Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity. X Maite Sampedro Pellicer, Affiliation: ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy X Maria Cristiana Papaleo, Affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy X Alessio Mengoni, Affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy X Luigi Ledda, Affiliation: Dipartimento di Agraria, University of Sassari, Sassari, Italy X Renato Fani, Affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy X Anna Benedetti, Affiliation: Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy X Claudia Dalmastr

Identificación de un nuevo gen responsable de una forma recesiva de distrofia de cinturas

[ES] Las Distrofias Musculares de Cinturas, LGMDs, son un grupo heterogéneo de enfermedades neurológicas raras, que se incluyen dentro de las llamadas distrofias musculares hereditarias. Se caracterizan por debilidad progresiva de la musculatura proximal, principalemente a nivel de la cintura pélvica y escapular. Hasta la fecha, los estudios genéticos clásicos han revelado 8 formas para la LGMD dominante y 15 formas para la LGMD recesiva y, se han identificado 18 genes causantes de la enfermedad. Se asocia a mutaciones en uno o más genes involucrados en la formación de las células musculares, por lo que la identificación de nuevas mutaciones ofrece importantes conocimientos acerca de los mecanismos de la enfermedad, de las vías biológicas y de las potenciales dianas terapéuticas. El presente proyecto de investigación se basa en resultados obtenidos en previos estudios y tiene como objetivo fundamental la identificación de un nuevo gen relacionado con una nueva forma de LGMD autosómica recesiva presente en una familia consanguínea. Para abordar este objetivo se realizaron análisis In Silico para predecir el grado de patogenicidad en las mutaciones candidatas e identificar la responsable de la expresión fenotípica. Además, se ha realizado un análisis de genotipado con la intención de descartar que la mutación se tratara de un polimorfismo poblacional. En conjunto, estos hallazgos parecen ser muy prometedores y sugieren que estamos ante una nueva forma de LGMD, no obstante se requieren más estudios que aborden esta hipótesis.[EN] Limb-girde muscular dystrophies, LGMDs, represent a heterogeneous group of rare neurological diseases, which are included in so-called hereditary muscular dystrophies. LGMD is characterized by progressive weakness and wasting, predominating in muscles of the pelvic and shoulder girdle. To date, classical genetic studies have revealed 8 forms of autosomal-dominant LGMDs and 15 forms of autosomal- recessive LGMDs, and 18 genes have been identified. LGMD is associated with mutations in one or more genes involved in the formation of muscle cells, therefore, the identification of new mutations provides important insights into the mechanisms of disease, biological pathways and potential therapeutic targets. This research project is based on results obtained in previous studies and the aim of this work is the identification of a new gene linked to a new form of autosomal recessive LGMD present in a consanguineous family. In order to address this objective, we performed In Silico analysis to predict the degree of pathogenicity in candidate mutations and identify the mutation responsible for the phenotypic expression. In addition, we have performed an analysis of genotyping which exclude that the mutation is a population polymorphism. The implications could be very relevant, and these findings suggest that this is a new form of LGMD; however, we need more studies to address this hypothesis.Sampedro Pellicer, M. (2012). Identificación de un nuevo gen responsable de una forma recesiva de distrofia de cinturas. http://hdl.handle.net/10251/27390Archivo delegad

UPGMA dendrogram of DGGE profiles of amplified 16S rDNA of bacterial communities recovered in CO, PA, MM, CV and TV, in spring and autumn, generated using Phoretix ID advanced analysis package.

<p>Designation of samples is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105515#pone-0105515-g001" target="_blank">Fig. 1</a>. The scale bar represents dissimilarity among samples. Consistency of each cluster was measured by the Cophenetic correlation coefficient shown at each node.</p

Effect of land-use and season on Eco-Physiological (EP) index of culturable bacteria (A) and diversity indices from CD-DGGE profiles (B).

<p>Effect of land-use and season on Eco-Physiological (EP) index of culturable bacteria (A) and diversity indices from CD-DGGE profiles (B).</p

Long-term effects of different land-use with increasing level of intensification in spring and autumn.

<p>Both pasture and managed meadow included spotted cork oak trees, which are key components of the Dehesatype landscape typical of this area of Sardinia. The cork-oak formation, pasture, and managed meadow have been converted to the current use and maintained unchanged for more than 30 years, whereas the non-tilled cover cropped vineyard and the tilled one were planted in 1985 and 1994, respectively. From the left to right: cork-oak forest (CO), hayland pasture rotation (PA), managed meadow (MM), grass covered vineyard (CV), tilled vineyard (TV).</p

Effect of land-use and season on soil physical-chemical and biological parameters.

<p>A) Heat map with hierarchal clustering of physical-chemical and biological parameters across the five Sardinia soils with different land uses at the two different sampling time points (May and November). The heat map was constructed using a maximum-minimum normalization of the data in order to represent each value in a range between 0 and 1. Higher values are represented by darker colors whereas lower ones are represented by lighter colors. CO = cork-oak forest; PA = hayland-pasture rotation; MM = managed meadow; TV =  tilled vineyard; CV =  grass covered vineyard. B) PCA ordination of data (axes 1 and 2) generated from physical-chemical and biological properties of the different types of land use in May and November.</p

Plot of the taxonomic composition of total bacterial community as inferred from taxonomic interpretation of T-RFLP profiles.

<p>Plot of the taxonomic composition of total bacterial community as inferred from taxonomic interpretation of T-RFLP profiles.</p