Can transposable element copy number distribution parameters be estimated from natural populations of Drosophila melanogaster?

The copy frequency distribution of a transposable element family in a Drosophila melanogaster natural population is generally characterised by the values of the Charlesworths' model parameters α and β (Charlesworth & Charlesworth, 1983). The estimation of these parameters is made using the observed distribution of the occupied sites in a population sample. Several results have been interpreted as due either to the influence of stochastic factors or to deterministic factors (transposition, excision, selection…). The accuracy of this method was tested by estimations performed on samples from simulated populations. The results show that with the sample size usually used for natural population studies, the confidence intervals are too large to reasonably deduce either the element copy number distribution or the values of transposition and excision rate and selective coefficients.     

Development and evaluation of a new device to effectively detach micro-organisms from food samples

Aims: To develop a new instrument of great versatility for recovering micro‐organisms from all types of food samples and to compare the effects with existing sample preparation methods. Methods and Results: To detach micro‐organisms from large‐size unbroken food samples such as apples, carrots, potatoes and tomatoes without preprocessing, the Spindle apparatus was newly developed. The Spindle was used to effectively detach micro‐organisms from large‐size samples. In a comparative study involving 51 food samples, treatment with the Spindle and Stomacher showed that recovery of total aerobic micro‐organisms (naturally occurring mesophilic microflora) and foodborne pathogens (from samples inoculated with Escherichia coli O157:H7, Salmonella Typhimurium and Listeria monocytogenes) for both methods was highly correlated (R² = 0·98). Furthermore, diluents treated by the Spindle contained much less food debris than those treated by stomaching. Conclusions: These results indicate that Spindle is a novel, effective alternative method for detaching micro‐organisms from food samples including four kinds of large‐size samples without the need for preprocessing. Significance and Impact of Study: The Spindle might be used to widely detaching micro‐organisms from all types of food samples for microbiological assay.     

Approche discriminante de la contribution de différents échelons microplanctoniques aux mesures globales d'ETS dans des échantillons d'eau de mer. a. Phytoplancton

Discriminating Approach of Various Microplanktonic-stage Contributions to Whole ETS Measurements in Sea-water Samples. a. Phytoplankton Data obtained from algal cell cultures were applied to various sea water samples in order to estimate the specific contribution of phytoplanktonic organisms to whole ETS (electron transport system) measurements of these samples which have been collected at eleven stations in the northwest Mediterranean Sea. When the phytoplankton ETS contributions were quantified by cell enumerations or by other indirect-biomass-indicator measurements, the results are in good accordance to the recorded ETS measurement values of the sample. More specific of the phytoplankton stage is the index used for such an estimation (as chlorophyll a), and better is the relationship between both estimated and measured ETS values.     

Occurrence of Salmonella spp in estuarine and coastal waters of Portugal

The presence of Salmonella and its relationship with indicator organisms of fecal pollution, such as total coliforms, fecal coliforms and fecal streptococci, was studied at two marine zones in Portugal. Seventeen different Salmonella serotypes were isolated and identified, S. virchow was the most frequently isolated (21.6%). In addition, a high percentage (35.1%) was recorded for some Salmonella serotypes of clinical significance, namely S. enteritidis, S. infantis, S. typhimurium and S. virchow. In any of the samples from the two zones Salmonella was not detected in the absence of any of the indicator organisms. However, the incidence of Salmonella as a function of indicator concentration intervals established by the EEC standards was 0, 10 and 19.3% at guide values of total coliforms, fecal coliforms and fecal streptococci, respectively in the Faro samples (south of Portugal). In contrast, Salmonella incidence rates of 37.5, 36.4 and 33.3% were recorded at the corresponding guide values the Caminha samples (north of Portugal). No significant correlations (p>0.005) were obtained between Salmonella and the indicators at the sampling stations; however, total coliforms and fecal streptococci were the indicators most closely related to Salmonella in Caminha and Faro samples, respectively. Survival experiments in Escherichia coli, Enterococcus faecalis and S. typhimurium, using diffusion chambers, were performed to verify whether the lack of correlation between indicators and Salmonella was due to different inactivation rates in seawater. The results indicate that survival percentages of the three microorganisms tested were similar after 48 h of exposure to seawater.     

Summary statistics of neutral mutations in longitudinal DNA samples

Longitudinal samples of DNA sequences are the DNA sequences sampled from the same population at different time points. For fast evolving organisms, e.g. RNA virus, these kind of samples have increasingly been used to study the evolutionary process in action. Longitudinal samples provide some interesting new summary statistics of genetic variation, such as the frequency of mutation of size i in one sample and size j in another, the average number of mutations accumulated since the common ancestor of two sequences each from a different sample, and number of private, shared and fixed mutations within samples. To make the results more applicable, we used in this study a general two-sample model, which assumes two longitudinal samples were taken from the same measurably evolving population. Inspired by the HIV study, we also studied a two-sample-two-stage model, which is a special case of two-sample model and assumes a treatment after the first sampling instantaneously changes the population size. We derived the formulas for calculating statistical properties, e.g. expectations, variances and covariances, of these new summary statistics under the two models. Potential applications of these results were discussed.     

Calorific and carbon values of marine and freshwater Protozoa

Calorific and carbon values were determined for a variety of marine and freshwater Protozoa (Noctiluca miliaris, Euplotes sp.,Eufolliculina sp. respectivelyTetrahymena pyriformis, Paramecium caudatum), their food sources(Bacteria, Dunaliella primolecta, Ceratium hirundinella), and for Protozoa-dominated plankton samples. Most calorific values lie close to the centre of the range covering organisms in general. Low values in some marine samples probably resulted from the retention of bound water in the dried material. When all results were combined with data selected from the literature, the dependence of calorific value on carbon content was highly significant. This relationship is probably also adequately described by an energy-carbon regression through the variety of organic compounds commonly found in organisms. Calorific value expressed per unit carbon is shown to vary little in Protozoa (mean conversion factor 46 J [mg C]^–1) or throughout the range of biological materials considered in this study (45 J [mg C]^–1).     

Diversity and morphological disparity of desmid assemblages in Central European peatlands

Morphological disparity has increasingly been used as an alternative measure of biological diversity based on the shape features of organisms. In this study, we investigated the species diversity and morphological disparity of benthic Desmidiales in Central European peatland pools. The shape features of cells were determined using the 3-D elliptical Fourier analysis of their frontal and lateral views. The resulting morphospace was used to calculate the contributions of localities and species to the morphological variation. In addition, the disparity of samples and their average cell complexity (indicating intricacy of cell shapes) was evaluated. These data were related to species diversity data and to the abiotic factors. Species diversity was positively correlated with pH and conductivity. The low-pH localities generally supported a more variable species composition than did slightly acidic to neutral localities. Conversely, the total nitrogen concentrations of these areas negatively correlated with species diversity. Interestingly, partial morphological disparity (measuring the contribution of a sample to the overall morphological variation) did not correlate with species diversity. On the contrary, several mountain peat bog localities had high disparity values, irrespective of their rather low species diversity. In addition, several samples from minerotrophic fens with high diversity had average or low values of partial morphological disparity. These results indicate the relative importance of mountain peat bogs for the total morphological diversity of Desmidiales within the region that could not be ascertained solely from species diversity data. The inner morphological disparity of samples was highly correlated with their species diversity. Species of the genus Micrasterias, Hyalotheca dissiliens and Desmidium species had the highest partial morphological disparity, thus indicating their marginal position within the morphospace. Micrasterias and Euastrum species had the highest complexity values. The average cell complexity of individual samples did not correlate with their diversity or disparity; however, it was positively correlated with the levels of total nitrogen and phosphorus, and illustrates a pattern different from that arrived at by species diversity data. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: J. Padisak     

Identification of <Emphasis Type="Italic">tertiary</Emphasis> butyl alcohol (TBA)-utilizing organisms in BioGAC reactors using <Superscript>13</Superscript>C-DNA stable isotope probing

Biodegradation of the gasoline oxygenates methyl tertiary-butyl ether (MTBE) and ethyl tertiary-butyl ether (ETBE) can cause tertiary butyl alcohol (TBA) to accumulate in gasoline-impacted environments. One remediation option for TBA-contaminated groundwater involves oxygenated granulated activated carbon (GAC) reactors that have been self-inoculated by indigenous TBA-degrading microorganisms in ground water extracted from contaminated aquifers. Identification of these organisms is important for understanding the range of TBA-metabolizing organisms in nature and for determining whether self-inoculation of similar reactors is likely to occur at other sites. In this study ¹³C-DNA-stable isotope probing (SIP) was used to identify TBA-utilizing organisms in samples of self-inoculated BioGAC reactors operated at sites in New York and California. Based on 16S rRNA nucleotide sequences, all TBA-utilizing organisms identified were members of the Burkholderiales order of the β-proteobacteria. Organisms similar to Cupriavidus and Methylibium were observed in both reactor samples while organisms similar to Polaromonas and Rhodoferax were unique to the reactor sample from New York. Organisms similar to Hydrogenophaga and Paucibacter strains were only detected in the reactor sample from California. We also analyzed our samples for the presence of several genes previously implicated in TBA oxidation by pure cultures of bacteria. Genes Mpe_B0532, B0541, B0555, and B0561 were all detected in ¹³C-metagenomic DNA from both reactors and deduced amino acid sequences suggested these genes all encode highly conserved enzymes. One gene (Mpe_B0555) encodes a putative phthalate dioxygenase-like enzyme that may be particularly appropriate for determining the potential for TBA oxidation in contaminated environmental samples.     

Characterization of microbial contamination in United States Air Force aviation fuel tanks

Bacteria and fungi, isolated from United States Air Force (USAF) aviation fuel samples, were identified by gas chromatograph fatty acid methyl ester (GC-FAME) profiling and 16S or 18S rRNA gene sequencing. Thirty-six samples from 11 geographically separated USAF bases were collected. At each base, an above-ground storage tank, a refueling truck, and an aircraft wing tank were sampled at the lowest sample point, or sump, to investigate microbial diversity and dispersion within the fuel distribution chain. Twelve genera, including four Bacillus species and two Staphylococcus species, were isolated and identified. Bacillus licheniformis, the most prevalent organism isolated, was found at seven of the 11 bases. Of the organisms identified, Bacillus sp., Micrococcus luteus, Sphinogmonas sp., Staphylococcus sp., and the fungus Aureobasidium pullulans have previously been isolated from aviation fuel samples. The bacteria Pantoea ananatis, Arthrobacter sp., Alcaligenes sp., Kocuria rhizophilia, Leucobacter komagatae, Dietza sp., and the fungus Discophaerina fagi have not been previously reported in USAF aviation fuel. Only at two bases were the same organisms isolated from all three sample points in the fuel supply distribution chain. Isolation of previously undocumented organisms suggests either, changes in aviation fuel microbial community in response to changes in aviation fuel composition, additives and biocide use, or simply, improvements in isolation and identification techniques.     

Inhibition of quantitative PCR analysis of fungal conidia associated with indoor air particulate matter

Environmental samples analyzed by quantitative PCR (qPCR) are subject to interference by inhibitors present in the environment being sampled. A controlled determination of the effect of inhibitors associated with sampling indoor air and the ability of internal standard controls to detect inhibition was carried out by filter collection of air samples followed by spiking of the filters with green fluorescent protein-expressing Aspergillus fumigatus conidia. Microscopic conidial counts were compared with qPCR results and correlated with levels of particulate matter and viable airborne microorganisms. Our data showed that PCR can be inhibited by masses of particulate matter as low as 50 μg and that the amount of inhibition was positively correlated with the mass of particulate (r = 0.75) and the number of non-filamentous organisms (r = 0.73). The use of internal standard DNA identified the presence of inhibitors and indicated the need for additional sample processing or qualification of sample results.     

TEMPORAL VARIATION IN ALLELE FREQUENCIES: TESTING THE RIGHT HYPOTHESIS

Although standard statistical tests (such as contingency chi-square or G tests) are not well suited to the analysis of temporal changes in allele frequencies, they continue to be used routinely in this context. Because the null hypothesis stipulated by the test is violated if samples are temporally spaced, the true probability of a significant test statistic will not equal the nominal α level, and conclusions drawn on the basis of such tests can be misleading. A generalized method, applicable to a wide variety of organisms and sampling schemes, is developed here to estimate the probability of a significant test statistic if the only forces acting on allele frequencies are stochastic ones (i.e., sampling error and genetic drift). Results from analyses and simulations indicate that the rate at which this probability increases with time is determined primarily by the ratio of sample size to effective population size. Because this ratio differs considerably among species, the seriousness of the error in using the standard test will also differ. Bias is particularly strong in cases in which a high percentage of the total population can be sampled (for example, endangered species). The model used here is also applicable to the analysis of parent-offspring data and to comparisons of replicate samples from the same generation. A generalized test of the hypothesis that observed changes in allele frequency can be satisfactorily explained by drift follows directly from the model, and simulation results indicate that the true α level of this adjusted test is close to the nominal one under most conditions.     

An Investigation of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> in Rectal-Collected Fecal Samples of Cows

In order to better understand the range and role of Bacillus thuringiensis (Bt) and its toxins in nature, we have undertaken a study of Bt taken directly from the rectum of 117 cows from 37 farms on the Caribbean island of Trinidad. Thirty-seven fecal samples (32%) were found to contain at least one Bt. Generally only one or two isolates with a particular crystal morphology were isolated from any one sample, however, a few samples contained more, up to 11 isolates, suggesting post-ingestion amplification. Bioassays using larvae of Musca domestica, Caenorhabditis elegans and Tetrahymena pyriformis showed no observable toxicity in gross bioassays. Very small dot-like parasporal bodies, not generally characteristic of Bt, were isolated from 44% of the samples, which in many instances appeared unstable and whose relation to Bt Cry protein-containing parasporal bodies is unknown. In conclusion, we find little evidence for a host adapted strain of Bt in the cows examined, nor toxicity to organisms that might logically be associated with either the cow or its feces. The presence of a large number of isolates containing small dot-like parasporal bodies, possibly either poly-β-hydroxybutyrate storage bodies or Cry proteins, was unexpected and merits further investigation.     

A Statistical Evaluation of Sediment Quality Triad Benthic Community Measurements in PAH-Impacted Sediments at a Manufactured Gas Plant Site along the Hudson River

The sediment quality triad (SQT) assumes that three measurements (sediment chemistry, laboratory bioassay, and benthic macroinvertebrate counts) comprise an independent assessment of impact, which when integrated using a weight-of-evidence approach provides a comprehensive assessment of risk. An SQT assessment was conducted on 41 sediment samples collected adjacent to a manufactured gas plant site on the freshwater reach of the Hudson River in New York State. The assessment shows that the benthic macroinvertebrate data did not correlate with either sediment or pore water polycyclic aromatic hydrocarbon (PAH) concentrations, nor did these data show consistent relationships to the results of laboratory bioassay testing (Hyalella azteca 28-day survival or biomass). The benthic community across the site and reference areas was comprised of few taxa, all of which were pollution-tolerant organisms with tolerance values greater than or equal to five. Only in significantly impacted sediment samples with PAH concentrations in the thousands of milligrams per kilogram, pore water concentrations above 100 toxic units, and visible non-aqueous phase liquid present in the sample did the benthic macroinvertebrate data show a response. In contrast, sediment and pore water PAH measurements and H. azteca toxicity testing provided consistent interpretation of impact. These results illustrate that benthic macroinvertebrate data may contain less information value and be a more challenging line of evidence to interpret in triad studies conducted in certain ecological settings; in this case, a large-order river with a relatively depauperate benthic community dominated by species tolerant of PAHs.     

The importance of accounting for the area of the medullary cavity in cross‐sectional geometry: A test based on the femoral midshaft

In cross‐sectional geometric (CSG) studies, both the subperiosteal and endosteal contours are considered important factors in determining bone bending rigidity. Recently, regression equations predicting CSG properties from a section's external dimensions were developed in a world‐wide sample of human long bones. The results showed high correlations between some subperiosteally derived and actual CSG parameters. We present a theoretical model that further explores the influence of endosteal dimensions on CSG properties. We compare two hypothetical femoral midshaft samples with the same total subperiosteal area but with percentages of cortical bone at the opposite ends of published human variation for population sample means. Even in this relatively uncommon scenario, the difference between the samples in the resultant means for predicted femoral polar second moment of area (J) appears to be modest: power analysis indicates that a minimum sample size of 61 is needed to detect the difference 90% of the time via a t‐test. Moreover, endosteal area can be predicted—although with substantial error—from periosteal area. Despite this error, including this relationship in subperiosteally derived estimates of J produces sample mean estimates close to true mean values. Power analyses reveal that when similar samples are used to develop prediction equations, a minimum sample of hundreds or more may be needed to distinguish a predicted mean J from the true mean J. These results further justify the use of regression equations estimating J from periosteal contours when analyzing behaviorally induced changes in bone rigidity in ancient populations, when it is not possible to measure endosteal dimensions. However, in other situations involving comparisons of individual values, growth trends, and senescence, where relative cortical thickness may vary greatly, inclusion of endosteal dimensions is still important. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments

The unsaturated subsurface (vadose zone) receives significant amounts of hazardous chemicals, yet little is known about its microbial communities and their capacity to biodegrade pollutants. Trichloroethylene (TCE) biodegradation occurs readily in surface soils; however, the process usually requires enzyme induction by aromatic compounds, methane, or other cosubstrates. The aerobic biodegradation of toluene and TCE by indigenous microbial populations was measured in samples collected from the vadose zone at unpolluted and gasoline-contaminated sites. Incubation at field moisture levels showed little activity on either TCE or toluene, so samples were tested in soil suspensions. No degradation occurred in samples suspended in water or phosphate buffer solution; however, both toluene and TCE were degraded in samples suspended in mineral salts medium. TCE degradation depended on toluene degradation, and little loss occurred under sterile conditions. Studies with specific nutrients showed that addition of ammonium sulfate was essential for degradation, and addition of other mineral nutrients further enhanced the rate. Additional studies with vadose sediments amended with nutrients showed similar trends to those observed in sediment suspensions. Initial rates of biodegradation in suspensions were faster in uncontaminated samples than in gasolinecontaminated samples, but the same percentages of chemicals were degraded. Biodegradation was slower and less extensive in shallower samples than deeper samples from the uncontaminated site. Two toluene-degrading organisms isolated from a gasoline-contaminated sample were identified as Corynebacterium variabilis SVB74 and Acinetobacter radioresistens SVB65. Inoculation with 10⁶ cells of C. variabilis ml^–1 of soil solution did not enhance the rate of degradation above that of the indigenous population. These results indicate that mineral nutrients limited the rate of TCE and toluene degradation by indigenous populations and that no additional benefit was derived from inoculation with a toluene-degrading bacterial strain. Correspondence to: K.M. Scow     

Proficiency testing of water microbiology laboratories in The Netherlands

In a 3-year period, four series of simulated water samples containing selected test strains were distributed to more than 50 laboratories in The Netherlands for bacteriological testing. Participating laboratories examined the samples by enrichment or membrane filtration methods, or both, for total coliform organisms, thermotolerant coliform organisms, faecal streptococci and standard plate counts (37 degrees and 22 degrees C) according to Dutch standard methods. The results were quantitatively satisfactory: the distribution of positive and negative results with subsamples conformed to stochastic variation; the standard deviation of membrane or plate counts was usually in the range which may be expected from a Poisson distribution, and there was good correspondence between average counts in participating laboratories and those expected from controls in the organizing laboratory. Problems of a qualitative nature were frequently encountered, however. Among them were a false positive response with a strain of Enterobacter cloacae in the thermotolerant coliform test; a false positive result with Clostridium perfringens in enrichment tests for total or thermotolerant coliform organisms and false positive results with Micrococcus varians in the faecal streptococcus test by membrane filtration. It is concluded that quality assessment should be a consistent activity in water microbiology laboratories. For this purpose, stable and well characterized reference materials are needed.     

Proficiency testing of water microbiology laboratories in The Netherlands

In a 3-year period, four series of simulated water samples containing selected test strains were distributed to more than 50 laboratories in The Netherlands for bacteriological testing. Participating laboratories examined the samples by enrichment or membrane filtration methods, or both, for total coliform organisms, thermotol-erant coliform organisms, faecal streptococci and standard plate counts (37˙ and 22˙C) according to Dutch standard methods. The results were quantitatively satisfactory: the distribution of positive and negative results with subsamples conformed to stochastic variation; the standard deviation of membrane or plate counts was usually in the range which may be expected from a Poisson distribution, and there was good correspondence between average counts in participating laboratories and those expected from controls in the organizing laboratory. Problems of a qualitative nature were frequently encountered, however. Among them were a false positive response with a strain of Enterobacter cloacae in the thermotolerant coliform test; a false positive result with Clostridium perfringens in enrichment tests for total or thermotolerant coliform organisms and false positive results with Micrococcus varians in the faecal streptococcus test by membrane filtration. It is concluded that quality assessment should be a consistent activity in water microbiology laboratories. For this purpose, stable and well characterized reference materials are needed.     

Note on a problem in probit analysis

The statistical treatment of dosage-mortality data when the number of survivors is counted but not the total number of organisms in each sample, the latter being estimated from an untreated sample, has been discussed by Wadley (1949), on the assumption of Poisson variation in the number of organisms per sample. The procedure to be followed when a wider hypothesis is made that the number of organisms has a negative binomial distribution is described here; both the arithmetical analysis of the results and the optimum arrangement of the samples are considered.     

Trophic interactions in soils as they affect energy and nutrient dynamics. II. Physiological responses of selected rhizosphere bacteria

Comparative microbial functions in the plant root zone were studied by evaluating rhizosphere-derivedPseudomonas andArthrobacter growth in chemostat culture and responses to root-exudate-related nutrients after varied starvation periods. These organisms were chosen to represent zymogenous and autochthonous microbes, respectively. In chemostat culture, thePseudomonas isolate showed increased energy charge and decreased populations with higher growth rates, whereas theArthrobacter had lower energy charge and cell population values which did not change appreciably with growth rate. The responses of these two types of organisms also differed with starvation. ThePseudomonas lost its ability to respire efficiently in the presence of several known root exudate components, whereas theArthrobacter isolate, in comparison, maintained a lower but more consistent ability to utilize these nutrients with increased starvation. TheArthrobacter also showed increased utilization of several substrates after starvation, suggesting its potential ability to function under restricted nutrient availability conditions. These results suggest thatPseudomonas-type organisms in the rhizosphere may best function in periods of more intense exudate release, whereas organisms of theArthrobacter- type may be more efficient at nutrient utilization during periods of lesser nutrient flux. Based on these data the rhizosphere-derivedPseudomonas isolate was considered to be an appropriate bacterium to use in more complex rhizosphere microcosm experiments where nutrient flux dynamics would be emphasized.     

浓香型白酒窖泥放线菌的群落结构及其多样性

以泸州老窖1、50、100和400年窖泥为研究对象,采用变性梯度凝胶电泳(DGGE)研究浓香型白酒窖泥放线菌的群落结构及其多样性。DGGE图谱显示,除1年样品外,其余窖底泥多样性指数(H)均低于同窖龄窖壁泥,但均匀度指数(EH)较高。不同窖池相同部位窖泥的群落结构变化趋势为:随窖龄的延长,窖壁泥H值逐渐上升,为1.74—2.28;窖底泥下降,为1.73—2.07。EH值均为波动下降,分别在0.986—0.991和0.971—0.994之间。窖底泥相似性系数(SC)逐渐上升,为0.46—0.82;窖壁泥为0.31—0.62。DGGE条带测序结果显示,窖泥放线菌归于Olsenella、Atopobium、Streptomyces和Corynebacterium 4个属。Olsenella和Atopobium属为共有的优势属,且在窖壁泥中的优势度(di)均随窖龄延长而降低,在窖底泥中升高。实验结果表明,浓香型白酒窖泥蕴藏着丰富的放线菌资源,群落结构和多样性存在差异,菌群演替呈现一定规律性。