Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.Peer reviewe

The Airway Microbiota in Cystic Fibrosis: A Complex Fungal and Bacterial Community—Implications for Therapeutic Management

International audienceBackground Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways. Methodology and Principal Findings Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus

Aeromonas: a book review

International audienc

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

International audienc

The significance of transparent exopolymeric particles (TEP) for microorganisms in Lake Pavin.

International audienc

A Comparison of Methods for Counting Viruses in Aquatic Systems

In this study, we compared different methods—including transmission electron microscopy—and various nucleic acid labeling methods in which we used the fluorochromes 4′,6′-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-2-methylmethyledene]-1-(3′-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>10(8) particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids

Rapid Quantification of Planktonic Ciliates: Comparison of Improved Live Counting with Other Methods

The following efficient and quantitatively valid method to filter concentrate and count live planktonic ciliates was developed and compared with other treatments: unconcentrated (raw) samples and centrifuged samples were counted live, and the effects of five different fixatives (HgCl(2), Lugol's iodine, formaldehyde, glutaraldehyde, and Champy-DaFano) on the counts were monitored. Samples originated from a eutrophic mountain lake (Lake Aydat, near Clermont-Ferrand, France). Overall, live filtered counts were similar to counts of raw samples, but they were significantly higher (2 to 2.3 fold, P < 0.05) by analysis of variance than counts from centrifuged samples. Nevertheless, some taxa, i.e., Halteria and Loxodes spp., were sensitive to filtration. The live filtered counts were also comparable to counts of raw HgCl(2)-fixed and settled samples. HgCl(2) and Lugol fixation consistently gave the highest total counts, while significantly lower counts were always obtained with Champy-DaFano-fixed samples. Losses due to fixation were insignificant for raw samples but were substantial and statistically significant in concentrated samples (15% after filtration and 71% after centrifugation, compared with counts from the corresponding live samples). Live counting of passively filter-concentrated ciliates has many advantages over other methods. It is two to four times quicker and more efficient. Ciliates are recognized with certainty, more species are identified, and enumeration of dead organisms (e.g., tintinnid loricas) is avoided. It should be recommended as a quantitatively valid alternative to classical methods for assessing planktonic ciliate populations

Dynamics and estimates of growth and loss rates from bacterioplankton in a temperate freshwater system

The growth rate and losses of bacterioplankton in the epilimnion of an oligo-mesotrophic reservoir were simultaneously estimated using three different methods for each process. Bacterial production was determined by means of the tritiated thymidine incorporation method, the dialysis bag method and the dilution method, while bacterial mortality was assessed with the dilution method, the disappearance of thymidine-labeled natural cells and ingestion of fluorescent bacterial tracers by heterotrophic flagellates. The different methods used to estimate bacterial growth rates yielded similar results. On the other hand, the mortality rates obtained with the dilution method were significantly lower than those obtained with the use of thymidine-labeled natural cells. The bacterial ingestion rate by flagellates accounted on average for 39% of total bacterial mortality estimated by the dilution method, but this value fell to 5% when the total mortality was measured by the thymidine-labeling method. Bacterial abundance and production varied in opposite phase to flagellate abundance and the various bacterial mortality rates. All this points to the critical importance of methodological aspects in the elaboration of quantitative models of matter and energy flows over the time through microbial trophic networks in aquatic systems, and highlights the role of bacterioplankton as a source of carbon for higher trophic levels in the studied system.NRC publication: Ye

Roles and mechanisms of parasitism in aquatic microbial communities

Next Generation Sequencing technologies are increasingly revealing that microbial taxa likely to be parasites or symbionts are probably much more prevalent and diverse than previously thought. Every well studied free-living species has parasites; parasites themselves can be parasitized. As a rule of thumb, there is an estimated 4 parasitic species for any given host, and the better a host is studied the more parasites are known to infect it. Therefore, parasites and other symbionts should represent a very large number of species and may far outnumber those with 'free-living' lifestyles. Paradoxically, free-living hosts, which form the bulk of our knowledge of biology, may be a minority! Microbial parasites typically are characterized by their small size, short generation time, and high rates of reproduction, with simple life cycle occurring generally within a single host. They are diverse and ubiquitous in the environment, comprising viruses, prokaryotes and eukaryotes. This Frontiers Research Topic sought to provide a broad overview but concise, comprehensive, well referenced and up-to-date state of the art for everyone involved with microbial parasites in aquatic microbial ecology