Impacts of agroecological practices on soil microbial communities in experimental open-field vegetable cropping systems.

This study aimed to determine the impact of different agroecological practices on the composition and diversity of edaphic bacterial and fungal communities. We designed two experimental agroecological vegetable cropping systems and analyzed their effects on soil microbial communities by pyrosequencing the 16S and 18S ribosomal RNA genes. Our results highlighted modifications to the Operational Taxonomic Units in both experimental systems compared with bare soil, particularly for the phyla Actinobacteria, Ascomycota, Bacteroidetes, and Mucoromycota. Multidimensional scaling plots based on beta diversity showed a clear distinction between the two experimental systems for fungi, whereas differences were observed between bare soil and the two experimental systems for bacteria. Overall, the agroecological systems enhanced soil microbial diversity. We showed a distinction between the two experimental systems and bare soil, correlated with the high total N and total P contents in the agroecological systems. Both experimental systems promoted soil enrichment with certain essential minerals. The agroecological systems had a positive impact on soil microbial communities, particularly by promoting the development of beneficial soil bacteria like Actinobacteria. In the two experimental systems, changes in the quality and quantity of organic matter (i.e. mulch, vermicompost, plant diversity) could have modified the abundance and diversity of microbial communities.

Phytochemical and Biological Study of Trophic Interaction between Pseudosphinx Tetrio L. Larvae and Allamanda Cathartica L.

In this article, we propose to explore the chemical interaction between Pseudosphinx tetrio L. and Allamanda cathartica L. using different analytical methods, including an innovative electrochemical approach (called electrochemical ecology) and multivariate analysis, and we investigate the potential antimicrobial effects (antibacterial and antifungal activities) of this interaction in order to gain a better understanding of their specific interaction. The analytical study presents a similar chemical profile between the leaves of healthy and herbivorous A. cathartica and the excretions of the caterpillars. The similar analytical profile of the leaves of A. cathartica and the excretions of P. tetrio, and the difference with the caterpillar bodies, suggests a selective excretion of compounds by the caterpillar. The measured antimicrobial activities support the physicochemical tests. The natural products found selectively in the excretions (rather than in the body) could explain the ability of P. tetrio to feed on this toxic Apocynaceae species.

KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies).

Summary: Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact: dcouvin@pasteur-guadeloupe.fr. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Comparative Transcriptome Profiling of Virulent and Attenuated Ehrlichia ruminantium Strains Highlighted Strong Regulation of map1- and Metabolism Related Genes.

The obligate intracellular pathogenic bacterium, Ehrlichia ruminantium, is the causal agent of heartwater, a fatal disease in ruminants transmitted by Amblyomma ticks. So far, three strains have been attenuated by successive passages in mammalian cells. The attenuated strains have improved capacity for growth in vitro, whereas they induced limited clinical signs in vivo and conferred strong protection against homologous challenge. However, the mechanisms of pathogenesis and attenuation remain unknown. In order to improve knowledge of E. ruminantium pathogenesis, we performed a comparative transcriptomic analysis of two distant strains of E. ruminantium, Gardel and Senegal, and their corresponding attenuated strains. Overall, our results showed an upregulation of gene expression encoding for the metabolism pathway in the attenuated strains compared to the virulent strains, which can probably be associated with higher in vitro replicative activity and a better fitness to the host cells. We also observed a significant differential expression of membrane protein-encoding genes between the virulent and attenuated strains. A major downregulation of map1-related genes was observed for the two attenuated strains, whereas upregulation of genes encoding for hypothetical membrane proteins was observed for the four strains. Moreover, CDS_05140, which encodes for a putative porin, displays the highest gene expression in both attenuated strains. For the attenuated strains, the significant downregulation of map1-related gene expression and upregulation of genes encoding other membrane proteins could be important in the implementation of efficient immune responses after vaccination with attenuated vaccines. Moreover, this study revealed an upregulation of gene expression for 8 genes encoding components of Type IV secretion system and 3 potential effectors, mainly in the virulent Gardel strain. Our transcriptomic study, supported by previous proteomic studies, provides and also confirms new information regarding the characterization of genes involved in E. ruminantium virulence and attenuation mechanisms.

Evaluation of changes to the Rickettsia rickettsii transcriptome during mammalian infection.

The lifecycle of Rickettsia rickettsii includes infection of both mammalian and arthropod hosts, with each environment presenting distinct challenges to survival. As such, these pathogens likely have distinctive transcriptional strategies for infection of each host. Herein, we report the utilization of next generation sequencing (RNAseq) and bioinformatic analysis techniques to examine the global transcriptional profile of R. rickettsii within an infected animal, and to compare that data to transcription in tissue culture. The results demonstrate substantial R. rickettsii transcriptional alteration in vivo, such that the bacteria are considerably altered from cell culture. Identification of significant transcriptional changes and validation of RNAseq by quantitative PCR are described with particular emphasis on known antigens and suspected virulence factors. Together, these results suggest that transcriptional regulation of a distinct cohort of genes may contribute to successful mammalian infection.

Failure of a heterologous recombinant Sca5/OmpB protein-based vaccine to elicit effective protective immunity against Rickettsia rickettsii infections in C3H/HeN mice.

Spotted fever group (SFG) rickettsial species are obligate intracellular tick-borne pathogens that are responsible for important human diseases. Previous reports have demonstrated the feasibility of using recombinant surface cell antigen Sca5/OmpB to elicit protective immunity against homologous challenges using murine models of Mediterranean spotted fever and Rocky Mountain spotted fever. In addition, the feasibility of generating cross-protective immunity against related rickettsial species has also been established, but the molecular basis for these phenomena was not explored. Here, we demonstrate that vaccination of C3H/HeN mice with a recombinant OmpB domain derived from Rickettsia conorii induced high titer humoral immune responses that are capable of recognizing the native OmpB protein at the R. rickettsii outer membrane, but this immunization was not sufficient to induce effective protective immunity. In contrast, animals vaccinated with a corresponding OmpB domain derived from R. rickettsii protected animals from fatal outcomes. These results demonstrate that vaccination with nearly identical antigens may not be an effective strategy to induce wide-ranging protective immunity against related SFG Rickettsia species.

Understanding Anaplasmataceae pathogenesis using "Omics" approaches.

This paper examines how "Omics" approaches improve our understanding of Anaplasmataceae pathogenesis, through a global and integrative strategy to identify genes and proteins involved in biochemical pathways key for pathogen-host-vector interactions. The Anaplasmataceae family comprises obligate intracellular bacteria mainly transmitted by arthropods. These bacteria are responsible for major human and animal endemic and emerging infectious diseases with important economic and public health impacts. In order to improve disease control strategies, it is essential to better understand their pathogenesis. Our work focused on four Anaplasmataceae, which cause important animal, human and zoonotic diseases: Anaplasma marginale, A. phagocytophilum, Ehrlichia chaffeensis, and E. ruminantium. Wolbachia spp. an endosymbiont of arthropods was also included in this review as a model of a non-pathogenic Anaplasmataceae. A gap analysis on "Omics" approaches on Anaplasmataceae was performed, which highlighted a lack of studies on the genes and proteins involved in the infection of hosts and vectors. Furthermore, most of the studies have been done on the pathogen itself, mainly on infectious free-living forms and rarely on intracellular forms. In order to perform a transcriptomic analysis of the intracellular stage of development, researchers developed methods to enrich bacterial transcripts from infected cells. These methods are described in this paper. Bacterial genes encoding outer membrane proteins, post-translational modifications, eukaryotic repeated motif proteins, proteins involved in osmotic and oxidative stress and hypothetical proteins have been identified to play a key role in Anaplasmataceae pathogenesis. Further investigations on the function of these outer membrane proteins and hypothetical proteins will be essential to confirm their role in the pathogenesis. Our work underlines the need for further studies in this domain and on host and vector responses to infection.

Tick-borne diseases in cattle: applications of proteomics to develop new generation vaccines.

Tick-borne diseases (TBDs) affect 80% of the world's cattle population, hampering livestock production throughout the world. Livestock industry is important to rural populations not only as food supply, but also as a source of income. Tick control is usually achieved by using acaricides which are expensive, deleterious to the environment and can induce chemical resistance of vectors; the development of more effective and sustainable control methods is therefore required. Theileriosis, babesiosis, anaplasmosis and heartwater are the most important TBDs in cattle. Immunization strategies are currently available but with variable efficacy. To develop a new generation of vaccines which are more efficient, cheaper and safer, it is first necessary to better understand the mechanisms by which these parasites are transmitted, multiply and cause disease; this becomes especially difficult due to their complex life cycles, in vitro culture conditions and the lack of genetic tools to manipulate them. Proteomics and other complementary post-genomic tools such as transcriptomics and metabolomics in a systems biology context are becoming key tools to increase knowledge on the biology of infectious diseases. Herein, we present an overview of the so called "Omics" studies currently available on these tick-borne pathogens, giving emphasis to proteomics and how it may help to discover new vaccine candidates to control TBDs.

Global gene expression profiling of Ehrlichia ruminantium at different stages of development.

Ehrlichia ruminantium (ER), the causative agent of heartwater on ruminants, is an obligate intracellular bacterium transmitted by ticks of the genus Amblyomma. Previous studies have shown that early stages of development may be critical for Ehrlichia pathogenicity. To gain insights into the biology of intracellular ER, we determined the genome-wide transcriptional profile of ER replicating inside bovine aortic endothelial cells using DNA microarrays. At intermediate and late stages of infection (reticulate and elementary bodies, respectively), a total of 54 genes were differentially expressed. Among them, we measured by q-RTPCR the overexpression of 11 of 14 genes. A number of genes involved in metabolism, nutrient exchange, and defense mechanisms, including those involved in resistance to oxidative stress, were significantly induced in ER reticulate bodies. This is consistent with the oxidative stress condition and nutrient starvation that seem to occur in Ehrlichia-containing vacuoles. During the lysis stage of development, when ER is infectious, we showed the overexpression of a transcription factor, dksA, which is also known to induce virulence in other pathogens such as Salmonella typhimurium. Our results suggest a possible role of these genes in promoting ER development and pathogenicity.

A new typing technique for the Rickettsiales Ehrlichia ruminantium: multiple-locus variable number tandem repeat analysis.

Ehrlichia ruminantium (ER) is a member of the order Rickettsiales transmitted by Amblyomma ticks. This obligatory intracellular bacterium is the causative agent of a fatal disease in ruminants, named heartwater. It represents a constraint on breeding development in sub-Saharan Africa and in the Caribbean. The genetic diversity of the strains of ER, which could be a limiting factor to obtain effective vaccines, needs to be better characterized. For this purpose, we developed a molecular typing technique based on the polymorphism of variable number tandem repeat (VNTR) sequences, MLVA (multiple locus VNTR analysis). Eight (out of 21) VNTR candidates were validated using 17 samples representing a panel of ER strains from different geographical origins from West, South Africa, and Caribbean areas and in ER infected ticks and goat tissues. This result demonstrated the ability of these VNTRs to type a wide range of strains. The stability of the selected VNTR markers was very good, at the time scale needed for epidemiological purposes: in particular, no difference in the VNTR profiles was observed between virulent and attenuated strains (for Gardel and Senegal strains) and between strains (Gardel and Blonde strains) isolated in the same area 19years apart. We validated the strong discriminatory power of MLVA for ER and found a high level of polymorphism between the available strains, with 10 different profiles out of 13 ER strains. The MLVA scheme described in this study is a rapid and efficient molecular typing tool for ER, which allows rapid and direct typing of this intracellular pathogen without preliminary culture and gives reliable results that can be used for further epidemiological studies.