Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic.
Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
ISME J. 2019 Apr;13(4):1056-1071. doi: 10.1038/s41396-018-0332-5. Epub 2019 Jan 4.
Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).
淡水环境中充满了微生物，这些微生物在培养物集中没有对应物，也无法从基因组存储库中的遗传数据中获得。目前，由于难以为最具代表性的进化枝建立生物体模型，我们对淡水细菌进化生态学的理解受到了阻碍。为了规避基于培养的技术固有的瓶颈，我们应用生态基因组学方法来揭示标志性的淡水谱系（如浮霉菌门）的进化历史和驱动基因组结构的过程。进化历史推断表明，沉积物/土壤浮霉菌过渡到水生环境，在那里它们产生了新的淡水特有进化枝。在所分析的进化枝中，最丰富的进化枝被发现具有最专门的生活方式（增加了调控基因回路，代谢调整以矿化蛋白性下沉聚集体，嗜冷行为），并拥有最小的淡水浮霉菌基因组，突出了由生态位定向进化形成的基因组结构（通过功能和途径的丧失，这些功能和途径在新获得的淡水生态位中不需要）。
