Assessing the role of host-microbe interaction in adaptation using Drosophila melanogaster and acetic acid bacteria as a model

尽管越来越明显的是，宿主相关微生物是适应的重要促进者，但今天旨在了解生物如何适应环境的大多数研究仍然只关注宿主生物。 我们的目标是通过使用D.黑腹菌和醋酸菌（AAB）作为模型。D.黑腹果蝇和AAB生活在这样的环境中，其中主要的食物来源，成熟的果实，是短暂的，通常是片状的，高糖和低氨基酸含量。在实验室缺乏氨基酸的条件下，AAB可促进果蝇生长，缩短发育时间达10天。因为我们和其他人已经表明，AAB通常与野生捕获的D。黑腹果蝇，这似乎是合理的假设，他们可以有助于苍蝇健身和适应自然条件下，以及。因此，与促进生长的AAB相关联并将其运输到新的食物源和产卵场所应该是苍蝇适应的。与此同时，不动的细菌可以受益于苍蝇介导的传播的短暂和斑块资源。因此，有利于D.具有有益AAB的黑腹果蝇可以有助于两个伴侣的适应，并且应该在细菌和苍蝇中显示出正选择的足迹。拟议的研究将集中在微生物共生体方面，迄今为止受到的关注较少。我们将研究宿主介导传播的机制和分子基础，以及它们如何有助于苍蝇健身。 因此，我们将（i）测量苍蝇介导的细菌传播，并将此特性与泛基因组关联研究（pan-GWAS）中的细菌基因和变体相关联，（ii）通过转录谱发现主要有益细菌与果蝇相互作用时活跃的基因，以及（iii）对pan-GWAS和转录谱中发现的基因和变体进行进化分析。最后，细菌的传播和苍蝇健身相关的功能的基因从泛GWAS和转录谱，显示正选择的证据将使用敲除技术和可用的大陆规模的微生物群落数据进行分析，以了解它们在环境适应的功能。 虽然其他研究，其中果蝇-微生物相互作用的调查，主要集中在实验室来源的细菌或细菌，很少遇到苍蝇在自然条件下，我们将集中在细菌，从野生捕获的D。黑胃，因此可能与进化相关。利用果蝇-AAB模型，我们可以利用大量的宿主基因组和遗传资源以及一套完整的微生物基因工程工具。这项拟议中的研究有能力改变我们对生物体如何适应的理解。

Although it is becoming more and more evident that host associated microbes are important facilitators of adaptation, most studies today that aim at understanding how organisms adapt to their environment still focus on the host organism alone. We aim at broadening this perspective by assessing how hosts and microbes interact in adaptation using D. melanogaster and acetic acid bacteria (AAB) as a model. D. melanogaster and AAB live in an environment where the primary food source, ripe fruit, is ephemeral, often patchy, high in sugar-, and low in amino acid content. Under amino acid poor conditions in the laboratory, AAB can promote Drosophila growth and shorten development time by up to 10 days. Because we and others have shown that AAB are commonly associated with wild-caught D. melanogaster, it seems reasonable to assume that they could contribute to fly fitness and adaptation under natural conditions as well. Accordingly, associating with, and transporting growth promoting AAB to new food sources and oviposition sites should be adaptive for flies. At the same time, immotile bacteria could benefit from fly-mediated dispersal on an ephemeral and patchy resource. As a consequence, genetic variants that favor association of D. melanogaster with beneficial AAB can contribute to adaptation of both partners and should show footprints of positive selection in bacteria and flies. The proposed research will focus on the microbial symbiont side that has received less attention so far. We will study the mechanisms and molecular underpinnings of host-mediated dispersal and how they contribute to fly fitness. Therefore, we will (i) measure fly mediated bacterial dispersal and associate this trait with bacterial genes and variants in a pan-genome wide association study (pan-GWAS), (ii) find genes via transcriptional profiling that are active when primarily beneficial bacteria interact with Drosophila, and (iii) perform evolutionary analysis on the genes and variants found in the pan-GWAS and the transcriptional profiling. Finally, bacterial dispersal and fly fitness related functions of the genes from pan-GWAS and transcriptional profiling that show evidence for positive selection will be analyzed using knockout techniques and available continental scale microbial community data to understand their function in environmental adaptation. While other studies, in which Drosophila-microbe interaction is investigated, focus mostly on lab-derived bacteria or bacteria that rarely encounter flies under natural conditions, we will focus on bacteria that were isolated from wild-caught D. melanogaster, and hence could be evolutionarily relevant. Using the Drosophila-AAB model we can draw on the large population genomic and genetic resources for the host as well as a full set of genetic engineering tools for the microbes. The proposed research has the power to transform our understanding of how organisms adapt.