Taxonomy and classification of Rickettsiae

During the recent 20 years the improvement of the methodological research basis including the molecular and genetic analysis of microorganisms parasites of eukaryotic cells, led to considerable changes in the taxonomy and classification of rickettsiae. This problem was not discussed in the Russian literature. At present the term "rickettsiae" conventionally embraces the group of microorganisms of the class Proteobacteria, nominated as species belonging to the genera Rickettsia, Orientia, Ehrlichia, Coxiella and Bartonella. An original scheme of the modern taxonomy of rickettsiae, pathogenic for man, is presented. The scheme is made with due regard to their phenotypic, clinico-epidemiological and genetic features.     

Taxonomy of Lactobacilli and Bifidobacteria

Genera Lactobacillus and Bifidobacterium include a large number of species and strains exhibiting important properties in an applied context, especially in the area of food and probiotics. An updated list of species belonging to those two genera, their phylogenetic relationships and other relevant taxonomic information are reviewed in this paper. The conventional nature of taxonomy is explained and some basic concepts and terms will be presented for readers not familiar with this important and fast-evolving area, which importance is often underestimated. The analysis of biodiversity and its cataloguing, i.e. taxonomy, constitute the basis for applications and scientific communication: reliable identification and correct naming of bacterial strains are not only primary aims of taxonomic studies, but also fundamental elements in an applied context, for the tracking of probiotic strains and a non fraudulent labelling of fermented milks and pharmaceutical products containing probiotic microorganisms. A number of resources freely available have been listed and their use is suggested for people concerned with different aspects of taxonomy. Some perspectives in taxonomy have been outlined, in particular considering the role of culture independent analyses to reveal the still unknown and uncultured microorganisms. Finally, the impact of the availability of whole-genome sequences in taxonomy is briefly explained: they have already begun to give insights on bacterial evolution, which will surely have implications on taxonomy, even if the analysis of data for lactic acid bacteria is still limited to few species.     

The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century

The beginning of modern microbiology can be traced back to the 1870s, and it was based on the development of new concepts that originated during the two preceding centuries on the role of microorganisms, new experimental methods, and discoveries in chemistry, physics, and evolutionary cell biology. The crucial progress was the isolation and growth on solid media of clone cultures arising from single cells and the demonstration that these pure cultures have specific, inheritable characteristics and metabolic capacities. The doctrine of the spontaneous generation of microorganisms, which stimulated research for a century, lost its role as an important concept. Microorganisms were discovered to be causative agents of infectious diseases and of specific metabolic processes. Microscopy techniques advanced studies on microorganisms. The discovery of sexuality and development in microorganisms and Darwin's theory of evolution contributed to the founding of microbiology as a science. Ferdinand Cohn (1828-1898), a pioneer in the developmental biology of lower plants, considerably promoted the taxonomy and physiology of bacteria, discovered the heat-resistant endospores of bacilli, and was active in applied microbiology.     

Halophilic anaerobic fermentative bacteria

In hypersaline environments bacteria are exposed to a high osmotic pressure caused by the surrounding high salt concentrations. Halophilic microorganisms have specific strategies for balancing the osmotic pressure and surviving in these extreme conditions. Halophilic fermentative bacteria form taxonomically and phylogenetically a coherent group mainly belonging to the order Halanaerobiales. In this review, halophilic anaerobic fermentative bacteria in terms of taxonomy and phylogeny, special characteristics, survival strategies, and potential for biotechnological applications in a wide variety of branches, such as production of hydrogen, are discussed.     

厌氧氨氧化细菌的研究进展

厌氧氨氧化是指微生物在无氧条件下,以NO2-为电子受体,将NH4+氧化成N2的过程,该过程主要由浮霉菌门下的厌氧氨氧化细菌参与.厌氧氨氧化细菌广泛存在于海洋生态系统、淡水生态系统、陆地生态系统及其他一些特殊生境中,其在废水生物脱氮和地球氮循环中扮演着重要角色.本文从厌氧氨氧化细菌的发现历程、种类、特性、代谢途径、分布、...     

醋酸菌多相分类研究进展

醋酸菌是一大群革兰氏染色阴性、绝对好氧的细菌的总称, 能将乙醇或糖类不完全氧化为有机酸。醋酸菌的分类在近30年经历了很大变化, 早期的分类系统主要以表型和生化特征为基础。如今, 大多采用结合表型、化学分类法和基因型数据的多相分类法对醋酸菌进行分类。本文综述了醋酸菌的多相分类研究进展, 主要介绍了醋酸菌的现行分类情况及表型分类、化学分类和基因分型等方法在醋酸菌分类中的应用。     

家蚕肠道细菌群体调查与分析

目前,环境微生物中绝大部分是无法获得纯培养的。为了比较全面地了解家蚕肠道的细菌群体结构,研究采用了非培养法和传统培养法相结合的方法进行调查分析。非培养法是先直接提取家蚕肠道中的微生物群体基因组DNA,用PCR法扩增细菌16S rRNA基因,建立16S rDNA文库;再以限制性片段长度多态性(RFLP)方法从文库中筛选可能不同细菌来源的克隆,并测定其核苷酸序列。将所获得的序列与GenBank数据库进行BLAST比对分析,并通过系统发育分析,推测它们可能代表的细菌种属,以及对家蚕生长发育所起的作用。结果表明,家蚕肠道中的细菌主要是节杆菌属、乳杆菌属、大肠杆菌属、芽胞杆菌属、葡萄球菌属、假单胞菌属。它们在家蚕消化利用桑叶和疾病预防中可能有着重要意义。非培养法和培养法均有各自的长处和不足,两者具有较强的互补性。     

真菌DNA条形码技术研究进展

DNA条形码(DNA barcoding)技术作为一门新兴的物种鉴定方法以其灵敏、精确、方便和客观的优势,在动植物和微生物的分类鉴定中已经得到广泛应用.真菌鉴定中常用作标准条形码的是核核糖体DNA内转录间隔区(Internal transcribed spacer,ITS),如今也有一些新型条形码被发现和应用到实际操作中,如微条形码、ND6、EF3.本文对DNA条形码技术的产生和发展做出了总结,通过研究其在真菌中应用的实际案例分析了DNA条形码技术的优缺点及发展趋势,并指出DNA条形码技术将以全新的视角来弥补传统分类学的不足,最终实现生物自身的序列变异信息与现有形态分类学的结合.     

Taxonomic heterogeneity of the collection strains of fluorescent pseudomonads

Typing of 13 strains of fluorescent pseudomonads from the Belarusian collection of nonpathogenic microorganisms (BIM) by ERIC-PCR and BOX-PCR revealed high level of genetic heterogeneity in bacteria, most of which have been previously identified as Pseudomonas fluorescens according to the classical scheme. Evaluation of the similarities of the 16S rRNA gene sequences and their phylogenetic analysis excluded affiliation of the bacteria under study within the same species and allowed them to be distributed within three relatively distant clusters of the genus Pseudomonas phylogenetic tree. While eight strains fell into the phylogenetic group of P. fluorescens, only one of them could be identified as P. fluorescens. Four strains clustered within the P. vancouverensis phylogenetic group, formed by new species, which have been described mainly according to the evaluation of genome relationships. One bacterium was related to a stable branch that did not contain any type strains of the known Pseudomonas spp. These results indicate taxonomic heterogeneity of collection strains of the fluorescent pseudomonads and demonstrate the necessity of identification of them considering the requirements of phylogenetic bacterial taxonomy.     

Indole-3-acetic acid: A widespread physiological code in interactions of fungi with other organisms

Plants as well as microorganisms, including bacteria and fungi, produce indole-3-acetic acid (IAA). IAA is the most common plant hormone of the auxin class and it regulates various aspects of plant growth and development. Thus, research is underway globally to exploit the potential for developing IAA-producing fungi for promoting plant growth and protection for sustainable agriculture. Phylogenetic evidence suggests that IAA biosynthesis evolved independently in bacteria, microalgae, fungi, and plants. Present studies show that IAA regulates the physiological response and gene expression in these microorganisms. The convergent evolution of IAA production leads to the hypothesis that natural selection might have favored IAA as a widespread physiological code in these microorganisms and their interactions. We summarize recent studies of IAA biosynthetic pathways and discuss the role of IAA in fungal ecology.     

Microbial metabolism of quorum-sensing molecules acyl-homoserine lactones, γ-heptalactone and other lactones

The cell-to-cell communication of microorganisms is known to be via exertion of certain chemical compounds (signal molecules) and is referred to as quorum sensing (QS). QS phenomenon is widespread in microbial communities. Several Gram-positive and Gram-negative bacteria and fungi use lactone-containing compounds (e.g. acyl-homoserine lactones (AHLs), γ-heptalactone, butyrolactone-I) as signalling molecules. The ability of microorganisms to metabolise these compounds and the mechanisms they employ for this purpose are not clearly understood. Many studies, however, have focused on identifying AHL and other lactone-degrading enzymes produced by bacteria and fungi. Various strains that are able to utilise these signalling molecules as carbon and energy sources have also been isolated. In addition, several reports have provided evidence on the involvement of lactones and lactone-degrading enzymes in numerous biological functions. These studies, although focused on processes other than metabolism of lactone signalling molecules, still provide insights into further understanding of the mechanisms employed by various microorganisms to metabolise the QS compounds. In this review, we consider conceivable microbial strategies to metabolise AHL and other lactone-containing signalling molecules such as γ-heptalactones.     

Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.     

Identification of 5-aminovaleric acid as a characteristic product of metabolism of various Clostridium species

An unusual ninhydrin-positive compound has been isolated from feces of accidentally contaminated Sprague-Dawley autbred rats and identified by mass spectrometry and 1H-NMR spectroscopy techniques as 5-aminovaleric acid. The described procedure of isolation, purification and structure determination can be recommended as a general method of identification of unusual ninhydrin-positive compounds in complex mixtures of biological origin. The 5-aminovaleric acid was found to be produced by an anaerobic bacterium Clostridium bifermentans. It is shown that not all Clostridium spp. excrete his amino acid and that the majority of microorganisms, normally inhabiting intestine of rats, simians and man, do not possess this ability. On the basis of data obtained, the test for 5-aminovaleric acid is proposed to be included into the taxonomy of bacteria.     

The potential of in situ hybridization and an immunogold assay to identify Legionella associations with other microorganisms.

Based on in vitro studies, bacteria in the genus Legionella are believed to multiply within protozoa such as amoebae in aquatic environments. Current methods used for detection of Legionella species, however, are not designed to show this relationship. Thus the natural intimate association of Legionella with other microorganisms remains to be clearly documented and the extent to which protozoa might be infected with Legionella species remains undefined. In this report we describe methods based on the use of Legionella specific reagents that would prove useful in describing its associations with other microorganisms. An immunogold and in situ hybridization technique have the potential to demonstrate the natural occurrence of Legionella species in free-living amoebae. In preliminary observations, however, bacteria reactive with Legionella specific reagents were often not intimately associated with amoebae. Bacteria occurred as free single cells, as cell aggregates, in proximity to other cells and debris, and only occasionally in close proximity to amoebae. Although some Legionella species replicate within amoebae, these preliminary observations suggest the bacteria may be encountered most frequently as extracellular microorganisms, either free-floating or in association with other structures or microorganisms. The future use of these techniques will aid in the elucidation of any naturally occurring relationships between Legionella species and other microorganisms.     

植物病原棒形细菌的分类研究进展

植物病原棒形细菌从棒杆菌属中独立出来之后,对于其中各菌分类地位的确立一直有较多争议。近年来已分别归入棒形杆菌属（Clavibacter）、短小杆菌属（Curtobacterium）、节杆菌属（Arthrobacter）、红球菌属（Rhodococcus）和拉氏杆菌属（Rathayibacter）5个属中。但此后又有人提出有些属中仍有异质性。这些分类上的变化主要是由于分类手段逐渐由传统的形态学分类方法向分子生物学方法和多相分类法过度。新的方法还在不断的完善之中。此外,植物病原棒形细菌分类系统的完善还有赖于植物病理学和微生物学家等多学科科学家的合作。     

Taxonomic position of the Rickettsiae: Current knowledge

Abstract: The term rickettsiae initially encompassed all intracellular bacteria. Early rickettsial taxonomy was based on a comparison of a few phenotypic characteristics and recently, molecular studies brought new bases for rickettsial taxonomy. All rickettsial species studied so far belong to the alpha and gamma groups of the Proteobacteria. Ehrlichiae complex groups Cowdria ruminantium, Anaplasma marginate and Wolbachia pipientis and the related parthenogenesis and cytoplasmic incompatibility bacteria, whereas Rochalimaea species group with Bartonella bacilliformis. Rickettsia tsutsugainushi may form an independent lineage, whereas molecular data allow to regroup serologically defined typhus and spotted fever group rickettsiae. The true scale of Rickettsia and Coxiella genera remain to be determined.     

《伯杰氏鉴定细菌学手册》和“伯杰氏国际系统微生物学学会”历史回顾、发展现状及未来展望

2023年是《伯杰氏鉴定细菌学手册》出版一百周年。《伯杰氏鉴定细菌学手册》的诞生，旨在建立起原核微生物分类的明确标准，开启对原核微生物分类学探索的使命。随着生物学、物理学、化学、分子生物学、生物信息学及其相关研究技术的发展及学科交叉，微生物分类学逐渐发展为以系统发育和多相分类为基础、研究微生物物种进化与生物学特性和物种间相关性的学科，因此新发现的微生物物种及其生物学特征信息增加迅猛，该手册在2015年改名为《伯杰氏古菌与细菌系统学手册》，并采用了电子版，使得更新快捷，为原核微生物系统分类学领域注入新的生机和活力。《伯杰氏鉴定细菌学手册》是微生物系统分类学的经典之作，为微生物学者提供微生物物种分类信息的同时，也在引领该领域的学者探索更为广阔的微生物世界。“伯杰氏国际系统微生物学学会”于2009年成立，旨在促进国际微生物领域的学术交流，推动原核微生物系统分类学的发展。本综述全面回顾了《伯杰氏鉴定细菌学手册》和“伯杰氏国际系统微生物学学会”的发展历史及最新进展，并对其未来发展方向进行了展望。     

Polar and Alpine Microbial Collection (PAMC): a culture collection dedicated to polar and alpine microorganisms

Microorganisms in polar areas may have important ecological roles in biogeochemical cycles and the food chain. They are adapted to polar environments by means of special physiological adaptation mechanisms that include cold-adapted enzymes and cryoprotectants such as exopolysaccharides. Culture collections for polar microorganisms can provide research resources for ecological and physiological studies. The Polar and Alpine Microbial Collection (PAMC) is a specialized culture collection for maintenance and distribution of polar and alpine microorganisms. A database system was developed to share important data fields with DarwinCore2 and Ocean Biogeographic Information System database schemas. Approximately 1,500 out of 5,500 strains maintained in PAMC have been identified and belonged primarily to the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Many of the microbial strains can grow at low temperature and produce proteases, lipases, and/or exopolysaccharides. PAMC provides search tools based on keywords such as taxonomy, geographical origin, habitat, and physiological characteristics. Biological materials and information provided by PAMC will be important resources for ecological and physiological studies on polar and alpine microorganisms.     

Microbial responses to environmental arsenic

Microorganisms have evolved dynamic mechanisms for facing the toxicity of arsenic in the environment. In this sense, arsenic speciation and mobility is also affected by the microbial metabolism that participates in the biogeochemical cycle of the element. The ars operon constitutes the most ubiquitous and important scheme of arsenic tolerance in bacteria. This system mediates the extrusion of arsenite out of the cells. There are also other microbial activities that alter the chemical characteristics of arsenic: some strains are able to oxidize arsenite or reduce arsenate as part of their respiratory processes. These type of microorganisms require membrane associated proteins that transfer electrons from or to arsenic (AoxAB and ArrAB, respectively). Other enzymatic transformations, such as methylation-demethylation reactions, exchange inorganic arsenic into organic forms contributing to its complex environmental turnover. This short review highlights recent studies in ecology, biochemistry and molecular biology of these processes in bacteria, and also provides some examples of genetic engineering for enhanced arsenic accumulation based on phytochelatins or metallothionein-like proteins.     

微生物腐蚀及腐蚀机理研究进展

在不同的环境中,不同种类的微生物能在材料上附着繁殖,其生命活动会引起或加剧材料的腐蚀。根据种类及功能的不同,腐蚀微生物可以分为硫酸盐还原菌、硫氧化菌、产酸菌、铁氧化细菌、铁还原细菌、硝酸盐还原菌以及产粘液细菌等。微生物腐蚀几乎能使所有现用的材料受到严重影响,破坏材料的结构与性能,在建筑、运输管道、工业环境(石油化工等)以及海洋环境中造成巨大的安全隐患和财产损失。本文概述了目前发现的腐蚀相关微生物的类群和特性,以及相对应的微生物腐蚀机理,为防护和控制材料的微生物腐蚀提供理论指导。