厌氧氨氧化细菌Candidatus Kuenenia stuttgartiensis铁的吸收利用研究进展

铁是影响微生物生长代谢的关键元素,它与蛋白质结合,起催化、氧化还原或调节作用.厌氧氨氧化(ANAMMOX)细菌的生长代谢严重依赖铁,尤其是含铁蛋白.ANAMMOX细菌的厌氧生活方式和厌氧氨氧化体的存在使其对铁代谢的模式不同于其他微生物.弄清ANAMMOX细菌的铁吸收代谢模式,可为获得其纯培养物奠定基础,有利于促进其在环...     

Revealing potential functions of VBNC bacteria in polycyclic aromatic hydrocarbons biodegradation

The bioremediation of polycyclic aromatic hydrocarbon (PAH)‐contaminated sites is not running smoothly, because of the lower activity of PAH‐degrading bacteria in actual bioremediation applications. The phenomenon of “viable but nonculturable” (VBNC) state may be a main limiting factor for their poor biodegradation capabilities of PAHs. Due to their abilities of entering into the VBNC state, most of bacterial populations with PAH‐degradation potential remain unculturable. Resuscitation of VBNC bacteria will enhance the degradation capability of indigenous bacteria which will eventually obtain their better capabilities in environmental bioremediation. Although evidences have been presented indicating that resuscitation of VBNC bacteria in polychlorinated biphenyl (PCB)‐contaminated environments not only significantly enhanced PCB degradation, but also obtained novel highly efficient PCB‐degrading bacteria, scanty information is available on the VBNC bacteria in PAH‐contaminated sites. VBNC bacteria, as a vast majority of potential microbial resource could be the repository of novel highly efficient PAH‐biodegraders. Therefore, studies need to be done on resuscitation of VBNC bacteria to overcome key bottlenecks in bioremediation of PAH‐contaminated sites. This mini‐review provides a new insight into the potential functions of VBNC bacteria in PAHs biodegradation.

Significance and Impact of the Study

As the vast majority microbial resource, viable but nonculturable (VBNC) bacteria, which showed their potential functions in polycyclic aromatic hydrocarbons (PAHs) biodegradation, can be of great significance in environmental bioremediation. It is therefore important to resuscitate VBNC bacteria for their better capabilities. Meanwhile, preventing the indigenous functional community from entering into the VBNC state will also maintain the high activity of PAH‐degrading bacteria in actual bioremediation applications. Undoubtedly, much more work needs to be done to reveal indigenous micro‐organisms in the VBNC state from the perspective of environmental functions.     

老年患者血培养病原菌分布及耐药性调查

目的了解老年患者血液感染的病原菌种类以及对抗菌药物的耐药状况。方法对2290份老年住院患者血培养标本中186例培养阳性检出菌及药敏结果进行统计学分析。结果在分离的172株细菌中,革兰阴性菌、革兰阳性菌及真菌分别占54.7%、34.9%和10.5%;革兰阴性菌中以大肠埃希菌占绝对优势(20.9%),假单胞菌其次(10.5%),革兰阳性菌中以凝固酶阴性葡萄球菌(CNS)占绝对优势(20.9%),金黄色葡萄球菌仅为2.9%。药敏试验表明老年菌血症的病原菌对常用抗菌药物的耐药严重,尤其是CNS及假单胞菌属细菌表现为较高的耐药率及多重耐药性。结论老年菌血症病原菌以机会致病菌感染比例较高,致病菌耐药问题严重,及时监测老年致病菌的变迁和耐药发展趋势以指导临床用药至关重要。     

The influence of cell size on marine bacterial motility and energetics

The influence of Brownian motion on marine bacteria was examined. Due to their small size, marine bacteria rotate up to 1,400 degrees in one second. This rapid rotation makes directional swimming difficult or impossible, as a bacterium may point in a particular direction for only a few tens of milliseconds on average. Some directional movement, however, was found to be possible if swimming speed is sufficiently great, over approximately 100 μm sec⁻¹. This led to the testable hypothesis that marine bacteria with radiii less than about 0.75 μm should exceed this speed. The result of the increased speed is that marine bacteria may spend in excess of 10% of their total energy budget on movement. This expenditure is 100 times greater than values for enteric bacteria, and indicates that marine bacteria are likely to be immotile below critical size-specific nutrient concentrations.     

Distribution of urea-decomposing bacteria in waters of lake suwa

The present study deals with the distribution of free and attached urea-decomposing bacteria in waters of Lake Suwa, one of the typical eutrophic lakes in Japan.Urea-decomposing bacteria are proved to be not an exceptional population among the populations of the heterotrophic bacteria studied. The percentage of attached urea-decomposing bacteria versus attached heterotrophic bacteria seems to be higher than that of free urea-decomposing bacteria versus free heterotrophic bacteria. Based on the assumption that most bacterial ureases are inducible ones, it is inferred that their ureases may not be induced under a such degree of urea concentration as is generally encountered in natural waters.     

Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp

The present paper provides an overview on the use of probiotic organisms as live supplements, with particular emphasis on Lactobacillus acidophilus and Bifidobacterium spp. The therapeutic potential of these bacteria in fermented dairy products is dependent on their survival during manufacture and storage. Probiotic bacteria are increasingly used in food and pharmaceutical applications to balance disturbed intestinal microflora and related dysfunction of the human gastrointestinal tract. Lactobacillus acidophilus and Bifidobacterium spp. have been reported to be beneficial probiotic organisms that provide excellent therapeutic benefits. The biological activity of probiotic bacteria is due in part to their ability to attach to enterocytes. This inhibits the binding of enteric pathogens by a process of competitive exclusion. Attachment of probiotic bacteria to cell surface receptors of enterocytes also initiates signalling events that result in the synthesis of cytokines. Probiotic bacteria also exert an influence on commensal micro-organisms by the production of lactic acid and bacteriocins. These substances inhibit growth of pathogens and also alter the ecological balance of enteric commensals. Production of butyric acid by some probiotic bacteria affects the turnover of enterocytes and neutralizes the activity of dietary carcinogens, such as nitrosamines, that are generated by the metabolic activity of commensal bacteria in subjects consuming a high-protein diet. Therefore, inclusion of probiotic bacteria in fermented dairy products enhances their value as better therapeutic functional foods. However, insufficient viability and survival of these bacteria remain a problem in commercial food products. By selecting better functional probiotic strains and adopting improved methods to enhance survival, including the use of appropriate prebiotics and the optimal combination of probiotics and prebiotics (synbiotics), an increased delivery of viable bacteria in fermented products to the consumers can be achieved.     

The role of oxygen in the viability of probiotic bacteria with reference to L. acidophilus and Bifidobacterium spp

The various therapeutic benefits of Lactobacillus acidophilus and Bifidobacterium spp. have resulted in their increased incorporation into dairy foods such as yoghurts. Currently however, the efficacy of these probiotic bacteria is limited by their poor survival during the shelf life of yoghurt. Oxygen toxicity is widely considered to be responsible for the cell deaths of these bacteria. The intestinal origins and the microaerophilic and anaerobic characteristics of L. acidophilus and Bifidobacterium spp. respectively, can render them susceptible to oxygen contained in the food products. This review discusses the influence of the dissolved oxygen in yogurt on the viability of these bacteria. Suggested techniques to protect these probiotic bacteria from oxygen toxicity are evaluated. Although the problem of oxygen toxicity in probiotic bacteria is regarded as significant, little is known however about the cellular interaction of these bacteria with oxygen. This review summarizes what is known about the biochemistry of oxygen toxicity in these bacteria. The various metabolic and biochemical responses of L. acidophilus and Bifidobacterium to oxygen are examined. Additionally, the importance of NADH oxidase and NADH peroxidase in the oxygen tolerance of these bacteria is evaluated and assays used to measure their cellular concentrations are discussed.     

Motility of flagellated bacteria in viscous environments.

The lowest viscosity that immobilized flagellated bacteria such as Psedomonas aeruginosa, Spirillum serpens, and Escherichia coli was 60 centipoise (cp). Much higher viscosities (1,000 cp and higher) were required to immobilize two flagellated bacteria selectively isolated from nature by methods based on their ability to migrate through agar gels. The latter finding indicates that certain flagellated bacteria have the ability to swim through environments of relatively high viscosity. It is suggested that these flagellated bacteria possess a specialized type of motility apparatus suited to viscous conditions present in their habitats.     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Contribution of SAR11 Bacteria to Dissolved Dimethylsulfoniopropionate and Amino Acid Uptake in the North Atlantic Ocean

SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of ³H-amino acids and [³⁵S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.     

Soft gel medium solidified with gellan gum for preliminary screening for root-associating,free-living nitrogen-fixing bacteria inhabiting the rhizoplane of plants

For preliminary screening for and characterization of free-living nitrogen-fixing bacteria from rhizoplane microflora, we used Winogradsky's mineral mixture-based nitrogen-free medium solidified with 0.3% gellan gum. The soft gel medium enabled some reference and wild free-living nitrogen-fixing bacteria to grow in characteristic colonies, including their reaction to oxygen and their motility change. Gellan gum is thus likely to be a better gel matrix than agarose for the investigation of root-associating, free-living nitrogen-fixing bacteria to identify their characteristic behaviors.     

新疆药用植物牛至内生细菌多样性与抗菌活性

【背景】植物内生菌作为微生物群落中一类非常重要的组成部分,在多个领域都有广泛的应用价值,如促进植物生长、抵抗病虫害、生物固氮、降解有毒有害化合物等。【目的】进一步丰富新疆野果林苹果腐烂病害的生防资源以及分析牛至内生细菌多样性特征。【方法】通过纯培养方法,对健康植物牛至组织进行内生细菌的分离纯化,并进行16S rRNA基因序列分析;再利用平板对峙法筛选具有抑制苹果腐烂病病原菌生长的内生细菌。【结果】共分离到168株内生细菌,最终确定为4门5纲8目12科17属,其中优势属为芽胞杆菌属(Bacillus)。由分离实验结果可知,M1号TSA培养基,M5号组氨酸-棉子糖培养基和M6号NA培养基是分离牛至内生细菌较为理想的培养基;采自新源县野果林的牛至内生细菌多样性较为丰富,在牛至根部内生细菌种类更多;通过拮抗实验共筛选出59株牛至内生细菌具有较好的抑菌效果。【结论】新疆药用植物牛至内生细菌的物种多样性较为丰富,而且富含一批有效抑制野苹果腐烂病病原菌生长的内生细菌菌株。因此,本研究在新疆野果林苹果腐烂病的生物防治和药用植物内生细菌种质资源的填补等方面具有重要意义。     

The association of Western flower thrips, Frankliniella occidentalis, with a near Erwinia species gut bacteria: transient or permanent?

Associations between insects and gut bacteria are ubiquitous. It is possible to make a distinction between permanent associations (called symbiosis), in which the same type of bacteria is present in more than one generation of the insect, and transient associations. Transient bacteria are ingested together with food but do not settle in the insect gut in such a way that they will be passed on to the next generation. In this study, we describe the permanent association between Western flower thrips (Frankliniella occidentalis), a polyphagous insect species that is a major pest worldwide, and one type of gut bacteria. On the basis of direct microscopic observations and counts of bacteria, it was found that thrips from the populations studied contained large numbers of bacteria in their hindgut. Bacteria were isolated from their host and grown on 10 different agar media. The number of bacteria isolated on agar media equaled the number of direct counts. All isolates had the same colony morphology. On the basis of their 16S rDNA sequence these bacteria were identified as Enterobacteriaceae, closely related to Escherichia coli. Isolates tested with API 20E biochemical tests were Erwinia species. This was the only type of bacteria found in all thrips individuals on any of the 10 different agar media. Universal primers, which would potentially pick up DNA from any bacterium present in the insect, were applied on crude DNA extracts from thrips with bacteria. We only found 16S rDNA sequences similar to those of the isolated thrips gut bacteria. The same type of bacteria was present in all life stages of the thrips and was found to persist in the thrips populations for at least 2 years (more than 50 generations).     

Bacterial Communities in Central European Bumblebees: Low Diversity and High Specificity

Recent studies on the microbial flora of the honeybee gut have revealed an apparently highly specific community of resident bacteria that might play a role in immune defence and food preservation for their hosts. However, at present, very little is known about the diversity and ecology of bacteria occurring in non-domesticated bees like bumblebees, which are of similar importance as honeybees for the pollination of agricultural and wild flowers. To fill this gap in knowledge, we examined six of the most common bumblebee species in Central Europe from three locations in Germany and Switzerland for their bacterial communities. We used a culture-independent molecular approach based on sequencing the 16S rRNA gene from a selection of individuals and examining a larger number of samples by terminal restriction fragment length polymorphism profiles. The gut flora was dominated by very few and mostly undescribed groups of bacteria belonging to the Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. This core set of bacteria was present in all of the examined bumblebee species. These bacteria are similar to, but distinct from, bacteria previously described from the honeybee gut. Significant differences were observed between the communities of bacteria in the different bumblebee species; the effect of sampling location was less strong. A novel group of Betaproteobacteria additionally shows evidence for host species-specific genotypes. The gut flora of bumblebees therefore is apparently composed of relatively few highly specialized bacteria, indicating a strong interaction and possibly important functions with their hosts.     

Origin of the bacterial SET domain genes: vertical or horizontal?

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.     

细菌生物膜与耐药性相关性研究进展

细菌生物膜是一种包裹于细胞外多聚物基质中不可逆的黏附于非生物或生物表面的微生物细胞菌落.生物膜状态下的细菌相对其浮游状态具有显著增强的耐药性,对人及动物细菌性感染具有重要研究价值.然而尽管动物细菌耐药性被广泛报道,却很少涉及细菌生物膜与其之间的相关性,本文综述了细菌生物膜的耐药机制并探讨了细菌生物膜与动物源性细菌耐药性的关系,可作为研究细菌耐药性及控制动物产品安全的参考.     

Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters

Quorum sensing (QS) in Gram-negative bacteria is generally assumed to be mediated by N-acyl-homoserine lactone molecules while Gram-positive bacteria make use of signaling peptides. We analyzed the occurrence in Gram-negative bacteria of peptides and transporters that are involved in quorum sensing in Gram-positive bacteria. Many class II bacteriocins and inducing factors produced by lactic acid bacteria (LAB) and competence stimulating peptides (CSPs) synthesized by streptococci are processed by their cognate ABC-transporters during their secretion. During transport, a conserved leader sequence, termed the double-glycine motif (GG-motif), is cleaved off by the N-terminal domain of the transporter, which belongs to the Peptidase C39 protein family. Several peptides containing a GG-motif were recently described in Gram-negative bacteria (Trends Microbiol 2001;9:164-8). To screen for additional putative GG-motif containing peptides, an in silico strategy based on MEME, HMMER2.2 and Wise2 was designed. Using a curated training set, a motif model of the leader peptide was built and used to screen over 120 fully sequenced bacterial genomes. The screening methodology was applied at the nucleotide level as probably many small peptide genes have not been annotated and may be absent from the non-redundant databases. It was found that 33% of the screened genomes of Gram-negative bacteria contained one or more transporters carrying a Peptidase C39 domain, compared to 44% of the genomes of Gram-positive bacteria. The transporters can be subdivided into four classes on the basis of their domain organization. Genes coding for putative peptides containing 23-142 amino acids and a GG-motif were found in close association with genes coding for Peptidase C39 domain containing proteins. These peptides show structural similarity to bacteriocins and peptide pheromones of Gram-positive bacteria. The possibility of signal transduction based on peptide signaling in Gram-negative bacteria is discussed.     

Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean

SAR11 bacteria are abundant in marine environments, often accounting for 35% of total prokaryotes in the surface ocean, but little is known about their involvement in marine biogeochemical cycles. Previous studies reported that SAR11 bacteria are very small and potentially have few ribosomes, indicating that SAR11 bacteria could have low metabolic activities and could play a smaller role in the flux of dissolved organic matter than suggested by their abundance. To determine the ecological activity of SAR11 bacteria, we used a combination of microautoradiography and fluorescence in situ hybridization (Micro-FISH) to measure assimilation of (3)H-amino acids and [(35)S]dimethylsulfoniopropionate (DMSP) by SAR11 bacteria in the coastal North Atlantic Ocean and the Sargasso Sea. We found that SAR11 bacteria were often abundant in surface waters, accounting for 25% of all prokaryotes on average. SAR11 bacteria were typically as large as, if not larger than, other prokaryotes. Additionally, more than half of SAR11 bacteria assimilated dissolved amino acids and DMSP, whereas about 40% of other prokaryotes assimilated these compounds. Due to their high abundance and activity, SAR11 bacteria were responsible for about 50% of amino acid assimilation and 30% of DMSP assimilation in surface waters. The contribution of SAR11 bacteria to amino acid assimilation was greater than would be expected based on their overall abundance, implying that SAR11 bacteria outcompete other prokaryotes for these labile compounds. These data suggest that SAR11 bacteria are highly active and play a significant role in C, N, and S cycling in the ocean.     

Anaerobic saccharolytic bacterial adhesion to raw starch granules

The experiment of bacteria adhesion onto starch granules is conducted. It is found that anaerobic saccharolytic bacteria have the highest adhesion ability in their growth and initial stage of stationary phase. Starch granules with a low crystallinity, low bulk density, and high water-holding capacity have a high adhesion capacity. The optimum temperature for both bacterial growth and their adhesion is 30 degrees C. The optimum pH for the bacterial adhesion range from 5.0 to 6.5. Anaerobic conditions cause an appreciable decrease in percentage of adhesion. The percentage of adhesion is not sensitive to the type of soluble saccharide on which bacteria were grown.