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.     

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.     

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。     

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.     

Flow cytometry applications in the food industry

Flow cytometry has become a valuable tool in food microbiology. By analysing large numbers of cells individually using light-scattering and fluorescence measurements, this technique reveals both cellular characteristics and the levels of cellular components. Flow cytometry has been developed to rapidly enumerate microorganisms; to distinguish between viable, metabolically active and dead cells, which is of great importance in food development and food spoilage; and to detect specific pathogenic microorganisms by conjugating antibodies with fluorochromes, which is of great use in the food industry. In addition, high-speed multiparametric data acquisition, analysis and cell sorting, which allow other characteristics of individual cells to be studied, have increased the interest of food microbiologists in this technique. This mini-review gives an overview of the principles of flow cytometry and examples of the application of this technique in the food industry.     

医学微生物学讨论式教学的意义

医学微生物学是医学基础课,为了提高教学质量,通过讨论式的微生物学教学方式,启发培养学生的多向思维能力、创新能力和开拓精神,拉近学生与现代生命科学发展的距离,使微生物学课程的学习成为对微生物学探索的开始,采用讨论微生物学新进展的教学方式,探索最合适的培养高素质人才的有效途径。     

生物工程专业微生物学实验教学改革探讨

针对生物工程专业微生物学实验教学改革中遇到的问题,结合自身教学实践,从实验时序性、开放性实验、考核考勤体制及教学方法等方面,提出如何提高微生物学实验教学质量、提高学生创新能力和学习能力。     

Research progress in genomics of environmental and industrial microorganisms

Microbes contribute to geochemical cycles in the ecosystem. They also play important roles in biodegradation and bioremediation of contaminated environments, and have great potential in energy conversion and regeneration. Up to date, at least 150 genomes of non-pathogenic microbes have been sequenced, of which, the majority are bacteria from various environments or of industrial uses. The emerging field ‘metagenomics’ in combination with the high-throughput sequencing technology offers opportunities to discover new functions of microbes in the environment on a large scale, and has become the ‘hot spot’ in the field of environmental microbiology. Seven genomes of bacteria from various extreme environments, including high temperature, high and low pressure, and extreme acidic regions, have been sequenced by researchers in China, leading to the discovery of metabolic pathways, genetic functions and new enzymes, which are related to the niches those bacteria occupy. These results were published in Nature, PNAS, Genome Research and other top international journals. In the meantime, several groups in China have started ‘metagenomics’ programs. The outcomes of these researches are expected to generate a considerable number of novel findings, taking Chinese researchers to the frontier of genomics for environmental and industrial microorganisms. Supported by the National High-tech Research Development Program of China (Grant No. 2007AA02Z106, 2007AA021303 and 2007AA020703) and the National Natural Science Foundation of China (Grant No. 30530010)     

Teaching of microbiology in Brazil: progress or stagnation?

There is a severe shortage of trained microbiologists in Brazil which is hampering the development and expansion of microbiology/biotechnology research, the development of the biotechnology industries and environmental control agencies. Even some medical areas are affected. The reason for this situation lies in the deficient teaching of microbiology, where undergraduate courses in the biological sciences contain little or no microbiology, and in the low number of professionals that are produced. There are a few post-graduates courses in microbiology but these have high costs and little capacity for expansion. There is a need for incentives for the establishment of more undergraduate university courses, more practical training in specific areas, courses for retraining or updating of professionals already at work and specific programmes by the funding agencies.The objective of this article is to encourage discussion about the present state and the future of the teaching of Microbiology in Brazil. It may also be useful for other countries in the same situation.J.R. Jardim Freire is with the Department of Soil Science, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 7712, 91540-000 Porto Alegre, RS, Brazil; W. Gambale is with the Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil.     

国外环境生物技术的发展和展望

环境生物技术在社会的发展中起着越来越重要的积极作用,相关产业也随之迅速发展起来,环境治理要依赖对生物,尤其是微生物及其生理,生化特性的了解和认识,从而可以对其生理,生化和遗传方面的性能加以利用。在这方面,分离解毒微生物及阐明毒物降解过程和机理仍是现在研究的焦点,与此同时,对遗传基因方面的研究和利用还有许多研究工作待进行,监测和跟踪微生物已进入到了分子水平,而传感监测方面已有一些可喜的成果正在向生产转化,生物修复作为消除污染的手段正治理中发挥巨大的作用,但环境保护的根本应是在于进行无污染产生的生产,也称之为绿色生产,未来的社会中,环境生物技术仍对将社会产生巨大的影响,对环境保护起到重要的作用,特别是在新型生物能源的开发和探索方面,本文同时也对世界不同地区在环境生物技术的发展及其特点进行了综述。     

快速发展中的环境微生物科学与技术—“第十二次全国环境微生物学学术研讨会”专刊序言

第十二次全国环境微生物学术研讨会于2009年11月在武汉华中科技大学顺利召开,本次会议围绕"环境微生物与人类健康"的主题,在环境微生物学前沿、微生物与环境健康及人类健康、环境微生物资源挖掘与利用,以及环境微生物技术与环境污染防治、生态修复、废弃物资源化利用和再生能源等诸多领域展开深入研讨,充分反映了我国环境微生物学界取得的最新进展,为了展现国内环境微生物及相关交叉领域科研工作者取得的最新进展,《微生物学通报》针对"第十二次全国环境微生物学术研讨会"组织出版了这期"环境微生物专刊",期望该专刊的出版有助于促进我国环境微生物学相关领域的交流和发展。     

Phylogenetic Estimation of Community Composition and Novel Eukaryotic Lineages in Base Mine Lake: An Oil Sands Tailings Reclamation Site in Northern Alberta

Reclamation of anthropogenically impacted environments is a critical issue worldwide. In the oil sands extraction industry of Alberta, reclamation of mining‐impacted areas, especially areas affected by tailings waste, is an important aspect of the mining life cycle. A reclamation technique currently under study is water‐capping, where tailings are capped by water to create an end‐pit lake (EPL). Base Mine Lake (BML) is the first full‐scale end‐pit lake in the Alberta oil sands region. In this study, we sequenced eukaryotic 18S rRNA genes recovered from 92 samples of Base Mine Lake water in a comprehensive sampling programme covering the ice‐free period of 2015. The 565 operational taxonomic units (OTUs) generated revealed a dynamic and diverse community including abundant Microsporidia, Ciliata and Cercozoa, though 41% of OTUs were not classifiable below the phylum level by comparison to 18S rRNA databases. Phylogenetic analysis of five heterotrophic phyla (Cercozoa, Fungi, Ciliata, Amoebozoa and Excavata) revealed substantial novel diversity, with many clusters of OTUs that were more similar to each other than to any reference sequence. All of these groups are entirely or mostly heterotrophic, as a relatively small number of definitively photosynthetic clades were amplified from the BML samples.     

Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats,are phylogenetically diverse and can be pathogenic

The type III secretion system (T3SS) is an important virulence factor of pathogenic bacteria, but the natural occurrence of variants of bacterial plant pathogens with deficiencies in their T3SS raises questions about the significance of the T3SS for fitness. Previous work on T3SS-deficient plant pathogenic bacteria has focused on strains from plants or plant debris. Here we have characterized T3SS-deficient strains of Pseudomonas syringae from plant and nonplant substrates in pristine nonagricultural contexts, many of which represent recently described clades not yet found associated with crop plants. Strains incapable of inducing a hypersensitive reaction (HR⁻) in tobacco were detected in 65% of 126 samples from headwaters of rivers (mountain creeks and lakes), snowpack, epilithic biofilms, wild plants and leaf litter and constituted 2 to 100% of the P. syringae population associated with each sample. All HR⁻ strains lacked at least one gene in the canonical hrp/hrc locus or the associated conserved effector locus, but most lacked all six of the genes tested (hrcC, hrpL, hrpK1, avrE1 and hrpW1) and represented several disparate phylogenetic clades. Although most HR⁻ strains were incapable of causing symptoms on cantaloupe seedlings as expected, strains in the recently described TA-002 clade caused severe symptoms in spite of the absence of any of the six conserved genes of the canonical T3SS according to PCR and Southern blot assays. The phylogenetic context of the T3SS variants we observed provides insight into the evolutionary history of P. syringae as a pathogen and as an environmental saprophyte.     

工业微生物学教学内容与方法改革探讨

工业微生物学单独作为教程的时间较短, 在教学内容和教学方法上, 还需经过多方面的改革探讨。从基础理论知识与科研, 实验教学及生产生活实践的有机结合等角度对教学内容改革进行了探讨;采用计算机辅助教学(CAI)模式, 把基于问题的学习(PBL)和基于案例的学习(CBS)的启发式教学方法相结合, 引入部分双语教学的方法, 对教学方法进行了改革。通过以上两方面的探讨实践, 学生对工业微生物学产生了较浓厚的兴趣, 达到了教改的目的。     

与时俱进的我国环境微生物学研究

环境微生物学作为微生物学与环境科学相结合的交叉学科,已经在环境污染治理、废弃物资源化利用和生物地球化学循环等方面发挥着重要作用。《微生物学通报》本期推出的"环境微生物学主题刊"报道了专论与综述16篇、研究报告17篇,内容涵盖环境微生物生态学及生物修复、环境微生物资源的发掘与利用、环境微生物学研究前沿、环境污染修复与微生物多样性、环境微生物生理学及生物制剂等应用领域,期望该主题刊的出版有助于加强我国环境微生物学研究者间的交流和合作,推动环境微生物学学科的进一步发展。