Enumeration and speciation of enterococci found in marine and intertidal sediments and coastal water in southern California

AIMS: To determine the levels and species distribution of enterococci in intertidal and marine sediments and coastal waters at two beaches frequently in violation of bacterial water standards. METHODS AND RESULTS: Faecal indicator bacteria were extracted from sediment and enumerated using membrane filtration. High levels of enterococci were detected in intertidal sediments in a seasonal river and near a storm drain outlet. Low levels were found in marine sediments at 10 m depths and in surf zone sand. Bacterial isolates presumptively identified as Enterococcus on mEI media were speciated. The predominant species found in both water and sediment included Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Enterococcus casseliflavus and Enterococcus mundtii. A number of isolates (11-26%) from regulatory water samples presumptively identified as enterococci on mEI media were subsequently identified as species other than Enterococcus. At both study sites, the distribution of species present in water was comparable with those in sediments and the distribution of species was similar in water samples passing and exceeding bacterial indicator standards. CONCLUSIONS: High levels of Enterococcus in intertidal sediments indicate retention and possible regrowth in this environment. SIGNIFICANCE AND IMPACT OF THE STUDY: Resuspension of enterococci that are persistent in sediments may cause beach water quality failures and calls into question the specificity of this indicator for determining recent faecal contamination.     

肠球菌在海水中的消亡机制研究进展

肠球菌作为近岸海域粪便污染的指示细菌和条件致病菌,在海水中的生长与消亡对水质监测以及公众健康具有重要影响.本文简述肠球菌在海水中的生理及分布特征,综述肠球菌在关键环境因子和生物因子影响下的消亡规律,并着重介绍肠球菌在细胞和分子水平的消亡机制与消亡动力学模型,同时对肠球菌的研究方向进行展望.通过构建肠球菌浓度预测模型,以...     

Arcobacter in Lake Erie beach waters: an emerging gastrointestinal pathogen linked with human-associated fecal contamination

The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. To better characterize the health risk posed by this emerging waterborne pathogen, we investigated the occurrence of Arcobacter spp. in Lake Erie beach waters. During the summer of 2010, water samples were collected 35 times from the Euclid, Villa Angela, and Headlands (East and West) beaches, located along Ohio's Lake Erie coast. After sample concentration, Arcobacter was quantified by real-time PCR targeting the Arcobacter 23S rRNA gene. Other fecal genetic markers (Bacteroides 16S rRNA gene [HuBac], Escherichia coli uidA gene, Enterococcus 23S rRNA gene, and tetracycline resistance genes) were also assessed. Arcobacter was detected frequently at all beaches, and both the occurrence and densities of Arcobacter spp. were higher at the Euclid and Villa Angela beaches (with higher levels of fecal contamination) than at the East and West Headlands beaches. The Arcobacter density in Lake Erie beach water was significantly correlated with the human-specific fecal marker HuBac according to Spearman's correlation analysis (r = 0.592; P < 0.001). Phylogenetic analysis demonstrated that most of the identified Arcobacter sequences were closely related to Arcobacter cryaerophilus, which is known to cause gastrointestinal diseases in humans. Since human-pathogenic Arcobacter spp. are linked to human-associated fecal sources, it is important to identify and manage the human-associated contamination sources for the prevention of Arcobacter-associated public health risks at Lake Erie beaches.     

岸滩粪便污染指示菌来源与影响因素研究进展

粪便污染指示菌(Fecal Indicator Bacteria,FIB),如大肠杆菌、肠球菌和耐热大肠菌等是用于指示水体中污染程度的微生物,但近年来的研究表明岸滩逐步成为FIB的重要储存库。微生物源示踪技术(MicrobialSourceTracking,MST)等方法被广泛应用于溯源岸滩FIB污染,但FIB进入岸滩环境后的生消机制尚不明确,因此影响FIB在岸滩上生存、消亡的各类因素仍是目前研究的热点。基于此,本文综述了岸滩生态系统中FIB的来源,同时结合国内外研究进展分析了影响FIB生存的非生物因素、生物因素及间隙流动等其他影响因素,并针对岸滩环境中FIB对人体健康的潜在风险提出相关建议,以期降低游客的患病风险,保障公共健康安全。     

Occurrence of Escherichia coli and enterococci in Cladophora (Chlorophyta) in nearshore water and beach sand of Lake Michigan

Each summer, the nuisance green alga Cladophora (mostly Cladophora glomerata) amasses along Lake Michigan beaches, creating nearshore anoxia and unsightly, malodorous mats that can attract problem animals and detract from visitor enjoyment. Traditionally, elevated counts of Escherichia coli are presumed to indicate the presence of sewage, mostly derived from nearby point sources. The relationship between fecal indicator bacteria and Cladophora remains essentially unstudied. This investigation describes the local and regional density of Escherichia coli and enterococci in Cladophora mats along beaches in the four states (Wisconsin, Illinois, Indiana, and Michigan) bordering Lake Michigan. Samples of Cladophora strands collected from 10 beaches (n = 41) were assayed for concentrations of E. coli and enterococci during the summer of 2002. Both E. coli and enterococci were ubiquitous (up to 97% occurrence), with overall log mean densities (+/- standard errors) of 5.3 (+/- 4.8) and 4.8 (+/- 4.5) per g (dry weight). E. coli and enterococci were strongly correlated in southern Lake Michigan beaches (P < 0.001, R(2) = 0.73, n = 17) but not in northern beaches (P = 0.892, n = 16). Both E. coli and enterococci survived for over 6 months in sun-dried Cladophora mats stored at 4 degrees C; the residual bacteria in the dried alga readily grew upon rehydration. These findings suggest that Cladophora amassing along the beaches of Lake Michigan may be an important environmental source of indicator bacteria and call into question the reliability of E. coli and enterococci as indicators of water quality for freshwater recreational beaches.     

An interpretation for the ROC curve and inference using GLM procedures

The accuracy of a medical diagnostic test is often summarized in a receiver operating characteristic (ROC) curve. This paper puts forth an interpretation for each point on the ROC curve as being a conditional probability of a test result from a random diseased subject exceeding that from a random nondiseased subject. This interpretation gives rise to new methods for making inference about ROC curves. It is shown that inference can be achieved with binary regression techniques applied to indicator variables constructed from pairs of test results, one component of the pair being from a diseased subject and the other from a nondiseased subject. Within the generalized linear model (GLM) binary regression framework, ROC curves can be estimated, and we highlight a new semiparametric estimator. Covariate effects can also be evaluated with the GLM models. The methodology is applied to a pancreatic cancer dataset where we use the regression framework to compare two different serum biomarkers. Asymptotic distribution theory is developed to facilitate inference and to provide insight into factors influencing variability of estimated model parameters.     

Spatio‐temporal variation of salt marsh seedling establishment in relation to the abiotic and biotic environment

Contrary to our expectations, soil salinity and moisture explained little of the spatial variation in plant establishment in the upper intertidal marsh of three southern California wetlands, but did explain the timing of germination. Seedlings of 27 species were identified in 1996 and 1997. The seedlings were abundant (maximum densities of 2143/m² in 1996 and 1819/m² in 1997) and predominantly annual species. CCAs quantified the spatial variation in seedling density that could be explained by three groups of predictor variables: (1) perennial plant cover, elevation and soil texture (16% of variation), (2) wetland identity (14% of variation) and (3) surface soil salinity and moisture (2% of variation). Increasing the spatial scale of analysis changed the variables that best predicted patterns of species densities. Timing of germination depended on surface soil salinity and, to a lesser extent, soil moisture. Germination occurred after salinity had dropped below a threshold or, in some cases, after moisture had increased above a critical level. Between 32% and 92% of the seedlings were exotic and most of these occurred at lower soil salinity than native species. However, Parapholis incurva and Mesembryanthemum nodiflorum were found in the same environments as the native species. In 1997, the year of a strong El Niño/Southern Oscillation event with high rainfall and sea levels, the elevation distribution of species narrowed and densities of P. incurva and other exotic species decreased but densities of native and rare species did not change. The ‘regeneration niche’ of wetland plant communities includes the effects of multiple abiotic and biotic factors on both the spatial and temporal variations in plant establishment.     

Annual variation in gobiid larval density in the northern Baltic Sea

The highest densities of gobiid larvae along the Finnish Baltic coast from 1974 to 1996 were found in the Åland Islands and the Archipelago Sea. The annual variation in gobiid densities was three-fold (from 1· 1 to 3·3 larvae m⁻²) with peak densities in the years 1977 and 1992 and the lowest density in 1987. No long-term trends in the density were found. The earliest gobiids were caught in the first half of May and the occurrence of larvae peaked at the end of June to early July.Within breeding seasons there was a positive correlation between water temperature at a depth of 1 m and the density of larvae. The density of larvae, however, did not correlate with mean summer temperature or the mean temperature of the previous summer. Instead larvae production was negatively affected by the severity of the previous winter as indicated by the maximum ice cover in the Baltic. The density of larvae was independent of larval density of the previous year suggesting that gobiid production primarily depends on the spawning stock size and may hence be regulated by density-independent factors.     

The influence of rainfall on the incidence of microbial faecal indicators and the dominant sources of faecal pollution in a Florida river

AIMS: An assessment of microbial densities in an urbanized Florida watershed was performed during a period of changing rainfall patterns to investigate the role of climate coupled with urbanization in declining water quality. METHODS AND RESULTS: Concentrations of traditional and alternative faecal indicators were assessed by standard methods over 24 months. Sources of faecal contamination were determined by antibiotic resistance analysis (ARA) of faecal coliform (FC) bacteria. Composite indices of indicator organisms based on a suite of microbial measurements were used to quantify pollution impacts in the river. ARA results found that FC from wild animal sources dominated during the drought, and the relative frequency of FC from human sources increased after cumulative rainfall increased to near-normal levels. CONCLUSIONS: Changes observed in faecal indicator densities and in FC sources during changing rainfall patterns strongly suggest a role of precipitation on the sources and extent of microbial pollution in urbanized coastal watersheds. SIGNIFICANCE AND IMPACT OF THE STUDY: Bacterial source tracking coupled with a composite index of microbial contamination resulted in a more complete picture of microbial pollution within the river, as opposed to the general practice of reliance on one indicator organism. Improved land use decisions in urban areas are necessary to insure maintenance of coastal environmental health under changing climate patterns and population density.     

A Protocol for Conducting Rainfall Simulation to Study Soil Runoff

Rainfall is a driving force for the transport of environmental contaminants from agricultural soils to surficial water bodies via surface runoff. The objective of this study was to characterize the effects of antecedent soil moisture content on the fate and transport of surface applied commercial urea, a common form of nitrogen (N) fertilizer, following a rainfall event that occurs within 24 hr after fertilizer application. Although urea is assumed to be readily hydrolyzed to ammonium and therefore not often available for transport, recent studies suggest that urea can be transported from agricultural soils to coastal waters where it is implicated in harmful algal blooms. A rainfall simulator was used to apply a consistent rate of uniform rainfall across packed soil boxes that had been prewetted to different soil moisture contents. By controlling rainfall and soil physical characteristics, the effects of antecedent soil moisture on urea loss were isolated. Wetter soils exhibited shorter time from rainfall initiation to runoff initiation, greater total volume of runoff, higher urea concentrations in runoff, and greater mass loadings of urea in runoff. These results also demonstrate the importance of controlling for antecedent soil moisture content in studies designed to isolate other variables, such as soil physical or chemical characteristics, slope, soil cover, management, or rainfall characteristics. Because rainfall simulators are designed to deliver raindrops of similar size and velocity as natural rainfall, studies conducted under a standardized protocol can yield valuable data that, in turn, can be used to develop models for predicting the fate and transport of pollutants in runoff.     

Prediction of N-myristoylation modification of proteins by SVM

Attachment of a myristoyl group to NH(2)-terminus of a nascent protein among protein post-translational modification (PTM) is called myristoylation. The myristate moiety of proteins plays an important role for their biological functions, such as regulation of membrane binding (HIV-1 Gag) and enzyme activity (AMPK). Several predictors based on protein sequences alone are hitherto proposed. However, they produce a great number of false positive and false negative predictions; or they cannot be used for general purpose (i.e., taxon-specific); or threshold values of the decision rule of predictors need to be selected with cautiousness. Here, we present novel and taxon-free predictors based on protein primary structure. To identify myristoylated proteins accurately, we employ a widely used machinelearning algorithm, support vector machine (SVM). A series of SVM predictors are developed in the present study where various scales representing physicochemical and biological properties of amino acids (from the AAindex database) are used for numerical transformation of protein sequences. Of the predictors, the top ten achieve accuracies of >98% (the average value is 98.34%), and also the area under the ROC curve (AUC) values of >0.98. Compared with those of previous studies, the prediction accuracies are improved by about 3 to 4%.     

Climatic control of trophic interaction strength: the effect of lizards on spiders

We investigated how temporal variation in rainfall influences the impact of lizards on spiders inhabiting small islands in Abaco, Bahamas. Annual censuses of web spiders were conducted on nine lizard islands and on eight no-lizard islands 1994–2003. Repeated-measures ANOVA showed that annual variation in spider density (time) and in the lizard effect on spider density (lizard × time) were both significant. Correlation coefficients between the lizard effect (ln ratio of no-lizard to lizard spider densities) and number of rainfall days were generally negative, and strengthened with length of the time period during which rainfall was measured prior to annual spider censuses. Spider density was also negatively correlated with rainfall days and strengthened with length of the prior time period. Longer time intervals included the hurricane season, suggesting that the strong negative correlations were linked to high rainfall years during which tropical storms impacted the region and reduced spider and lizard densities. Split-plot ANOVA showed that rainfall during the hurricane season had a significant effect on the lizard effect and on spider density. Results in this study are opposite to those found in our previous 10-year study (1981–1990) conducted in the Exuma Cays, a moderately xeric region of the Bahamas, where the relation between rainfall and the lizard effect on spider density was positive. Combined data from the Exuma and Abaco studies produce a unimodal relation between trophic interaction strength and rainfall; we suggest that the negative effect of storms associated with rainfall was paramount in the present study, whereas the positive bottom-up effect of rainfall prevailed in our previous study. We conclude that climatic variability has a major impact on the trophic interaction and suggest that a substantial change in precipitation in either direction may weaken the interaction significantly.     

Climate Change and Microbiological Water Quality at California Beaches

Daily microbiological water quality and precipitation data spanning 6?years were collected from monitoring stations at southern California beaches. Daily precipitation projected for the twenty-first century was derived from downscaled CNRM CM3 global climate model. A time series model of Enterococcus concentrations that was driven by precipitation, matched the general trend of empirical water quality data; there was a positive association between precipitation and microbiological water contamination (P?相似文献   

Modelling the population dynamics of Penilia avirostris (Branchiopoda,Ctenopoda) in a tropical bay

An ecological model for the simulation of the population dynamics of the cladoceran Penilia avirostris in Guanabara Bay, a tropical Brazilian bay, was developed. The simulated curve gave a good fit, in time and intensity, to the exponential increase and decrease in densities of P. avirostris during the March-July 2000 period. The densities of embryos, young individuals, males, and parthenogenic and gamogenic females were the state variables. Parameters of the model were varied within the range of field and literature data. Predation was considered as the main factor affecting mortality, the death rate being a function of the density of chaetognaths, the dominant invertebrate predator in Guanabara Bay. Input of resting eggs into the model as a “seed” source of embryos provided a good fit to the exponential increase of Penilia density. The observed sharp decreases and collapses of the population could not be explained by mortality or a shift from parthenogenic to gamogenic reproduction only. To provide an explanation, it was necessary to introduce an output forcing function, which probably represents physical factors such as water mass exchanges by tide- and wind-driven currents.     

Evaluation of Proxy Tests for SFSN: Evidence for Mixed Small and Large Fiber Dysfunction

Background

Though intra-epidermal nerve fiber density (IENFD) is considered the gold standard for diagnosis of small fiber sensory neuropathy (SFSN), we aimed to determine if novel threshold values derived from standard tests of small or large fiber function could serve as diagnostic alternatives.

Methods

Seventy-four consecutive patients with painful polyneuropathy and normal nerve conduction studies (NCS) were defined as SFSN cases or controls by distal IENFD <5.4 and ≥5.4 fibers/mm, respectively. Diagnostic performance of small fiber [cooling (CDT) and heat perception (HP) thresholds, axon reflex-mediated neurogenic vasodilatation] and large fiber function tests [vibration perception thresholds (VPT) and sural nerve conduction parameters] were determined by receiver operating-characteristic (ROC) curve analyses.

Results

The 26(35%) SFSN cases had mean IENFD 3.3±1.7 fibers/mm and the 48(65%) controls 9.9±2.9 fibers/mm. Male gender (p = 0.02) and older age (p = 0.02) were associated with SFSN cases compared to controls. VPT were higher and CDT lower in SFSN cases, but the largest magnitude of differences was observed for sural nerve amplitude. It had the greatest area under the ROC curve (0.75) compared to all other tests (p<0.001 for all comparisons) and the optimal threshold value of ≤12 µV defined SFSN cases with 80% sensitivity and 72% specificity.

Conclusion

In patients presenting with polyneuropathy manifestations and normal NCS, though small fiber function tests were intuitively considered the best alternative measures to predict reduced IENFD, their diagnostic performance was poor. Instead, novel threshold values within the normal range for large fiber tests should be considered as an alternative strategy to select subjects for skin biopsy in diagnostic protocols for SFSN.     

The response of sap flow to pulses of rain in a temperate Australian woodland

In water-limited systems, pulses of rainfall can trigger a cascade of plant physiological responses. However, the timing and size of the physiological response can vary depending on plant and environmental characteristics, such as rooting depth, plant size, rainfall amount, or antecedent soil moisture. We investigated the influence of pulses of rainfall on the response of sap flow of two dominant evergreen tree species, Eucalyptus crebra (a broadleaf) and Callitris glaucophylla (a needle leaved tree), in a remnant open woodland in eastern Australia. Sap flow data were collected using heat-pulse sensors installed in six trees of each species over a 2 year period which encompassed the tail-end of a widespread drought. Our objectives were to estimate the magnitude that a rainfall pulse had to exceed to increase tree water use (i.e., define the threshold response), and to determine how tree and environmental factors influenced the increase in tree water use following a rainfall pulse. We used data filtering techniques to isolate rainfall pulses, and analysed the resulting data with multivariate statistical analysis. We found that rainfall pulses less than 20 mm did not significantly increase tree water use (P > 0.05). Using partial regression analysis to hold all other variables constant, we determined that the size of the rain event (P < 0.05, R ² = 0.59), antecedent soil moisture (P < 0.05, R ² = 0.29), and tree size (DBH, cm, P < 0.05, R ² = 0.15), all significantly affected the response to rainfall. Our results suggest that the conceptual Threshold-Delay model describing physiological responses to rainfall pulses could be modified to include these factors. We further conclude that modelling of stand water use over an annual cycle could be improved by incorporating the T-D behaviour of tree transpiration. Responsible Editor: Stephen S.O. Burgess     

Occurrence of Escherichia coli and Enterococci in Cladophora (Chlorophyta) in Nearshore Water and Beach Sand of Lake Michigan

Each summer, the nuisance green alga Cladophora (mostly Cladophora glomerata) amasses along Lake Michigan beaches, creating nearshore anoxia and unsightly, malodorous mats that can attract problem animals and detract from visitor enjoyment. Traditionally, elevated counts of Escherichia coli are presumed to indicate the presence of sewage, mostly derived from nearby point sources. The relationship between fecal indicator bacteria and Cladophora remains essentially unstudied. This investigation describes the local and regional density of Escherichia coli and enterococci in Cladophora mats along beaches in the four states (Wisconsin, Illinois, Indiana, and Michigan) bordering Lake Michigan. Samples of Cladophora strands collected from 10 beaches (n = 41) were assayed for concentrations of E. coli and enterococci during the summer of 2002. Both E. coli and enterococci were ubiquitous (up to 97% occurrence), with overall log mean densities (± standard errors) of 5.3 (± 4.8) and 4.8 (± 4.5) per g (dry weight). E. coli and enterococci were strongly correlated in southern Lake Michigan beaches (P < 0.001, R² = 0.73, n = 17) but not in northern beaches (P = 0.892, n = 16). Both E. coli and enterococci survived for over 6 months in sun-dried Cladophora mats stored at 4°C; the residual bacteria in the dried alga readily grew upon rehydration. These findings suggest that Cladophora amassing along the beaches of Lake Michigan may be an important environmental source of indicator bacteria and call into question the reliability of E. coli and enterococci as indicators of water quality for freshwater recreational beaches.     

Variability of palmprint ridge density in a North Indian population and its use in inference of sex in forensic examinations

Fingerprints and palmprints are unique to an individual, and these biometric characters are used in the identification of individuals. In the recent past, ridge density (ridge count in a defined area) has been explored for its applicability in inference of sex from the fingerprints and palmprints recovered at the crime scene. The present research aims to study the variability of palmprint ridge density in a North Indian population, and its significance in inference of sex in forensic examinations. The sample consisted of 157 healthy young adults (110 females and 47 males) from Shimla city in North India. Bilateral palmprints were taken from all the participants following standard methods. The palmprints were manually analyzed in four defined areas of each palmprint that included the central prominent part of the thenar eminence (P1), the mount distal to the axial triradius on the hypothenar region (P2), the mount proximal to the triradius of the second digit (P3) and the mount proximal to the triradius of the fifth digit (P4). The ridge density was calculated diagonally using a square measuring 5 mm × 5 mm. The sex differences in palmprint ridge densities were statistically analyzed for each of the designated areas using statistical considerations. Receiver operating characteristic (ROC) curve analysis was done to test the overall ability of the palmprint ridge densities obtained from each area in inference of sex. The mean palmprint ridge density was found to be significantly greater in females than in males in all the four defined areas of the palmprint. Ridge densities in P3 and P4 areas of the palmprint showed statistically significant bilateral differences in both males and females. The study observed variations in the ridge density between the four designated areas of the palmprint. Based on the area under the ROC curve (AUC), maximum sexing potential for the palmprint ridge density was observed in the P4 area, followed by P3 area on both right and left sides. ROC analysis of the total palmprint ridge density indicated that the sexing accuracy from the right and left palmprint ridge densities was 70.2% and 71.8% respectively. The study shows variability of palmprint ridge density among sexes and in different regions of the palm on both sides. In view of the considerable overlapping in male and female values and lower levels of accuracy obtained in ROC analysis, the present research concludes that the palmprint ridge density cannot be used as an effective tool in inference of sex. However, in absence of other more reliable means/evidence, it still can be considered as a supportive trait in sex inference.     

应用热脉冲系统对桉树人工林树液流通量的研究

应用热脉冲式树液流测定系统和自动气象站 1 999年 9月～ 2 0 0 0年 9月的观测资料 ,探讨了广东省湛江市雷州半岛两个桉树人工林树液流通量 (Sap flux density,SFD)的时空动态及其与环境因子的相关关系。河头和纪家两地桉树林的树液流变化具有明显的昼夜节律性 ,大约从清晨 7:0 0开始萌动 ,1 2 :0 0以后达到峰值 ,夏季连续 4 d中 (2 0 0 0年 6月 1 5日～ 6月 1 8日 )河头 SFD最大值 44.2 1± 4.5 ml/ (cm2 · h) ,纪家 2 9.2± 7.2 ml/ (cm2· h)。此后 ,SFD逐渐减小 ,一直到日落前后降至最低值。树液流在不同的季节具有不同的昼夜节律性变化规律。两地 SF D值的季节波动节律相似 ,湿季时相对较大。但是河头日平均 SFD值 (2 4 36± 1 1 92 .5 ml/ (cm2 · d) )要比纪家 (1 70 3± 82 4 .5 ml/ (cm2 · d) )高 ,这主要是由于两地土壤质地的差异所导致的。在所选时段内 ,SFD的最大值出现在河头的冬季和纪家的夏季 ,这是由于这两天的大气饱和水气压差 ,太阳辐射和土壤有效持水量都比较高的缘故。在空间上 ,从形成层到心材 ,SF D最初有所增加 ,随后持续减小。整个观测期间两地 SFD的极大值均出现在 6月中旬 ,河头为 51 .53ml/ (cm2· h) ,而纪家为 39.85ml/ (cm2 · h) ,显然 ,由于环境条件的限制 ,主要是土