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C Pedrós-Alió

Publications and source records attributed to C Pedrós-Alió.

At least 19 recordsLinked to original sources

Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas.

We analyzed microbial eukaryote diversity in perennially cold arctic marine waters by using 18S rRNA gene clone libraries. Samples were collected during concurrent oceanographic missions to opposite sides of the Arctic Ocean Basin and encompassed five distinct water masses. Two deep water Arctic Ocean sites and the convergence of the Greenland, Norwegian, and Barents Seas were sampled from 28 August to 2 September 2002. An additional sample was obtained from the Beaufort Sea (Canada) in early October 2002. The ribotypes were diverse, with different communities among sites and between the upper mixed layer and just below the halocline. Eukaryotes from the remote Canada Basin contained new phylotypes belonging to the radiolarian orders Acantharea, Polycystinea, and Taxopodida. A novel group within the photosynthetic stramenopiles was also identified. One sample closest to the interior of the Canada Basin yielded only four major taxa, and all but two of the sequences recovered belonged to the polar diatom Fragilariopsis and a radiolarian. Overall, 42% of the sequences were <98% similar to any sequences in GenBank. Moreover, 15% of these were <95% similar to previously recovered sequences, which is indicative of endemic or undersampled taxa in the North Polar environment. The cold, stable Arctic Ocean is a threatened environment, and climate change could result in significant loss of global microbial biodiversity.

Animals↗

High-diversity biofilm for the oxidation of sulfide-containing effluents.

In the present work, we describe for the first time the utilization of a complex microbial biofilm for the treatment of sulfide-containing effluents. A non-aerated packed-column reactor was inoculated with anoxic lake sediment and exposed to light. A biofilm developed in the column and showed a stable oxidation performance for several weeks. Microbial species composition was analyzed by microscopy, pigment analysis and a bacterial 16S rRNA gene clone library. Colorless sulfur bacteria, green algae and purple sulfur bacteria were observed microscopically. Pigment composition confirmed the presence of algae and purple sulfur bacteria. The clone library was dominated by alpha-Proteobacteria (mostly Rhodobacter group), followed by gamma-Proteobacteria (Chromatiaceae-like and Thiothrix-like aerobic sulfur oxidizers) and the Cytophaga- Flavobacterium- Bacteroides group. Plastid signatures from algae were also present and a few clones belonged to both the beta- ( Rhodoferax sp., Thiobacillus sp.) and delta-Proteobacteria ( Desulfocapsa sp.) and to the low G+C Gram-positive bacteria (Firmicutes group). The coexistence of aerobic, anaerobic, phototrophic and chemotrophic microorganisms in the biofilm, the species richness found within these metabolic groups (42 operational taxonomic units) and the microdiversity observed within some species could be very important for the long-term functioning and versatility of the reactor.

Base Sequence↗

Dissolved primary production and the strength of phytoplankton- bacterioplankton coupling in contrasting marine regions.

We analyzed the strength of phytoplankton-bacterioplankton coupling by comparing the rate of particulate (PPP) and dissolved primary production (DPP) with bacterial carbon demand (BCD) in four contrasting marine regions: offshore and coastal waters of the Southern Ocean, a coastal area of the NE Atlantic, and a coastal-offshore transect in the NW Mediterranean. We measured bacterial heterotrophic production (BHP) and estimated BCD from a literature model. Average phytoplanktonic percent extracellular release [PER = DPP/(DPP + PPP)] was 18-20% in the Antarctic (offshore and coastal, respectively), 16% in the NW Mediterranean, and 7% in the NE Atlantic. A significant inverse relationship was found between PER and total system productivity with pooled data. On average BHP amounted to <5% of total primary production in all regions. However, the strength of phytoplankton-bacterioplankton coupling, estimated as the potential importance of DPP in meeting BCD, differed greatly in the four regions. DPP was highly correlated to BCD in offshore Antarctic waters and was sufficient to meet BCD. In contrast, BCD exceeded DPP and bore no significant relationship in the remaining regions. The data suggest that a strong dependence of bacteria on algal extracellular production is only expected in open-ocean environments isolated from coastal inputs of DOC.

Algorithms↗

Studying marine microorganisms from space.

Microorganisms are but a few micrometers in diameter and are not visible to the naked eye. Yet, the large numbers of microorganisms present in the oceans and the global impact of their activities make it possible to observe them from space. Here a few examples of how microorganisms can be studied from satellites are presented. The first case is the best known: the main pigment used in photosynthesis (chlorophyll a) can be determined from satellites. These kinds of studies have contributed a tremendous amount of understanding about the distribution and dynamics of primary production in the oceans. Two other examples will concern analysis of heterotrophic prokaryotic production and estimates of dimethyl sulfide (DMS) concentration and flux to the atmosphere. These three processes are of fundamental importance for the functioning of the biosphere. Marine microbes carry out about half of the total primary production in the planet. A substantial fraction of the respiration in the oceans is due to the activity of heterotrophic prokaryotes. Finally, the flux of DMS to the atmosphere is believed to constitute one of the mechanisms by which the biota can regulate climate. The global implications of microbial processes in the oceans can only be addressed with the help of satellites.

Chlorophyll↗

Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton.

Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.

Animals↗

Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing.

Very small eukaryotic organisms (picoeukaryotes) are fundamental components of marine planktonic systems, often accounting for a significant fraction of the biomass and activity in a system. Their identity, however, has remained elusive, since the small cells lack morphological features for identification. We determined the diversity of marine picoeukaryotes by sequencing cloned 18S rRNA genes in five genetic libraries from North Atlantic, Southern Ocean, and Mediterranean Sea surface waters. Picoplankton were obtained by filter size fractionation, a step that excluded most large eukaryotes and recovered most picoeukaryotes. Genetic libraries of eukaryotic ribosomal DNA were screened by restriction fragment length polymorphism analysis, and at least one clone of each operational taxonomic unit (OTU) was partially sequenced. In general, the phylogenetic diversity in each library was rather great, and each library included many different OTUs and members of very distantly related phylogenetic groups. Of 225 eukaryotic clones, 126 were affiliated with algal classes, especially the Prasinophyceae, the Prymnesiophyceae, the Bacillariophyceae, and the Dinophyceae. A minor fraction (27 clones) was affiliated with clearly heterotrophic organisms, such as ciliates, the chrysomonad Paraphysomonas, cercomonads, and fungi. There were two relatively abundant novel lineages, novel stramenopiles (53 clones) and novel alveolates (19 clones). These lineages are very different from any organism that has been isolated, suggesting that there are previously unknown picoeukaryotes. Prasinophytes and novel stramenopile clones were very abundant in all of the libraries analyzed. These findings underscore the importance of attempts to grow the small eukaryotic plankton in pure culture.

Animals↗

Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques.

We used denaturing gradient gel electrophoresis (DGGE) to study the diversity of picoeukaryotes in natural marine assemblages. Two eukaryote-specific primer sets targeting different regions of the 18S rRNA gene were tested. Both primer sets gave a single band when used with algal cultures and complex fingerprints when used with natural assemblages. The reproducibility of the fingerprints was estimated by quantifying the intensities of the same bands obtained in independent PCR and DGGE analyses, and the standard error of these estimates was less than 2% on average. DGGE fingerprints were then used to compare the picoeukaryotic diversity in samples obtained at different depths and on different dates from a station in the southwest Mediterranean Sea. Both primer sets revealed significant differences along the vertical profile, whereas temporal differences at the same depths were less marked. The phylogenetic composition of picoeukaryotes from one surface sample was investigated by excising and sequencing DGGE bands. The results were compared with an analysis of a clone library and a terminal restriction fragment length polymorphism fingerprint obtained from the same sample. The three PCR-based methods, performed with three different primer sets, revealed very similar assemblage compositions; the same main phylogenetic groups were present at similar relative levels. Thus, the prasinophyte group appeared to be the most abundant group in the surface Mediterranean samples as determined by our molecular analyses. DGGE bands corresponding to prasinophytes were always found in surface samples but were not present in deep samples. Other groups detected were prymnesiophytes, novel stramenopiles (distantly related to hyphochytrids or labyrinthulids), cryptophytes, dinophytes, and pelagophytes. In conclusion, the DGGE method described here provided a reasonably detailed view of marine picoeukaryotic assemblages and allowed tentative phylogenetic identification of the dominant members.

Animals↗

5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient.

Natural prokaryotic assemblages from two multi-pond solar salterns and pure cultures of both marine bacteria and halophilic archaea were analyzed and compared by electrophoretic analysis of 5S rRNAs. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied. The culture-independent, PCR-free, fingerprinting analysis covered two objectives: (i) to compare natural assemblages among them and with results previously obtained through a PCR-dependent approach and (ii) to estimate the in situ relevance of those prokaryotic groups obtained with classical culture methodologies. Natural assemblages were analyzed through cluster analysis of quantitative 5S rRNA band patterns. The resulting groups were in accordance with environmental parameters (i.e., NaCl concentration) and with the clustering obtained after a PCR-dependent approach, showing the formation of three salinity-based groups of samples (<10%, 10-25% and >25% salinity). Similarities between the laboratory strains tested and dominant community members were studied by comparing 5S rRNA band patterns. The lack of match obtained after cluster analysis indicated that the prokaryotic populations relevant in the ponds below 25% salinity were neither Flavobacteria nor haloarchaeal strains belonging to the genera Halococcus, Haloarcula and Halobacterium. Members of Proteobacteria and Gram-positive bacteria were found to match bands in these samples. The 5S rRNA fingerprint from the dominant community members in the ponds above 30% salinity did not fit any of the cultured halophilic archaea studied, in agreement with earlier PCR results. This is consistent with a greater bias introduced by culture-dependent methods than by those based on PCR, especially for archaeal populations.

Journal Article↗

Spatial differences in bacterioplankton composition along the Catalan coast (NW Mediterranean) assessed by molecular fingerprinting.

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments was used to compare surface bacterioplankton assemblages along the Catalan coast (NW Mediterranean). Samples from three coastal stations were compared with samples taken inside the Barcelona harbour and open sea samples taken during a cruise. The bacterial assemblage of each sample showed a characteristic and reproducible DGGE fingerprint. Between 17 and 35 bands were detected in each sample, and about 40% of the bands accounted for more than 80% of the band intensity in each sample. The presence of bands as well as their relative intensity was used to compare bacterial assemblages. Clear differences between the harbour samples and the coastal samples were evident during all periods. Marked temporal changes in the bacterial assemblages were detectable for the coastal sites, suggesting seasonal succession of coastal bacterioplankton. During each season, two stations presented a very similar bacterial composition (Barcelona and Masnou) whereas bacterial assemblages in Blanes were slightly different. These differences were consistent with the different hydrography of the area. Diversity indices calculated from DGGE fingerprints were relatively similar for all samples analysed, even though harbour samples were expected to present lower diversity values.

Journal Article↗

Comparative analysis shows that bacterivory, not viral lysis, controls the abundance of heterotrophic prokaryotic plankton.

Empirical models derived from literature data were used to compare the factors controlling prokaryotic abundance (PN) and prokaryotic heterotrophic production (PHP) in solar salterns. These empirical relationships were generated as multiple linear regressions with PN or PHP as dependent variables, while the independent variables were chosen to reflect the likely sources of organic matter, inorganic nutrients and temperature. These variables were then measured in solar salterns and the predictions made by the general relationships were compared to actual saltern values of PN and PHP. Saltern ponds of salinity higher than 100 per thousand departed significantly from the general relationships, while the ponds of salinity lower than 100 per thousand fitted well within the range of values predicted by the general models. The most likely explanation for the discrepancy of the former was the absence of bacterivory. This hypothesis was tested with data from other very different aquatic systems: karstic lakes with anaerobic hypolimnia and two marine areas in the Mediterranean and the Southern Ocean. The anoxic regions of karstic lakes departed significantly from the predictions of the general model, while the oxic layers conformed to the predictions. As in the case of salterns, this difference could be explained by the presence of significant predation in the oxic, but not in the anoxic, layers of these lakes. Finally, two marine areas with similar predation pressure on prokaryotes but very different impacts of viral lysis were tested. In all cases, PN values conformed to the predictions, suggesting that lysis due to viruses is not the main factor controlling PN in aquatic systems, which is more likely to be determined by the balance between bacterivory and resource supply. The present work also demonstrates the usefulness of empirical comparative analyses to generate predictions and to draw inferences on the functioning of microbial communities.

Journal Article↗

Comparison of pure cultures and natural assemblages of planktonic photosynthetic sulfur bacteria by low molecular mass RNA fingerprinting.

Pure cultures of phototrophic sulfur bacteria were compared to natural populations that bloom in karstic lakes by electrophoretic analysis of low molecular mass RNA molecules (lmwRNA) and microscopy. Similarities between dominant community members, field isolates and reference strains were established by comparing the lmwRNA band patterns through dendrograms produced with Euclidean distances and the average linkage clustering method, by a single, quick, one-step method. The fingerprinting analysis had three objectives: (i) to compare microbial assemblages from different geographical locations, (ii) to compare those organisms which grow in pure culture to those forming planktonic blooms and (iii) to give a preliminary view of the identity of the predominant community members. The lmwRNA analysis yielded a number of clusters consistent with the microscopic observations and allowed rapid comparison of the microbial communities without the need to isolate their individual components. The fingerprints of natural communities were different from most of the laboratory strains tested. Purple sulfur bacteria responsible for the blooms analyzed in karstic lakes were more closely related to the Thiocystis group than to the classical strains extensively studied in the laboratory.

Journal Article↗

The microbial food web along salinity gradients.

The microbial food web was studied along a gradient of salinity in two solar salterns used for the commercial production of salt. The different ponds in the salterns provide a wide range of ecosystems with food webs of different complexities. Abundance of prokaryotes, cell volume, prokaryotic heterotrophic production, chlorophyll a, abundance of heterotrophic flagellates, ciliates and phytoplankton were determined in several ponds in each saltern. Increases in salinity resulted in a progressive reduction in the abundance and number of different groups of eukaryotic microorganisms present, but an increase in biomass of prokaryotes. Maximal activity of both phyto- and bacterioplankton was found at a salinity of around 100 per thousand, where there was also a maximum in chlorophyll a concentration. Growth rates of heterotrophic prokaryotes decreased with increasing salinity. Bacterivory disappeared above 250 per thousand salinity, whereas other loss factors such as viral lysis appeared to be of minor importance throughout the gradient [Guixa-Boixereu et al. (1996) Aquat. Microb. Ecol. 11, 215-227].

Journal Article↗

Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom.

The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that Roseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the alpha Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing Cytophagales and delta Proteobacteria) were primarily found in deeper waters (200 to 500 m).

Alphaproteobacteria↗

Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis.

The microbial assemblages of Lake Cisó and Lake Vilar (Banyoles, northeast Spain) were analyzed in space and time by microscopy and by performing PCR-denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 16S rRNA gene fragments. Samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. Although the lakes have the same climatic conditions and the same water source, the limnological parameters were different, as were most of the morphologically distinguishable photosynthetic bacteria enumerated by microscopy. The phylogenetic affiliations of the predominant DGGE bands were inferred by performing a comparative 16S rRNA sequence analysis. Sequences obtained from Lake Cisó samples were related to gram-positive bacteria and to members of the division Proteobacteria. Sequences obtained from Lake Vilar samples were related to members of the Cytophaga-Flavobacterium-Bacteroides phylum and to cyanobacteria. Thus, we found that like the previously reported differences between morphologically distinct inhabitants of the two lakes, there were also differences among the community members whose morphologies did not differ conspicuously. The changes in the species composition from winter to spring were also marked. The two lakes both contained sequences belonging to phototrophic green sulfur bacteria, which is consistent with microscopic observations, but these sequences were different from the sequences of cultured strains previously isolated from the lakes. Euryarchaeal sequences (i.e., methanogen- and thermoplasma-related sequences) also were present in both lakes. These euryarchaeal group sequences dominated the archaeal sequences in Lake Cisó but not in Lake Vilar. In Lake Vilar, a new planktonic population related to the crenarchaeota produced the dominant archaeal band. The phylogenetic analysis indicated that new bacterial and archaeal lineages were present and that the microbial diversity of these assemblages was greater than previously known. We evaluated the correspondence between the abundances of several morphotypes and DGGE bands by comparing microscopy and sequencing results. Our data provide evidence that the sequences obtained from the DGGE fingerprints correspond to the microorganisms that are actually present at higher concentrations in the natural system.

Archaea↗

A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces.

We compared the phylogenetic compositions of marine planktonic archaeal populations in different marine provinces. Samples from eight different environments were collected at two depths (surface and aphotic zone), and 16 genetic libraries of PCR-amplified archaeal 16S rRNA genes were constructed. The libraries were analyzed by using a three-step hierarchical approach. Membrane hybridization experiments revealed that most of the archaeal clones were affiliated with one of the two groups of marine archaea described previously, crenarchaeotal group I and euryarchaeotal group II. One of the 2,328 ribosomal DNA clones analyzed was related to a different euryarchaeal lineage, which was recently recovered from deep-water marine plankton. In temperate regions (Pacific Ocean, Atlantic Ocean, and Mediterranean Sea) both major groups were found at the two depths investigated; group II predominated at the surface, and group I predominated at depth. In Antarctic and subantarctic waters group II was practically absent. The clonal compositions of archaeal libraries were investigated by performing a restriction fragment length polymorphism (RFLP) analysis with two tetrameric restriction enzymes, which defined discrete operational taxonomic units (OTUs). The OTUs defined in this way were phylogenetically consistent; clones belonging to the same OTU were closely related. The clonal diversity as determined by the RFLP analysis was low, and most libraries were dominated by only one or two OTUs. Some OTUs were found in samples obtained from very distant places, indicating that some phylotypes were ubiquitous. A tree containing one example of each OTU detected was constructed, and this tree revealed that there were several clusters within archaeal group I and group II. The members of some of these clusters had different depth distributions.

Animals↗

Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment.

A method for analyzing virus assemblages in aquatic environments was developed and used for studying the highest-salinity ponds (from 13.4 to 35% salinity) from a multi-pond solar saltern in Alicante, Spain. The protocol consisted of a series of concentration and purification steps including tangential flow filtration and ultracentrifugation, followed by the preparation of total viral nucleic acids that were subsequently separated by pulsed-field gel electrophoresis. For every sample analyzed, a characteristic DNA pattern was obtained, whose complexity was related to viral diversity. The comparison of our results with a similar analysis carried out with marine virus assemblages shows that, as expected, the viral diversity corresponding to the analyzed hypersaline environment is considerably lower than that of a marine environment.

Bacteriophages↗

Effects of temperature, sulfide, and food abundance on growth and feeding of anaerobic ciliates.

The trophic role of ciliates in anaerobic food webs has not been assessed experimentally. In order to obtain basic information necessary to interpret field situations, we studied the effects of temperature, sulfide concentration, and food abundance on the growth and feeding activities of two anaerobic ciliates, Plagiopyla nasuta and Metopus es. The growth rate of P. nasuta increased with temperature from 8 to 18 degrees C (Q(10) = 2.0) and remained constant in the range between 18 and 24 degrees C (0.22 day). Sulfide concentrations of between 0 and 1 mM did not affect the feeding activities, but concentrations greater than 2 mM were inhibitory. The functional response of P. nasuta feeding on fluorescently labeled heterotrophic and phototrophic bacteria was investigated. In both cases, the parameters of the functional response were almost identical when expressed in terms of biovolume: the maximal uptake rate (U(m)) was 1,800 mum ciliate h and the half-saturation constant for ingestion (k) was 1.5 x 10 mum ml. The functional response of M. es feeding on heterotrophic bacteria was found to be similar to that of P. nasuta. These ciliates needed high bacterial abundances in order to maintain their growth (k of about 4 x 10 bacteria ml), implying that they will frequently be food limited in planktonic environments. Both the maximal uptake rates and the maximal clearance rates were comparable to those of aerobic ciliates. By combining the growth and feeding data, we estimated gross growth efficiencies of 12 and 13% for P. nasuta and M. es, respectively. These results indicate that the feeding rates of anaerobic ciliates are similar to those of aerobic ciliates. Their slower growth must, therefore, be due to the lower gross growth efficiency (likely due to anaerobic metabolism).

Journal Article↗

Role of anaerobic ciliates in planktonic food webs: abundance, feeding, and impact on bacteria in the field.

We studied the dynamics of two populations of anaerobic ciliates, Plagiopyla sp. and Metopus sp., and of their potential prey, heterotrophic and phototrophic purple bacteria, in Lake Cisó throughout a 1-year cycle. The abundance of both ciliates was very low (less than 2 individuals per ml). During mixing, Plagiopyla ciliates exhibited high clearance rates (about 100 nl ciliate h), its integrated abundance increased with a net doubling time of 47 days, and its potential doubling times, as calculated from the number of bacteria consumed, ranged between 5 and 8 days. During stratification, the activity of Plagiopyla ciliates was reduced and the population decreased; this was related to the higher amounts of sulfide present. The impact of predation by the Plagiopyla population on bacterioplankton was found to be insignificant, less than 0.1% of bacterial biomass consumed per day. Thus, anaerobic ciliates cannot control the bacterioplankton in Lake Cisó because of both the low abundance over the period studied and the low feeding rates during certain periods. A review of available field studies suggests that this conclusion can be extrapolated to most other anoxic systems.

Journal Article↗