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Fernandez C.,University of Concepcion | Fernandez C.,CNRS Microbial Oceanography Laboratory | Farias L.,University of Concepcion | Ulloa O.,University of Concepcion
PLoS ONE | Year: 2011

Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 μmol m-2 d-1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 μmol m-2 d-1) than the oxic euphotic layer (48±68 μmol m-2 d-1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions. © 2011 Fernandez et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Berdjeb L.,French National Institute for Agricultural Research | Ghiglione J.-F.,CNRS Microbial Oceanography Laboratory | Jacquet S.,French National Institute for Agricultural Research
Applied and Environmental Microbiology | Year: 2011

Bacterioplankton plays a central role in the microbial functioning of lacustrine ecosystems; however, factors that constrain its structural variation are still poorly understood. Here we evaluated the driving forces exerted by a large set of environmental and biological parameters on the temporal and spatial dynamics of free-living bacterial community structures (BCS) in two neighboring perialpine lakes, Lake Bourget and Lake Annecy, which differ in trophic status. We analyzed monthly data from a 1-year sampling period at two depths situated in the epi-and hypolimnia for each lake. Overall, denaturing gradient gel electrophoresis (DGGE) revealed significant differences in the BCS in the two lakes, characterized by a higher number of bands in the oligotrophic ecosystem (i.e., Lake Annecy). The temporal dynamics of BCS differed greatly between depths and lakes, with temporal scale patterns being much longer in the mesotrophic Lake Bourget. Direct-gradient multivariate ordination analyses showed that a complex array of biogeochemical parameters was the driving force behind BCS shifts in both lakes. Our results indicated that 60 to 80% of the variance was explained only by the bottom-up factors in both lakes, indicating the importance of nutrients and organic matter from autotrophic origin in controlling the BCS. Top-down regulation by flagellates together with ciliates or viruses was found only in the hypolimnion and not in the epilimnion for both lakes and explained less than 18% of the bacterial community changes during the year. Our study suggests that the temporal dynamics of the free-living bacterial community structure in deep perialpine lakes are dependent mainly on bottom-up factors and to a lesser extent on top-down factors, whatever the specific environmental conditions of these lakes. © 2011, American Society for Microbiology.

Ghiglione J.F.,French National Center for Scientific Research | Ghiglione J.F.,CNRS Microbial Oceanography Laboratory | Murray A.E.,Desert Research Institute
Environmental Microbiology | Year: 2012

Marine bacterioplankton studies over the annual cycle in polar systems are limited due to logistic constraints in site access and support. Here, we conducted a comparative study of marine bacterioplankton sampled at several time points over the annual cycle (12 occasions each) at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish a better understanding of the extent and nature of variation in diversity and community structure at these different latitudes (49-64S). Molecular methods targeting the 16S rRNA gene (DGGE, CE-SSCP and tag pyrosequencing) suggest a strong seasonal pattern with higher richness in winter and a clear influence of phytoplankton bloom events on bacterioplankton community structure and diversity in both locations. The distribution of sequence tags within Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions. At both sites, several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed intense seasonal variation often with similar trends at both sites. This enhanced understanding of variability in dominant groups of bacterioplankton over the annual cycle contributes to an expanding baseline to understand climate change impacts in the coastal zone of polar oceans and provides a foundation for comparison with open ocean polar systems. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Paniel N.,CNRS Microbial Oceanography Laboratory | Baudart J.,CNRS Microbial Oceanography Laboratory | Hayat A.,Clarkson University | Barthelmebs L.,University of Perpignan
Methods | Year: 2013

The increasing concerns about food and environmental safety have prompted the desire to develop rapid, specific, robust and highly sensitive methods for the detection of microorganisms to ensure public health. Although traditional microbiological methods are available, they are labor intensive, unsuitable for on-site and high throughput analysis, and need well-trained personnel. To circumvent these drawbacks, many efforts have been devoted towards the development of biosensors, using nucleic acid as bio-recognition element. In this review, we will focus on recent significant advances made in two types of DNA-based biosensors, namely genosensors, and aptasensors. In genosensor approach, DNA or RNA target is detected through the hybridization reaction between DNA or RNA and ssDNA sensing element, while in aptasensor method, DNA or RNA aptamer, capable of binding to a target molecule with high affinity and specificity, plays the role of receptor. The goal ofthis article is to review the innovative methods that have been emerged in genosensor and aptasensor during recent years. Particular attention is given to recent advances and trends in selection of biorecognition element, DNA immobilization strategies and sensing formats. © 2013 Elsevier Inc.

Baudart J.,CNRS Microbial Oceanography Laboratory | Lebaron P.,CNRS Microbial Oceanography Laboratory
Journal of Applied Microbiology | Year: 2010

Aims: We developed an improved Fluorescent In Situ Hybridization FISH-based method to detect viable Escherichia coli cells by solid phase cytometry (SPC), and results were compared to those obtained by the standard culture method. Methods and Results: The method includes a direct viable count (DVC) assay, multi-probes labelled and unlabelled (helpers) to detect specifically viable E. coli cells and to enhance SPC cell counts. We demonstrate that helpers increase the fluorescence intensity of hybridized E. coli cells as detected by SPC and assess the high specificity of the DVC-FISH procedure on a large panel of cultured strains. Application to seawater, freshwater and wastewater samples showed a good correlation between SPC cells counts and standard plate counts. Conclusion: The high specificity of the procedure was demonstrated as well as its accuracy for detecting and counting viable E. coli cells in environmental samples. Significance and Impact of the Study: The developed approach may be used to monitor faecal contamination sources and to investigate the occurrence of viable E. coli in natural environments. © 2010 The Society for Applied Microbiology.

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