古大湖湿地盐碱土壤微生物群落结构及多样性分析

以黑龙江省古大湖湿地原生、林地、耕地及湖岸盐碱土壤微生物为研究对象,基于高通量测序方法,分析4种生境类型条件下土壤细菌和真菌群落结构及多样性。结合土壤理化指标,进一步分析影响微生物群落多样性的环境因子。结果表明:细菌群落中变形菌门的相对丰度值最高,真菌群落中为子囊菌门。同一生境细菌群落多样性具有相似性,而真菌具有一定的差异;不同生境间两者均具有差异。耕地土壤和林地土壤的细菌群落多样性接近,但与湖岸土壤真菌的更相近。前两者中细菌群落多样性较高,其次为原生土壤,而湖岸土壤中的最低。耕地土壤与湖岸土壤真菌群落多样性较高,原生土壤较低,而林地土壤中最低。与真菌相比,细菌的群落多样性受土壤环境因子影响更大,其中pH值、含水量对土壤细菌和真菌群落多样性均具有显著影响。     

Evaluation of the Phene Plate generalized microplate for metabolic fingerprinting and for measuring fermentative capacity of mixed bacterial populations

The Phene Plate (PhP) generalized microplate for metabolic fingerprinting and for measuring the fermentative capacity of intestinal bacteria was evaluated. Twelve bacterial species, representing those commonly found in the intestine of humans and animals were employed. Mixtures of bacteria were inoculated in duplicate onto the PhP microplates. Anaerobic conditions were achieved by either incubating the plates under nitrogen atmosphere or by covering the microplates with mineral oil before incubation. Different metabolic fingerprints based on the pattern of substrate utilization were obtained for each bacterial mixture. Metabolic responses of bacterial samples were similar under both anaerobic conditions although the rate of carbohydrate utilization was higher in plates covered with mineral oil. A fermentative capacity value based on the number and the degree of fermented carbohydrates was established for each mixture which differed as the composition of the mixture changed but in general it was higher in samples with more bacterial species. The PhP generalized microplate may thus be used for studying the functional status and metabolic potential of intestinal floras.     

Comparison of bacterial indicators and sampling programs for drinking water systems.

A total of 48 French villages were selected for a survey of water quality from February 1983 to June 1984 as part of an epidemiological study conducted in the rural area of the Rhône-Alpes region. Water samples were collected and analyzed on a weekly basis in each village. Bacteriological analysis of each water sample included enumeration of standard plate count bacteria, total and thermotolerant coliforms, and fecal streptococci. The water quality regulations are examined as to the analysis frequency, the volume of samples, and the relationship between the various bacterial indicators. Analyzing 300-ml, instead of 100-ml, samples tends to generate better information on single water samples. However, if many samples are analyzed over time from the same community, the value of using large volumes of water samples is diminished. The comparisons between bacterial indicators showed that the information obtained from the various indicators was very similar. However, fecal streptococci had a better predictive value of a negative test than coliforms with respect to the French standards.     

Comparison of bacterial indicators and sampling programs for drinking water systems

A total of 48 French villages were selected for a survey of water quality from February 1983 to June 1984 as part of an epidemiological study conducted in the rural area of the Rh?ne-Alpes region. Water samples were collected and analyzed on a weekly basis in each village. Bacteriological analysis of each water sample included enumeration of standard plate count bacteria, total and thermotolerant coliforms, and fecal streptococci. The water quality regulations are examined as to the analysis frequency, the volume of samples, and the relationship between the various bacterial indicators. Analyzing 300-ml, instead of 100-ml, samples tends to generate better information on single water samples. However, if many samples are analyzed over time from the same community, the value of using large volumes of water samples is diminished. The comparisons between bacterial indicators showed that the information obtained from the various indicators was very similar. However, fecal streptococci had a better predictive value of a negative test than coliforms with respect to the French standards.     

Kinetics of Escherichia coli destruction by microwave irradiation.

The kinetics of destruction of Escherichia coli cells suspended in a solution by microwave irradiation with a microwave oven were studied. During radiation at several powers, the temperature of 0.01 M phosphate buffer (PB), pH 7.0, in a glass beaker increased linearly at a rate of A (degrees Centigrade per second) according to the exposure time. When E. coli cells suspended in PB were exposed in the same beaker, the number of viable cells decreased according to the exposure time and the power used. The survival curve was approximated to a set of three linear parts. For each part, a rate constant of destruction (k) and an extrapolated starting temperature (T0) at several powers were estimated. Thereafter, the relationships between A and k and between A and T0 were studied. When a flat petri dish was used, the A value of exposed PB was lower and bacterial destruction was inhibited; the survival curve was similar to a curve predicted from the A value by using the relationships between the parameters. As the concentration of salt in the solution increased (from 0 to 1.35 M), the A value decreased and bacterial destruction was more suppressed. No remarkable difference between the destruction profiles for microwave exposure and conventional heating, which had the potential to generate an equal A value, was detected. These results showed that the parameter A of an irradiated solution is essential when kinetics of bacterial destruction by microwave exposure are studied and that the destruction profile can be interpreted mostly by means of thermal effects.     

Kinetics of Escherichia coli destruction by microwave irradiation.

The kinetics of destruction of Escherichia coli cells suspended in a solution by microwave irradiation with a microwave oven were studied. During radiation at several powers, the temperature of 0.01 M phosphate buffer (PB), pH 7.0, in a glass beaker increased linearly at a rate of A (degrees Centigrade per second) according to the exposure time. When E. coli cells suspended in PB were exposed in the same beaker, the number of viable cells decreased according to the exposure time and the power used. The survival curve was approximated to a set of three linear parts. For each part, a rate constant of destruction (k) and an extrapolated starting temperature (T0) at several powers were estimated. Thereafter, the relationships between A and k and between A and T0 were studied. When a flat petri dish was used, the A value of exposed PB was lower and bacterial destruction was inhibited; the survival curve was similar to a curve predicted from the A value by using the relationships between the parameters. As the concentration of salt in the solution increased (from 0 to 1.35 M), the A value decreased and bacterial destruction was more suppressed. No remarkable difference between the destruction profiles for microwave exposure and conventional heating, which had the potential to generate an equal A value, was detected. These results showed that the parameter A of an irradiated solution is essential when kinetics of bacterial destruction by microwave exposure are studied and that the destruction profile can be interpreted mostly by means of thermal effects.     

A statistical model for interpreting the antibiogram

Up to now, to interpret antibiotic susceptibility tests, the common practice has been to use: first, breakpoints without any quantitative justification, secondly, concordance curves between the different measurement techniques; these are not well adapted to the heterogeneous character of bacterial populations. We hereby propose another method: it is based on a global data analysis for each bacterial species, each antibiotic family and each measurement technique. So, we have drawn up a new model for the interpretation, both global and data-processed; it is based on qualifying classes, which are obtained and interpreted by hierarchical ascendent classification, principal components analysis, and comparison with pharmacological data. It can be used by any biologist. What is more, justified breakpoints with a numerical risk and quality control are defined. There are also some additional uses: evaluation of the effect of new antibiotics, standardization of new measurement techniques, detection of the emergence of new bacterial resistance in patients, guidance for research into unknown resistance mechanisms and characters.     

Bacterial stress enrichment enhances anaerobic hydrogen production in cattle manure sludge

Methodology was evaluated to selectively enrich hydrogen-producing species present in biological sludge produced during organic wastewater treatment. The influence of bacterial stress enrichment on anaerobic hydrogen-producing microorganisms was investigated in batch tests using serum bottles. Enrichment conditions investigated included application of acute physical and chemical stresses: wet heat, dry heat and desiccation, use of a methanogen inhibitor, freezing and thawing, and chemical acidification with and without preacidification of the sludge at pH 3. For each enrichment sample, cultivation pH value was set at an initial value of 7. After application of selective enrichment (by bacterial stress), hydrogen production was significantly higher than that of untreated original sludge. Hydrogen production from the inocula with bacterial stress enrichment was 1.9–9.8 times greater when compared with control sludge. Chemical acidification using perchloric acid showed the best hydrogen production potential, irrespective of preacidification. Enhancement is due to the selective capture of hydrogen-producing sporeformers, which induces altered anaerobic fermentative metabolism.     

Dynamics and estimates of growth and loss rates of bacterioplankton in a temperate freshwater system

The growth rate and losses of bacterioplankton in the epilimnion of an oligo-mesotrophic reservoir were simultaneously estimated using three different methods for each process. Bacterial production was determined by means of the tritiated thymidine incorporation method, the dialysis bag method and the dilution method, while bacterial mortality was assessed with the dilution method, the disappearance of thymidine-labeled natural cells and ingestion of fluorescent bacterial tracers by heterotrophic flagellates. The different methods used to estimate bacterial growth rates yielded similar results. On the other hand, the mortality rates obtained with the dilution method were significantly lower than those obtained with the use of thymidine-labeled natural cells. The bacterial ingestion rate by flagellates accounted on average for 39% of total bacterial mortality estimated by the dilution method, but this value fell to 5% when the total mortality was measured by the thymidine-labeling method. Bacterial abundance and production varied in opposite phase to flagellate abundance and the various bacterial mortality rates. All this points to the critical importance of methodological aspects in the elaboration of quantitative models of matter and energy flows over the time through microbial trophic networks in aquatic systems, and highlights the role of bacterioplankton as a source of carbon for higher trophic levels in the studied system.     

Identification of the bacterial community of maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing

The bacterial community of maple sap was characterized by analysis of samples obtained at the taphole of maple trees for the 2001 and 2002 seasons. Among the 190 bacterial isolates, 32 groups were formed according to the similarity of the banding patterns obtained by amplified ribosomal DNA restriction analysis (ARDRA). A subset of representative isolates for each ARDRA group was identified by 16S rRNA gene fragment sequencing. Results showed a wide variety of organisms, with 22 different genera encountered. Pseudomonas and Ralstonia, of the gamma- and beta-Proteobacteria, respectively, were the most frequently encountered genera. Gram-positive bacteria were also observed, and Staphylococcus, Plantibacter, and Bacillus were the most highly represented genera. The sampling period corresponding to 50% of the cumulative sap flow percentage presented the greatest bacterial diversity according to its Shannon diversity index value (1.1). gamma-Proteobacteria were found to be dominant almost from the beginning of the season to the end. These results are providing interesting insights on maple sap microflora that will be useful for further investigation related to microbial contamination and quality of maple products and also for guiding new strategies on taphole contamination control.     

Partition-mediated plasmid pairing

Plasmid partition systems are essential for the stability and thus the survival of low-copy-number plasmids in growing bacterial populations. The partition reaction is responsible for proper intracellular distribution of plasmids in the bacterial cell cycle. One common step in most partition models is the pairing of plasmids to each other by partition components. Here, evidence that supports the pairing of plasmids via their partition complexes is reviewed, and discussed in light of recent observations that many plasmids, including those without active partition systems are clustered in limited groups inside bacterial cells.     

Lattice-Boltzmann model for bacterial chemotaxis

We present a new numerical approach for modeling bacterial chemotaxis and the fate and transport of a chemoattractant in bulk liquids. This Lattice-Boltzmann method represents the microorganisms and the chemoattractant by quasi-particles that move, collide, and react with each other on a two-dimensional numerical lattice. We use the model to simulate traveling bands of bacteria along self-generated gradients in substrate concentration in bulk liquids. Particularly, we simulate Pseudomonas putida that respond chemotactically to naphthalene dissolved in water. We find that only a fraction of a bacterial slug injected into a domain containing the chemoattractant at constant concentration forms a traveling band as the slug length exceeds a critical value. An expanding bacterial ring forms as one injects a droplet of bacteria into a two-dimensional domain.     

INDISIM, an individual-based discrete simulation model to study bacterial cultures.

An individual-based model has been developed and designed to simulate the growth and behaviour of bacterial colonies. The simulator is called INDISIM, which stands for INDividual DIScrete SIMulations. INDISIM is discrete in space and time, and controls a group of bacterial cells at each time step, using a set of random, time-dependent variables for each bacterium. These variables are used to characterize its position in space, biomass, state in the cellular reproduction cycle as well as other individual properties. The space where the bacterial colony evolves is also discrete. A physical lattice is introduced, subject to the appropriate boundary conditions. The lattice is subdivided into spatial cells, also defined by a set of random, time-dependent variables. These variables may include concentrations of different types of particles, nutrients, reaction products and residual products. Random variables are used to characterize the individual bacterium and the individual particle, as well as the updating of individual rules. Thus, the simulations are stochastic rather than deterministic. The whole set of variables, those that characterize the bacterial population and the environment where they evolve, enables the simulator to study the behaviour of each microorganism-such as its motion, uptake, metabolism, and viability-according to given rules suited for the system under study. These rules require the input of only a few parameters. Once this information is inputted, INDISIM simulates the behaviour of the system providing insights into the global properties of the system from the assumptions made on the properties of the individual bacteria. The relation between microscopic and global properties of the bacterial colony is obtained by using statistical averaging. In this work INDISIM has been used to study (a) biomass distributions, (b) the relationship between the rate of growth of a bacterial colony and the nutrient concentration and temperature, and (c) metabolic oscillations in batch bacterial colonies. The simulation results are found to be in very good qualitative agreement with available experimental data, and provide useful insights into the mechanisms involved in each case.     

细菌萜类合成酶的生物信息学分析

【目的】目前对于萜类合成酶(Terpenoid synthase,TPS)的研究主要集中在植物和真菌中,而对细菌TPS的系统研究尚少。建立在大量已经被测序的细菌基因组基础上,利用生物信息学方法,对细菌TPS在全基因组范围内进行识别、分类和功能分析。【方法】利用TPS的隐马尔科夫模型(Pfam编号为PF03936)搜索自建的细菌蛋白质组数据库,预测出细菌TPS。对这些候选TPS的蛋白序列用MAFFT 7.130b进行多序列比对,并利用MEGA 6.0对多序列比对结果进行进化分析。利用MEME和PredictProtein分别进行细菌TPS的基序(Motifs)和点突变分析。【结果】建立在生物信息学分析的基础上,1 423条细菌TPS被识别,它们分布在8个门中,即放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)、酸杆菌门(Acidobacteria)和衣原体门(Chlamydiae)。进化分析表明细菌TPS可分为4大类,Motifs分析表明除了各类之间保守的基序(Motifs)外,还有特异的Motifs,这暗示着细菌TPS在不同类别之间的功能分化。点突变分析表明,细菌TPS不同位点的氨基酸突变对TPS功能的影响不同。【结论】细菌TPS主要分布于8个门中,其中在2个门中细菌TPS尚未见报道,即厚壁菌门(Firmicutes)与酸杆菌门(Acidobacteria)。基于进化分析,可以把细菌TPS分为4类,各类之间的差异可能是由类特异的Motifs决定的,另外细菌TPS不同氨基酸位点的突变分析为今后验证TPS的功能提供了很好的理论基础。     

Modeling, simulation, and optimization of bacterial leaching reactors

Bacterial leaching represents an unusual problem in biochemical engineering, because the substrate for bacterial growth is not supplied directly, but is a product of another reaction, the leaching of mineral particles. In addition, leaching is a heterogeneous reaction dependent on the particle-size distribution in the feed and on the kinetics of particle shrinkage. In this study, these effects are incorporated in the material balance for each mineral by the number balance. Examination of the number balance gives rise to a novel analysis of the competing technologies for leaching. The model is completed by the addition of material balances for the ferrous and ferric ions, the dissolved oxygen, and for each bacterial species to the number balance for each mineral present in the feed. The model is compared with pilot plant data for three different ores. It is shown that the model is in excellent agreement with the data. The performance of a bacterial leaching reactor is explored using the model, and the washout and sensitivity criteria are determined. It is shown that there are three washout conditions, in which the leaching conversion drops to zero. The washout conditions are dependent on the growth rate of the bacteria, on the rate of dissolution of the mineral, and on the rate of mass transfer of oxygen to the reactor. The critical washout condition is that arising from the rate of mineral dissolution. The optimization of a plant in which continuous tank reactors are configured in series is addressed. This analysis shows that the primary reactor should be between 1.5 and 2 times the size of each of the secondary reactors in a series combination.     

Purification and characterization of mouse liver xanthine oxidase

Xanthine oxidase (EC 1.1.3.22) is purified to homogeneity from mouse liver after induction with bacterial lipopolysaccharide. The enzyme has an apparent molecular weight of 300,000 in its native state and it is suggested to be constituted of two identical subunits of Mr 150,000 each. The isoelectric point is 6.7 and the apparent Km value for xanthine is 3.4 microM. The amino acid composition of mouse xanthine oxidase is quite similar to that of Drosophila xanthine dehydrogenase.     

The use of alkaline phosphatase-labelled oligonucleotide probes as culture confirmation reagents for the identification of commercially important bacteria

A range of rRNA-targeted alkaline phosphatase-labelled oligonucleotide probes was tested for use as culture confirmation reagents for the rapid identification of micro-organisms. The probes were specific to clinically important bacteria ( Helicobacter pylori and Mycobacterium tuberculosis ), fish and shellfish pathogens ( Renibacterium salmoninarum and Vibrio vulnificus ), food spoilage bacteria ( Listeria spp. and L. monocytogenes ), for bacteria of biotechnological importance ( Streptomyces spp.) and for bacteria associated with the oil industry (Sulphate-reducing bacteria, SRB). A universal bacterial probe and a eukaryotic probe were included in the study as positive and negative controls, respectively. A total of 93 bacterial strains was screened. With the exception of a large number of cross-reactions of the SRB probe (specificity value of 29·4%) and a single cross-reaction of the R. salmoninarum probe (specificity value of 97·7%), dot blot analysis indicated that each probe hybridized 100% specifically to the organisms tested. A simple culture confirmation method was then developed using these probes to enable the identification of bacterial colonies using a simple hybridization procedure.     

Antimicrobial activity of lysozyme isoforms: Key molecular features

Increasing bacterial resistance towards antibiotics has stimulated research for novel antimicrobials. Proteins acting on bacterial membranes could be a solution. Lysozyme has been proven active against E. coli by disruption of both outer and cytoplasmic membranes, with dry‐heating increasing lysozyme activity. Dry‐heated lysozyme (DH‐L) is a mixture of isoforms (isoaspartyl, native‐like and succinimide lysozymes), giving rise to two questions: what effects does each form have, and which physicochemical properties are critical as regards the antibacterial activity? These issues were investigated by fractionating DH‐L, analyzing structural properties of each fraction, and testing each fraction in vivo on bacteria and in vitro on membrane models. Positive net charge, hydrophobicity and molecular flexibility of the isoforms seem key parameters for their interaction with E. coli membranes. The succinimide lysozyme fraction, the most positive, flexible and hydrophobic, shows the highest antimicrobial activity, induces the strongest bacterial membrane disruption and is the most surface active on model lipid monolayers. Moreover, each fraction appears less efficient than DH‐L against E. coli , indicating a synergetic cooperation between lysozyme isoforms. The bacterial membrane modifications induced by one isoform could facilitate the subsequent action of the other isoforms.     

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.