第二章微生物多样性总结
微生物种群多样性(Microbial species diversity)
Species diversity is an index that incorporates the number of species in an area and also their relative abundance. It is generally a much more useful value than species richness.
微生物生态系统多样性(Microbial ecosystem diversity)
Ecosystem diversity refers to the diversity of a place at the level of ecosystems. It is contrasted with biodiversity, which refers to variation in species rather than ecosystems.
organotrophs and heterotrophs: carbon and energy are obtained
from organic chemicals (heterotrophs, E.coli, pathogens)
Ecological diversity
-salinity: from fresh water to marine and hypersaline environments (Dead sea and the Great Salt Lake, halophiles)
Types of OTUs OTUs种类
35
LB
WSA
CSEA
28
21
14
7
0
0
20
40
60
80
100
120
土壤细菌Hha I酶切数量
Number of soil bacteria digested by Hha I
不同培养基培养的细菌种系型丰度趋势线
Types of OTUs OTUs种类
28
0.1 ×0.15-0.13 m 0.2-0.3 ×0.5-1.0 m 0.1 - 0.25 m dia
0.7-0.8 ×2-3 m 0.4-0.7 ×1-3 m 0.8-1.0 m dia
4-5 m 5 ×100 m
Metabolic diversity
Phototrophs: energy is obtained from light
How does “abundance” influence this balance?
“…one reason for the high genomic diversity observed in prokaryotic communities in soil and sediments is the large populations of organisms and the capacity to accumulate large numbers of mutations.”
1.5 微生物多样性价值
❖ 科研价值 ❖ 经济价值 ❖ 生态价值
Estimates of biodiversity are problematic
Cultivated
Uncultivated (16S rDNA clone diversity)
第二节 微生物多样性研究方法
1) 传 统 平 板 培 养 方 法 ( traditional culture-dependent methods) 2) 群落水平生理学方法(community level physiological profile,CLPP) 3) 生物标记法(Biomakers) 4) 分子微生物学方法(Molecular microbial diversity )
-cell shapes: rods, cocci, spirals, filaments,amorphous, starshaped, squares,……
-cell organization: multicellular from pairs and tetrads to filaments, sheets, rosettes, microbial mats,……
Small bacteria
Bacteroides spp Bordetella pertussis Mycoplasma spp
Medium bacteria
Bacillus spp E. coli S. aureus
Large Bacteria
Anabaena spp Achromatium spp
-hydrostatic pressure: from 1 to 1400 atm (barophiles)
1.4 微生物多样性影响因素(Drive factors)
❖ 营养物质 ❖ 环境因素 ❖ 生物关系
Diversity theories
Diversity arises from the balance between speciation and extinction rates.
——From Wikipedia, the free encyclopedia
1.3 微生物多样性表现形式
❖ 形态多样性(Morphological diversity) ❖ 代谢多样性(Metabolic diversity) ❖ 生态多样性(Ecological diversity)
Morphological diversity
2.3 脂肪酸谱图法(PLFAs、WCFA-FAMEs和其它方法)
磷脂是构成生物细胞膜的主要成分,约占细胞干重的5%。在 细胞死亡时,细胞膜很快被降解,磷脂脂肪酸被迅速的代谢掉,因 此它只在活细胞中存在,十分适合于微生物群落的动态监测。另一 个重要因素是脂肪酸具有属的特异性,特殊的甲基脂肪酸已经被作 为微生物分类的依据。磷脂脂肪酸谱图分析法首先将磷脂脂肪酸部 分提取出来,然后用气相色谱分析,得出PLFA谱图。
heted from organic compounds
(halophilic Archaea and others)
autotrophs: carbon is obtained by fixing CO2 (most cyanobacteria,
2.1 传统平板培养方法
传统培养分离方法是将定量样品接种于培养基中,在一定的 温度下培养一定的时间,然后对生长的菌落计数和计算含量,并 通过在显微镜下观察其形态构造,结合培养分离过程生理生化特 性的观察鉴定种属分类特性。培养分离方法采用配比简单的营养 基质和固定的培养温度,还忽略了气候变化和生物相互作用的影 响,这种人工环境与原生境的偏差使得可培养的种类大大减少(仅 占环境微生物总数的0.1%~10%)。而且,此方法繁琐耗时,不能 用于监测种群结构的动态变化。
-cells size: average 1 to 5 microns range 0.1 to 660 microns (Thiomargarita namibiensis , giant sulfur bacteruim in Namibian sediments)
Dimensions of some bacteria
微生物多样性(Microbial Diversity)是一定区域范围 内的所有微生物种类和它们的生态环境总和。
1.2 微生物多样性的三个层次
微生物遗传多样性(Microbial genetic diversity)
Genetic diversity is a level of biodiversity that refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.
-temperature: from –12 to 113oC (Pyrolobus) and beyond (121oC)
-pH: from 0 (Thiobacillus thiooxidans) to 13 (Plectonema nostocorum) pH 0 is 1M HCl
-redox potential: from –450mV (methanogens)to + 850mV (iron bacteria)
0~48h
48~96h
96~192h
21
14
7
0
0
20
40
60
80
100
土壤细菌Hha I酶切数量
Number of soil bacteria digested by Hha I
不同培养时间培养的细菌种系型丰度趋势线
2.2 BIOLOG 鉴定系统
该方法最初由美国的BIOLOG公司于1989年开发成功,最初应用于纯种微生 物鉴定,至今已经能够鉴定包括细菌、酵母菌和霉菌在内的2000多种病原微生物 和环境微生物。
2.4 荧光原位杂交技术(fluorescent in situ hybridization, FISH)
荧光原位杂交是在20世纪80年代末在放射性原位杂交技术的 基础上发展起来的一种非放射性分子细胞遗传技术,以荧光标记取 代同位素标记而形成的一种新的原位杂交方法。它根据已知微生 物不同分类级别上种群特异的DNA序列,以利用荧光标记的特异 寡聚核苷酸片段作为探针,与环境基因组中DNA分子杂交,检测 该特异微生物种群的存在与丰度。该方法的特点是可以进行样品 的原位杂交,应用于环境中特定微生物种群鉴定、种群数量分析 及其特异微生物跟踪检测,是目前在分子微生物生态学领域应用 比较广泛的方法之一。