Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern
Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern
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DOI：
10.1046/j.1462-2920.2002.00297.x
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发表时间：
2002-06-01
影响因子：
5.1
通讯作者：
Pedrós-Alió, C
中科院分区：
文献类型：
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作者：
Casamayor, EO;Massana, R;Pedrós-Alió, C
居住在多池太阳盐场的微生物群落进行了分析和比较，使用SSU rRNA聚合酶链反应（PCR）为基础的指纹图谱进行了平行的四个实验室。从海水（3.7%）NaCl沉淀（37%）的盐度梯度进行了研究，细菌，古细菌和真核生物，实验室应用自己的技术和协议，对同一组样品。从所有盐浓度检索所有三个域的成员。三个指纹技术：变性梯度凝胶电泳（DGGE），核糖体内部间隔区分析（RISA），和末端限制性片段长度多态性（T-RFLP）。此外，每个实验室都使用自己的生物量收集方法和DNA提取方案。使用DGGE和RISA用不同的“结构域特异性”引物组处理原核生物。由一个实验室使用DGGE和T-RFLP分析真核生物，但靶向相同的18 S rDNA位点。指纹图谱通过聚类分析和非度量多维标度图进行比较。这项工作允许快速比较微生物组合，并确定每个实验室提供的图片与其他实验室的图片相似的程度。在原核生物中形成两个主要的、基于盐度的样品组（4-15%和22-37%盐度）在所有实验室中是一致的。当出现其他聚类时，这是在每种情况下使用的特定技术和方案的结果，但更多地受到所使用的引物组的影响。真核微生物从池塘到池塘的变化更多; 4-5%和8-37%的盐度，但检测到两个主要群体。在最初的池塘中，Eukarya的操作分类单位（OTU）的数量最多，而Eukarya的条带数量最少。伪像出现在DGGE从池塘微生物丰富度极低。另一方面，不同的16 S rDNA片段具有相同的限制或内转录间隔区（ITS）长度的T-RFLP和RISA分析，分别是主要的限制，在池塘中具有最高的OTU丰富度。然而，尽管特定的分类组成可能会因方案而异，但微生物组合的一般结构得到了保持。
Microbial communities inhabiting a multipond solar saltern were analysed and compared using SSU rRNA polymerase chain reaction (PCR)-based fingerprintings carried out in parallel by four laboratories. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied for Bacteria, Archaea and Eukarya, and laboratories applied their own techniques and protocols on the same set of samples. Members of all three domains were retrieved from all salt concentrations. Three fingerprinting techniques were used: denaturing gradient gel electrophoresis (DGGE), ribosomal internal spacer analysis (RISA), and terminal-restriction fragments length polymorphism (T-RFLP). In addition, each laboratory used its own biomass collection method and DNA extraction protocols. Prokaryotes were addressed using DGGE and RISA with different 'domain-specific' primers sets. Eukaryotes were analysed by one laboratory using DGGE and T-RFLP, but targeting the same 18S rDNA site. Fingerprints were compared through cluster analysis and non-metric multidimensional scaling plots. This exercise allowed fast comparison of microbial assemblages and determined to what extent the picture provided by each laboratory was similar to those of others. Formation of two main, salinity-based groups of samples in prokaryotes (4-15% and 22-37% salinity) was consistent for all the laboratories. When other clusters appeared, this was a result of the particular technique and the protocol used in each case, but more affected by the primers set used. Eukaryotic microorganisms changed more from pond to pond; 4-5% and 8-37% salinity were but the two main groups detected. Archaea showed the lowest number of bands whereas Eukarya showed the highest number of operational taxonomic units (OTUs) in the initial ponds. Artefacts appeared in the DGGE from ponds with extremely low microbial richness. On the other hand, different 16S rDNA fragments with the same restriction or internal transcribed spacer (ITS) length were the main limitations for T-RFLP and RISA analyses, respectively, in ponds with the highest OTUs richness. However, although the particular taxonomic composition could vary among protocols, the general structure of the microbial assemblages was maintained.