Seasonal and vertical distribution of planktonic bacteria and heterotrophic nanoflagellates in the middle Adriatic Sea

Temporal and spatial patterns of bacteria and heterotrophic nanoflagellates (HNF) were studied monthly from January 1997 to December 1998 in the middle Adriatic Sea. Bacterial and HNF relationships with phytoplankton biomass and temperature were analyzed to examine how the relative importance of bottom-up and top-down factors may shift over seasons and locations. For the coastal area, an inconsistent relationship between bacterial abundance and chlorophyll a and a stronger relationship between bacterial abundance and bacterial production suggest that other substrates than those of phytoplankton origin are important for bacteria. The analysis of simultaneous effects of temperature and bacterial production on bacterial abundance showed that the effect of temperature obscured the effects of bacterial production, suggesting that bacterial growth itself is highly temperature-dependent. The relationship between HNF abundance and bacterial abundance was slightly improved by the inclusion of in situ temperature, bacterial production or both parameters, as additional independent variables. About 60% of the variability in HNF abundance can be explained by bacterial abundance, bacterial production and temperature. In the open sea, tight coupling of bacterial abundance with chlorophyll a concentrations implied that phytoplankton-derived substrates have a dominant role in controlling bacterial abundance. During the colder months, bacterial abundance was high enough to support higher HNF abundance than observed, suggesting that predation exerted a minor depressing influence on bacterial abundance during that period. During the spring-summer period, HNF controlled bacterial standing stocks by direct cropping of bacterial production.Communicated by: H.-D. Franke     

Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics

Long distance atmospheric transport of bacterial cells is often implied as a driver of the apparent cosmopolitan distribution of bacterial taxa. Surprisingly, efforts to measure immigration in bacterial communities are rare. An 8-week time series of within-lake bacterial community composition and atmospheric deposition rates and composition were used to estimate the influence of immigration on bacterial community dynamics in two north temperate lakes. Characterization of bacterial community dynamics using automated ribosomal intergenic spacer analysis suggested moderate overlap in composition between the lakes and atmospherically deposited cells. However, taxa that appeared to be delivered by atmospheric deposition had a relatively minor influence on lake bacterial community dynamics. The weak influence of immigrating bacterial taxa suggests that a species-sorting concept best describes aquatic bacterial metacommunity dynamics.     

迟钝爱德华氏菌菌蜕系统的构建

菌蜕系统（Bacterial Ghost,BG）的形成是利用噬菌体PhiX174的裂解蛋白E在革兰阴性菌细胞膜形成一个跨膜孔道结构,使细菌胞内物质由孔道排出而引起死亡。这种基因灭活的过程不引起细菌表面结构的任何理化变性,因此生成的细菌空壳具有与活菌相同功能的膜抗原结构,可诱导机体的体液免疫和细胞免疫应答。检测和比较了在铁调控启动子PyncE和温度调控启动子PR/cI控制下的E基因对迟钝爱德华氏菌菌蜕系统（EBG）的生成效率。结果显示,2种启动子均能成功生成EBG,电镜下可观察到细菌两端有直径约为80～400 nm的孔洞。传统菌蜕系统所用的热启动子在诱导后3 h开始裂解,8 h后细菌停止死亡;而新型铁诱导启动子在诱导后2 h细菌即完全停止生长。本研究为将来开发菌蜕载体疫苗防治爱德华氏菌症奠定了基础。     

水生细菌生物量的估算方法*

细菌的生物量是海洋微生物研究的关键参数之一。目前,细菌生物量估算方法主要根据其体积的大小进行换算,但换算的方式也不尽一致。对细菌体积和细菌碳含量主要的测定方法、体积与生物量之间换算系数、换算模式进行介绍,评述。认为流式细胞术是测定细菌体积较为合适的方法,X-射线微量分析法是测定单个细菌生物量(碳含量)最合适的方法,异速生长模式是目前生物量换算过程较为常用的模式。     

Distinct successional patterns and processes of free-living and particle-attached bacterial communities throughout a phytoplankton bloom

1. Understanding the successional patterns of microbial communities during a phytoplankton bloom is crucial for predicting the compositional and functional stability of lake ecosystems in response to the disturbance of a bloom. Previous studies on bacterial communities associated with blooms have rarely studied the dynamics of these communities. The successional patterns of bacterial communities within different micro-habitats (i.e. water column versus particles) and mechanisms that shape these communities that differ in composition and structure remain unclear.
2. We selected a eutrophic urban lake to investigate the succession of bacterial communities during a bloom. We divided the bacterial communities into free-living (FL) and particle-attached (PA) groups based on their different lifestyles. The amplicon-based 16S rRNA gene high-throughput sequencing technology was used to obtain bacterial community composition and phylogenetic structure.
3. Our study showed distinct successional patterns between FL and PA bacterial communities, and the two bacterial lifestyles showed different responses and resilience to the bloom, in terms of diversity and relative abundance of bacterial taxa. Alpha-diversity of the PA bacterial community decreased during the bloom, whereas that of the FL bacterial community increased. More taxa in the FL bacterial community showed resilience after the disturbance than in the PA bacterial community.
4. The influence of phytoplankton blooms on the assembly of the bacterial community can be viewed as niche selection that led to the decrease in the relative importance of stochastic processes in shaping both FL and PA bacterial communities. This study shows the ecological significance of the bacterial community response to bloom events in lakes. It also shows that assembly processes differ for bacterial communities that have different lifestyles in lake ecosystems disturbed by phytoplankton blooms.

     

Transport of bacteria in porous media and its enhancement by surfactants for bioaugmentation: A review

The success of bioaugmentation processes for groundwater bioremediation requires efficient transport of bacteria in the subsurface environment. In this paper, the factors that influence transport of bacterial cells in porous media are reviewed and the effects of surfactants on the transport are discussed. Movement of bacterial cells in porous media is a process driven by advection and hydrodynamic dispersion forces of fluids. Immobilization of bacterial cells takes place due to processes such as adsorption and straining. Blocking and ripening along with bacterial migration process decrease and increase the retention of cells in porous media, respectively. Physicochemical properties of the porous media, groundwater chemistry, and properties of the bacterial cells affect the transport behavior. Surfactants have the potential to modify bacterial surface properties for both bacterial cells and medium solids, and thus enhance bacterial transport.     

Bacteria, phages and septicemia

The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion.     

Using light scatter signal to estimate bacterial biovolume by flow cytometry.

BACKGROUND: In the past decade, flow cytometry has become a useful and precise alternative to microscopic bacterial cell counts in aquatic samples. However, little evidence of its usefulness for the evaluation of bacterial biovolumes has emerged in from the literature. METHODS: The light scattering and cell volume of starved bacterial strains and natural bacterial communities from the Black Sea were measured by flow cytometry and epifluorescence microscopy, respectively, in order to establish a relationship between light scattering and cell volume. RESULTS: With the arc-lamp flow cytometer, forward angle light scatter (FALS) was related to cell size in both the starved strains and natural communities, although regression parameters differed. We tested the predictive capacity of the FALS verous cell size relationship in a bacterial community from the North Sea. That analysis showed that a reliable bacterial biovolume prediction of a natural bacterial community can be obtained from FALS using a model generated from natural bacterial community data. CONCLUSIONS: Bacterial biovolume is likely to be related to FALS measurements. It is possible to establish a generally applicable model derived from natural bacterial assemblages for flow cytometric estimation of bacterial biovolumes by light scatter.     

水稻种子的细菌含量和群落结构及其影响因素分析

【目的】种子是植物微生物群代际传递的重要途径，但种子携带的微生物群落尚缺乏系统的研究。本研究以水稻种子为模型，定量分析种子的细菌含量、测定种子的细菌群落结构、探究地域与品种对细菌含量及群落结构的影响和鉴定水稻种子的核心菌群。【方法】选取18个水稻品种，每个品种分别来自中国海南和天津2个地域，共36组样本。每组样本包含5或10个DNA样本，每个DNA样本由3粒种子提取的总DNA构成。使用细菌特异性16S rDNA介导的荧光定量PCR技术测定种子的细菌含量，并分析影响因素；使用16S rDNA扩增子测序技术测定种子的细菌群落结构，并用生物信息学方法分析了影响因素和核心菌群。【结果】本研究测定了1 080粒水稻种子的细菌含量，发现经过表面除菌的水稻种子内部存在共栖细菌，平均每克种子的细菌含量为1.53×10⁶。水稻品种对种子的细菌含量有显著影响，而地域无影响。测定180个扩增子文库的细菌群落结构，发现水稻种子的菌群与水稻植株有相似之处，均以变形菌门为主要的细菌门类；地域对水稻种子的细菌群落结构有重要影响，不同地域的水稻种子在主坐标分析(principal co-ordinate analysis, PCoA)中有明显分离；而粳稻和籼稻之间无显著差异。还发现水稻种子存在核心菌群，且相对丰度高达总菌群的85.56%。【结论】本研究系统地揭示了水稻种子的细菌含量、群落结构及其影响因素，为利用种传微生物促进水稻健康提供了数据和方法支持。     

细菌基因突变的策略及应用

细菌病仍然是目前危害人类和动物的重要疾病。细菌突变技术是重要的细菌学研究技术,包括传统的物理、化学、生物学等方法及现代的基因突变技术。基因突变技术是目前细菌学研究的重点,不同的基因突变技术采用的策略不同。细菌基因突变技术的开发和应用为细菌疫苗研制、细菌基因功能研究和基因治疗提供了新的技术手段。     

血清降钙素原与传统感染检测指标对细菌性血流感染的临床诊断价值比较

目的比较血清降钙素原(PCT)和传统感染检测指标在细菌性血流感染中的诊断价值。方法选取我院2018年1月至11月59例血培养显示细菌感染阳性患者为血培养阳性组,选取同期63例血培养阴性患者为血培养阴性组,分析两组患者白细胞(WBC)、中性粒细胞(NEU)计数和血清PCT水平,比较PCT、WBC和NEU对细菌性血流感染的诊断阳性率和ROC曲线下面积。结果两组患者WBC、NEU计数和血清PCT水平差异均有统计学意义(均P<0.05),PCT对细菌性血流感染的诊断阳性率和ROC曲线下面积显著大于WBC和NEU(均P<0.05)。PCT诊断细菌性血流感染的灵敏度为96.6%,特异度为95.2%。结论血清PCT对细菌性血流感染具有较高的诊断价值。     

Nutritional influences on the gut microbiota and the consequences for gastrointestinal health

The human colonic microbiota degrades dietary substrates that are indigestible in the upper GIT (gastrointestinal tract), releasing bacterial metabolites, some of which are important for gut health. Advances in molecular biology techniques have facilitated detailed analyses of the composition of the bacterial community resident in the lower GIT. Such analyses have indicated that more than 500 different bacterial species colonize an individual, and that, although there is much functional consistency in the resident bacterial groups, there is considerable inter-individual variation at the species/strain level. The bacterial community develops during early childhood until it reaches an adult-like composition. Whereas colonization and host factors influence the species composition, dietary factors also have an important impact, with specific bacterial groups changing in response to specific dietary interventions. Since bacterial species have different metabolic activities, specific diets have various consequences for health, dependent on the effect exerted on the bacterial population.     

Bacterial succession during 500?years of soil development under agricultural use

Soil bacterial succession under intensive anthropogenic disturbances is not well known. Using terminal restriction fragment length polymorphisms and 454 pyrosequencing of 16S rRNA genes, this study investigated how soil bacterial diversity and community structure changed under two agricultural land uses (paddy rice and upland cropping) in relation to soil development along a 500-year chronosequence created by intermittent reclamation of estuarine salt marshes. Multivariate analysis revealed orderly changes in soil physicochemical properties and bacterial community structure with time, confirming the occurrence of soil development and bacterial succession. Patterns of soil development and bacterial succession resembled each other, with recent land uses affecting their trajectories but not the overall direction. Succession of bacterial community structure was mainly associated with changes in ??-Proteobacteria and Verrucomicrobia. Two stages of bacterial succession were observed, a dramatic-succession stage during the first several decades when bacterial diversity increased evidently and bacterial community structure changed rapidly, and a long gradual-succession stage that lasted for centuries. Canonical correspondence analysis identified soil Na⁺, potentially mineralizable nitrogen, total phosphorous, and crystallinity of iron oxyhydrates as potential environmental drivers of bacterial succession. To conclude, orderly succession of soil bacterial communities occurred along with the long-term development of agroecosystems, which in turn was associated with soil physicochemical changes over time.     

Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism.

We describe a new method for studying the structure and diversity of bacterial communities in the natural ecosystem. Our approach is based on single-strand-conformation polymorphism (SSCP) analysis of PCR products of 16S rRNA genes from complex bacterial populations. A pair of eubacterial universal primers for amplification of the variable V3 region were designed from the 16S rRNA sequences of 1,262 bacterial strains. The PCR conditions were optimized by using genomic DNAs from five gram-positive and seven gram-negative strains. The SSCP analysis of the PCR products demonstrated that a bacterial strain generated its characteristic band pattern and that other strains generated other band patterns, so that the relative diversity in bacterial communities could be measured. In addition, this method was sensitive enough to detect a bacterial population that made up less than 1.5% of a bacterial community. The distinctive differences between bacterial populations were observed in an oligotrophic lake and a eutrophic pond in a field study. The method presented here, using combined PCR amplification and SSCP pattern analyses of 16S rRNA genes, provides a useful tool to study bacterial community structures in various ecosystems.     

Phospholipid-Derived Fatty Acids and Quinones as Markers for Bacterial Biomass and Community Structure in Marine Sediments

Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.     

Bacteria-lectin interactions in phytohemagglutinin-induced bacterial overgrowth of the small intestine

The mechanism of phytohemagglutinin-induced bacterial overgrowth of the small bowel in the rat was studied. Interaction of the lectin with bacterial isolates selected at random from those that comprised the major population of the overgrowth was determined. In both bacterial agglutination assays and glycocalyx stabilization, no specific association between lectin and bacteria was seen. In three independent binding assays phytohemagglutinin was not found to increase bacterial adherence to washed intestinal mucosa. Phytohemagglutinin would not appear to act, therefore, as a direct ligand to mediate bacterial adherence or to modify the mucosal surface to increase bacterial adherence.     

Profiling and monitoring of microbial populations by denaturing high-performance liquid chromatography

We describe a new molecular technique for the analysis of microbial species and complex microbial populations based on the separation of PCR-amplified 16S rDNA fragments by denaturing high-performance liquid chromatography (DHPLC). Using marine bacterial samples, we determined the optimum conditions for the analysis of bacterial species and the examination of complex bacterial assemblages obtained from different environments. The incorporation of a 40-bp GC clamp into the amplification primer was essential to effectively discriminate genetic differences in DHPLC-primers with a 20-, 10-, or 0-bp GC clamp length were less efficient. A 64.5 degrees C column temperature in DHPLC allowed optimal separation of species in a complex bacterial population. PCR-DHPLC analysis of bacterial assemblages demonstrated profiles with distinguishable peaks, which constituted the different populations and their degree of abundance. Fraction collection and DNA sequencing from profile peaks enabled bacterial identification. PCR-DHPLC analysis can also provide opportunities for describing bacterial communities, cloning bacteria, and monitoring bacterial populations in environments of interest.     

我国马铃薯软腐病防治的研究进展

马铃薯软腐病是马铃薯细菌性病害中最严重的一种,简要介绍了我国马铃薯软腐病的病原菌、病害性状以及对病害的防治方法。利用现代生物技术手段人为地操纵细菌群体感应系统,将会成为提高植物抗病性的新方法、新途径。