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At least 163 records · Page 9Linked to original sources
PubMed2002

Planktonic nitrate-reducing bacteria and sulfate-reducing bacteria in some western Canadian oil field waters.

Oil fields that use water flooding to enhance oil recovery may become sour because of the production of H(2)S from the reduction of sulfate by sulfate-reducing bacteria (SRB). The addition of nitrate to produced waters can stimulate the activities of nitrate-reducing bacteria (NRB) and control sulfide production. Many previous studies have focused on chemolithotrophic bacteria that can use thiosulfate or sulfide as energy sources while reducing nitrate. Little attention has been given to heterotrophic NRB in oil field waters. Three different media were used in this study to enumerate various types of planktonic NRB present in waters from five oil fields in western Canada. The numbers of planktonic SRB and bacteria capable of growth under aerobic conditions were also determined. In general, microbial numbers in the produced waters were very low (<10 ml x (-1)) in samples taken near or at wellheads. However, the numbers increased in the aboveground facilities. No thiosulfate-oxidizing NRB were detected in the oil field waters, but other types of NRB were detected in 16 of 18 produced water samples. The numbers of heterotrophic NRB were equal to or greater than the number of sulfide-oxidizing, chemolithotrophic NRB in 12 of 15 samples. These results showed that each of the oil fields contained NRB, which might be stimulated by nitrate amendment to control H(2)S production by SRB.

Animals↗
PubMed2004

Molecular evidence links cryptic diversification in polar planktonic protists to Quaternary climate dynamics.

It is unknown how pelagic marine protists undergo diversification and speciation. Superficially, the open ocean appears homogeneous, with few clear barriers to gene flow, allowing extensive, even global, dispersal. Yet, despite the apparent lack of opportunity for genetic isolation, diversity is prevalent within marine taxa. A lack of candidate isolating mechanisms would seem to favor sympatric over allopatric speciation models to explain the diversity and biogeographic patterns observed in the oceans today. However, the ocean is a dynamic system, and both current and past circulation patterns must be considered in concert to gain a true perspective of gene flow through time. We have derived a comprehensive picture of the mechanisms potentially at play in the high latitudes by combining molecular, biogeographic, fossil, and paleoceanographic data to reconstruct the evolutionary history of the polar planktonic foraminifer Neogloboquadrina pachyderma sinistral. We have discovered extensive genetic diversity within this morphospecies and that its current "extreme" polar affinity did not appear until late in its evolutionary history. The molecular data demonstrate a stepwise progression of diversification starting with the allopatric isolation of Atlantic Arctic and Antarctic populations after the onset of the Northern Hemisphere glaciation. Further diversification occurred only in the Southern Hemisphere and seems to have been linked to glacial-interglacial climate dynamics. Our findings demonstrate the role of Quaternary climate instability in shaping the modern high-latitude plankton. The divergent evolutionary history of N. pachyderma sinistral genotypes implies that paleoceanographic proxies based on this taxon should be calibrated independently.

Animals↗
PubMed2004

Bacteriophage Phi S1 infection of Pseudomonas fluorescens planktonic cells versus biofilms.

This communication focuses on the efficacy of a specific lytic phage, phage Phi S1, as a control agent of Pseudomonas fluorescens biofilms. The effect of phage infection temperature and the host growth temperature were evaluated. The results obtained showed that the phage infection process was temperature dependent and that the optimum temperature of infection of planktonic cells and biofilms was 26 degrees C. At this temperature, bacteriophage Phi S1, at a multiplicity of infection (MOI) of 0.5 infected both planktonic cells and biofilms causing a biomass reduction of about 85% in both cases.

Bacteriophages↗
PubMed2005

Ecological specialization of mixotrophic plankton in a mixed water column.

In recent years, the population dynamics of plankton in light- or nutrient-limited environments have been studied extensively. Their evolutionary dynamics, however, have received much less attention. Here, we used a modeling approach to study the evolutionary behavior of a population of plankton living in a mixed water column. Initially, the organisms are mixotrophic and thus have both autotrophic and heterotrophic abilities. Through evolution of their trophic preferences, however, they can specialize into separate autotrophs and heterotrophs. It was found that the light intensity gradient enables evolutionary branching and thus may result in the ecological specialization of the mixotrophs. By affecting the gradient, other environmental properties also acquire influence on this evolutionary process. Intermediate mixing intensities, large mixing depths, and high nutrient densities were found to facilitate evolutionary branching and thus specialization. Later results may explain why mixotrophs are often more dominant in oligotrophic systems while specialist strategies are associated with eutrophic systems.

Adaptation, Physiological↗
PubMed1998

Increasing resistance of planktonic and biofilm cultures of Burkholderia cepacia to ciprofloxacin and ceftazidime during exponential growth.

The change in resistance of Burkholderia cepacia to ceftazidime and to ciprofloxacin during the exponential phase and up to the onset of stationary phase was assessed along the growth curve in batch culture. B. cepacia was grown in planktonic culture and in a biofilm on a membrane support. Resistance increased progressively during the exponential phase, being increased by ten-fold about every four generations. Bacteria grown in a biofilm were about 15 times more resistant than equivalent planktonic-grown bacteria. The growth rate was not the key factor for the development of resistance. The growth phase and the mode of growth have a fundamental impact on the susceptibility of B. cepacia towards antimicrobial agents. Bacteria growing at the same rate may differ greatly in their resistance to antimicrobial agents.

Animals↗
PubMed1996

Molecular phylogeny of symbiotic dinoflagellates from planktonic foraminifera and radiolaria.

Recent analyses of the small subunit ribosomal DNA (srDNA) from dinoflagellate symbionts of cnidaria have confirmed historical descriptions of a diverse but well-defined clade, Symbiodinium, as well as several other independent symbiont lineages (Rowan 1991; Rowan and Powers 1992; Sadler et al. 1992; McNally et al 1994). Dinoflagellates also occur as intracellular symbionts in a number of pelagic protistan taxa, but the srDNA of these symbionts has not been examined. We analyzed the srDNA sequences of the symbiotic dinoflagellates from four planktonic foraminiferal species and six radiolarian species. The symbionts from these sarcodines formed two distinct lineages within the dinoflagellates. Within each lineage, symbionts obtained from different host species showed few, if any, srDNA sequence differences. The planktonic foraminiferal symbionts were most closely related to Gymnodinium simplex and the Symbiodinium clade, whereas the radiolarian symbionts were most closely related to the dinoflagellate symbiont from the oceanic chondrophore, Velella velella. Therefore, although the dinoflagellate symbionts of foraminifera appear to be a sister taxon of the symbionts from benthic foraminifera and invertebrates, the symbionts of radiolaria are distinct and arose from an independent lineage of dinoflagellate symbionts that shares common ancestry with the symbiont of at least one pelagic metazoan. The lack of srDNA variability within the sarcodine symbiont lineages suggests that coevolution of host and symbiont has not occurred.

Animals↗
PubMed2003

Evolution as a critical component of plankton dynamics.

Microevolution is typically ignored as a factor directly affecting ongoing population dynamics. We show here that density-dependent natural selection has a direct and measurable effect on a planktonic predator-prey interaction. We kept populations of Brachionus calyciflorus, a monogonont rotifer that exhibits cyclical parthenogenesis, in continuous flow-through cultures (chemostats) for more than 900 days. Initially, females frequently produced male offspring, especially at high population densities. We observed rapid evolution, however, towards low propensity to reproduce sexually, and by 750 days, reproduction had become entirely asexual. There was strong selection favouring asexual reproduction because, under the turbulent chemostat regime, males were unable to mate with females, produced no offspring, and so had zero fitness. In replicated chemostat experiments we found that this evolutionary process directly influenced the population dynamics. We observed very specific but reproducible plankton dynamics which are explained well by a mathematical model that explicitly includes evolution. This model accounts for both asexual and sexual reproduction and treats the propensity to reproduce sexually as a quantitative trait under selection. We suggest that a similar amalgam of ecological and evolutionary mechanisms may drive the dynamics of rapidly reproducing organisms in the wild.

Animals↗
PubMed2004

Recognizing plankton images from the shadow image particle profiling evaluation recorder.

We present a system to recognize underwater plankton images from the shadow image particle profiling evaluation recorder (SIPPER). The challenge of the SIPPER image set is that many images do not have clear contours. To address that, shape features that do not heavily depend on contour information were developed. A soft margin support vector machine (SVM) was used as the classifier. We developed a way to assign probability after multiclass SVM classification. Our approach achieved approximately 90% accuracy on a collection of plankton images. On another larger image set containing manually unidentifiable particles, it also provided 75.6% overall accuracy. The proposed approach was statistically significantly more accurate on the two data sets than a C4.5 decision tree and a cascade correlation neural network. The single SVM significantly outperformed ensembles of decision trees created by bagging and random forests on the smaller data set and was slightly better on the other data set. The 15-feature subset produced by our feature selection approach provided slightly better accuracy than using all 29 features. Our probability model gave us a reasonable rejection curve on the larger data set.

Algorithms↗
PubMed2006

Switch from planktonic to sessile life: a major event in pneumococcal pathogenesis.

Two main patterns of gene expression of Streptococcus pneumoniae were observed during infection in the host by quantitative real time RT-PCR; one was characteristic of bacteria in blood and one of bacteria in tissue, such as brain and lung. Gene expression in blood was characterized by increased expression of pneumolysin, pspA and hrcA, while pneumococci in tissue infection showed increased expression of neuraminidases, metalloproteinases, oxidative stress and competence genes. In vitro situations with similar expression patterns were detected in liquid culture and in a newly developed pneumococcal model of biofilm respectively. The biofilm model was dependent on addition of synthetic competence stimulating peptide (CSP) and no biofilm was formed by CSP receptor mutants. As one of the differentially expressed gene sets in vivo were the competence genes, we exploited competence-specific tools to intervene on pneumococcal virulence during infection. Induction of the competence system by the quorum-sensing peptide, CSP, not only induced biofilm formation in vitro, but also increased virulence in pneumonia in vivo. In contrast, a mutant for the ComD receptor, which did not form biofilm, also showed reduced virulence in pneumonia. These results were opposite to those found in a bacteraemic sepsis model of infection, where the competence system was downregulated. When pneumococci in the different physiological states were used directly for challenge, sessile cells grown in a biofilm were more effective in inducing meningitis and pneumonia, while planktonic cells from liquid culture were more effective in inducing sepsis. Our data enable us, using in vivo gene expression and in vivo modulation of virulence, to postulate the distinction - from the pneumococcal point of view - between two main types of disease. During bacteraemic sepsis pneumococci resemble planktonic growth, while during tissue infection, such as pneumonia or meningitis, pneumococci are in a biofilm-like state.

Animals↗
PubMed2006

Detection of free-living and plankton-bound vibrios in coastal waters of the Adriatic Sea (Italy) and study of their pathogenicity-associated properties.

Culturable vibrios were isolated from water and plankton fractions collected during an 18-month sampling study performed along the north-central coast of the Adriatic Sea (Italy). Unculturable Vibrio vulnificus and V. parahaemolyticus were detected in plankton fractions by polymerase chain reaction amplification of DNA sequences for cytotoxin-haemolysin and thermolabile haemolysin respectively. The presence of V. parahaemolyticus, V. vulnificus and V. cholerae virulence genes and the expression of pathogenicity-associated traits were analysed in all isolates. The results showed the spreading of these properties among the environmental isolates and confirm the need of both monitoring the presence of vibrios in coastal areas and studying their pathogenicity potential in order to properly protect human health.

Copepoda↗
PubMed2006

Common evolutionary origin of planktonic and benthic nitrogen-fixing oscillatoriacean cyanobacteria from tropical oceans.

The filamentous cyanobacteria belonging to the genus Hydrocoleum (Blennothrix) are among the most common mat-forming cyanobacteria in tropical oceans. We present here the evidence that these benthic cyanobacteria are morphologically and phylogenetically very close to the planktonic species of Trichodesmium. Genetic relationship was established independently with regard to sequences of the 16S rRNA gene, nifH gene, and phycocyanin and phycoerythrin intergenic spacers. The species of both genera formed a common distinct branch in phylogenetically reconstructed cyanobacterial trees, suggesting that the main constituents of cyanobacterial benthos and plankton have an early common origin and both represent major contributors to nitrogen budget of tropical oceans today as in the distant geological past.

Animals↗
PubMed2006

Cell surface lectin-binding glycoconjugates on marine planktonic protists.

Carbohydrate-protein interactions appear to play an important role in the phagocytosis of microbial prey by free-living protozoa. The present study utilizes FITC-labelled plant lectins to investigate the presence and localization of cell surface glycoconjugates on live and fixed planktonic protists (Dunaliella primolecta, Oxyrrhis marina, Goniomonas amphinema, Paraphysomonas vestita and Euplotes vannus). With live flagellate preparations, lectins primarily bound to external cell surfaces, with minimal internal staining observed. In contrast, cell fixation permeabilized cell membranes, allowing lectins to bind to internal structures, such as nuclear membranes and food vacuoles, interfering with the characterization of cell surface glycoconjugates. The method developed to label cell surface sugar moieties of live planktonic protists successfully overcomes the problems associated with fixation, and thus provides a useful protocol for future studies on protistan cell surface carbohydrate characterization.

Animals↗
PubMed1967

Planktonic Foraminifera: field experiment on production rate.

In a study of the rate of production of four species of planktonic Foraminifera in the region of the California Current it was found that their life spans are of the order of 1 month. Reproduction seems to take place mainly in the upper hundred meters. Results are in contrast to previous evidence presented in favor of yearly life cycles and maturing at great depth in other species of planktonic Foraminifera.

Ecology↗
PubMed1997

Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel.

Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters.

Animals↗
PubMed2000

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↗
PubMed2005

High motility reduces grazing mortality of planktonic bacteria.

We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 microm s(-1) as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 microm s(-1)) and a highly motile strain (>45 microm s(-1)) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 microm(3). Grazing mortality was lowest for cells of >0.5 microm(3) and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (< or =0.1 microm(3), >50 microm s(-1)) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.

Animals↗
PubMed2006

Planktonic replication is essential for biofilm formation by Legionella pneumophila in a complex medium under static and dynamic flow conditions.

Legionella pneumophila persists for a long time in aquatic habitats, where the bacteria associate with biofilms and replicate within protozoan predators. While L. pneumophila serves as a paradigm for intracellular growth within protozoa, it is less clear whether the bacteria form or replicate within biofilms in the absence of protozoa. In this study, we analyzed surface adherence of and biofilm formation by L. pneumophila in a rich medium that supported axenic replication. Biofilm formation by the virulent L. pneumophila strain JR32 and by clinical and environmental isolates was analyzed by confocal microscopy and crystal violet staining. Strain JR32 formed biofilms on glass surfaces and upright polystyrene wells, as well as on pins of "inverse" microtiter plates, indicating that biofilm formation was not simply due to sedimentation of the bacteria. Biofilm formation by an L. pneumophila fliA mutant lacking the alternative sigma factor sigma(28) was reduced, which demonstrated that bacterial factors are required. Accumulation of biomass coincided with an increase in the optical density at 600 nm and ceased when the bacteria reached the stationary growth phase. L. pneumophila neither grew nor formed biofilms in the inverse system if the medium was exchanged twice a day. However, after addition of Acanthamoeba castellanii, the bacteria proliferated and adhered to surfaces. Sessile (surface-attached) and planktonic (free-swimming) L. pneumophila expressed beta-galactosidase activity to similar extents, and therefore, the observed lack of proliferation of surface-attached bacteria was not due to impaired protein synthesis or metabolic activity. Cocultivation of green fluorescent protein (GFP)- and DsRed-labeled L. pneumophila led to randomly interspersed cells on the substratum and in aggregates, and no sizeable patches of clonally growing bacteria were observed. Our findings indicate that biofilm formation by L. pneumophila in a rich medium is due to growth of planktonic bacteria rather than to growth of sessile bacteria. In agreement with this conclusion, GFP-labeled L. pneumophila initially adhered in a continuous-flow chamber system but detached over time; the detachment correlated with the flow rate, and there was no accumulation of biomass. Under these conditions, L. pneumophila persisted in biofilms formed by Empedobacter breve or Microbacterium sp. but not in biofilms formed by Klebsiella pneumoniae or other environmental bacteria, suggesting that specific interactions between the bacteria modulate adherence.

Animals↗
PubMed2006

Cryptococcus neoformans cells in biofilms are less susceptible than planktonic cells to antimicrobial molecules produced by the innate immune system.

The human pathogenic fungus Cryptococcus neoformans can form biofilms on polystyrene plates and medical devices in a process that requires capsular polysaccharide release. Although biofilms are known to be less susceptible to antimicrobial drugs, little is known about their susceptibility to antimicrobial molecules produced by the innate immune system. In this study, we investigated the susceptibility of C. neoformans cells in biofilm and planktonic states to oxidative and nonoxidative antimicrobial molecules produced by phagocytic cells. The effects of various immune effector molecules on the fungal mass, metabolic activity, and architecture of C. neoformans biofilms were measured by colony counts, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide reduction, and confocal microscopy, respectively. Biofilms were more resistant than planktonic cells to oxidative stress but remained vulnerable to cationic antimicrobial peptides. However, melanized biofilms were significantly less susceptible to antimicrobial peptides than nonmelanized biofilms. These results suggest that the biofilm phenotype increases resistance against host immune mechanisms, a phenomenon that could contribute to the ability of biofilm-forming microbes to establish persistent infections.

Amino Acid Sequence↗