Now you see them, now you don't - tracking hidden dormant bacteria in the environment

当你在晚上熟睡时，什么会把你吵醒？是警报声还是鸟叫声？是吐司或咖啡的味道让你清醒吗？你会因为太热或太冷而醒来吗？或者像我一样，一个小小的人类醒来，引起你的注意。我的研究是关于细菌如何进入“睡眠”或“冬眠”行为，以确保它们在环境中的生存，以及它们使用什么线索从这种冬眠状态中“醒来”。细菌有聪明的方法来确保它们在环境中的压力时期存活下来。这些压力可能是温度变化，缺乏营养，或者可能来自抗生素暴露或氯化处理。细菌在压力下生存的唯一途径是进入可逆的休眠状态。这些休眠细胞以降低的速度利用营养物质，并改变大小和形状，以更好地保护自己免受不利条件的影响。此外，休眠细胞无法通过常规测试检测到，这使得它们难以研究。它们可以保持这种“类似睡眠”的状态，直到周围环境的有利条件恢复，在那里它们“重新醒来”并繁殖，导致对环境有害的细菌大量繁殖，在某些情况下对人类健康有害。科学家们仍然不知道细菌是如何从这种休眠状态中“醒来”的，也不知道它们是如何从休眠状态转变为活跃的细胞群的。我将使用在海洋和河口环境中发现的弧菌来研究细菌的休眠。弧菌物种在低盐度和温暖的温度下茁壮成长，只在温暖的月份出现在环境中。在冬季没有检测到弧菌，并且假设细菌由于寒冷的温度而死亡。然而，一小部分细胞进入休眠状态以在冬季条件下生存。当夏季回归时，营养水平和海水温度增加，休眠的弧菌细胞“重新唤醒”并成长为细菌种群。最近，使用先进的流式细胞术技术，我能够从环境中分离出处于休眠期的弧菌细胞，并将它们唤醒，重新成为活跃的可检测群体。利用这种能力来识别和操纵休眠细胞将首次允许我在细菌休眠领域探索新的概念领域。在此期间，我将与英国Cefas和植物与食品研究所等政府机构合作（新西兰），海产品业（里昂海鲜）和国际研究所（ICDDR，B，海洋研究所（挪威），IZSUM（意大利），巴塞罗那大学，阿拉斯加大学费尔班克斯和乔治梅森大学（美国）），以获得整个地球仪的弧菌物种在夏季丰富，因此可能包含细菌休眠细胞在凉爽的月份地区的环境样本。我将揭示休眠细胞在环境中的地理分布，以及它们是否存在于特定的生态位中（例如，沉积物、水柱、贝类、牡蛎肠）。我将观察休眠细胞如何对环境的变化做出反应，并确定帮助这些休眠细胞复苏并使它们重新出现为不断增长的群体的机械过程。我的研究计划将导致发现和开发新的诊断测试，以识别环境中早期休眠细菌的存在，这将减轻全球弧菌细菌新发疾病的风险。

When you are in a deep sleep at night what wakes you up? Is it the sound of an alarm or the birds tweeting? Is it the smell of toast or coffee that stirs you awake? Do you wake up because your too hot or too cold? Or like me a tiny human wakes up and gets your attention. My research is about how bacteria enter a 'sleep-like' or 'hibernation-like' behaviour to ensure their survival in their environment and what cues they use to 'wake up' from this state of hibernation. Bacteria have clever ways to ensure they survive during periods of stress in their environment. These stresses may be a change in temperature, a lack of nutrients or it may come from antibiotic exposure or chlorination treatment. One-way bacteria survive the stress is by entering into a reversible state of dormancy. These dormant cells utilise nutrients at a reduced rate and change in size and shape to better protect themselves from unfavourable conditions. Furthermore, dormant cells are not detectable by routine tests making them difficult to study. They can stay in this 'sleep like' state until favourable conditions in the surrounding environment return, where they 'reawaken' and reproduce to cause bacterial blooms that are hazardous to the environment and in some cases human health. Scientists still do not know how bacteria are able to 'wake up' from this state of dormancy or what cues they use to change from a dormant state into an active growing population of cells.I will use Vibrio species found in the marine and estuarine environment to study bacterial dormancy. Vibrio species thrive in low salinity and warm temperatures and only appear in the environment during the warmer months. Vibrio bacteria are not detected in the winter, and it is assumed that the bacteria die due to the cold temperatures. However, a small proportion of the cells enter the dormant state to survive the winter conditions. When summer returns, nutrient levels and sea temperatures increase, and dormant Vibrio cells 'reawaken' and grow into bacterial populations. Recently, using advanced flow cytometry techniques, I was able to isolate Vibrio cells in the dormant phase from the environment, and wake them up into an active detectable population again. Using this ability to identify and manipulate dormant cells will for the first time, allow me to explore new conceptual territory in the field of bacterial dormancy.During this fellowship, I will collaborate with government agencies such as Cefas (UK) and Plant & Food Research Institute (New Zealand), seafood industry (Lyons Seafood), and international institutes (ICDDR,B, Institute of Marine Research (Norway), IZSUM (Italy), University of Barcelona, University of Alaska Fairbanks and George Mason University (USA)) to obtain environmental samples across the globe from areas where Vibrio species are abundant in the summer and thus likely to contain bacterial dormant cells during cooler months. I will uncover the geographical spread of dormant cells in the environment and whether they are present in specific niches, (e.g., sediment, water column, shellfish, oyster gut). I will look to see how dormant cells respond to changes in their environment, and identify the mechanistic processes that aid resuscitation of these dormant cells and allow them to re-emerge as a growing population. My research programme will lead to finding and developing new diagnostic tests to identify the presence of dormant bacteria early in the environment that will mitigate risks against emerging diseases from Vibrio bacteria worldwide.