Most microbiome research focusses on the taxonomic composition at the species level to understand the impact of environmental factors, but intraspecific diversity has largely been ignored. To address this significant knowledge gap, we took advantage of the simple, culturable microbiome of Drosophila. First, we documented that natural populations of D. simulans harbor three diverged clades of Lactiplantibacillus plantarum, a key nutritional symbiont. We studied the distinct ecological roles of these three clades by exposing flies with their native microbiome to two temperature regimes in the laboratory. Tracking the three clades within the complete Drosophila microbiome over a period of more than 10 years at two temperatures, we identified strikingly distinct dynamics in response to the selection regime. We confirmed the functional differentiation of the three clades using in vitro growth measurements and in vivo mono-association assays. Our results highlight that environmental selection operates at the subspecies level. Therefore, we conclude that the functional diversification of the microbiome can only be understood when intra- and interspecific diversity is considered.
大多数微生物组研究聚焦于物种层面的分类组成以理解环境因素的影响，但种内多样性在很大程度上被忽视了。为填补这一重大知识空白，我们利用了果蝇简单且可培养的微生物组。首先，我们记录了自然种群中的拟果蝇存在三个分化明显的植物乳杆菌分支，这是一种关键的营养共生菌。通过在实验室中将携带天然微生物组的果蝇暴露于两种温度条件下，我们研究了这三个分支的不同生态功能。在超过10年的时间里，我们在两种温度下追踪了果蝇完整微生物组中的这三个分支，发现它们对选择条件的反应存在显著不同的动态变化。通过体外生长测量和体内单关联实验，我们证实了这三个分支的功能分化。我们的结果表明，环境选择在亚种层面发挥作用。因此，我们得出结论：只有同时考虑种内和种外多样性，才能理解微生物组的功能多样化。
Gracia Alvira, J. B. et al. · CC-BY 4.0