat en la comprensió dels fenòmens intrínsecs a la fase de latència, que és de gran interès en l’àmbit de la microbiologia predictiva. Aquest estudi, realitzat al llarg de quatre anys, s’ha abordat des de la metodologia Individual-based Modelling (IbM) amb el simulador INDISIM (INDividual DIScrete SIMulation), que ha estat millorat per poder fer-ho. INDISIM ha permès estudiar dues causes de la fase de latència de forma separada, i abordar l’estudi del comportament del cultiu des d’una perspectiva mesoscòpica. S’ha vist que la fase de latència ha de ser estudiada com un procés dinàmic, i no definida per un paràmetre. L’estudi de l’evolució de variables com la distribució de propietats individuals entre la població (per exemple, la distribució de masses) o la velocitat de creixement, han permès distingir dues etapes en la fase de latència, inicial i de transició, i aprofundir en la comprensió del que passa a nivell cel•lular. S’han observat experimentalment amb citometria de flux diversos resultats previstos per les simulacions. La coincidència entre simulacions i experiments no és trivial ni casual: el sistema estudiat és un sistema complex, i per tant la coincidència del comportament al llarg del temps de diversos paràmetres interrelacionats és un aval a la metodologia emprada en les simulacions. Es pot afirmar, doncs, que s’ha verificat experimentalment la bondat de la metodologia INDISIM.

Natural Capital's perception by Kodagu communities: a comparative study (Karnataka, India)

When we ask ourselves about a concrete definition of “Natural Capital” we can find a large and wide range of conceptions, which are attached to it. These can turn out to be confusing and contradictory in some cases. In theory, through books and different studies we know natural resources are composed by all the natural actives originated by the nature itself. Besides, these conform a patrimony for society as them are translated into a path towards economy: The Natural Capital. May not the Natural Capital be an easy conception to put in terms of economy it turns out to be an important capacitor for economy growth in most countries. In any case, we can clearly distinguish two ways as Natural Capital can be seen. One may elaborate a definition about it by reading what others have previously written, those who usually are quite far from the direct use of natural resources. On the other hand it would also be interesting to conform a definition of it by asking people who are constantly in contact with natural resources and consequently contribute to form the Natural Capital.

Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on E. coli have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with E. coli. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion.

Intermediary and structural determinants of early childhood health in Colombia: exploring the role of communities

This study examines how structural determinants influence intermediary factors of child health inequities and how they operate through the communities where children live. In particular, we explore individual, family and community level characteristics associated with a composite indicator that quantitatively measures intermediary determinants of early childhood health in Colombia. We use data from the 2010 Colombian Demographic and Health Survey (DHS). Adopting the conceptual framework of the Commission on Social Determinants of Health (CSDH), three dimensions related to child health are represented in the index: behavioural factors, psychosocial factors and health system. In order to generate the weight of the variables and take into account the discrete nature of the data, principal component analysis (PCA) using polychoric correlations are employed in the index construction. Weighted multilevel models are used to examine community effects. The results show that the effect of household’s SES is attenuated when community characteristics are included, indicating the importance that the level of community development may have in mediating individual and family characteristics. The findings indicate that there is a significant variance in intermediary determinants of child health between-community, especially for those determinants linked to the health system, even after controlling for individual, family and community characteristics. These results likely reflect that whilst the community context can exert a greater influence on intermediary factors linked directly to health, in the case of psychosocial factors and the parent’s behaviours, the family context can be more important. This underlines the importance of distinguishing between community and family intervention programmes.

Discovering similarities in the time use patterns of the Spanish Autonomous Communities by Fuzzy techniques

In 2000 the European Statistical Office published the guidelines for developing theHarmonized European Time Use Surveys system. Under such a unified framework,the first Time Use Survey of national scope was conducted in Spain during 2002–03. The aim of these surveys is to understand human behavior and the lifestyle ofpeople. Time allocation data are of compositional nature in origin, that is, they aresubject to non-negativity and constant-sum constraints. Thus, standard multivariatetechniques cannot be directly applied to analyze them. The goal of this work is toidentify homogeneous Spanish Autonomous Communities with regard to the typicalactivity pattern of their respective populations. To this end, fuzzy clustering approachis followed. Rather than the hard partitioning of classical clustering, where objects areallocated to only a single group, fuzzy method identify overlapping groups of objectsby allowing them to belong to more than one group. Concretely, the probabilistic fuzzyc-means algorithm is conveniently adapted to deal with the Spanish Time Use Surveymicrodata. As a result, a map distinguishing Autonomous Communities with similaractivity pattern is drawn.Key words: Time use data, Fuzzy clustering; FCM; simplex space; Aitchison distance

Indicator taxa of benthic diatom communities: a case study in Mediterranean streams

A key issue in the implementation of the Water Framework Directive is the classification of streams and rivers using biological quality parameters and type-specific reference conditions. Four groups of stream types were defined in NE Spain on the basis of 152 diatom samples by means of detrended correspondence analysis and classification techniques. Diatom analysis was restricted to epilithic taxa, and the sites included gradients ranging from near-natural streams to sites with poor ecological quality. The main gradient shows a clear separation of sites in relation to the degree of human influence: polluted streams (mainly located in the lowlands) differ from streams in mountainous areas and in the Pyrenees. A second gradient is related to physiographical features. Headwater streams can be distinguished by their catchment geology. The type-specific diatom taxa for the stream types studied were determined by using indicator species analysis (IndVal). The type-specific taxa from near-natural streams are coincident with the indicator taxa for high ecological status. Human impact reduced the typological heterogeneity of the diatom community composition. Overall, the diatom communities in NE Spain exhibit a regional distribution pattern that closely corresponds with that observed in river systems elsewhere. Physiographical differences are only evident in undisturbed sites, while nutrient enrichment and other human disturbances may mask the regional differences in the distribution of diatom communities

Biodiversity and global change in Mediterranean benthic communities: perspectives over large spatial and long temporal scales

Many terrestrial and marine systems are experiencing accelerating decline due to the effects of global change. This situation has raised concern about the consequences of biodiversity losses for ecosystem function, ecosystem service provision, and human well-being. Coastal marine habitats are a main focus of attention because they harbour a high biological diversity, are among the most productive systems of the world and present high anthropogenic interaction levels. The accelerating degradation of many terrestrial and marine systems highlights the urgent need to evaluate the consequence of biodiversity loss. Because marine biodiversity is a dynamic entity and this study was interested global change impacts, this study focused on benthic biodiversity trends over large spatial and long temporal scales. The main aim of this project was to investigate the current extent of biodiversity of the high diverse benthic coralligenous community in the Mediterranean Sea, detect its changes, and predict its future changes over broad spatial and long temporal scales. These marine communities are characterized by structural species with low growth rates and long life spans; therefore they are considered particularly sensitive to disturbances. For this purpose, this project analyzed permanent photographic plots over time at four locations in the NW Mediterranean Sea. The spatial scale of this study provided information on the level of species similarity between these locations, thus offering a solid background on the amount of large scale variability in coralligenous communities; whereas the temporal scale was fundamental to determine the natural variability in order to discriminate between changes observed due to natural factors and those related to the impact of disturbances (e.g. mass mortality events related to positive thermal temperatures, extreme catastrophic events). This study directly addressed the challenging task of analyzing quantitative biodiversity data of these high diverse marine benthic communities. Overall, the scientific knowledge gained with this research project will improve our understanding in the function of marine ecosystems and their trajectories related to global change.

An analysis of the metabolic patterns of two rural communities affected by soy expansion in the North of Argentina

The soy expansion model in Argentina generates structural changes in traditional lifestyles that can be associated with different biophysical and socioeconomic impacts. To explore this issue, we apply an innovative method for integrated assessment - the Multi Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM) framework - to characterize two communities in the Chaco Region, Province of Formosa, North of Argentina. These communities have recently experienced the expansion of soy production, altering their economic activity, energy consumption patterns, land use, and human time allocation. The integrated characterization presented in the paper illustrates the differences (biophysical, socioeconomic, and historical) between the two communities that can be associated with different responses. The analysis of the factors behind these differences has important policy implications for the sustainable development of local communities in the area.

Banks and development: Jewish communities in the Italian Renaissance and current economic performance

Are differences in local banking development long-lasting? Do they affect long-term economic performance?I answer these questions by relying on an historical development that occurred in Italian cities during the 15thcentury. A sudden change in the Catholic doctrine had driven the Jews toward money lending. Cities thatwere hosting Jewish communities developed complex banking institutions for two reasons: first, the Jews werethe only people in Italy who were allowed to lend for a profit and, second, the Franciscan reaction to Jewishusury led to the creation of charity lending institutions, the Monti di Pietà, that have survived until today andhave become the basis of the Italian banking system. Using Jewish demography in 1500 as an instrument, Iprovide evidence of (1) an extraordinary persistence in the level of banking development across Italian cities (2)large effects of current local banking development on per-capita income. Additional firm-level analyses suggestthat well-functioning local banks exert large effects on aggregate productivity by reallocating resources towardmore efficient firms. I exploit the expulsion of the Jews from the Spanish territories in Italy in 1541 to arguethat my results are not driven by omitted institutional, cultural and geographical characteristics. In particular,I show that, in Central Italy, the difference in current income between cities that hosted Jewish communitiesand cities that did not exists only in those regions that were not Spanish territories in the 16th century.