Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
Microbiol Mol Biol Rev. 2011 Mar;75(1):14-49. doi: 10.1128/MMBR.00028-10.
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
淡水细菌处于生物地球化学循环的中心，控制着湖泊的水质。尽管如此，对于具有功能意义的湖内细菌的身份和生态学特性，我们知之甚少。分子研究已经确定了许多丰富的湖内细菌，但用于探索的方法在分类学或系统发育的广度上存在很大差异。正因为如此，在淡水细菌中形成了不一致且重叠的命名结构，这给识别这些群体之间一致的生态特征造成了重大障碍。迫切需要一个统一的领域论述。在这里，我们根据所有已发表的来自湖泊透光层的 16S rRNA 基因序列构建了一个新的淡水湖系统发育，并提出了一个统一的词汇来讨论淡水分类群。有了这个新的词汇，我们回顾了关于湖内细菌的生态学、生理生态学和分布的现有信息，并强调了新鉴定的枝原体。在我们综述的第二部分，我们对汇编的数据进行了荟萃分析，确定了细菌枝原体在生物群系之间以及在湖泊环境梯度中的分布模式。最后，我们强调了这一综述可以为未来的研究提供一个连贯的框架。
