Isotope-fluorescence activated cell sorting to allocate C utilization in the soil microbial black box

光合作用固定大气中的二氧化碳(CO2)碳(C)，并将其并入植物组织。当植物部分死亡时，碳被转移到土壤中，并从活的植物根的活动中转移到土壤中。碳从根到土壤的转移称为根沉积。根际沉积物含有多种碳化合物，它们是生活在靠近植物根的土壤(根际)中微生物的食物来源。当根际微生物消耗根际沉淀物时，它们会将一些碳转化为细胞，一些转化为土壤有机质，一些转化为二氧化碳。在可能消耗根际沉淀物C的根际生活的各种微生物群落中，重要的是了解某一特定群体消耗的C的比例。这一知识之所以重要，是因为：1.微生物消耗根际碳的效率决定了土壤中储存了多少碳，以及有多少碳回到了大气中。据估计，土壤微生物通过消耗根际沉积物释放的二氧化碳大约是燃烧化石燃料向大气释放的二氧化碳的十倍。碳转化为二氧化碳和土壤有机质的效率可能因微生物种类的不同而不同。因此，给定物种消耗的根际沉淀物C的数量对大气CO2浓度和土壤C储量有影响。2.生活在根际的微生物类型可以不同地影响植物生长，有些是有益的(例如，它们固定了氮)，有些是有害的(例如，它们会引起疾病)。因此，哪些微生物以牺牲根部沉积为代价而生长并提高其活性，对植物的营养和健康有影响。在现实的土壤条件下，很难评估微生物群体消耗的根际沉淀物C的量。目前的方法使用稳定的碳(13C)同位素来追踪根际微生物的DNA中的根沉淀物C。13C DNA被分离出来，并作为DNA指纹图谱的基础，以识别消费微生物。然而，这种方法不是非常敏感，也不是定量的；它告诉你哪些微生物物种正在消耗13C，但不能告诉你他们消耗了多少13C。关于特定微生物物种在特定环境条件下消耗根际沉淀物的定量知识很重要，因为这将使我们能够更好地了解根际生态，因此，在农业中，让我们：(A)更好地预测系统将如何应对变化的环境和采用新的作物生产做法；(B)操纵根际，使之受益，例如，改善根际有益微生物的性能，从而促进投入更少、更可持续的农业。因此，该研究项目的目的是评估一种新方法的潜力，以量化选定微生物物种对根际沉积物的消耗。新方法结合了三项成熟的技术：(I)使用碳同位素来追踪微生物的碳消耗；(Ii)用荧光染料标记属于感兴趣物种或组的微生物细胞；(Iii)对荧光细胞进行分类并量化碳同位素含量。该项目将从简单的实验开始。这些措施包括将一种细菌类型接种到土壤中，这种细菌具有不寻常的能力来消耗一种特定的化学物质，这种化学物质也将被添加到土壤中。然后，实验将继续进行设计，包括量化接种细菌和本地细菌在模拟根际沉积的设置中的碳消耗，以及那些包含真正的豆子和小麦植株的设置。经过优化后，新的方法将成为一种可广泛应用的平台技术，以增进对植物-土壤系统的了解并提出问题。

Photosynthesis fixes carbon dioxide (CO2) carbon (C) from the atmosphere and incorporates it into plant tissues. The C is then transferred to soil when plant parts die, and from the activities of living plant roots. The transfer of C from root to soil is called rhizodeposition. Rhizodeposits contain a diverse range of C compounds that serve as a food source for microbes living in the soil close to plant roots (the rhizosphere). When rhizosphere microbes consume rhizodeposits they convert some of the C into cells, some to soil organic matter and some to CO2. Out of the diverse microbial community living in the rhizosphere that could potentially be consuming rhizodeposit C, it is important to know the proportion of C consumption that a particular group is responsible for. This knowledge is important because: 1. The efficiency with which microbes consume rhizodeposit C determines how much C is stored in the soil and how much goes back to the atmosphere. It is estimated that release of CO2 through consumption of rhizodeposits by soil microorganisms is about ten times greater than CO2 release to the atmosphere due to the burning of fossil fuels. It is probable that the efficiency of conversion of C to CO2 and soil organic matter differs depending upon the microbial species responsible. Thus, the quantity of rhizodeposit C consumed by a given species has consequences for atmospheric CO2 concentrations and soil C storage. 2. The types of microbes living in the rhizosphere can affect plant growth differently, some are beneficial (e.g. they fix nitrogen), some are detrimental (e.g. they cause disease). Thus, which microbial species grow and increase their activity at the expense of rhizodeposits has consequences for plant nutrition and health. Assessing the amount of rhizodeposit C consumed by microbial groups under realistic soil conditions is difficult. Current methodology uses the stable isotope of C (13C) to trace the rhizodeposit C in to the DNA of rhizosphere microbes. The 13C DNA is separated and used as a basis for DNA fingerprinting to identify the consuming microbes. However, this method is not very sensitive and it is not quantitive; it tells you which microbial species are consuming the 13C, but not how much of the 13C they have consumed. Quantitative knowledge regarding the consumption of rhizodeposits by particular microbial species under defined environmental conditions is important as it will allow us to understand the ecology of the rhizosphere better and therefore, in agriculture, let us: (a) make better predictions regarding how the system will respond to the changing environment and the adoption of new crop production practices; (b) manipulate the rhizosphere for benefit, for example, in the improvement of the performance of beneficial microbes in the rhizosphere which will promote lower input, more sustainable agriculture. Therefore, the aim of the research project is to assess the potential of a new method to quantify the consumption of rhizodeposits by chosen microbial species. The new method brings together three well-established techniques: (i) use of C isotopes to trace microbial C consumption; (ii) labelling microbial cells belonging to a species or group of interest with a fluorescent dye; (iii) sorting the fluorescent cells and quantifying the C isotope content. The project will start off with simple experiments. These will involve the inoculation of a bacterial type to soil, which has the unusual ability to consume a particular chemical, which will also be added to the soil. Experiments will then progress to designs involving quantification of C consumption by both inoculated and native bacteria in set-ups which mimic rhizodeposition and those which contain real bean and wheat plants. When optimized, the new methodology will serve as a platform technology that can be applied broadly to enhance understanding and ask questions regarding the plant-soil system.