Spatial variability of microbial indicators and assessment of tillage systems on the soil microbiological functioning on organic farming.

Reduction tillage, in modifying the soil microorganisms’ environment, modifies their potential to supply plants nutrients. This is of primary importance in organic farming as the nutrients availability is mainly dependent on the organic matter degradation by microorganisms. To study the effect of tillage on soil physical and microbiological properties, we compare 4 tillage practises (deep and shallow ploughing, chisel and no tillage) in an experimental field near Lyon. Our objective is to link a structural statement with a microbiological functioning in order to study the microorganisms’ abilities to supply nitrogen and phosphorus. For such studies, it is of primary importance to use a convenient sampling design as the microbiological properties are highly variable in space and time. So, we first studied, before the treatments differentiation, the spatial variability of some microbiological properties. We first present this study briefly and its utilities for the future assessment of the tillage practises on the soil microbiological functioning

Discrimination and Aggregative Patterns among and between populations of Entamoeba spp.

Kin recognition facilitates the evolution of cooperation in animals, but its relevance in microorganisms and their behavior toward relatives remains unclear. The Entamoeba lineage constitutes an ideal model to determine the behavioral and signaling cues needed for aggregative preference. Chemical cues have been reported for E. histolytica but not E. dispar, suggesting cell-communication between con-specifics and behavioral differences with relevance for disease. Entamoeba varieties have been reported as ‘morphologically undistinguishable’. Two strains of E. invadens have been isolated from different hosts (VK-1: NS - Varanus komodoensis and IP1- serpentes) but were classified within the same ‘species’. Trophozoites of each strain aggregate only with members of their own variety, suggesting they are able to associate based on behavioral and chemical communication. Adaptations to different environments and horizontal gene exchange could have influenced diversification of each lineage. Measurable aggregation and behavioral cues in fluorescence micrographs of Entamoeba varieties suggest that these characteristics should be included in phylogenetic studies

Characterization of CRISPR-Cas Systems in Serratia marcescens Isolated from Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Curculionidae)

The CRISPR-Cas adaptive immune system has been attracting increasing scientific interest for biological functions and biotechnological applications. Data on the Serratia marcescens system are scarce. Here, we report a comprehensive characterisation of CRISPR-Cas systems identified in S. marcescens strains isolated as secondary symbionts of Rhynchophorus ferrugineus, also known as Red Palm Weevil (RPW), one of the most invasive pests of major cultivated palms. Whole genome sequencing was performed on four strains (S1, S5, S8, and S13), which were isolated from the reproductive apparatus of RPWs. Subtypes I-F and I-E were harboured by S5 and S8, respectively. No CRISPR-Cas system was detected in Si or S13. Two CRISPR arrays (4 and 51 spacers) were detected in S5 and three arrays (11, 31, and 30 spacers) were detected in S8. The CRISPR-Cas systems were located in the genomic region spanning from ybhR to phnP, as if this were the only region where CRISPR-Cas loci were acquired. This was confirmed by analyzing the S. marcescens complete genomes available in the NCBI database. This region defines a genomic hotspot for horizontally acquired genes and/or CRISPR-Cas systems. This study also supplies the first identification of subtype I-E in S. marcescens

Influential cited references in FEMS Microbiology Letters: lessons from Reference Publication Year Spectroscopy (RPYS)

The journal FEMS Microbiology Letters covers all aspects of microbiology including virology. On which scientific shoulders do the papers published in this journal stand? Which are the classic papers used by the authors? We aim to answer these questions in this study by applying the Reference Publication Year Spectroscopy (RPYS) analysis to all papers published in this journal between 1977 and 2017. In total, 16 837 publications with 410 586 cited references are analyzed. Mainly, the studies published in the journal FEMS Microbiology Letters draw knowledge from methods developed to quantify or characterize biochemical substances such as proteins, nucleic acids, lipids, or carbohydrates and from improvements of techniques suitable for studies of bacterial genetics. The techniques frequently used for studying the genetic of microorganisms in FEMS Microbiology Letters' studies were developed using samples prepared from microorganisms. Methods required for the investigation of proteins, carbohydrates, or lipids were mostly transferred from other fields of life science to microbiology

Extensive horizontal gene transfer in cheese-associated bacteria.

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities

Assembling the Tree of Life in Europe (AToLE)

A network of scientists under the umbrella of 'Assembling the Tree of Life in Europe (AToLE)' seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.
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Synthetic microbial ecosystems : an exciting tool to understand and apply microbial communities

Many microbial ecologists have described the composition of microbial communities in a plenitude of environments, which has greatly improved our basic understanding of microorganisms and ecosystems. However, the factors and processes that influence the behaviour and functionality of an ecosystem largely remain black boxes when using conventional approaches. Therefore, synthetic microbial ecology has gained a lot of interest in the last few years. Because of their reduced complexity and increased controllability, synthetic communities are often preferred over complex communities to examine ecological theories. They limit the factors that influence the microbial community to a minimum, allowing their management and identifying specific community responses. However, besides their use for basic research, synthetic ecosystems also found their way towards different applications, like industrial fermentation and bioremediation. Here, we review why and how synthetic microbial communities are applied for research purposes and for which applications they have been and could be successfully used

Clinical metagenomics.

Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health