Lecture 12-3Microbial Evolution and Systematics 微生物进化与系统分类

School of Life Science and TechnologyShanghai Jiao Tong University

Chapter 11 inBROCK BIOLOGY OF MICROORGANISMS

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Contents

I. EARLY EARTH, THE ORIGIN OF LIFE, AND MICROBIAL DIVERSIFICATION

II. METHODS FOR DETERMINING EVOLUTIONARY RELATIONSHIPS

III. MICROBIAL EVOLUTIONIV. MICROBIAL TAXONOMY AND PHYLOGENETICS

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IV. Microbial Taxonomy and phylogenetics 微生

物分类学与系统发生学

Phylogenetics系统发生学-the study of phylogeny• family history of microbes• Genotype-based

Taxonomy分类学-science of classification, consists of two major subdisciplines:分类学的两个方面

• Identification 鉴定

• Nomenclature 命名

• Phenotype-based

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12.10 Conventional/Classical Taxonomy 传统/经典分类法

Characteristics of taxonomic value include morphology, Motility, Nutrition, physiology & ecology分类学特征

包括形态学、运动性、营养需求、生理学、生

态学特征

GC ratios can be a part of classical bacterial taxonomy

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Example of methods for identification 鉴定方法举例

Figure: 11-20

Most of the analyses require：1. pure culture of the organism2. solely phenotypic criteria

鉴定中需要纯培养物和独特的表型特征

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GC ratios in Classical Taxonomy

The same GC ratio-maybe not relatedDifferent GC ratio-surely unrelatedConclusion: Occasionally helpful but generally of minimal value

Figure: 11-21DNA base composition(GC%)

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12.11 Molecular taxonomy (chemotaxonomy) 分子分类法(化学分类法) p.320

12.11.1 DNA:DNA hybridization

12.11.2 Ribotyping核糖核酸图谱分型

12.11.3 FAME analysis脂肪酸甲酯分析法

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Figure: 11-22a

12.11.1 Genomic hybridization as a taxonomic tool 基因

组杂交法

a) DNA is isolated from test organisms. One of the DNAs is labeled (Organism 1)

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(b) Actual hybridization experiment. Excess unlabeled DNA is added in each experiment to prevent labeled DNA from reannealing with itself. Following hybridization, hybridized DNA is separated from unhybridized DNA before measuring radioactivity in the hybridized DNA only.

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c) Results. Hybridization values of 70% or above ⇒ the same species; values of at least 20-30% ⇒ two organisms in same genus. Hybridization of DNAs from totally unrelated organisms occurs at less than 10%

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12.12 Species Concept in Microbiology 微生物学中种的概念 p.324

Plants and animals: a species is considered a population of individuals that can interbreed under natural conditions, produce fertile offspring, and that is reproductively isolatedfrom other populations.高等动植物中种的概念: 该群体中的个

体之间可以在自然条件下交配, 产生可繁殖的后代, 并且和其

它群体的生物有生殖隔离.

Prokaryotes are haploid and reproduce asexually. Concepts like “the production of fertile offspring” have no meaning. 原核生物为单倍体,无性繁殖.

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Bacterial Species and Higher Taxa

A prokaryote whose 16S rRNA sequence differs by more than3% from that of all other organisms should be considered a new species. 原核生物的16SrRNA序列与其它所有生物的序列

差异大于3%，则它为一个新种。

Greater than 5-7% difference in 16S rRNA gene sequence to be different genus 16S rRNA差异大于5-7%则为不同属

70% DNA:DNA hybridization for the same species 大于70%的

DNA：DNA杂交率为同种

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Figure: 11-25

Relationship between 16S rRNA sequence similarity and genomic DNA hybridization between different pairs of organisms

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Points in the orange box represent combinations where 16S sequence similarity (>97%) and genomic hybridization (>70%) were both very high; thus, in each case, the two organisms tested were clearly the same species.

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Points in the green box represent combinations that indicate the two organisms tested were different species, and both methods show this.

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Points in the blue box indicate that the two test organisms were different species as measured by genomic DNA hybridization but not by 16S sequencing. (Why?)

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Taxonomic hierarchy分类等级

Species- Allochromatium warmingii种Genus- Allochromatium属Family- Chromatiacae科Order- Chromatiales目Class- Zymobacteria纲Phylum- Gamma Proteobacteria门(Kingdom-Bacteria界)Domain-Bacteria域

Shanghai Jiao Tong UniversityFigure: 11-23 Possible mechanism of bacterial speciation

新种产生的可能机制

When a beneficial mutation occurs within an ecotype, the cell will eventually form a population that will replace the original ecotype. As this occurs repeatedly within a given ecotype, a genetically distinct population of cells arises that represents a new species.

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10.11 The Bible of microbiologists-Bergey’s Manual伯杰氏手册

Bergey‘s Manual of Determinative Bacteriology-1st ed 1923伯杰氏细菌学鉴定手册

Bergey’s Manual of Systematic Bacteriology-2nd

ed 2001伯杰氏细菌系统分类学手册

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The First Edition of Bergey’s Manual of Systematic Bacteriology

4 volumes with 33 sections.Procaryotic groups are divided in the following manner:

Volume 1- Gram-negative bacteria of general, medical, or industrial importance;常见的、医学及工业重要的G-菌

Volume 2- Gram-positive bacteria other than actinomycetes;除放线菌外的G+菌

Volume 3- Gram-negative bacteria with distinctive properties, cyanobacteria, and archaea;有特殊性状的G-菌,蓝细菌及古生

菌

Volume 4- Actinomycetes (gram-positive filamentous bacteria)放线菌(丝状G+菌)

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The Second Edition of Bergey’s Manual of Systematic Bacteriology5 volumes:Volume 1- The Archaea, and the Deeply Branching and Phototrophic

Bacteria古生菌,深分支细菌和光合细菌

Volume 2- The Proteobateria 变形杆菌

Volume 3- The Low G+C Gram-Positive BacteriaVolume 4- The High G+C Gram-Positive BacteriaVolume 5- The Planctomycetes泛霉状菌, Spirochaetes螺旋体,

Fibrobacteres丝杆菌, Bacteroidetes拟杆菌, and Fusobacteria梭形杆菌

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