Sex and Death: testing the evolutionary benefit of recombination using a bacterium and bacteriophage model

背景虽然细菌通过二元分裂进行繁殖，但它们并不是纯粹的克隆。有时，它们能够从环境中提取来自其他细菌细胞的DNA，并将其与自己的遗传物质重组。这个过程被称为转变。就像植物和动物的性别一样，DNA的这种改组增加了种群中的遗传变异。自然选择的过程需要种群中的这种遗传变异，才能选择最合适的个体。因此，进行有性繁殖(或更广泛地说，重组)的有机体种群可以被认为更快地适应他们的环境。然而，只有在环境不断变化的情况下，重组才会受到青睐。否则，重组最终会瓦解它创造的最合适的DNA组合。强选择和连续波动选择的最强候选者是寄生虫攻击。寄生虫和宿主被困在持续的军备竞赛中：宿主对他们的寄生虫产生抵抗力，寄生虫进化以克服这种抵抗力，以此类推。这一场景是根据刘易斯·卡罗尔的《镜花水月》命名的，在书中，红皇后告诉爱丽丝：你需要尽你所能地奔跑，才能保持原地不动。目的红皇后假说特别可能适用于细菌，原因有两个。首先，细菌经常受到致命病毒(噬菌体)的攻击，对新的耐药性具有非常强的选择性。其次，细菌的重组比许多动植物的重组要“便宜”。例如，细菌不依赖有性繁殖，只有在需要时才会求助于有性繁殖。虽然已经发展了许多理论，但对红皇后假说的实验测试很少。在这里，我们建议实验地将已知频繁重组的水生细菌气单胞菌与噬菌体共同进化。可用于转化的游离DNA的质量将被实验操纵。这将使我们第一次量化“细菌性行为”是否有助于适应寄生虫病毒。转化会导致种群中所有的多态重新洗牌，而不仅仅是那些与抗噬菌体相关的多态。因此，我们还将包括一种温度处理，其中高温、压力大的温度需要额外的适应，预期重组具有更大的潜在好处。应用和益处细菌和噬菌体是检验红皇后假说的理想模型系统，但对人类健康和经济也非常重要。各种气单胞菌都是机会致病菌，可引起广泛的感染。气单胞菌是一种正在上升的病原体，在对2004年亚洲海啸幸存者的一项研究中发现，它是软组织和皮肤感染的最常见原因。噬菌体是导致细菌死亡的重要因素。随着细菌对抗生素耐药性水平的提高，噬菌体疗法作为一种替代策略重新引起人们的兴趣，通过使用噬菌体作为“进化的抗生素”来预防和抗击感染。重要的是，这个项目将测试与噬菌体的共同进化是否选择增加转化。因此，旨在限制病原菌负面影响的噬菌体疗法实际上可以通过转化提高细菌进化毒力或抗生素耐药性的能力。发现更高温度下重组的任何增加的好处，可能对应对气候变化的进化变化具有重要影响。这将是第一项明确将噬菌体共同进化和转化联系在一起的研究，这是微生物学中的两种主要进化力量，必将产生令人兴奋的新见解，与抗击机会性病原体特别相关。

General SummaryBackgroundAlthough bacteria reproduce through binary fission, they are not purely clonal. On occasion, they are capable of taking up DNA from the environment derived from other bacterial cells and recombine it with their own genetic material. This process is termed transformation. Just as in plant and animal sex, this shuffling of DNA increases the genetic variation in the population. The process of natural selection needs such genetic variation in the population to be able to select the fittest individuals. Populations of organisms that engage in sex (or more generally recombination) could thus be assumed to adapt more quickly to their environment. However, recombination is only favoured when the environment is ever-changing. If not, recombination would eventually disassemble the fittest combinations of DNA it had created. The strongest candidate for both strong and continuously fluctuating selection is that of parasite attack. Parasites and hosts are locked in a continuing arms race: hosts develop resistance against their parasites, and parasites evolve to overcome this resistance and so on and so forth. This scenario is named 'the Red Queen Hypothesis' after Lewis Carroll's book Through the Looking-Glass, where the Red Queen tells Alice: 'It takes all the running you can do, to keep in the same place'. AimThe Red Queen Hypothesis is especially likely to be applicable to bacteria for two reasons. First, bacteria are frequently attacked by deadly viruses (bacteriophages), exerting very strong selection for novel resistance. Second, bacterial recombination is 'cheaper' than that of many plants and animals. For instance, bacteria do not rely on sex for reproduction and could resort to it only when needed. Although a lot of theory has been developed, experimental tests of the Red Queen Hypothesis are rare. Here, we propose to experimentally coevolve the aquatic bacterium Aeromonas, known to frequently recombine, with phage. The quality of free DNA available for transformation will be experimentally manipulated. This will allow us to for the first time quantify whether 'bacterial sex' can aid adaptation to parasitic viruses. Transformation results in the reshuffling of all polymorphisms in the population, not only those associated with resistance to phage. We therefore will also include a temperature treatment where high, stressful temperature requires additional adaptation with an expected greater potential benefit of recombination. Applications and BenefitsBacteria and phage are an ideal model system to test the Red Queen Hypothesis, but are also of great importance to human health and the economy. Various Aeromonas species are opportunistic pathogens causing a wide range of infections. Aeromonas is a pathogen on the rise and has been found to be the most common cause of soft tissue and skin infections in a study on survivors of the 2004 tsunami in Asia. Bacteriophages are important agents of bacterial mortality. With increasing levels of bacterial resistance to antibiotics, phage therapy has received renewed interest as an alternative strategy to prevent and fight infection by using phages as 'evolving antibiotics'. Importantly, this project will test whether coevolution with phage selects for increased transformation. Phage therapy designed to limit the negative impact of pathogenic bacteria thus could actually result in the increased capability of bacteria to evolve virulence or antibiotic resistance through transformation. Finding any increased benefit of recombination at higher temperature could have important implications for evolutionary change in response to climate change. This will be the first study explicitly linking phage coevolution and transformation, two main evolutionary forces in microbiology, and is bound to yield exciting new insights with special relevance to fighting an opportunistic pathogen.