A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

A metaproteomic survey of surface coastal waters near Palmer Station on the Antarctic Peninsula, West Antarctica, was performed, revealing marked differences in the functional capacity of summer and winter communities of bacterioplankton. Proteins from Flavobacteria were more abundant in the summer metaproteome, whereas winter was characterized by proteins from ammonia-oxidizing Marine Group I Crenarchaeota. Proteins prevalent in both seasons were from SAR11 and Rhodobacterales clades of Alphaproteobacteria, as well as many lineages of Gammaproteobacteria. The metaproteome data were used to elucidate the main metabolic and energy generation pathways and transport processes occurring at the microbial level in each season. In summer, autotrophic carbon assimilation appears to be driven by oxygenic photoautotrophy, consistent with high light availability and intensity. In contrast, during the dark polar winter, the metaproteome supported the occurrence of chemolithoautotrophy via the 3-hydroxypropionate/4-hydroxybutyrate cycle and the reverse tricarboxylic acid cycle of ammonia-oxidizing archaea and nitrite-oxidizing bacteria, respectively. Proteins involved in nitrification were also detected in the metaproteome. Taurine appears to be an important source of carbon and nitrogen for heterotrophs (especially SAR11), with transporters and enzymes for taurine uptake and degradation abundant in the metaproteome. Divergent heterotrophic strategies for Alphaproteobacteria and Flavobacteria were indicated by the metaproteome data, with Alphaproteobacteria capturing (by high-affinity transport) and processing labile solutes, and Flavobacteria expressing outer membrane receptors for particle adhesion to facilitate the exploitation of non-labile substrates. TonB-dependent receptors from Gammaproteobacteria and Flavobacteria (particularly in summer) were abundant, indicating that scavenging of substrates was likely an important strategy for these clades of Southern Ocean bacteria. This study provides the first insight into differences in functional processes occurring between summer and winter microbial communities in coastal Antarctic waters, and particularly highlights the important role that ‘dark'' carbon fixation has in winter.     

Anaerobic bacteria from the digestive tract of North Atlantic fin whales (Balaenoptera physalus)

Abstract Samples were collected from the forestomach and colon of North Atlantic fin whales ( Balaenoptera physalus ) landed at the commercial whaling station at Hvalfjördur, Iceland during three whaling seasons. Techniques were used to enrich for and enumerate anaerobic bacteria, methanogens, and sulfate reducers. Anaerobic bacteria ranged from 10⁸ to 10¹⁰ per ml of digesta in the colon, and from 10⁵ to 10⁹ per ml of digesta in the forestomach. Methanogens and sulfate-reducing bacteria were found in the majority of forestomach and colon samples, with sulfate-reducing bacteria usually occuring at higher concentrations. Enteric bacteria, Vibrio , and Listonella spp. were found in the colon. Volatile fatty acids were detected in significant concentrations in the forestomach of many of the whales. These results support previous findings which suggest that a microbial fermentation occurs in the forestomach of baleen whales.     

Winogradsky and modern microbiology

The 150th anniversary of the birth of Sergei N. Winogradsky is a special date for general microbiology. Apart from the discovery of chemosynthesis, the development of the elective method, the application of the direct method, and formulation of microbial ecology problems, Winogradsky, in his pioneering studies, addressed fundamental aspects of the naturalistic Weltanschauung from the position of a microbiologist who studies the role of microorganisms in nature. These problems are still important today. Expanding knowledge throws light on them from different angles of view and highlights them with varying degrees of completeness, but the problems remain beyond time. It may be useful for contemporary microbiologists to realize the extent to which they would recognize their own work in the system of questions and answers stated a hundred years ago.     

Separation of histones from Physarum polycephalum by ion-paired, reverse-phase high-performance liquid chromatography

A rapid, one-step method for the efficient purification of murine monoclonal antibodies from tissue culture supernatants is described. This process is based on affinity chromatography on protein A-Sepharose columns. It was found that murine monoclonal antibodies raised against tick-borne encephalitis virus frequently eluted at more than one pH value and these pH values did not always correspond to those of antibodies of the same subclass from polyclonal mouse sera. The two populations of antibody molecule eluting at different pH values showed no variation in molecular weight, isoelectric profiles, specific enzyme-linked immunosorbent assay titer, or antibody subclass.     

A comparison of methods for total community DNA preservation and extraction from various thermal environments

The widespread use of molecular techniques in studying microbial communities has greatly enhanced our understanding of microbial diversity and function in the natural environment and contributed to an explosion of novel commercially viable enzymes. One of the most promising environments for detecting novel processes, enzymes, and microbial diversity is hot springs. We examined potential biases introduced by DNA preservation and extraction methods by comparing the quality, quantity, and diversity of environmental DNA samples preserved and extracted by commonly used methods. We included samples from sites representing the spectrum of environmental conditions that are found in Yellowstone National Park thermal features. Samples preserved in a non-toxic sucrose lysis buffer (SLB), along with a variation of a standard DNA extraction method using CTAB resulted in higher quality and quantity DNA than the other preservation and extraction methods tested here. Richness determined using DGGE revealed that there was some variation within replicates of a sample, but no statistical difference among the methods. However, the sucrose lysis buffer preserved samples extracted by the CTAB method were 15-43% more diverse than the other treatments.     

改革医学微生物学实验教学模式, 培养学生动手能力

根据预防医学专业的教学要求与培养目标, 围绕如何在实验教学中培养学生的动手能力, 对预防医学专业的医学微生物学实验课程体系中的教学计划、教学内容、教学方法和手段、实验考核方法进行了探索, 构建了适合于预防医学专业的医学微生物学实验教学模式。通过问卷调查结果显示, 该实验教学模式有利于培养学生的动手能力、科研思维、综合分析与解决问题能力, 有利于培养学生的合作意识和团队精神, 显示出传统实验教学方法不可比拟的优越性。     

Exploring the bovine rumen bacterial community from birth to adulthood

The mammalian gut microbiota is essential in shaping many of its host''s functional attributes. One such microbiota resides in the bovine digestive tract in a compartment termed as the rumen. The rumen microbiota is necessary for the proper physiological development of the rumen and for the animal''s ability to digest and convert plant mass into food products, making it highly significant to humans. The establishment of this microbial population and the changes occurring with the host''s age are important for understanding this key microbial community. Despite its importance, little information about colonization of the microbial populations in newborn animals, and the gradual changes occurring thereafter, exists. Here, we characterized the overall bovine ruminal bacterial populations of five age groups, from 1-day-old calves to 2-year-old cows. We describe the changes occurring in the rumen ecosystem after birth, reflected by a decline in aerobic and facultative anaerobic taxa and an increase in anaerobic ones. Some rumen bacteria that are essential for mature rumen function could be detected as early as 1 day after birth, long before the rumen is active or even before ingestion of plant material occurs. The diversity and within-group similarity increased with age, suggesting a more diverse but homogeneous and specific mature community, compared with the more heterogeneous and less diverse primary community. In addition, a convergence toward a mature bacterial arrangement with age was observed. These findings have also been reported for human gut microbiota, suggesting that similar forces drive the establishment of gut microbiotas in these two distinct mammalian digestive systems.     

开展微生物学兴趣小组活动提高综合素质教育

在实施微生物学课堂教学的同时开展生物学兴趣小组活动,以学生学习为主体,充分发挥学生的主动性,对于培养学生的动手,动脑能力,提高微生物学综合素质,是一个有效的方法,实践表明,兴趣小组活动不仅有利于学生自身发展,还促进了老师的教学和科研工作。     

DNA芯片技术在微生物学研究中的应用

DNA芯片技术作为一种高通量的核酸分析方法,已经成为“后基因组时代”中研究海量序列信息的重要分析工具之一。本简述了目前一些常用以及和新出现的DNA芯片的技术原理,并从微生物基因表达谱研究,微生物基因组学研究以及微生物检测鉴定研究等多个方面概述了DNA芯片技术在微生物学中的应用,同时在对DNA芯片技术的不足进行简要分析的基础上,展望了其进一步应用的前景。     

新生儿咽部微群落研究

本文调查了一周龄新生长的口咽部菌群,结果显示有约５０％的５－７天龄的新生儿其咽部正常的甲型链球菌群未能建立,易于为致病性较强的菌株定植,这段时间是这部份新生儿的敏感“窗期”。表皮葡萄球菌也是在新生儿口咽部最早定值的“先驱菌”之一,但对新生儿似无保护作用,其致病作用表现得亦不明显。     

Multi-species biofilms defined from drinking water microorganisms provide increased protection against chlorine disinfection

A model biofilm, formed of multiple species from environmental drinking water, including opportunistic pathogens, was created to explore the tolerance of multi-species biofilms to chlorine levels typical of water-distribution systems. All species, when grown planktonically, were killed by concentrations of chlorine within the World Health Organization guidelines (0.2–5.0?mg?l^?1). Higher concentrations (1.6–40-fold) of chlorine were required to eradicate biofilm populations of these strains, ～70% of biofilms tested were not eradicated by 5.0?mg?l^?1 chlorine. Pathogenic bacteria within the model multi-species biofilms had an even more substantial increase in chlorine tolerance; on average ～700–1100?mg?l^?1 chlorine was required to eliminate pathogens from the biofilm, 50–300-fold higher than for biofilms comprising single species. Confocal laser scanning microscopy of biofilms showed distinct 3D structures and multiple cell morphologies and arrangements. Overall, this study showed a substantial increase in the chlorine tolerance of individual species with co-colonization in a multi-species biofilm that was far beyond that expected as a result of biofilm growth on its own.     

The plant pathogen Rhodococcus fascians. History,disease symptomatology,host range,pathogenesis and plant–pathogen interaction

Since 1927, outbreaks of the leafy gall disease caused by Rhodococcus fascians on annual and perennial herbaceous plants have put the ornamental plant industry at risk. More recently, Pistachio Bushy top syndrome (PBTS), a serious disease emerging in the Western United States, has been declared as a natural disaster by the U.S. Department of Agriculture. Recent developments indicate that the taxonomic position of R. fascians should be re-evaluated and circumscribed from other members of the genus. Due to the broad host range of this bacterium, economically important crops are in a vulnerable position especially with new members within the genus becoming able to interact synergistically with R. fascians to cause symptom development. The virulence strategies employed by R. fascians and the involvement of cytokinins (CKs) in its pathogenicity have been the subject of much controversy in the last years. Additionally, the detection of virulent strains of R. fascians from symptomatic tissues has been problematic for many researchers. This review focuses on plant–pathogen interaction in context with more recent findings on the association of CKs in virulence of R. fascians. Current knowledge on the worldwide distribution of the pathogen, a historical recap of its discovery and the economic impact of the disease caused by R. fascians are also described here.     

Enterococcus faecalis can be distinguished from Enterococcus faecium via differential susceptibility to antibiotics and growth and fermentation characteristics on mannitol salt agar

Enterococcus faecalis and Enterococcus faecium are both human intestinal colonizers frequently used in medical bacteriology teaching laboratories in order to train students in bacterial identification....