Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME, USA.
ISME J. 2012 Jan;6(1):113-23. doi: 10.1038/ismej.2011.84. Epub 2011 Jun 30.
Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.
最近的发现表明，光异养生物（含视蛋白的细菌（RBs）和需氧厌氧光养生物（AAPs））和化能自养生物可能对海洋和淡水生态系统的生产力具有重要意义。然而，它们的丰度和分类身份在很大程度上仍然未知。我们使用单细胞和宏基因组 DNA 测序的组合来研究栖息在温带、物理化学性质多样的淡水湖中透光带的主要光异养生物和化能自养生物。通过荧光激活细胞分选和全基因组多次置换扩增生成的 712 个单扩增基因组的多基因座测序表明，大多数世界性的淡水菌群都包含光异养生物。这些至少占浮游细菌的 10-23%，并且 RBs 是主要部分。我们的数据表明，放线菌，包括 acI、Luna 和 acSTL 等菌群，是主要的淡水 RBs。我们大大拓宽了已知的淡水 RBs 的分类范围，包括 Alpha、Beta、Gamma 和 Deltaproteobacteria、Verrucomicrobia 和 Sphingobacteria。通过对单细胞进行测序，我们发现了视蛋白基因在门间水平基因转移和重组的证据，并确定了参与这些进化过程的特定分类群。我们的数据表明，普遍存在的β变形菌 Polynucleobacter spp. 是温带淡水湖中主要的 AAP。此外，在几个β变形菌、拟杆菌门和γ变形菌的单细胞中发现了 RuBisCO（核酮糖 1,5-二磷酸羧化酶/加氧酶）基因，这表明化能自养生物在好氧细菌浮游生物中的普遍性可能比以前认为的更高。这项研究表明，单细胞 DNA 测序在解决有关未培养微生物代谢潜力和进化历史的先前未解决的问题方面具有强大的功能，而这些微生物在大多数自然环境中占据主导地位。
