Winans Nathan J, Walter Alec, Chouaia Bessem, Chaston John M, Douglas Angela E, Newell Peter D
Department of Entomology, Cornell University, Ithaca, NY, USA.
Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, USA.
Mol Ecol. 2017 Sep;26(17):4536-4550. doi: 10.1111/mec.14232. Epub 2017 Jul 24.
Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two habitat types are ecologically and evolutionarily distinct is largely unknown. This study investigated the scale and pattern of genetic differentiation between bacteria of the family Acetobacteraceae isolated from the guts of Drosophila fruit flies, plant material and industrial fermentations. Genome-scale analysis of the phylogenetic relationships and predicted functions was conducted on 44 Acetobacteraceae isolates, including newly sequenced genomes from 18 isolates from wild and laboratory Drosophila. Isolates from the external environment and Drosophila could not be assigned to distinct phylogenetic groups, nor are their genomes enriched for any different sets of genes or category of predicted gene functions. In contrast, analysis of bacteria from laboratory Drosophila showed they were genetically distinct in their universal capacity to degrade uric acid (a major nitrogenous waste product of Drosophila) and absence of flagellar motility, while these traits vary among wild Drosophila isolates. Analysis of the competitive fitness of Acetobacter discordant for these traits revealed a significant fitness deficit for bacteria that cannot degrade uric acid in culture with Drosophila. We propose that, for wild populations, frequent cycling of Acetobacter between Drosophila and the external environment prevents genetic differentiation by maintaining selection for traits adaptive in both the gut and external habitats. However, laboratory isolates bear the signs of adaptation to persistent association with the Drosophila host under tightly defined environmental conditions.
在动物体内以及外部环境中均已鉴定出多种细菌类群，但来自这两种栖息地类型的相关细菌在生态和进化上的差异程度在很大程度上尚不清楚。本研究调查了从果蝇肠道、植物材料和工业发酵中分离出的醋杆菌科细菌之间的遗传分化规模和模式。对44株醋杆菌科分离株进行了系统发育关系和预测功能的基因组规模分析，其中包括来自野生和实验室果蝇的18株新测序基因组。来自外部环境和果蝇的分离株无法归入不同的系统发育组，它们的基因组也没有富集任何不同的基因集或预测基因功能类别。相比之下，对来自实验室果蝇的细菌分析表明，它们在降解尿酸（果蝇的主要含氮废物）的普遍能力以及缺乏鞭毛运动方面在遗传上是不同的，而这些特征在野生果蝇分离株中有所不同。对具有这些性状差异的醋化醋杆菌的竞争适应性分析表明，在与果蝇共培养时，不能降解尿酸的细菌存在显著的适应性缺陷。我们提出，对于野生种群而言，醋杆菌在果蝇和外部环境之间的频繁循环通过维持对在肠道和外部栖息地均具有适应性的性状的选择来防止遗传分化。然而，实验室分离株表现出在严格定义的环境条件下适应与果蝇宿主持续关联的迹象。
