Long-term impact of sustainable land management practices on soil bacterial community in an almond orchard in south Spain

[SPA] Una estructura de comunidad bacteriana saludable es uno de los principales indicadores de calidad del suelo. Las prácticas agrícolas modernas en las que se aplican labranza intensa y fertilizantes químicos continúan poniendo en juego el equilibrio ambiental y la sostenibilidad de la producción día a día. En este estudio, nuestro objetivo fue evaluar el efecto a largo plazo de prácticas sostenibles de bajos insumos, como la labranza reducida y el abono verde sobre la comunidad bacteriana edáfica en un cultivo de almendros del sur de España. La labranza reducida y la adición de abono verde han demostrado la estructura de la comunidad bacteriana más estable y la abundancia de especies con respecto a los métodos convencionales. El carbono orgánico del suelo y la comunidad bacteriana se mejoran con un enfoque sostenible de bajos insumos. [ENG] A healthy bacterial community structure is one of the main aspects of soil quality indicators. Modern agricultural practices, where intense tillage and chemical fertilizers are applied, continue to put environmental balance and sustainability of production at stake day by day. In this study, we aimed to assess the long-term effect of low-input sustainable practices such as reduced tillage and green manure on soil bacterial communities in an almond orchard from south Spain. Reduced tillage and addition of green manure has shown the most stable bacterial community structure and species abundance with respect to conventional practice. Soil organic carbon and bacterial community are improved by low-input sustainable approach.This work was conducted as a part of the European Commission Horizon 2020 project Diverfarming [grant agreement 728003]

Impact of different crop rotation sequences and management practices on soil bacterial diversity in Northern Netherlands

[SPA] La identificación de la estructura y diversidad bacteriana edáfica proporciona una visión enorme de la calidad del suelo debido a las intensas relaciones bioquímicas entre el microbioma del suelo y las plantas que interactúan. El objetivo de este estudio fue evaluar cómo diferentes sistemas de cultivo diversificados bajo dos diferentes tipos de manejo (convencional y biodinámico) afectan a la diversidad bacteriana del suelo. La comunidad bacteriana del suelo se identificó a través de la secuenciación de próxima generación de genes de codificación del RNAr 16S bacteriano. Los resultados mostraron que diferentes secuencias de rotaciones de cultivos, el periodo de implementación de las rotaciones y la práctica de manejo tienen una fuerte influencia en la biomasa microbiana, la biodiversidad bacteriana y la abundancia de diferentes filos bacterianos. [ENG] Identification of soil bacterial community structure and diversity provides a huge insight into soil quality due to the intense biochemical relationships between soil microbiome and interacting plants. The aim of this study was to assess how different diversified cropping systems under two different management (conventional and biodynamic) can affect soil bacterial diversity. Soil bacterial community was identified through next-generation sequencing of 16S rRNA coding genes of soil bacteria. The findings showed that different sequences of crop rotations, period of implementation of rotations and management practice had a strong influence on soil microbial biomass, bacterial biodiversity and the abundance of different bacterial phyla, without a specific trend regulated by these factors.This work was supported by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003]

A depth study of changed bacterial structure from soil under different cropping systems by co-occurrence network approach

[SPA] Debido al desgaste de los suelos por el uso indiscriminado de pesticidas y herbicidas, la búsqueda de alternativas a la agricultura convencional ha ido ganando interés alrededor del mundo. En este sentido, los microorganismos son importantes, ya que están incluidos en muchas funciones indispensables en los suelos, como la fijación de nitrógeno. En este trabajo se estudiaron 3 tipos de agricultura diferentes i) convencional, ii) ecológica con estiércol y iii) ecológica con compost, con el objetivo de estudiar los cambios ocurridos en las comunidades bacterianas, así como su funcionalidad, las parcelas estaban ubicadas en Cartagena (España). Para estudiar estas funciones, se utilizó el gen 16S obtenido a través de la secuenciación masiva y seguidamente se realizaron aproximaciones matemáticas a través de PICRUSt para predecir la función de esos microorganismos en el suelo. Por otro lado, se realizó un análisis de redes ecológicas moleculares (MENA) para estudiar las interacciones entre esas bacterias. Los resultados de esta investigación mostraron como el compost puede incrementar algunas rutas metabólicas y puede influir en la organización bacteriana, favoreciendo la modulación y las conexiones entre los nodos. [ENG] Due to soil degradation caused by indiscriminate use of pesticides and herbicides, search for sustainable alternatives to conventional agriculture has taken interest around the world. In this sense, microorganisms are important since they are involved in many indispensable functions on soils such a nitrogen fixation. In this work, three different cropping systems were studied i) conventional ii) organic with manure and iii) organic with compost, with the aim to study changes occurred on bacterial communities as well as their functionality. Experimental plots were located in Cartagena (Spain). To study these functions, 16S gen obtain through high-throughput then a mathematical approximations using PICRUST algorithm were used to predict functionality on soils. On the other hand, a molecular ecological network analysis (MENA) was made to study the interactions among these bacteria. Results of this research showed how compost can enhance some metabolic pathways and can influence the bacterial organization favoring modulation and connections among nodes.Este proyecto está financiado por la Unión Europea a través del proyecto del Programa Horizonte 2020 Diverfarming (GA 728003)

Long-term adoption of reduced tillage and green manure improves soil physicochemical properties and increases the abundance of beneficial bacteria in a Mediterranean rainfed almond orchard

Soil health and function is one of the most important components for sustainable management of woody orchards. Intensive use of machinery and tillage creates heavy pressure on agroecosystems by altering the soil physicochemical and biological characteristics. In this study we aimed to assess the changes in soil physicochemical properties and the soil bacterial community structure, as well as the main drivers involved in shifts in the microbial community following 10 years implementing reduced tillage and reduced tillage plus green manure in a rainfed Mediterranean almond orchard. The treatments were: i) conventional tillage (CT); ii) reduced tillage (RT); and iii) reduced tillage and diversification with Avena sativa and Vicia sativa (RTD). After ten years, the results showed that the different managements had no significant effect on almond yields. RTD significantly increased total organic carbon (TOC), with an average content of 19.5 g kg−1 compared to 17.1 g kg−1 in CT. RTD also contributed to an increase in the fraction of soil macro-aggregates. Both RT and RTD significantly increased soil total nitrogen (NT) and particulate organic carbon (POC). However, other physical and chemical variables such as exchangeable Ca, Mg and K, bioavailable Fe, Cu, Zn and Mn, cation exchange capacity, bulk density, wilting point and field capacity were not significantly affected by the management. The bacterial community significantly changed with management: RTD showed a higher relative abundance of the family Solirubrobacteraceae and the genera Streptomyces and Solirubrobacter. The bacterial community structure was explained by changes in TOC, POC, pH, and NT values. Thus, a combination of reduced tillage and green manure could represent an appropriate sustainable management for rainfed almond orchards in very fragile environmental conditions, due to an increase in soil organic matter, total nitrogen, and the higher presence of beneficial bacteria related to soil productivityThis work was supported by the European Commission Horizon 2020 project Diverfarming [grant agreement 728003].Peer reviewe

Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers

Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea.This study was supported by EUROLEGUME project. This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 613781. European Investment Funds by FEDER/COMPETE/ POCI – Operational Competitiveness and Internationalization Programme, under Project POCI-01-0145-FEDER-006958 and National Funds by FCT – Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013. MMA was partially supported by the Feed the Future Innovation Lab for Climate Resilient Cowpea (USAID Cooperative Agreement AID-OAA-A-13-00070), which is directed by TJC. The funding entities had no role in the design of the study, collection, analysis and interpretation of data, or in writing the manuscript.info:eu-repo/semantics/publishedVersio

pcrEfficiency: a Web tool for PCR amplification efficiency prediction

<p>Abstract</p> <p>Background</p> <p>Relative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.</p> <p>Results</p> <p>We have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.</p> <p>Conclusions</p> <p>pcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at <url>http://srvgen.upct.es/efficiency.html</url> under the GPL v2 license.</p

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena

Continuous-time modeling of cell fate determination in Arabidopsis flowers

<p>Abstract</p> <p>Background</p> <p>The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored.</p> <p>Results</p> <p>We propose an ordinary differential equation (ODE) model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant <it>Arabidopsis thaliana</it>. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known) experimental expression data. The model is validated by simulation studies of known mutant plants.</p> <p>Conclusions</p> <p>The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in <it>Arabidopsis</it>, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.</p

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution