Application of multi-omics to identify and target microbial bloom control in legacy nuclear ponds

背景核储存池的安全运行对于继续向英国提供低碳核电至关重要，而从历史运营中退役遗留的核储存池系统仍然是该行业面临的数十亿GB的重大挑战。优化塞拉菲尔德遗址遗留池塘的管理和处理对于减少危险、降低纳税人的成本和保护环境至关重要。然而，微生物对工厂运行的影响正在变得明显，因为遗留池塘中微生物水华的形成导致这些设施内的能见度降低，并导致下游水处理系统受到污染。因此，控制微生物生长，使退役计划按时并符合预算，变得越来越重要。曼彻斯特地质微生物学小组最近通过与Sellafield Ltd.和国家核实验室的合作，在一个液压连接的遗留池塘网络中发现了离散的微生物群(见上文参考文献)。例如，尖端的DNA测序和代谢组谱已经确定了光合藻(Megraw等人。2018)和蓝藻(Foster等人2020a)，适应高辐射水平和与池塘相关的其他极端环境(例如高PH值)，并可能在控制优先放射性核素的去向方面发挥作用(Megraw等人)。2018和福斯特等人。2020b)。相比之下，与室内池塘相关的低光强并没有支持光合作用群落的广泛增长，导致由氢维持的独特微生物群(通过辐射分解反应产生；Ruiz-Lopez等人，2020)。这些研究扩展了我们对工程环境中极端微生物的知识，也有助于巩固控制战略，例如通过仔细控制净化周期(Foster等人，2020a)。研究问题和目的这项新的研究将集中在一个封闭的池塘系统，该系统已被证明对微生物水华很敏感，但不能通过清洗系统进行控制。在EPSRC的支持下，IAA最近的工作导致在这个池塘中发现了一个离散的微生物群，并帮助微调了一种新的特定物种的声学方法来控制生物量(正在为REF开发的Des Impact案例中)。现在，我们希望通过一个新的EPSRC案例项目，在Sellafield和NNL的这些积极的初步结果的基础上再接再厉，该项目将：1.使用基于DNA的高通量16/18S rRNA基因测序来监控池塘的长期运营，并帮助微调靶向超声治疗。应用互补的多组学方法研究池塘内的适应战略。3.开发以培养为基础的方法，以(1)确认在受到严格限制的实验室系统中的适应战略，(2)量化微生物定居对放射性核素命运的影响，以及(3)试验控制战略，例如，用杀菌剂处理来加强声学作用。方法和培训将采用跨学科方法，并酌情培训以培养为基础的微生物学、DNA提取和测序(16S/18S rRNA和基因组测序)、生物信息学、转录组和蛋白质组分析、地球化学和放射化学分析以及尖端成像和光谱学等技术。学生将在不同的范围内工作，从小规模的实验室实验到更大的工业规模的培养系统，与CASE合作伙伴(Sellafield Ltd)一起验证控制措施。这个项目与提供训练有素的环境科学家的需求非常一致，他们能够使用现场的真实核材料，并能够为英国核设施退役的显著成本节约做出贡献，包括与管理和退役Sellafield相关的数十亿GB成本。

Background The safe operation of nuclear storage ponds is crucial to the continued provision of low carbon nuclear power to the UK, while decommissioning of legacy pond systems from historic operations remains a significant £multi-billion challenge to the industry. Optimising the management and treatment of the legacy ponds on the Sellafield site is crucial to reduce the hazards, reduce the cost to the tax-payer and protect the environment. However, the impact of microorganisms on plant operations is becoming evident, as the formation of microbial blooms in legacy ponds leads to reduced visibility within these facilities and fouling of downstream water treatment systems. As a result, controlling microbial growth is of growing importance, to keep decommissioning schedules on time and to budget. Recent work from the Manchester Geomicrobiology group, via collaborations with Sellafield Ltd. and the National Nuclear Laboratory, have identified discrete microbiomes in a network of hydraulically-linked legacy ponds (see references above). For example, cutting edge DNA-sequencing and metabolomic profiling has identified photosynthetic algae (MeGraw et al. 2018) and cyanobacteria (Foster et al. 2020a) in outdoor ponds, adapted to high radiation levels and other extremes (e.g. high pH) associated with the ponds, and potentially playing a role in controlling the fate of priority radionuclides (MeGraw et al. 2018 and Foster et al. 2020b). In contrast the low light intensities associated with indoor ponds, has not supported the widespread growth of photosynthetic communities, resulting in unique microbiomes sustained by hydrogen (generated through radiolysis reactions; Ruiz-Lopez et al, 2020). These studies have extended our knowledge of extremophile microbiology in engineered environments, and have also helped underpin control strategies, for example through carefully controlled purging cycles (Foster et al, 2020a). Research questions and objectives This new study will focus on a closed-pond system, that has proved susceptible to microbial blooms, but cannot be controlled by purge systems. Recent IAA work supported by EPSRC has resulted in the identification of a discrete microbiome in this pond, and helped fine-tune a novel species-specific sonication approach for biomass control (featured in a DEES Impact Case being developed for REF). We now wish to build on these positive initial results with Sellafield and NNL, via a new EPSRC CASE project which will:1. Use DNA-based high-throughput 16/18S rRNA gene sequencing to monitor long-term operation of the pond and help fine-tune targeted sonication treatments.2. Apply complementary multi-omics approaches to study adaptation strategies within the pond. 3. Develop culture-based approaches to (i) confirm adaptation strategies in carefully constrained laboratory systems, (ii) quantify the impacts of microbial colonisation on radionuclide fate, and finally (iii) test control strategies e.g. biocide treatments to augment sonication. Methods and training A cross-disciplinary approach will be adopted with training in techniques including culture-based microbiology, DNA extraction and sequencing (16S/18S rRNA and genome sequencing), bioinformatics, transcriptomic and proteomic analyses, geochemical and radiochemical profiling, and cutting-edge imaging and spectroscopy as appropriate. The student will work at various scales, from small-scale laboratory experiments, through to larger industrial scale culture systems, to verify control measures with the CASE partner (Sellafield Ltd).This project aligns strongly with the need to deliver highly trained environmental scientists, able to work with real nuclear materials from site, and able to contribute to significant cost savings in the decommissioning of UK nuclear sites, including the £multibillion costs associated with managing and decommissioning Sellafield.