The Structure of Bacterial Complexes in the Protva River Floodplain

The synecological analysis of bacterial communities from the Protva River floodplain biogeocenosis showed that all of their horizons contain spirilla, which are typical hydrobionts, and pigmented coryneform bacteria associated with the herbaceous plants of the floodplain meadows. The alluvial meadow soils of the inundated regions of the floodplain differ from the unflooded regions of the floodplain in that they have a more diverse bacterial population that is continuously distributed over the soil profile.     

Effect of Cell Moisture on the Thermal Inactivation Rate of Bacterial Spores

Thermal inactivation rates were determined for two strains of Bacillus subtilis var. niger spores after equilibration to various relative humidity (RH) levels. In these tests, small thin stainless-steel squares were each inoculated with a drop of spore suspension and equilibrated to 11, 33, or 85% RH. Following equilibration, the squares were placed on a hot plate preheated to 108, 125, 136, 164, or 192 C for various exposure times and then assayed for surviving organisms. The results revealed that spores of the A strain of B. subtilis were least resistant if preequilibrated to 11% RH and most resistant if preequilibrated to 85% RH. The same trend was obtained at all temperatures except 192 C, at which, no difference was noted, probably because the rapid kill time approaches the heat-up time of the stainless-steel square. The B strain of B. subtilis spores showed an opposite RH effect; that is, the cells preequilibrated to 11% RH were the most resistant. Because the two strains of spores were grown on different media, further studies were conducted at 136 C after subculturing the cells on different media. When the B strain was subcultured on the A strain medium, the pattern was reversed; the cells preequilibrated to low RH were then least resistant. Although it was not possible to reverse these cells to the original pattern by subculturing on the original B strain medium again, the pattern was altered to the point that there was no significant difference in heat resistance of these cells regardless of the preequilibration RH. The same result was obtained when the A strain was grown on the B strain medium; that is, the thermal resistance could not be reversed, but it was altered from the point where the low RH equilibrated cells were least resistant initially to the point where there was no significant difference in any of the cells regardless of what RH was used for preequilibration. The thermal resistance of spores seemed to be dependent on (i) the medium on which the spores are grown, (ii) the RH on which they are exposed before heating, and (iii) some genetic characteristic of the cell.     

Effect of Temperature and Gas Velocity on the Dry-Heat Destruction Rate of Bacterial Spores

Spores of Bacillus subtilis were dried in vacuo for use in dry-heat thermal destruction tests. Survivor curve tests were conducted in a specifically designed dry-heat oven. This oven provided accurate temperature control and permitted air or nitrogen to be passed over the spores during the lethal treatment. Experiments were carried out at various flow rates of the two gases (air and nitrogen) and various temperatures, and the data were expressed as survivor curves from which the decimal reduction time (D value) was obtained. Linear regression analysis methods were used to compute the slope of the survivor curves. The results indicated that as the flow rate of gas is increased, the effect of temperature on the destruction rate of the spores is lessened, the z value becoming very large. It is believed that the higher flow rates of dry gas cause greater dehydration of the spores and that spore moisture loss is one of the major factors in determining the dry-heat thermal destruction rate of bacterial spores.     

Effect of Nutrient Inflow on the Bacterial Flora in the River Sakuragawa,Japan

The relationship between nutrient level and microorganisms in the waters of the River Sakuragawa, Japan, was studied from 1976 to 1977. Statistical analyses show that the organic nutrients for the bacteria were mainly autochthonous, and that the water system of the River Sakuragawa was never polluted enough to fall into a condition that could be classified as dystrophic.     

Effect of Immunohistochemistry on Molecular Analysis of Tissue Samples: Implications for Microdissection Technologies

Laser-based tissue microdissection is an important tool for the molecular evaluation of histological sections. The technology has continued to advance since its initial commercialization in the 1990s, with improvements in many aspects of the process. More recent developments are tailored toward an automated, operator-independent mode that relies on antibodies as targeting probes, such as immuno–laser capture microdissection or expression microdissection (xMD). Central to the utility of expression-based dissection techniques is the effect of the staining process on the biomolecules in histological sections. To investigate this issue, the authors analyzed DNA, RNA, and protein in immunostained, microdissected samples. DNA was the most robust molecule, exhibiting no significant change in quality after immunostaining but a variable 50% to 75% decrease in the total yield. In contrast, RNA in frozen and ethanol-fixed, paraffin-embedded samples was susceptible to hydrolysis and digestion by endogenous RNases during the initial steps of staining. Proteins from immunostained tissues were successfully analyzed by one-dimensional electrophoresis and mass spectrometry but were less amenable to solution phase assays. Overall, the results suggest investigators can use immunoguided microdissection methods for important analytic techniques; however, continued improvements in staining protocols and molecular extraction methods are key to further advancing the capability of these methods.     

Effect of Physical Factors on Bacterial Distribution in the Jordan River Mouth Area in Israel

The Jordan River mouth is an area of complicated hydrography and variable and vulnerable ecology. It has changeable water and sediment regimes, for example, large spatial gradients of biological, chemical, physical, and hydrological characteristics. The Jordan River enters Lake Kinneret in the north and carries with it sewage from the Upper Galilee; thus the river is the major source of enteric bacteria in the lake. This research is based on theoretical analysis as well as on biological-hydrodynamical measurements along a discharging free, turbulent jet flow. Three components of velocities were recorded downstream from the exit cross-section for a distance of 700 m, and the mean streamwise velocity turbulence intensity and the turbulence scale were calculated. The measuring devices were an original three-dimensional velocity-fluctuation meter. Results of these measurements show that the Jordan River flows through the whole transect until it reaches the crest of a bar. After this, there is a separated exponential flow from the bottom and upper layers for ~100m after the bar. Fecal coliforms, Escherichia coli, and Klebsiella spp. were enumerated as colony-forming units from samples taken along the Jordan River path as it entered Lake Kinneret. Bacterial numbers were similar in surface and bottom waters in front of the bar. Behind the bar, however, there was a sharp decrease of bacterial numbers in the surface water, probably because of photooxidative stress. Despite the more protective environment of the bottom waters, the numbers here also decreased, indicating that the bar is a physical barrier for bacterial distribution. Furthermore, we found a significant effect of the flow velocity of Jordan River water on the bacterial distribution in Lake Kinneret. When the velocity is high, bacteria are distributed over a longer distance, regardless of their numbers in Jordan River mouth.     

Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins

Actin is an abundant protein that constitutes a main component of the eukaryotic cytoskeleton. Its polymerization and depolymerization are regulated by a variety of actin-binding proteins. Their functions range from nucleation of actin polymerization to sequestering G-actin in 1∶1 complexes. The kinetics of forming these complexes, with rate constants varying at least three orders of magnitude, is critical to the distinct regulatory functions. Previously we have developed a transient-complex theory for computing protein association mechanisms and association rate constants. The transient complex refers to an intermediate in which the two associating proteins have near-native separation and relative orientation but have yet to form short-range specific interactions of the native complex. The association rate constant is predicted as k_a = k_a0, where k_a0 is the basal rate constant for reaching the transient complex by free diffusion, and the Boltzmann factor captures the bias of long-range electrostatic interactions. Here we applied the transient-complex theory to study the association kinetics of seven actin-binding proteins with G-actin. These proteins exhibit three classes of association mechanisms, due to their different molecular shapes and flexibility. The 1000-fold k_a variations among them can mostly be attributed to disparate electrostatic contributions. The basal rate constants also showed variations, resulting from the different shapes and sizes of the interfaces formed by the seven actin-binding proteins with G-actin. This study demonstrates the various ways that actin-binding proteins use physical properties to tune their association mechanisms and rate constants to suit distinct regulatory functions.     

Rate of Bacterial Mortality in Aquatic Environments

A method is proposed which provides a minimum estimate of the rate of bacterial mortality in growing natural populations of planktonic bacteria. This estimate is given by the rate of decrease of radioactivity from the DNA of a [³H]thymidine-labeled natural assemblage of bacteria after all added thymidine has been exhausted from the medium. Results obtained from river water, estuarine water, and seawater show overall bacterial mortality rates in the range 0.010 to 0.030 h⁻¹, in good agreement with the range of growth rates measured in the same environments. Use of selective filtration through Nuclepore filters (pore size, 2 μm) allowed us to determine the contribution of microzooplankton grazing to overall bacterial mortality. Grazing rates estimated by this method ranged from 0 to 0.02 h⁻¹.     

甘肃不同矿区样品中的细菌多样性

甘肃矿产资源丰富,矿区酸性矿坑水(acid mine drainage,AMD)及周边土壤中嗜酸微生物种类丰富,具有相当大的研究价值.本研究通过Illumina高通量测序方法,对甘肃省4个矿区AMD及周边土壤中的细菌群落组成、相似性及功能组成进行分析.结果 表明,煤矿样品GNM细菌物种组成最为丰富,金矿样品LNJ1与紫金矿样品LNZJK细菌组成最相似,与属于铜矿的BYT物种较相近,与LNJ1同地区的LNJ2样品细菌组成相比较远.所有样品细菌主要分为放线菌门(Actinobacteria)、拟杆菌门(Bacteriodetes)、厚壁菌门(Firmicutes)和变形菌门(Proteobacteria)四大门,其中变形菌门(Proteobacteria)丰度最高.放线菌门(Actinobacteria)中不动杆菌属(Acinetobacter)、类诺卡氏属(Nocardioides)和芽球菌属(Blastococcus)表现出较高丰度;厚壁菌门(Firmicutes)中微小杆菌属(Exiguobacterium)和芽孢杆菌属(Bacillus)表现出较高丰度,且微小杆菌属(Exiguobacterium)丰度极高.通过功能预测发现,与煤矿样品GNM相比,LNJ1、LNJ2、BYT和LNZJK4个金属矿区样品中的微生物具有较强的氨基酸与碳源的转运与代谢、转录等功能以及较低的能量生产与转运、无机离子转运与代谢能力.通过探究AMD中的细菌多样性及其与重金属之间的相互关系,了解AMD采样区微生物群落结构,以期挖掘出更为丰富的具有重金属抗性的菌株资源,以应用于生物浸矿和环境修复等领域.     

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou''s evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.     

一株苯酚降解菌的筛选、鉴定及其降解特性

本研究采用逐量分批驯化的方法,从造纸废水中分离得到一株能够以苯酚为唯一碳源生长的苯酚降解菌株F5-1.经形态观察、生理生化特性鉴定及16S rDNA序列分析,将该菌株鉴定为克雷伯菌(Klebsie-lla sp.).该菌株能够在7 h时完全降解初始浓度为100 mg/L的苯酚,降解苯酚主要发生在生长对数期;在pH 5.0～9.0,NaCl浓度0～80 g/L,温度20～40℃范围内,菌株F5-1均可有效降解初始浓度为100～1 200 mg/L的苯酚;能够耐受的最大苯酚浓度为1 500 mg/L.本研究结果表明,F5-1菌株对处理环境条件复杂的含酚废水具有潜在的应用前景.     

Rate Constants and the Variation of Random Concentration Curves in a 2-Compartment System

In biology and medicine many substances and drugs enter the system not at regular time intervals but rather according to a random process. In the present article a situation is investigated where input enters a 2-compartment system according to a Poisson process. The arising two random concentration curves y(t), one for the central and one for the peripheral compartment are discussed (shot noise). The equations for E[y(t)] and Var [y(t)] are derived. The dependence of E[y(t)] and Var [y(t)] and of the index of dispersion ID[y(t)] on the rate parameters is analysed and discussed in both compartments. The arising calculations were considerably simplified by means of “Mathematica”, a computer program which allows to perform symbolic calculations.     

Effect of Hard Detergents on Algae in a High-Rate-Oxidation Pond

Regular concentrations of hard detergents in domestic wastewater do not affect algal growth in a high-rate-oxidation pond. The addition of nonionic hard detergent at concentrations above 60 mg/liter decreased the algal concentration in the batch culture, and complete lysis of algal cells was observed within a few days at a detergent concentration of 100 mg/liter.     

Quantification of Bacterial Uropathogens in Preclinical Samples Using Real-Time PCR Assays

Uropathogenic Escherichia coli (UPEC) and Staphylococcus saprophyticus (S. saprophyticus) are responsible for the majority of community-acquired urinary tract infections (UTI). Agar plating, a gold standard for detection of bacterial uropathogens, is labor intensive, limited for distinguishing between environmental contaminants and pathogens, and fails to effectively detect mixed infections. A reliable method for specific and sensitive quantitative assessment of infections would allow cost-effective evaluation of large numbers of experimental samples. A methodology such as quantitative PCR (qPCR) addresses the limitations of agar plating. We developed and validated highly specific and sensitive qPCR assays to assist researchers in the evaluation of potential vaccines and interventions in preclinical models of UPEC and S. saprophyticus UTI. The developed UPEC PCR targeted a highly conserved region of the UPEC hemolysin D (hlyD) gene that reproducibly detected type strains CFT073 and J96 over a 9 log range with high precision. To quantify S. saprophyticus genomes, a separate qPCR assay targeting the Trk transport gene was developed with an 8 log range. Neither assay detected bacterial species predicted to be sample contaminants. Using our optimized workflow that includes automated steps, up to 200 urine or tissue samples can be processed in as few as 3 h. Additionally, sequence comparisons of our primers and probe to other UTI bacterial strains indicated the broad applicability of these assays. These optimized qPCR assays provide a cost-effective and time-saving method for quantification of bacterial burdens in tissues and body fluids to assess the effectiveness of candidate vaccines or interventions.     

Effect of Temperature on the Taxonomic Structure of Soil Bacterial Communities during Litter Decomposition

Microbiology - Effect of temperature on succession changes of the saprotrophic bacterial community of gray forest soil in the course of decomposition of aspen leaves and branches was studied in...     

Dimethyl Sulfide Production from Dimethylsulfoniopropionate in Coastal Seawater Samples and Bacterial Cultures

Dimethyl sulfide (DMS) was produced immediately after the addition of 0.1 to 2 μM β-dimethylsulfonio-propionate (DMSP) to coastal seawater samples. Azide had little effect on the initial rate of DMS production from 0.5 μM added DMSP, but decreased the rate of production after 6 h. Filtration of water samples through membrane filters (pore size, 0.2 μm) greatly reduced DMS production for approximately 10 h, after which time DMS production resumed at a high rate. Autoclaving completely eliminated the production of DMS. The antibiotics chloramphenicol, tetracycline, kanamycin, and vancomycin all had little effect on the accumulation of DMS over the first few hours of incubation, but produced significant inhibition thereafter. The effects of individual antibiotics were additive. Chloroform over a range of concentrations (0.25 to 1.25 mM) had no effects on DMS production. Similarly, organic amendments, including acrylate, glucose, protein, and starch, did not affect DMS accumulation from DMSP. Acrylate, a product of the enzymatic cleavage of DMSP, was metabolized in seawater samples, and two strains of bacteria were isolated with this compound as the growth substrate. These bacteria produced DMS from DMSP. The sensitivity to inhibitors with respect to growth and DMSP-lyase activity varied from strain to strain. These results illustrate the significant potential for microbial conversion of dissolved DMSP to DMS in coastal seawater.     

Molecular Detection of Hepatitis E Virus in Sewage Samples

Human hepatitis E virus (HEV) is considered an emerging pathogen in industrialized countries. In Italy, the true burden of HEV infection is unknown. Molecular HEV screening of raw sewage samples from 11 wastewater treatment plants yielded 19 positives (16%; 18 genotype I, 1 genotype III) evenly distributed throughout Italy. Evidence that HEV could be establishing itself in our region is accumulating and may justify more active surveillance to monitor its spread.Hepatitis E is a self-limited, enterically transmitted acute viral hepatitis that occurs most frequently in epidemic outbreaks and often spreads by way of fecally contaminated drinking water (5, 20). Hepatitis E virus (HEV) infections are caused by a positive-sense, nonenveloped RNA virus of the Hepevirus genus. The four major genotypes (GI to GIV), all belonging to a single serotype, are known to infect humans. While GI and GII are restricted to humans, GIII and GIV are zoonotic and may infect animals (swine, chickens, deer, mongooses, and rabbits), as well as humans, in both industrialized and nonindustrialized countries (18, 19). GI consists of epidemic strains circulating in Africa and Asia. GII is found in Mexico and Africa. GIII is widely distributed, mainly—but not exclusively—in the United States, Europe, and Japan. GIV is present in Asia (16). An HEV strain belonging to a fifth genotype has been identified in birds (12).HEV is transmitted by the fecal-oral route. Large waterborne outbreaks with high attack rates among young adults have been described in regions characterized by poor sanitary conditions (22). Hepatitis E is responsible for over 50% of cases of acute viral hepatitis in countries where the disease is endemic (Central and Southeast Asia, North and West Africa, and Mexico), where seroprevalence rates range from 15% to 60% (8). North America and Europe have traditionally been considered areas where HEV is not endemic, with acute infection diagnosed rarely and largely confined to travelers returning from areas where the disease is endemic. The high rates of HEV IgG positivity reported in different studies, however, suggest that unrecognized or subclinical infection is common (8). In Europe, increasing numbers of HEV infections not associated with travel have been recently reported (15).HEV infection may vary in severity from asymptomatic to fulminant. Case fatality rates range between 0.5% and 4% overall but may reach 25% among pregnant women (1). In industrialized countries, the case fatality rate seems to be higher than in areas where the disease is endemic, since infection occurs more frequently in elderly people with chronic liver disease, a subgroup of patients with a case fatality rate approaching 70% (26).HEV, which is shed in the feces of infected individuals, has been detected in sewage samples, suggesting that HEV contamination of aquatic environments may also be present (2, 6, 7, 23). In Italy, the true burden of HEV infection is still unknown and there are no available studies on the presence of this virus in sewage. The prevalence of anti-HEV antibodies among healthy individuals has been found to be approximately 1% in the northern regions and up to 5% in the southern regions, including Sicily and Sardinia. Higher prevalence rates have been found among drug users (especially HIV-infected individuals), hemodialysis patients, and patients with chronic hepatitis C, suggesting that HEV may be transmitted not only by the fecal-oral route (the main mode of transmission) but also parenterally (27).The objective of the present study was to investigate the occurrence of HEV through the molecular screening of raw sewage samples collected from urban wastewater treatment plants (WTPs) in different regions of Italy.