A Monitoring Sensor Management System for Grid Environments

Large distributed systems such as Computational Grids require a large amount of monitoring data be collected for a variety of tasks such as fault detection, performance analysis, performance tuning, performance prediction, and scheduling. Ensuring that all necessary monitoring is turned on and that data is being collected can be a very tedious and error-prone task. We have developed an agent-based system to automate the execution of monitoring sensors and the collection of event data.     

Multielement compositions of marine phytoplankton samples from coastal areas of japan by instrumental neutron activation analysis

Phytoplankton samples were collected during spring bloom of diatoms from three coastal areas of Japan using a NORPAC P-25 net (25-Μm opening) with a NGG52 prenet (335-Μm opening), and 25 major and trace elements have been analyzed by INAA. Concentration ranges of analyzed phytoplankton samples are much wider than the concentration ranges compiled by Bowen (1979) except for As, and data of marine phytoplankton samples for Br, Sb, Hf, Sc, La, Ce, Sm, and Eu were not included in the compilation. The 25 analyzed elements have been categorized into three groups: elements showing positive correlation with Br, positive correlation with Al, and no positive correlation with Br or Al. The marine phytoplankton samples have been plotted on a Masuzawa-Koyama-Terazaki (MKT) plot and it proved that the MKT plot is applicable to marine phytoplankton samples.     

Properties of Bacteria Isolated from Deep-Sea Sediments

Thirty-eight isolates were subjected to taxonomic analysis by computer. Of the 38 isolates, 31 were from sediment samples collected at depths from 9,400 to 10,400 meters in the Philippine and Marianas Trenches of the Pacific Ocean, and 7 cultures were from seawater samples collected at various depths from surface to 4,000 meters and from several locations in the Pacific Ocean. A total of 116 characteristics were determined for each isolate, coded, and transferred to punch cards. Similarity values were obtained by computer analysis, with the use of two recently developed computer programs. Five distinct phenetic clusters were observed from the numerical analyses. Four of the clusters were identified as species of the genus Pseudomonas, and one, as an aerogenic species of Aeromonas. Group IV was identified as pigmented Pseudomonas fluorescens, and the major cluster, consisting of groups I and II, which merged at a species level of similarity, was treated as a new species of Pseudomonas. The 38 strain data were compared with data for 132 marine and nonmarine strains previously subjected to computer taxonomic analysis. The barotolerant deep-sea strains, with the exception of the deep-sea P. fluorescens isolates, clustered separately from all other marine strains.     

Molecular detection of betanodaviruses from apparently healthy wild marine invertebrates

One hundred eighteen samples (21 species) of wild marine invertebrates were collected from western and southern coastal area of Korean Peninsula. Four of 78 (18 species) samples collected at Namhae (South) area were positive for nodavirus in nested PCR test. Of the 40 samples (5 species) collected at Hwanghae (West) areas, all samples were negative for nodavirus in both RT-PCR and nested PCR tests. Positive nested PCR results were obtained from the following species: Charybdis bimaculata Charybdid crab; Pandalus hypsinotus Southern humpback shrimp and Mytilus galloprovincialis Mediterranean mussel. Phylogenetic analysis based on the partial nucleotide sequence (177 bases) of the RNA2 coat protein gene showed that the four strains were highly homologous (100%) and closely related to that of the known betanodaviruses, redspotted grouper nervous necrosis virus (RGNNV). These results indicate that nodavirus is present from wild marine invertebrates in the southern coastal areas of Korean Peninsula. These subclinically infected marine invertebrates may constitute an inoculum source for betanodavirus infection and cause mortality in cultured fishes in Korea.     

Discovery of novel metabolites from marine actinomycetes

Recent findings from culture-dependent and culture-independent methods have demonstrated that indigenous marine actinomycetes exist in the oceans and are widely distributed in different marine ecosystems. There is tremendous diversity and novelty among the marine actinomycetes present in marine environments. Progress has been made to isolate novel actinomycetes from samples collected at different marine environments and habitats. These marine actinomycetes produce different types of new secondary metabolites. Many of these metabolites possess biological activities and have the potential to be developed as therapeutic agents. Marine actinomycetes are a prolific but underexploited source for the discovery of novel secondary metabolites.     

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.     

Peptaibols: stable markers of fungal development in the marine environment

Different peptaibols were observed in both fresh and frozen marine sediments collected from a marine area devoted to bivalve culture (Fier d'Ars, Atlantic coast, France). The identification of the peptaibols was based on a three-step mass-spectrometric analysis: observation of doubly charged ions with a characteristic isotopic profile, cleavage and observation of C- and N-terminal fragments, and partial sequencing of the N-terminal segments. The MS characteristics indicated numerous similarities between the peptaibols detected and those produced by different strains of Trichoderma species isolated from fresh sediments. Peptaibols were also detected in mussel samples collected at the same site. This constitutes the first observation of contamination of the marine human-food chain by fungal metabolites. Since peptaibols were readily observed both in fresh sediments and in samples kept frozen for several years, these compounds can be considered as stable markers of the development of Trichoderma in the marine environment.     

Investigation of bacterial diversity in Brazilian tropical estuarine sediments reveals high actinobacterial diversity

Phylogenetic and statistical analyses of 16S rRNA gene libraries were used for the investigation of actinobacterial communities present in two tropical estuarine sediments (Santos-São Vicente estuary, Brazil). The libraries were constructed from samples collected at the brackish end of the estuary, highly hydrocarbon-contaminated, and at the marine end, uncontaminated. Clones from the marine end of the estuary were all related to sequences from non-cultured Actinobacteria and unidentified bacteria recovered from a wide range of environmental samples, whereas clones from the brackish end were mainly related to sequences from cultured Actinobacteria. Statistical analyses showed that the community recovered from the hydrocarbon-contaminated sediment sample, at the brackish end, was less diverse than the uncontaminated one, at the marine end, and that the communities from the two libraries were differently structured, suggesting that these may have not originated from the same community. The recognition of the spatial pattern of actinobacterial distribution in a natural environment is a first step towards understanding the way these communities are organized, providing valuable data for further investigations of their taxonomic and functional diversity.     

The detection of spatial variation in widespread marine species: methods and bias in the analysis of population structure in the crown of thorns starfish (Echinodermata: Asteroidea)

The basic assumptions that widespread marine species should show little spatial variation in genetic structure, given their high potential for dispersal on ocean currents, is being questioned. This has taken some time because there are few studies of widespread marine species over oceanic scales, few data sets that have the high density of sampling required for the detection of fine population structure, and there is little incentive to look further if initial analyses suggest the expected result. The interpretation of the population genetic structure of crown-of-thorns starfish (Acanthaster planci) has been found to vary considerably depending on the sample set included in the analyses and on the method of analysis used. Scatter plots of genetic distance or , and spatial autocorrelation approaches gave markedly different results ranging from no structure to isolation by distance. Only visual examination of maps of patterns of variation in allele variation first detected that crown-of-thorns starfish occupy large regions with little between population differentiation, but between which there are markedly higher levels of differentiation. These findings highlight the care required in interpreting population structure, particularly where there are few sample points. Many marine species may have population structures where sharp genetic disjunctions, not associated with any obvious environmental boundaries, separate regions of relative genetic homogeneity. Such population structures are very different from those traditionally assumed and are not yet understood. Further advances in understanding the genetic structure of marine species will demand an iterative approach where a greater number of samples are collected over particular regions identified by earlier interpretations.     

Biogeography and systematics of Hildenbrandia (Rhodophyta,Hildenbrandiales) in North America: inferences from morphometrics and rbcL and 18S rRNA gene sequence analyses

Morphometric analysis and phylogenetic analysis of sequences of the rbcL chloroplast gene (which codes for the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme) and the nuclear 18S ribosomal RNA (rRNA) gene were carried out on 26 specimens of marine and freshwater Hildenbrandia from North America. Nineteen marine specimens were collected from Alaska to Costa Rica on the Pacific coast and from Newfoundland to Connecticut on the Atlantic coast. Seven freshwater samples were collected from Texas, Costa Rica, St Lucia and Puerto Rico. Three groups of samples were distinguished by morphometric analysis: one containing all freshwater samples (H. angolensis Welwitsch ex West et West), one consisting of a marine sample with parallel tetrasporangial divisions (H. occidentalis Setchell ex Gardner) and one group with non-parallel tetrasporangial divisions (H. rubra (Sommerfelt) Meneghini. These groupings were partially incongruent with those obtained by analyses of the molecular data. Parsimony and distance analyses of the rbcL gene resulted in trees in which Atlantic and Pacific clades were largely resolved. However, an Alaskan sample was included in the Atlantic group, which may indicate a trans-Arctic invasion event. The freshwater samples were paraphyletic for the rbcL gene, among the marine collections, which supports the concept of multiple invasions establishing the freshwater populations in North America. The 18S rRNA gene sequence data indicate that the freshwater samples are monophyletic with the exception of the unresolved position of the H. occidentalis sample. The freshwater samples form a monophyletic clade when multiple outgroups are used. The rbcL data appear to be mutationally saturated above approximately 17% divergence, which makes interpretation of phylogenetic signal among distant groups difficult. This may be a result of the asexual reproduction of the alga.     

Beyond the benchtop and the benthos: Dataset management planning and design for time series of ocean carbonate chemistry associated with Durafet®-based pH sensors

To better understand the impact of ocean acidification on marine ecosystems, an important ongoing research priority for marine scientists is to characterize present-day pH variability. Following recent technological advances, autonomous pH sensor deployments in shallow coastal marine environments have revealed that pH dynamics in coastal oceans are more variable in space and time than the discrete, open-ocean measurements that are used for ocean acidification projections. Data from these types of deployments will benefit the research community by facilitating the improved design of ocean acidification studies as well as the identification or evaluation of natural and human-influenced pH variability. Importantly, the collection of ecologically relevant pH data and a cohesive, user-friendly integration of results across sites and regions requires (1) effective sensor operation to ensure high-quality pH data collection and (2) efficient data management for accessibility and broad reuse by the marine science community. Here, we review the best practices for deployment, calibration, and data processing and quality control, using our experience with Durafet®-based pH sensors as a model. Next, we describe information management practices for streamlining preservation and distribution of data and for cataloging different types of pH sensor data, developed in collaboration with two U.S. Long Term Ecological Research (LTER) sites. Finally, we assess sensor performance and data recovery from 73 SeaFET deployments in the Santa Barbara Channel using our quality control guidelines and data management tools, and offer recommendations for improved data yields. Our experience provides a template for other groups contemplating using SeaFET technology as well as general steps that may be helpful for the design of data management for other complex sensors.     

Field Observations on the Acute Effect of Crude Oil on Glucose and Glutamate Uptake in Samples Collected from Arctic and Subarctic Waters

The acute effects of crude oil on glucose uptake rates by marine microorganisms were studied in 215 water and 162 sediment samples collected from both arctic and subarctic marine waters. The mean percentage reduction of glucose uptake rates ranged from 37 to 58 in the water samples exposed to crude oil and from 14 to 36 in the sediment samples. Substrate uptake kinetic studies indicated that the observed reductions by microbial populations exposed to crude oil were caused by metabolic inhibition. The effect of crude oil was less in sediments than in the water samples, with the difference being significant at the P < 0.0002 level. With the exception of one sediment study, all of the differences observed in the uptake rates between treated and nontreated samples were statistically significant. A high degree of variability was observed in the degree which glucose and glutamate uptake rates were altered in water samples exposed to crude oil. In some cases, uptake rates were greater in the samples exposed to crude oil. Data on samples collected in Cook Inlet suggested that areas where pelagic microorganisms are most probably chronically exposed to crude oil are also the areas where the effects of crude oil on glucose uptake are the lowest. Two studies indicated that after pelagic populations are exposed to crude oil for several days, the heterotrophic population adjusts to the presence of crude oil.     

A computational method for quantifying morphological variation in scleractinian corals

Morphological variation in marine sessile organisms is frequently related to environmental factors. Quantifying such variation is relevant in a range of ecological studies. For example, analyzing the growth form of fossil organisms may indicate the state of the physical environment in which the organism lived. A quantitative morphological comparison is important in studies where marine sessile organisms are transplanted from one environment to another. This study presents a method for the quantitative analysis of three-dimensional (3D) images of scleractinian corals obtained with X-ray Computed Tomography scanning techniques. The advantage of Computed Tomography scanning is that a full 3D image of a complex branching object, including internal structures, can be obtained with a very high precision. There are several complications in the analysis of this data set. In the analysis of a complex branching object, landmark-based methods usually do not work and different approaches are required where various artifacts (for example cavities, holes in the skeleton, scanning artifacts, etc.) in the data set have to be removed before the analysis. A method is presented, which is based on the construction of a medial axis and a combination of image-processing techniques for the analysis of a 3D image of a complex branching object where the complications mentioned above can be overcome. The method is tested on a range of 3D images of samples of the branching scleractinian coral Madracis mirabilis collected at different depths. It is demonstrated that the morphological variation of these samples can be quantified, and that biologically relevant morphological characteristics, like branch-spacing and surface/volume ratios, can be computed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biological indicators in marine and coastal waters: a statistical and modelling analysis of the MARS campaign

We perform a statistical analysis of ecological data collected in the MARS project from marine environments of the Red and Mediterranean Seas in Israel, and the North Sea in Germany. In the study of fish parasite data, we examine the basic premise that the complex host lifecycles of heteroxenous (h) parasites make them more sensitive to pollution than monoxenous (m) parasites which have only one host. Unlike results from analyses of earlier survey data, we find that the pooled h/m index for a community is not a clear indicator of environmental stress as originally hypothesized. This is due to the relatively large seasonal variability at the sampling sites over the course of the 3-year survey. Other possible indicators for water pollution gradients are checked, including species richness, diversity and prevalence of parasite populations. A theoretical model of host-parasite population dynamics that makes the presence of ecological thresholds transparent is offered to help explain the abrupt transitions prominent in the distributions of parasites at different sites under different pollution loadings. Heavy metal and chlorinated hydrocarbon data collected from fish tissue samples and molluscs of the three seas are assessed as bioindicators for pollution monitoring. The xenobiotic loads and indices of defence system activity and tissue damage are shown to have great potential as monitoring bioindicators.     

Enchanced accuracy of coliform testing in seawater by a modification of the most-probable-number method.

A 1-year study of marine water sample from six beach locations showed that the most-probable-number method failed to recover significant numbers of coli-forms. Modifying this method by transferring, after 48 h, presumptive negatives (growth and no gas production) to confirmed and fecal coliform media significantly improved recovery. Tests which were presumptive negative but confirmed as fecal coliform positive were designated as false negatives. Most-probable-number method false negatives occurred throughout the year, with 143 of 270 samples collected producing false negatives. More than 50% of fecal coliform false-negative isolates were Escherichia coli. Inclusion of false-negative tubes into the coliform most-probable-number method data resulted in increased violation of the California ocean water contact sports standard at all sites. More than 20% of the samples collected were in violation of this standard. These data indicate that modification of the most-probable-number method increases detection of coliform numbers in the marine environment.     

Enchanced accuracy of coliform testing in seawater by a modification of the most-probable-number method.

A 1-year study of marine water sample from six beach locations showed that the most-probable-number method failed to recover significant numbers of coli-forms. Modifying this method by transferring, after 48 h, presumptive negatives (growth and no gas production) to confirmed and fecal coliform media significantly improved recovery. Tests which were presumptive negative but confirmed as fecal coliform positive were designated as false negatives. Most-probable-number method false negatives occurred throughout the year, with 143 of 270 samples collected producing false negatives. More than 50% of fecal coliform false-negative isolates were Escherichia coli. Inclusion of false-negative tubes into the coliform most-probable-number method data resulted in increased violation of the California ocean water contact sports standard at all sites. More than 20% of the samples collected were in violation of this standard. These data indicate that modification of the most-probable-number method increases detection of coliform numbers in the marine environment.     

Quantifying disturbances in benthic communities—comparison of the community disturbance index (CDI) to other multivariate methods

A multivariate index assessing community stress in marine benthic count data is compared to other multivariate methods. Both ordinations and clustering methods are included in the comparison and so is AMBI (AZTI marine biotic index). The community disturbance index (CDI) requires the data to contain undisturbed reference samples. If this requirement is met, the calculations are carried out in two steps. Firstly, the reference samples are separated and used to build a model representing the natural variation. Subsequently, the remaining samples are compared to the model and the respective disturbance indices are calculated. The CDI has the same sensitivity as the traditional multivariate methods. Additionally, one obtains a quantification of the relative level of disturbance. The comparison is performed using data from monitoring surveys at three different oilfields in the North Sea: Troll, Ekofisk and Oseberg-Brage. The samples are collected in 1996, 1990 and 1996, respectively.     

Morbillivirus ecology in polar bears (Ursus maritimus)

Polar bear (Ursus maritimus) morbillivirus infection was initially reported by Follmann and co-workers in 1996, based upon serologic results using canine distemper virus (CDV). The impetus for the evaluation of polar bear populations for morbillivirus infections was prompted by epidemics of canine distemper-like disease in seal populations in the north Atlantic regions of Greenland, Europe, and Russia. Since marine morbilliviruses have been further characterized into three major species, phocine distemper virus (PDV), dolphin morbillivirus (DMV) and porpoise morbillivirus (PMV), it was of value to determine the origin of the polar bear infection. One hundred serum samples were selected from a group of sera collected from regions of Alaska and Russia and tested by differential serum neutralization assay against the three major marine morbilliviruses and CDV, to determine the predominant virus infecting the polar bear. Polar bears had higher serum antibody titers to CDV than they did to PDV, DMV, and PMV. These data suggest that polar bears are being infected with a morbillivirus of terrestrial origin. Furthermore, based on the high serum antibody prevalence in the population, the virus may be indigenous to the polar bear and not necessarily the result of interspecies transmission from other arctic mammals susceptible to CDV and/or marine morbilliviruses. Accepted: 20 December 1999