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1.
Cytometry A ; 103(3): 260-268, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-35929601

RESUMO

Marine viruses make up an essential compartment of the marine ecosystem. They are the most abundant organisms and represent one of the biggest sources of unknown biodiversity. Viruses also have an important impact on bacterial and algal mortality in the ocean, and as such have a major influence on microbial diversity and biogeochemical cycling. However, little is known about the abundance and distribution patterns of viruses across the oceans and seas. Over the last 20 years, flow cytometry has been the technique of choice to detect and count the viral particles in natural samples. Nevertheless, due to their small size, the detection of marine viruses is still extremely challenging. In this article we describe how a new generation of flow cytometer which uses the side scatter (SSC) of violet photons from a 405 nm laser beam helps to improve the resolution for detecting marine viruses. To the best of our knowledge, this is the first report where virioplankton has been detected in aquatic samples using flow cytometry with a 405 nm violet SSC instead of a 488 nm blue SSC.


Assuntos
Ecossistema , Vírus , Oceanos e Mares
2.
Proc Natl Acad Sci U S A ; 114(31): 8319-8324, 2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28716941

RESUMO

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.


Assuntos
Ciclo do Carbono/fisiologia , Nitrificação/fisiologia , Oxigênio/metabolismo , Fotossíntese/fisiologia , Prochlorococcus/metabolismo , Anaerobiose , Organismos Aquáticos/metabolismo , Clorofila/metabolismo , Aquecimento Global , México , Microbiota/fisiologia , Nitrogênio/metabolismo , Oceanos e Mares , Peru
3.
Environ Microbiol ; 20(10): 3601-3615, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30063098

RESUMO

Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.


Assuntos
Bactérias/isolamento & purificação , Diatomáceas/microbiologia , Microbiota , Bacteroidetes/isolamento & purificação , Água Doce , Processos Heterotróficos , Filogenia , Proteobactérias/isolamento & purificação , Taiwan
4.
Curr Top Microbiol Immunol ; 377: 191-210, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24271566

RESUMO

Hyperspectral cytometry is an emerging technology for single-cell analysis that combines ultrafast optical spectroscopy and flow cytometry. Spectral cytometry systems utilize diffraction gratings or prism-based monochromators to disperse fluorescence signals from multiple labels (organic dyes, nanoparticles, or fluorescent proteins) present in each analyzed bioparticle onto linear detector arrays such as multianode photomultipliers or charge-coupled device sensors. The resultant data, consisting of a series of characterizing every analyzed cell, are not compensated by employing the traditional cytometry approach, but rather are spectrally unmixed utilizing algorithms such as constrained Poisson regression or non-negative matrix factorization. Although implementations of spectral cytometry were envisioned as early as the 1980s, only recently has the development of highly sensitive photomultiplier tube arrays led to design and construction of functional prototypes and subsequently to introduction of commercially available systems. This chapter summarizes the historical efforts and work in the field of spectral cytometry performed at Purdue University Cytometry Laboratories and describes the technology developed by Sony Corporation that resulted in release of the first commercial spectral cytometry system-the Sony SP6800. A brief introduction to spectral data analysis is also provided, with emphasis on the differences between traditional polychromatic and spectral cytometry approaches.


Assuntos
Células/citologia , Citometria de Fluxo/métodos , Animais , Citometria de Fluxo/instrumentação , Humanos , Estatística como Assunto
5.
Appl Environ Microbiol ; 80(16): 4821-31, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24907329

RESUMO

When immersed in seawater, substrates are rapidly colonized by both micro- and macroorganisms. This process is responsible for important economic and ecological prejudices, particularly when related to ship hulls or aquaculture nets. Commercial antifouling coatings are supposed to reduce biofouling, i.e., micro- and macrofoulers. In this study, biofilms that primarily settled on seven different coatings (polyvinyl chloride [PVC], a fouling release coating [FRC], and five self-polishing copolymer coatings [SPC], including four commercial ones) were quantitatively studied, after 1 month of immersion in summer in the Toulon Bay (Northwestern Mediterranean Sea, France), by using flow cytometry (FCM), microscopy, and denaturing gradient gel electrophoresis. FCM was used after a pretreatment to separate cells from the biofilm matrix, in order to determine densities of heterotrophic bacteria, picocyanobacteria, and pico- and nanoeukaryotes on these coatings. Among diatoms, the only microphytobenthic class identified by microscopy, Licmophora, Navicula, and Nitzschia were determined to be the dominant taxa. Overall, biocide-free coatings showed higher densities than all other coatings, except for one biocidal coating, whatever the group of microorganisms. Heterotrophic bacteria always showed the highest densities, and diatoms showed the lowest, but the relative abundances of these groups varied depending on the coating. In particular, the copper-free SPC failed to prevent diatom settlement, whereas the pyrithione-free SPC exhibited high picocyanobacterial density. These results highlight the interest in FCM for antifouling coating assessment as well as specific selection among microbial communities by antifouling coatings.


Assuntos
Fenômenos Fisiológicos Bacterianos/efeitos dos fármacos , Biofilmes/efeitos dos fármacos , Incrustação Biológica/prevenção & controle , Diatomáceas/fisiologia , Polímeros/farmacologia , Água do Mar/microbiologia , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/isolamento & purificação , Diatomáceas/classificação , Diatomáceas/efeitos dos fármacos , Diatomáceas/isolamento & purificação , Mar Mediterrâneo , Cloreto de Polivinila/farmacologia , Navios
6.
Cytometry A ; 83(5): 508-20, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23526804

RESUMO

Multispectral and hyperspectral flow cytometry (FC) instruments allow measurement of fluorescence or Raman spectra from single cells in flow. As with conventional FC, spectral overlap results in the measured signal in any given detector being a mixture of signals from multiple labels present in the analyzed cells. In contrast to traditional polychromatic FC, these devices utilize a number of detectors (or channels in multispectral detector arrays) that is larger than the number of labels, and no particular detector is a priori dedicated to the measurement of any particular label. This data-acquisition modality requires a rigorous study and understanding of signal formation as well as unmixing procedures that are employed to estimate labels abundance. The simplest extension of the traditional compensation procedure to multispectral data sets is equivalent to an ordinary least-square (LS) solution for estimating abundance of labels in individual cells. This process is identical to the technique employed for unmixing spectral data in various imaging fields. The present study shows that multispectral FC data violate key assumptions of the LS process, and use of the LS method may lead to unmixing artifacts, such as population distortion (spreading) and the presence of negative values in biomarker abundances. Various alternative unmixing techniques were investigated, including relative-error minimization and variance-stabilization transformations. The most promising results were obtained by performing unmixing using Poisson regression with an identity-link function within a generalized linear model framework. This formulation accounts for the presence of Poisson noise in the model of signal formation and subsequently leads to superior unmixing results, particularly for dim fluorescent populations. The proposed Poisson unmixing technique is demonstrated using simulated 8-channel, 2-fluorochrome data and real 32-channel, 6-fluorochrome data. The quality of unmixing is assessed by computing absolute and relative errors, as well as by calculating the symmetrized Kullback-Leibler divergence between known and approximated populations. These results are applicable to any flow-based system with more detectors than labels where Poisson noise is the dominant contributor to the overall system noise and highlight the fact that explicit incorporation of appropriate noise models is the key to accurately estimating the true label abundance on the cells. © 2013 International Society for Advancement of Cytometry.


Assuntos
Citometria de Fluxo/métodos , Modelos Lineares , Modelos Estatísticos , Células Sanguíneas/citologia , Corantes Fluorescentes , Humanos , Distribuição de Poisson
7.
PLoS One ; 18(10): e0292536, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37871046

RESUMO

Sixteen years (2005-2020) of zooplankton monitoring in the Bay of Marseille (N-W Mediterranean Sea) are analyzed in relation to physical, meteorological, climatic and biotic data. Samples were collected every two weeks by a vertical haul (0-55 m) of a 200 µm plankton net. Different indices characterizing the mesozooplankton are compared: biomass dry weight of four size fractions between 200 and 2000 µm; abundances of the whole of the mesozooplankton and of 13 main taxonomic groups defined from plankton imagery; seasonal onset timing of each zooplankton group; and two other types of indices: the first characterized diversity based on abundance data, and the second was derived from zooplankton size spectra shape. The clearest pattern in the environmental compartment was an overall decreasing trend in nutrients, shifts in phytoplankton metrics (i.e. size structure and particulate organic matter), and changes in winter conditions (i.e. increasing temperatures, precipitation and NAO). Interannual patterns in the mesozooplankton community were: (i) a decrease of total abundance (ii) a decrease in biomass for the four size fractions, with an earlier decrease for the 1000-2000 µm size fraction (in 2008); (iii) a reduced dominance of copepods (calanoids and oithonoids) and a concomitant increase in abundance of other taxonomic groups (crustaceans, pteropods, chaetognaths, salps) which induced higher diversity; (iv) a first shift in size spectra towards smaller sizes in 2009, when the 1000-2000 µm size fraction biomass decreased, and a second shift towards larger sizes in 2013 along with increased diversity; and (iv) a later onset in the phenology for some zooplankton variables and earlier onset for salps. Concomitant changes in the phytoplankton compartment, winter environmental conditions, zooplankton community structure (in size and diversity) and zooplankton phenology marked by a shift in 2013 suggest bottom-up control of the pelagic ecosystem.


Assuntos
Ecossistema , Zooplâncton , Animais , Mar Mediterrâneo , Baías , Biomassa , Plâncton , Fitoplâncton
8.
Sci Total Environ ; 857(Pt 3): 159619, 2023 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-36280086

RESUMO

Along with their important diversity, coastal ecosystems receive various amounts of nutrients, principally arising from the continent and from the related human activities (mainly industrial and agricultural activities). During the 20th century, nutrients loads have increased following the increase of both the global population and need of services. Alongside, climate change including temperature increase or atmospheric circulation change has occurred. These processes, Ecosystem state changes are hard to monitor and predict. To study the long-term changes of nutrients concentrations in coastal ecosystems, eleven French coastal ecosystems were studied over 20 years as they encompass large climatic and land pressures, representative of temperate ecosystems, over a rather small geographical area. Both univariate (time series decomposition) and multivariate (relationships between ecosystems and drivers) statistical analyses were used to determine ecosystem trajectories as well as typologies of ecosystem trajectories. It appeared that most of the French coastal ecosystems exhibited trajectories towards a decrease in nutrients concentrations. Differences in trajectories mainly depended on continental and human influences, as well as on climatic regimes. One single ecosystem exhibited very different trajectories, the Arcachon Bay with an increase in nutrients concentrations. Ecosystem trajectories based on ordination techniques were proven to be useful tools to monitor ecosystem changes. This study highlighted the importance of local environments and the need to couple uni- and multi-ecosystem studies. Although the studied ecosystems were influenced by both local and large-scale climate, by anthropogenic activities loads, and that their trajectories were mostly similar based on their continental influence, non-negligible variations resulted from their internal functioning.


Assuntos
Mudança Climática , Ecossistema , Humanos , Atividades Humanas , Nutrientes
9.
Cytometry A ; 81(1): 35-44, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22173900

RESUMO

Despite recent progress in cell-analysis technology, rapid classification of cells remains a very difficult task. Among the techniques available, flow cytometry (FCM) is considered especially powerful, because it is able to perform multiparametric analyses of single biological particles at a high flow rate-up to several thousand particles per second. Moreover, FCM is nondestructive, and flow cytometric analysis can be performed on live cells. The current limit for simultaneously detectable fluorescence signals in FCM is around 8-15 depending upon the instrument. Obtaining multiparametric measurements is a very complex task, and the necessity for fluorescence spectral overlap compensation creates a number of additional difficulties to solve. Further, to obtain well-separated single spectral bands a very complex set of optical filters is required. This study describes the key components and principles involved in building a next-generation flow cytometer based on a 32-channel PMT array detector, a phase-volume holographic grating, and a fast electronic board. The system is capable of full-spectral data collection and spectral analysis at the single-cell level. As demonstrated using fluorescent microspheres and lymphocytes labeled with a cocktail of antibodies (CD45/FITC, CD4/PE, CD8/ECD, and CD3/Cy5), the presented technology is able to simultaneously collect 32 narrow bands of fluorescence from single particles flowing across the laser beam in <5 µs. These 32 discrete values provide a proxy of the full fluorescence emission spectrum for each single particle (cell). Advanced statistical analysis has then been performed to separate the various clusters of lymphocytes. The average spectrum computed for each cluster has been used to characterize the corresponding combination of antibodies, and thus identify the various lymphocytes subsets. The powerful data-collection capabilities of this flow cytometer open up significant opportunities for advanced analytical approaches, including spectral unmixing and unsupervised or supervised classification.


Assuntos
Citometria de Fluxo/instrumentação , Análise de Célula Única/instrumentação , Animais , Anticorpos Monoclonais/química , Citometria de Fluxo/métodos , Humanos , Linfócitos/citologia , Linfócitos/metabolismo , Camundongos , Análise de Célula Única/métodos
10.
Cytometry A ; 79(4): 263-75, 2011 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21387542

RESUMO

Analytical flow cytometry (FCM) is well suited for the analysis of phytoplankton communities in fresh and sea waters. The measurement of light scatter and autofluorescence properties of particles by FCM provides optical fingerprints, which enables different phytoplankton groups to be separated. A submersible version of the CytoSense flow cytometer (the CytoSub) has been designed for in situ autonomous sampling and analysis, making it possible to monitor phytoplankton at a short temporal scale and obtain accurate information about its dynamics. For data analysis, a manual clustering is usually performed a posteriori: data are displayed on histograms and scatterplots, and group discrimination is made by drawing and combining regions (gating). The purpose of this study is to provide greater objectivity in the data analysis by applying a nonmanual and consistent method to automatically discriminate clusters of particles. In other words, we seek for partitioning methods based on the optical fingerprints of each particle. As the CytoSense is able to record the full pulse shape for each variable, it quickly generates a large and complex dataset to analyze. The shape, length, and area of each curve were chosen as descriptors for the analysis. To test the developed method, numerical experiments were performed on simulated curves. Then, the method was applied and validated on phytoplankton cultures data. Promising results have been obtained with a mixture of various species whose optical fingerprints overlapped considerably and could not be accurately separated using manual gating.


Assuntos
Citometria de Fluxo , Fitoplâncton , Animais , Automação Laboratorial , Separação Celular/instrumentação , Separação Celular/métodos , Citometria de Fluxo/instrumentação , Citometria de Fluxo/métodos , Água Doce , Filogenia , Fitoplâncton/classificação , Fitoplâncton/citologia , Fitoplâncton/metabolismo , Água do Mar
11.
Extremophiles ; 15(3): 347-58, 2011 May.
Artigo em Inglês | MEDLINE | ID: mdl-21424516

RESUMO

Here, we combined flow cytometry (FCM) and phylogenetic analyses after cell sorting to characterize the dominant groups of the prokaryotic assemblages inhabiting two ponds of increasing salinity: a crystallizer pond (TS) with a salinity of 390 g/L, and the non-crystallizer pond (M1) with a salinity of 200 g/L retrieved from the solar saltern of Sfax in Tunisia. As expected, FCM analysis enabled the resolution of high nucleic acid content (HNA) and low nucleic acid content (LNA) prokaryotes. Next, we performed a taxonomic analysis of the bacterial and archaeal communities comprising the two most populated clusters by phylogenetic analyses of 16S rRNA gene clone library. We show for the first time that the presence of HNA and LNA content cells could also be extended to the archaeal populations. Archaea were detected in all M1 and TS samples, whereas representatives of Bacteria were detected only in LNA for M1 and HNA for TS. Although most of the archaeal sequences remained undetermined, other clones were most frequently affiliated to Haloquadratum and Halorubrum. In contrast, most bacterial clones belonged to the Alphaproteobacteria class (Phyllobacterium genus) in M1 samples and to the Bacteroidetes phylum (Sphingobacteria and Salinibacter genus) in TS samples.


Assuntos
Archaea/classificação , Bactérias/classificação , Citometria de Fluxo , Filogenia , Microbiologia da Água , Água/química , Alphaproteobacteria/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , Bacteroidetes/classificação , Biodiversidade , DNA Arqueal/isolamento & purificação , DNA Bacteriano/isolamento & purificação , Halorubrum/classificação , Processos Heterotróficos , RNA Ribossômico 16S/genética , Ribotipagem , Salinidade , Sphingobacterium/classificação , Tunísia
12.
Front Microbiol ; 12: 697801, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34456886

RESUMO

Located from 35° to 45° latitude in both hemispheres, the transition zone is an important region with respect to the planktonic biogeography of the sea. However, to the best of our knowledge, there have been no reports on the existence of a tintinnid community in the transition zone. In this research, tintinnids along two transects across the North Pacific Transition Zone (NPTZ) were investigated in summer 2016 and 2019. Eighty-three oceanic tintinnid species were identified, 41 of which were defined as common oceanic species. The common oceanic species were further divided into five groups: boreal, warm water type I, warm water type II, transition zone, and cosmopolitan species. Undella californiensis and Undella clevei were transition zone species. Other species, such as Amphorides minor, Dadayiella ganymedes, Dictyocysta mitra, Eutintinnus pacificus, Eutintinnus tubulosus, Protorhabdonella simplex, and Steenstrupiella steenstrupii, were the most abundant in the NPTZ but spread over a much larger distribution region. Species richness showed no obvious increase in the NPTZ. Boreal, transition zone, and warm water communities were divided along the two transects. Tintinnid transition zone community mainly distributed in regions with water temperatures between 15 and 20°C. The tintinnid lorica oral diameter size classes were dominated by the 24-28 µm size class in three communities, but the dominance decreased from 66.26% in the boreal community to 48.85% in the transition zone community and then to 22.72% in the warm water community. Our research confirmed the existence of tintinnid transition zone species and community. The abrupt disappearance of warm water type I species below 15°C suggested that this group could be used as an indicator of the northern boundary of the NPTZ.

13.
Sci Rep ; 11(1): 281, 2021 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-33431943

RESUMO

One pathway by which the oceans influence climate is via the emission of sea spray that may subsequently influence cloud properties. Sea spray emissions are known to be dependent on atmospheric and oceanic physicochemical parameters, but the potential role of ocean biology on sea spray fluxes remains poorly characterized. Here we show a consistent significant relationship between seawater nanophytoplankton cell abundances and sea-spray derived Cloud Condensation Nuclei (CCN) number fluxes, generated using water from three different oceanic regions. This sensitivity of CCN number fluxes to ocean biology is currently unaccounted for in climate models yet our measurements indicate that it influences fluxes by more than one order of magnitude over the range of phytoplankton investigated.


Assuntos
Atmosfera/química , Microbiota , Água do Mar/microbiologia , Clima
14.
Cytometry A ; 77(10): 911-24, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21290465

RESUMO

Heterogeneity within natural phytoplankton communities makes it very difficult to analyze parameters at the single-cell level. Flow cytometric sorting is therefore a useful tool in aquatic sciences, as it provides material for post-sort analysis and culturing. Sorting subpopulations from natural communities, however, often requires handling morphologically diverse and complex particles with various abundances. Long particles, such as filament-forming cyanobacteria (>100-µm long), prove very difficult to handle. These potentially toxic organisms are widespread in eutrophic systems and have important ecological consequences. Being able to sort filamentous cyanobacteria efficiently and as viable cells is therefore highly desirable when studying factors associated with their toxicity and occurrence. This unconventional sorting requires extensive user experience and special instrument setup. We have investigated the effect of hydrodynamic and electromechanical components of a flow cytometer, and sorting protocol on the quantitative sorting efficiency of these long particles using two filamentous cyanobacterial strains with average lengths of ∼100 and ∼300 µm. Sorting efficiency ranged from 9.4 to 96.0% and was significantly affected by filament length, sorting envelope, drop delay (dd), and for the long species also by tip size, but not by cycle time. Filaments survived sorting and were not damaged. The optimal settings found for the modular MoFlo® cell-sorter to sort the filaments were a 100-µm flow tip at 30 psi (207 kPa) with a three-droplet envelope in Enrich mode while using an extended analysis time of 17.6 µs and an intermediate plate charge and deflection percentage combination of 3,000 V/60%, combined with a dd 0 for the cultures with 100-µm filaments and dd +1 for the culture with 300-µm filaments. To the best of our knowledge, the filaments up to 1063.5 µm sorted in this study are the longest ever sorted.


Assuntos
Separação Celular/métodos , Cianobactérias/citologia , Citometria de Fluxo/instrumentação , Adesão Celular , Movimento Celular , Sobrevivência Celular , Células Cultivadas , Cianobactérias/metabolismo , Citometria de Fluxo/métodos
15.
Microbiologyopen ; 9(6): 1207-1224, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32180355

RESUMO

The shallow Caroline Seamount is located in the tropical western Pacific Ocean. Its summit is 57 m below the surface and penetrates the euphotic zone. Therefore, it is ideal for the study of the influence of seamount on plankton distribution. Here, virioplankton abundance and distribution were investigated by flow cytometry (FCM) in the Caroline Seamount in August and September 2017. The total abundance of virus-like particles (VLP) was in the range of 0.64 × 106 -18.77 × 106  particles/ml and the average was 5.37 ± 3.75 × 106  particles/ml. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensities were identified. Above the deep chlorophyll maximum (DCM), two medium fluorescence virus (MFV) subclusters were discriminated. Between the DCM and the deeper layers, only one MFV subcluster was resolved. In general, low fluorescence viruses (LFV) comprised the most abundant subclusters. In the 75-150 m water column, however, the MFV abundance was higher than the LFV abundance. High fluorescence viruses (HFV) constituted the least abundant subcluster throughout the entire water column. Virioplankton abundance was significantly enhanced at the seamount stations. Environmental factors including water temperature and nitrate concentration were the most correlated with the variation in virioplankton abundance at the seamount stations. Interactions between shallow seamounts and local currents can support large virus standing stocks, causing a so-called indirect "seamount effect" on the virioplankton.


Assuntos
Plâncton/virologia , Vírus/classificação , Biodiversidade , Ecossistema , Fluorescência , Oceano Pacífico , Vírus/genética , Vírus/isolamento & purificação
16.
Cytometry A ; 75(2): 163-8, 2009 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19051328

RESUMO

ELF97 phosphate (ELF-P) is a useful compound for assessing the phosphorus-related status of planktonic aquatic populations. The technique has been successfully applied to phytoplankton and more recently to heterotrophic prokaryotes in both freshwater and marine samples. We have used a recently developed protocol that enables the detection by flow cytometry of ELF alcohol (ELFA), the product of ELF-P hydrolysis. This protocol allows for identification of the fraction of cells able to express phosphatase activity (i.e., ELFA-labeled). This protocol is also very valuable in the study of time kinetics in this ELFA-labeling. The percentage of ELFA-labeled cells, the relative median ELFA fluorescence per cell, and the absolute ELFA fluorescence were determined in both freshwater (lake) and marine samples. The incubation time necessary to reach a stable percentage of active cells with maximal fluorescence intensity varied widely among samples. We highlight very subtle but important problems of discrimination between active and nonactive cells and of estimation of per-cell activity and we underline the importance of studying time kinetics of ELFA-labeling to determine the appropriate incubation time and thus making sample comparisons more relevant. Working on time kinetics of ELFA-labeling is promising for phosphomonoester hydrolysis rate determination at single cell level.


Assuntos
Bactérias/isolamento & purificação , Água Doce/microbiologia , Monoéster Fosfórico Hidrolases/análise , Fitoplâncton/isolamento & purificação , Quinazolinonas/química , Água do Mar/microbiologia , Bactérias/enzimologia , Citometria de Fluxo , Cinética , Compostos Organofosforados/química , Fitoplâncton/enzimologia , Coloração e Rotulagem
17.
MethodsX ; 6: 1133-1146, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31193445

RESUMO

Sterilization is essential for discriminating biotic responses from abiotic reactions in laboratory experiments investigating biogeochemical processes of complex natural samples. However, the conventional methods used to effectively sterilize materials or culture media do not allow sterilizing complex natural samples while maintaining biogeochemical balances. The aim of this study was to develop a low-cost and easy-to-use method to obtain geochemically unmodified and sterilized samples from complex lacustrine or coastal marine ecosystems. In preliminary assays, the impact of several sterilization methods (autoclaving, chemical poisoning, microwave, UV irradiation) on the trace metals balances was studied using borosilicate glass (BG), fluorinated ethylene-propylene (FEP) or polyethylene terephthalate (PET) bottles. Unlike other methods, UV sterilization had minor effects on the distribution of dissolved trace metals. Additional tests using complex lacustrine and coastal marine samples under 10 g/L sediments were performed using a homemade UV sterilization chamber designed to simultaneously irradiate a large number samples. Results showed: •very reproducible UV tests in BG and FEP bottles•faster sterilization using FEP bottles than using BG bottles•low variations of dissolved trace metals concentrations, except for Al, Cu, Fe and Zn.

18.
J Microbiol Methods ; 75(2): 269-78, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18639593

RESUMO

It has been demonstrated that ELF97-phosphate (ELF-P) is a useful tool to detect and quantify phosphatase activity of phytoplankton populations at a single cell level. Recently, it has been successfully applied to marine heterotrophic bacteria in culture samples, the cells exhibiting phosphatase activity being detected using epifluorescence microscopy. Here, we describe a new protocol that enables the detection of ELF alcohol (ELFA), the product of ELF-P hydrolysis, allowing the detection of phosphatase positive bacteria, using flow cytometry. Bacteria from natural samples must be disaggregated and, in oligotrophic waters, concentrated before they can be analyzed by flow cytometry. The best efficiency for disaggregating/separating bacterial cell clumps was obtained by incubating the sample for 30 min with Tween 80 (10 mg l(-1), final concentration). A centrifugation step (20,000 g; 30 min) was required in order to recover all the cells in the pellet (only 7+/-2% of the cells were recovered from the supernatant). The cells and the ELFA precipitates were resistant to these treatments. ELFA-labelled samples were stored in liquid nitrogen for up to four months before counting without any significant loss in total or ELFA-labelled bacterial cell abundance or in the ELFA fluorescence intensity. We describe a new flow cytometry protocol for detecting and discriminating the signals from both ELFA and different counterstains (4',6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI)) necessary to distinguish between ELFA-labelled and non ELFA-labelled heterotrophic bacteria. The method has been successfully applied in both freshwater and marine samples. This method promises to improve our understanding of the physiological response of heterotrophic bacteria to P limitation.


Assuntos
Bactérias/citologia , Bactérias/enzimologia , Citometria de Fluxo/métodos , Água Doce/microbiologia , Monoéster Fosfórico Hidrolases/metabolismo , Água do Mar/microbiologia , Bactérias/crescimento & desenvolvimento , Centrifugação , Filtração/métodos , Processos Heterotróficos , Kit de Reagentes para Diagnóstico
19.
Curr Protoc Cytom ; 85(1): e42, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29958333

RESUMO

In aquatic environments, free heterotrophic bacteria play an extremely important role due to their high biomass, wide panel of metabolisms, and ubiquity, as well as the toxicity of certain species. This unit presents a nucleic-acid double-staining protocol (NADS) for flow cytometry that can distinguish fractions of viable, damaged, or membrane-compromised cells within the free-bacterial community. The NADS protocol is based on the simultaneous utilization of two nucleic acid stains-membrane-permeant SYBR Green and membrane-impermeant propidium iodide (PI). The efficiency of the double staining on fresh samples is magnified by the FRET from SYBR Green to PI when both are bound to the nucleic acids. Full quenching of SYBR Green fluorescence by PI identifies cells with a compromised membrane, partial quenching indicates cells with a slightly damaged membrane, and lack of quenching characterizes cells with an intact membrane. Samples do not require any pretreatment and this protocol can be performed almost anywhere. © 2018 by John Wiley & Sons, Inc.


Assuntos
Bactérias/citologia , Bactérias/metabolismo , Membrana Celular/metabolismo , Citometria de Fluxo/métodos , Microbiologia da Água , Benzotiazóis , Diaminas , Viabilidade Microbiana , Compostos Orgânicos/química , Propídio/química , Quinolinas
20.
Nat Commun ; 9(1): 953, 2018 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-29507291

RESUMO

Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO2 on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2-20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.


Assuntos
Carbono/metabolismo , Diatomáceas/fisiologia , Fitoplâncton/fisiologia , Estações do Ano , Biomassa , Contagem de Células , Clorofila/metabolismo , Código de Barras de DNA Taxonômico , Diatomáceas/ultraestrutura , Geografia , Sedimentos Geológicos , Mar Mediterrâneo , Fitoplâncton/classificação , Fitoplâncton/ultraestrutura
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