Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia lagoon)

The VAHINE mesocosm experiment, conducted in the low-nutrient low-chlorophyll waters of the Noumea lagoon (coastal New Caledonia) was designed to trace the incorporation of nitrogen (N) fixed by diazotrophs into the food web, using large volume (50 m(3)) mesocosms. This experiment provided a unique opportunity to study the succession of different N-2-fixing microorganisms (diazotrophs) and calculate in situ net growth and mortality rates in response to fertilization with dissolved inorganic phosphate (DIP) over a 23-day period, using quantitative polymerase chain reaction (qPCR) assays targeting widely distributed marine diazotroph lineages. Inside the mesocosms, the most abundant diazotroph was the heterocyst-forming Richelia associated with Rhizosolenia (Het-1) in the first half of the experiment, while unicellular cyanobacterial Group C (UCYN-C) became abundant during the second half of the experiment. Decreasing DIP concentrations following the fertilization event and increasing temperatures were significantly correlated with increasing abundances of UCYN-C. Maximum net growth rates for UCYN-C were calculated to range between 1.23 +/- 0.07 and 2.16 +/- 0.07 d(-1) in the mesocosms, which are among the highest growth rates reported for diazotrophs. Outside the mesocosms in the New Caledonia lagoon, UCYN-C abundances remained low, despite increasing temperatures, suggesting that the microbial community response to the DIP fertilization created conditions favorable for UCYN-C growth inside the mesocosms. Diazotroph community composition analysis using PCR targeting a component of the nitrogenase gene (nifH) verified that diazotrophs targeted in qPCR assays were collectively among the major lineages in the lagoon and mesocosm samples, with the exception of Crocosphaera-like phylotypes, where sequence types not typically seen in the oligotrophic ocean grew in the mesocosms. Maximum net growth and mortality rates for nine diazotroph phylotypes throughout the 23-day experiment were variable between mesocosms, and repeated fluctuations between periods of net growth and mortality were commonly observed. The field population of diazotrophs in the New Caledonian lagoon waters appeared to be dominated by Het-1 over the course of the study period. However, results from both qPCR and PCR analysis indicated a diverse field population of diazotrophs was present in the lagoon at the time of sampling. Two ecotypes of the Braarudosphaera bigelowii symbiont unicellular group A (UCYN-A) were present simultaneously in the lagoon, with the recently described B. bigelowii/UCYN-A2 association present at higher abundances than the B. bigelowii/UCYN-A1 association

Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen

Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease

Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs

Homologous recombination is a key in contributing to bacteriophages genome repair, circularization and replication. No less than six kinds of recombinase genes have been reported so far in bacteriophage genomes, two (UvsX and Gp2.5) from virulent, and four (Sak, Redβ, Erf and Sak4) from temperate phages. Using profile–profile comparisons, structure-based modelling and gene-context analyses, we provide new views on the global landscape of recombinases in 465 bacteriophages. We show that Sak, Redβ and Erf belong to a common large superfamily adopting a shortcut Rad52-like fold. Remote homologs of Sak4 are predicted to adopt a shortcut Rad51/RecA fold and are discovered widespread among phage genomes. Unexpectedly, within temperate phages, gene-context analyses also pinpointed the presence of distant Gp2.5 homologs, believed to be restricted to virulent phages. All in all, three major superfamilies of phage recombinases emerged either related to Rad52-like, Rad51-like or Gp2.5-like proteins. For two newly detected recombinases belonging to the Sak4 and Gp2.5 families, we provide experimental evidence of their recombination activity in vivo. Temperate versus virulent lifestyle together with the importance of genome mosaicism is discussed in the light of these novel recombinases. Screening for these recombinases in genomes can be performed at http://biodev.extra.cea.fr/virfam

Lytic failure in cross-inoculation assays between phages and prokaryotes from three aquatic sites of contrasting salinity

Little is known about the ability of phages to successfully colonize contrasting aquatic niches. We conducted experimental cross-infections between viruses and prokaryotes from three tropical sites of West Africa, with distinct salinities: a freshwater reservoir, a marine coastal station and a hypersaline lake. A cellular poison-based method (potassium cyanide) revealed that the addition of native viruses (regardless of the water type) consistently stimulated viral production. Conversely, in all incubations conducted with allochtonous (non-native) viruses, their overall production was not promoted, which suggests a lytic failure. Prokaryotic heterotrophic production increased in fresh and marine water supplemented with native viruses, but not in the hypersaline water. These results point to the role of the viral shunt in low-salinity environments, where the release of bioavailable lysis products might be of high nutritional value for the noninfected prokaryotes. In contrast, in hypersaline water where glycerol is a major carbon and energy source for the heterotrophic community, dissolved organic matter (DOM) of lytic origin may represent a less important DOM source for prokaryotes. Finally, our results suggest that cosmopolitan phages capable of moving between biomes are probably rare in aquatic habitats, supporting the common idea that most wild phages are relatively limited in their host range

Development and validation of a multiplex qPCR assay for detection and relative quantification of HPV16 and HPV18 E6 and E7 oncogenes

International audienceHuman papillomaviruses (HPV) play a key role in promoting human anogenital cancers. Current high-risk HPV screening or diagnosis tests involve cytological or molecular techniques mostly based on qualitative HPV DNA detection. Here, we describe the development of a rapid quantitative polymerase chain reaction (qPCR) detection test of HPV16 and HPV18 oncogenes (E6 and E7) normalized on human gene encoding GAPDH. Optimized qPCR parameters were defined, and analytical specificities were validated. The limit of detection was 10 1 for all genes tested. Assay performances were evaluated on clinical samples (n = 96). Concordance between the Xpert HPV assay and the triplex assay developed here was 93.44% for HPV16 and 73.58% for HPV18. HPV co-infections were detected in 15 samples. The systems developed in the present study can be used in complement to traditional HPV tests for specifically validating the presence of HPV16 and/or HPV18. It can also be used for the follow-up of patients with confirmed infection and at risk of developing lesions, through the quantification of E6 and E7 oncogene expression (mRNA) normalized on the GAPDH expression levels

Effects of freshwater and seawater mixing on virio- and bacterioplankton in a tropical estuary

International audience1. Estuaries are interesting sites to examine virus-bacteria interactions since they may vary gradually or abruptly in salinity, which presumably requires physiological, genetic and ecological adaptations. To explore such adjustments in tropical areas, freshwater and seawater samples were collected in the estuarine system of the River Senegal and experimentally subjected to abrupt mixing of seawater with freshwater and vice versa. 2. Production rates of freshwater bacteria (measured by the tritiated thymidine incorporation method) and of viruses (measured by the dilution method) sharply declined immediately after seawater addition, which was followed by a spectacular recovery of the surviving bacterial and viral populations within 24 and 48 h, respectively. 3. Conversely, neither marine bacteria nor viruses were significantly affected by mixing with freshwater. This suggests that the turbulent front between ascending tidal sea water and outwelling fluvial freshwater is a more favourable environment for marine bacterioplankton, which may take advantage of massive bursts of freshwater cells resulting from osmotic shock. 4. In both mixing experiments, the dynamics of virioplankton production followed that of the bacteria within 24 h, suggesting that viruses can rapidly respond to dramatic shifts in the abundance and community composition of bacterial hosts

Stocks and soil-plant transfer of macro-nutrients and trace metals in temperate New Zealand estuarine mangroves

Aims Rapid expansion of temperate mangroves in New Zealand over the last decades has prompted an increase in resource consents for removal. However, little is known about the capacity of temperate mangroves to store elements, including pollutants. The main objectives of this study were to assess the stocks and soil-plant transfer of macro-nutrients (C, N, P, K, Mg, Ca, S) and trace metals (Fe, Mn, Al, Ni, Cu, Zn, Co, Cr) within temperate mangrove soils.MethodsSoil samples and root, leaf and wood tissues were analysed for their total and available elemental concentrations over a wide range of environmental conditions along the head-mouth textural, salinity and nutrient gradients of the estuary. Physico-chemical characteristics of the soil of the different sites studied were also determined.ResultsMangrove soils with lower Eh and currents upstream of the estuary trapped larger amount of macro-nutrients and heavy metals in the soils than downstream. This results in higher translocation of macro elements from the soil toward the above-ground biomass and higher translocation of heavy metals from the soil toward the litterfall, likely as a mechanism to avoid long term metal toxicity in the root system.ConclusionsThis multi-elemental study provides a comprehensive understanding of soil- plant transfers in temperate mangroves and can be used to better evaluate the ecological services of these ecosystems

Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport

International audienceIllegal bushmeat traffic is an important threat to biodiversity conservation of several endangered species and may contribute to the emergence and spread of infectious diseases in humans. The hunting, manipulation and consumption of wildlife-based products, especially those of primate origin, may be a threat to human health; however, few studies have investigated the role of bushmeat trade and consumption as a potential source of human infections to date. In this study, we report the screening of viral pathogens in African simian game seized by French customs at Toulouse Blagnac Airport. Epifluorescence microscopy revealed the presence of virus-like particles in the samples, and further metagenomic sequencing of the DNA and RNA viromes confirmed the presence of sequences related to the Siphoviridae, Myoviridae and Podoviridae bacteriophage families; some of them infecting bacterial hosts that could be potentially pathogenic for humans. To increase the sensitivity of detection, twelve pan-generic PCRs targeting several viral zoonoses were performed, but no positive signal was detected. A large-scale inventory of bacteria, viruses and parasites is urgently needed to globally assess the risk for human health of the trade, manipulation and consumption of wildlife-related bushmeat

Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport

International audienceIllegal bushmeat traffic is an important threat to biodiversity conservation of several endangered species and may contribute to the emergence and spread of infectious diseases in humans. The hunting, manipulation and consumption of wildlife-based products, especially those of primate origin, may be a threat to human health; however, few studies have investigated the role of bushmeat trade and consumption as a potential source of human infections to date. In this study, we report the screening of viral pathogens in African simian game seized by French customs at Toulouse Blagnac Airport. Epifluorescence microscopy revealed the presence of virus-like particles in the samples, and further metagenomic sequencing of the DNA and RNA viromes confirmed the presence of sequences related to the Siphoviridae, Myoviridae and Podoviridae bacteriophage families; some of them infecting bacterial hosts that could be potentially pathogenic for humans. To increase the sensitivity of detection, twelve pan-generic PCRs targeting several viral zoonoses were performed, but no positive signal was detected. A large-scale inventory of bacteria, viruses and parasites is urgently needed to globally assess the risk for human health of the trade, manipulation and consumption of wildlife-related bushmeat

Sedimentary and elemental dynamics as a function of the elevation profile in a semi-arid mangrove toposequence

The effect of elevation and seasonal variations on the elemental status of sediments was investigated along a semi-arid mangrove profile in the Heart of Voh, New Caledonia. As other mangroves in the world, this mangrove site experienced an increase of tidal range that led to the recent colonisation of salt flats at the highest elevations landward by Avicetuda marina (Forsk.) Vierh subsp. australasica (Walp.) J. Everett. This young Avicennia stand was compared with an old Avicennia stand at lower elevations on its edge. Down the elevation profile, the sediment properties of a short Rhizophora stylosa Griff stand were compared with a taller Rhizophora stand seaward that experienced longer immersion periods. Our results show that centimetre-scale variation in elevation significantly affects all sediment properties along the semi-arid profile and induces a strong seasonal variation in reduction potential and pH at high elevations over the year. We suggest that during the dry season, the oxygenated sediments enhanced the oxidation of organic matter (OM), which led to the dissolution of Fe-S compounds and the subsequent acidification of the sediments. This in turn induced a loss of metal content (Fe, Cu Ni, Mn) compared to the sediments at lower elevation. Moreover, our results show that the accumulation of OM during the colonisation phase by Avicennia coincided with higher water content and higher total and exchangeable concentrations of N, P, Mg and K within the surface sediments than in the old Avicennict stand. The tall Rhizophora stand at the borders of the channel was characterized by an increase in elevation, denser sediments and a depletion of elements in several horizons of the depth profile compared to the short Rhizophora landward. These results provide a better understanding of i) the impact of elevation differences on major and minor elements in a semi-arid mangrove ecosystem, and ii) the changes of sediment properties mediated by a pioneer species within the early phase of succession in hypersaline mangroves