Intracellular Behaviour of Non- Strains within Three Amoeba Strains, Including C2c Maky.

Legionellosis, an often-lethal pneumonia, is generally associated with contamination by . This bacterium can persist in the environment and resist chemical treatment when it is internalized by amoebae. In addition, there is increasing medical proof that other species can be causative agents of Legionellosis.

Proteomics and Lipidomics Investigations to Decipher the Behavior of C2c Maky According to Different Culture Modes.

C2c Maky is a free-living amoeba that has demonstrated its ability to inhibit the intracellular multiplication of some strains, which are pathogenic bacteria inhabiting the aquatic environment. The Amoeba, an industry involved in the treatment of microbiological risk in the water and plant protection sectors, has developed a natural biocide based on the property of to manage the proliferation of the pathogen in cooling towers. In axenic liquid medium, amoebas are usually cultivated in adhesion on culture flask.

A New Active Substance Derived from Lyzed C2c Maky Cells to Fight Grapevine Downy Mildew.

Downy mildew of grapevine is one of the most destructive grapevine diseases worldwide. Nowadays, downy mildew control relies almost exclusively on the use of chemical pesticides, including copper products, which are efficient but controversial due to their environmental toxicity. Natural plant protection products have become important solutions in the quest for the sustainable production of food and pest management.

Mitigation of Expression of Virulence Genes in Internalized in the Free-Living Amoeba C2c Maky.

is a human pathogen responsible for a severe form of pneumonia named Legionnaire disease. Its natural habitat is aquatic environments, being in a free state or intracellular parasites of free-living amoebae, such as . This pathogen is able to replicate within some amoebae.

Insight into the Lifestyle of Amoeba during Bioreactor Growth Using Transcriptomics and Proteomics.

C2c maky is a thermophilic free-living amoeba strain that showed ability to eliminate , a pathogenic bacterium living in the aquatic environment. The amoeba industry has proposed the use of as a natural biocide to control proliferation in cooling towers. Here, transcriptomic and proteomic studies were carried out in order to expand knowledge on produced in a bioreactor.

Intracellular Behaviour of Three Strains within Three Amoeba Strains, Including C2c Maky.

is a facultative intracellular pathogen found in aquatic environments as planktonic cells within biofilms and as intracellular parasites of free-living amoebae such as . This pathogen bypasses the elimination mechanism to replicate within amoebae; however, not all amoeba species support the growth of . C2c Maky, a non-pathogenic amoeba, was previously demonstrated to possess the ability to eliminate the strain Paris.

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH.

Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH.

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome.

For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised.

Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions.

To diversify their genetic material, and thereby allow adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightning-related electrical phenomena may constitute an additional gene-transfer mechanism occurring in nature. The presence in clouds of bacteria such as Pseudomonas syringae capable of forming ice nuclei that lead to precipitation, and that are likely to be involved in triggering lightning, led us to postulate that natural electrotransformation in clouds may contribute to the adaptive potential of these bacteria.

Microbial soil community analyses for forensic science: Application to a blind test.

Soil complexity, heterogeneity and transferability make it valuable in forensic investigations to help obtain clues as to the origin of an unknown sample, or to compare samples from a suspect or object with samples collected at a crime scene. In a few countries, soil analysis is used in matters from site verification to estimates of time after death. However, up to date the application or use of soil information in criminal investigations has been limited.

Soil characterisation by bacterial community analysis for forensic applications: A quantitative comparison of environmental technologies.

The ubiquity and transferability of soil makes it a resource for the forensic investigator, as it can provide a link between agents and scenes. However, the information contained in soils, such as chemical compounds, physical particles or biological entities, is seldom used in forensic investigations; due mainly to the associated costs, lack of available expertise, and the lack of soil databases. The microbial DNA in soil is relatively easy to access and analyse, having thus the potential to provide a powerful means for discriminating soil samples or linking them to a common origin.

Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes.

Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs.

Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments.

The ethyl tert-butyl ether (ETBE) degradation capacity and phylogenetic composition of five aerobic enrichment cultures with ETBE as the sole carbon and energy source were studied. In all cases, ETBE was entirely degraded to biomass and CO2. Clone libraries of the 16S rRNA gene were prepared from each enrichment.

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.

A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced.

Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer.

Ethyl tert-butyl ether (ETBE) enrichment was obtained by adding contaminated groundwater to a mineral medium containing ETBE as the sole carbon and energy source. ETBE was completely degraded to biomass and CO2 with a transient production of tert-butanol (TBA) and a final biomass yield of 0.37 ± 0.

Development of a new tool to improve gene transfer frequency calculations.

Gene transfer frequency can be determined experimentally on plates, but the methods currently in use do not discriminate between independent transfers and clonal multiplication of initial transformants. In order to overcome this bias, we engineered an Acinetobacter baylyi population in which cells differed by a specific molecular signature and used it as recipient in transformation experiments. Our results suggest that a corrective factor of 0.

Metagenomic exploration of antibiotic resistance in soil.

The ongoing development of metagenomic approaches is providing the means to explore antibiotic resistance in nature and address questions that could not be answered previously with conventional culture-based strategies. The number of available environmental metagenomic sequence datasets is rapidly expanding and henceforth offer the ability to gain a more comprehensive understanding of antibiotic resistance at the global scale. Although there is now evidence that the environment constitutes a vast reservoir of antibiotic resistance gene determinants (ARGDs) and that the majority of ARGDs acquired by human pathogens may have an environmental origin, a better understanding of their diversity, prevalence and ecological significance may help predict the emergence and spreading of newly acquired resistances.

Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria.

The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation.

Dissimilar pH-dependent adsorption features of bovine serum albumin and alpha-chymotrypsin on mica probed by AFM.

We studied bovine serum albumin (BSA) and alpha-chymotrypsin adsorption onto mica surfaces over a large pH range by atomic force microscopy (AFM) measurements in liquid. Data analyses (height, roughness and roughness factor) brought new insights on the conformation of proteins in soil environments, with mica as a model of soil phyllosilicates and non-hydrophobic surfaces. Validation of AFM approach was performed on BSA, whose behavior was previously described by nuclear magnetic resonance and infra-red spectroscopic methods.

Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach.

We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.

Evaluation of functional gene enrichment in a soil metagenomic clone library.

We evaluated the use of mixed oligonucleotide probes hybridized to metagenomic clones spotted on high density membranes. The pooled probes included oligonucleotides designed for genes associated with denitrification, antibiotic resistance, and dehalogenation among others. Pyrosequence comparison between the clones and the original DNA demonstrated the utility of clone screening with pooled probes.

Antibiotic-resistant soil bacteria in transgenic plant fields.

Understanding the prevalence and polymorphism of antibiotic resistance genes in soil bacteria and their potential to be transferred horizontally is required to evaluate the likelihood and ecological (and possibly clinical) consequences of the transfer of these genes from transgenic plants to soil bacteria. In this study, we combined culture-dependent and -independent approaches to study the prevalence and diversity of bla genes in soil bacteria and the potential impact that a 10-successive-year culture of the transgenic Bt176 corn, which has a blaTEM marker gene, could have had on the soil bacterial community. The bla gene encoding resistance to ampicillin belongs to the beta-lactam antibiotic family, which is widely used in medicine but is readily compromised by bacterial antibiotic resistance.

Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a sphingomonas strain that degrades various polycyclic aromatic hydrocarbons.

In this study, the enzymes involved in polycyclic aromatic hydrocarbon (PAH) degradation in the chrysene-degrading organism Sphingomonas sp. strain CHY-1 were investigated. [14C]chrysene mineralization experiments showed that PAH-grown bacteria produced high levels of chrysene-catabolic activity.