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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.

Medlin L.K.,CNRS Microbial Oceanography Laboratory | Kooistra W.H.C.F.,Stazione Zoologica Anton Dohrn
Diversity | Year: 2010

We review the application of molecular methods to estimate biodiversity in the marine environment. All of the methods reviewed here, which are at the forefront of molecular research, can be applied to all organisms in all habitats, but the case studies used to illustrate the points are derived from marine photosynthetic eukaryotic protists. It has been accepted that we know less than 10% of the identified diversity in the marine microbial world and the marine micro- and pico-eukaryotes are no exception. Even the species that we think we can easily recognize are often poorly described, and even less is known of their life histories and spatial and temporal trends in their abundance and distribution. With new molecular and analytical techniques, we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. Biogeochemical reactions performed by marine photosynthetic microbial organisms constitute a major sustaining component of ecosystem functioning, and therefore, affect climate changes. New interpretations of how environmental, ecological and evolutionary processes control and structure marine ecosystem biodiversity can be made so that we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study without good analytical methods. © 2010 by the authors; licensee MDPI, Basel, Switzerland.

Fernandez C.,University of Concepción | Fernandez C.,CNRS Microbial Oceanography Laboratory | Farias L.,University of Concepción | Ulloa O.,University of Concepción
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.

Chatelain M.,CNRS Microbial Oceanography Laboratory | Guizien K.,CNRS Microbial Oceanography Laboratory
Water Research | Year: 2010

A one-dimensional vertical unsteady numerical model for diffusion-consumption of dissolved oxygen (DO) above and below the sediment-water interface was developed to investigate DO profile dynamics under wind waves and sea swell (high-frequency oscillatory flows with periods ranging from 2 to 30 s). We tested a new approach to modelling DO profiles that coupled an oscillatory turbulent bottom boundary layer model with a Michaelis-Menten based consumption model. The flow regime controls both the mean value and the fluctuations of the oxygen mass transfer efficiency during a wave cycle, as expressed by the non-dimensional Sherwood number defined with the maximum shear velocity (Sh). The Sherwood number was found to be non-dependent on the sediment biogeochemical activity (μ). In the laminar regime, both cycle-averaged and variance of the Sherwood number are very low (over(S h, -) < 0.05, VAR (S h) < 0.1 %). In the turbulent regime, the cycle-averaged Sherwood number is larger (over(S h, -) ≈ 0.2). The Sherwood number also has intra-wave cycle fluctuations that increase with the wave Reynolds number (VAR(Sh) up to 30%). Our computations show that DO mass transfer efficiency under high-frequency oscillatory flows in the turbulent regime are water-side controlled by: (a) the diffusion time across the diffusive boundary layer and (b) diffusive boundary layer dynamics during a wave cycle. As a result of these two processes, when the wave period decreases, the Sh minimum increases and the Sh maximum decreases. over(S h, -) values vary little, ranging from 0.17 to 0.23. For periods up to 30 s, oxygen penetration depth into the sediment did not show any intra-wave fluctuations. Values for the laminar regime are small (≤1 mm for μ = 2000 g m-3 d-1) and decrease when the flow period increases. In the turbulent regime, the oxygen penetration depth reaches values up to five times larger than those in the laminar regime, becoming asymptotic as the maximum shear velocity increases. © 2009 Elsevier Ltd. All rights reserved.

Beier S.,Uppsala University | Beier S.,CNRS Microbial Oceanography Laboratory | Bertilsson S.,Uppsala University
Limnology and Oceanography | Year: 2011

We investigated to what extent chitinolytic bacteria subsidize bacterial populations that do not produce chitinolytic enzymes but still use the products of chitin hydrolysis. Applying single-cell techniques to untreated and chitin-enriched lake water, we show that the number of planktonic cells taking up chitin hydrolysis products by far exceeds the number of cells expressing chitinases. Flavobacteria, Actinobacteria, and specifically members of the abundant and ubiquitous freshwater Ac1 cluster of the Actinobacteria, increased in abundance and were enriched in response to the chitin amendment. Flavobacteria were frequently observed in dense clusters on chitin particles, suggesting that they are actively involved in the hydrolysis and solubilization of chitin. In contrast, Actinobacteria were exclusively planktonic. We propose that planktonic Actinobacteria contain commensals specialized in the uptake of small hydrolysis products without expressing or possibly even possessing the machinery for chitin hydrolysis. More research is needed to assess the importance of such ''cheater'' substrate acquisition strategies in the turnover and degradation of polymeric organic matter in aquatic ecosystems. © 2011, by the American Society of Limnology and Oceanography, Inc.

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.

Khan M.T.,King Abdullah University of Science and Technology | Manes C.L.O.,King Abdullah University of Science and Technology | Manes C.L.O.,CNRS Microbial Oceanography Laboratory | Aubry C.,King Abdullah University of Science and Technology | Croue J.-P.,King Abdullah University of Science and Technology
Water Research | Year: 2013

The complexity of Reverse Osmosis (RO) membrane fouling phenomenon has been widely studied and several factors influencing it have been reported by many researchers. This original study involves the investigation of two different fouling profiles produced at a seawater RO desalination plant installed on a floating mobile barge. The plant was moved along the coastline of the Red Sea in Saudi Arabia. The two locations where the barge was anchored showed different water quality. At the second location, two modules were harvested. One of the modules was pre-fouled by inorganics during plant operation at the previous site while the other was installed at the second site. Fouled membranes were subjected to a wide range of chemical and microbiological characterization procedures. Drastically different fouling patterns were observed in the two membranes which indicates the influence of source water quality on membrane surface modification and on fouling of RO membranes. © 2012 Elsevier Ltd.

Beier S.,Uppsala University | Beier S.,CNRS Microbial Oceanography Laboratory | Bertilsson S.,Uppsala University
Frontiers in Microbiology | Year: 2013

Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities. © 2013 Beier and Bertilsson.

Paniel N.,CNRS Microbial Oceanography Laboratory | Baudart J.,CNRS Microbial Oceanography Laboratory
Talanta | Year: 2013

Monitoring seawater, particularly recreational water, for indicator bacteria presence is required to protect the public from exposure to fecal pollution and to guarantee the safety of the swimming areas. Two methods for the detection and quantification of Escherichia coli DNA were developed: a colorimetric assay in a microplate and an electrochemical biosensor. These assays were based on the double hybridization recognition of a single-strand DNA capture probe immobilized onto the microplate or the screen-printed carbon electrode to its complementary ssDNA, which is hybridized with an ssDNA signal probe labeled with horseradish peroxidase enzyme. The hybridization recognition step used the colorimetric monitoring of the oxidation state of the 3,3′,5,5′-tetramethylbenzidine. The electrochemical monitoring of the oxidation state of 5 methyl-phenazinium methyl sulfate was allowed when the horseradish-peroxidase was in the presence of the mediator (5 methyl-phenazinium methyl sulfate and hydrogen peroxide). These approaches allow for the detection and quantification of 102 to 103 cells of E. coli in 5 l of seawater samples in less than 5 h. Detection was achieved without a nucleic acid amplification step. The specificity of the two methods against E. coli was demonstrated by testing a panel of bacteria. The two methods can be used for on-site monitoring of seawater quality. © 2013 Elsevier B.V.

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.

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