微生物令人吃惊的多样性向科学家提出了一些棘手的问题，如在任何一个给定环境中有多少种不同细菌共同生活在一起？它们之间是什么关系？甚至还包括什么样的东西才算是细菌这样一个问题。研究人员利用从海水中提取出的DNA对这些问题进行了研究。尽管数以千计的在基因组成上明显不同的细菌共同生活在这些海水中，但它们多数都能归入彼此关系非常相近的类别中，这些类别与其他类别明显不同。预计执行类似生态功能的生物也存在这种情况，在微生物世界中这可能就代表着一个物种。
Fine-scale phylogenetic architecture of a complex bacterial community
Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.
