Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea
Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea
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DOI：
10.1128/aem.69.5.2430-2443.2003
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发表时间：
2003-05-01
影响因子：
4.4
通讯作者：
Scanlan, DJ
中科院分区：
文献类型：
--
作者：
Fuller, NJ;Marie, D;Scanlan, DJ
从红海和其他几个海洋环境中的31个新的培养分离物的16 S核糖体DNA（rDNA）测序的海洋聚球藻属的成员之间的系统发育关系进行了确定。这揭示了一个大的遗传多样性与早期的工作一致的海洋聚球藻集群，但也确定了三个新的分支以前没有认识到。系统发育分析表明，一个分支，含有耐盐菌株缺乏藻红蛋白（PE），包括菌株的能力，或不，利用硝酸盐作为唯一的N源，其中聚集在MC-A（聚球藻亚群5.1）谱系。海洋聚球藻基因组中存在两个拷贝的16 S rRNA基因，对来自聚球藻属菌株VVH 7803的这些拷贝和来自聚球藻属菌株WH 8102的基因组信息的克隆和测序表明它们是相同的。基于16 S rDNA序列信息，设计了海洋聚球藻属的分支特异性寡核苷酸，并对其特异性进行了优化。使用斑点杂交技术，这些探针被用来确定在1999年4月期间的最大聚球藻的时间在红海的海洋聚球藻种群的原位社区结构。一个单一的分支的基因型代表的优势被发现，这些基因型是常见的菌株分离到文化。相反，缺乏PE的菌株也相对容易分离到培养物中，仅代表聚球藻种群的一小部分。对应于充分研究的实验室菌株的基因型在红海的分层水柱中也表现不佳。
Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain VVH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.