Role of interactions between soil microbes in shaping ecosystem carbon cycling

-土壤中含有对生态系统功能至关重要的微生物种类繁多。土壤中的微生物群落是土壤碳循环的重要驱动力，它们控制着最近植物碳输入的命运，并决定着同化碳的稳定性。我们的工作表明，更高的微生物生长产量，以及分配给生物合成的更大比例的底物，增加了群落在土壤中储存碳的能力。我们还知道，土壤非生物因素，如水分水平和资源可获得性，可以影响微生物的生长产量，从而影响碳封存。然而，微生物群落内的生物相互作用在决定碳循环速率中的作用还没有被探索。土地利用对土壤中微生物的多样性和功能有很大的影响。在土地利用强度较低的土壤中，较高的持水量和较高的资源利用率导致较高的微生物密度、较高的功能多样性和较大的微生物生物量。随着微生物栖息地的连通性增强，在低集约化土壤群落中微生物相互作用的可能性比在高集约化土地利用中的更大。个体之间的生物相互作用可以从防御、对抗和竞争，到细胞信号、共代谢和共生。相反，在高集约土地利用中，社区的资源限制和较高的流转可能会导致社区成员之间的竞争和对抗。这些相互作用如何影响群落动态和生态系统过程尚不清楚。2.项目目标：该项目旨在通过实地评估和有针对性的实验室实验相结合的方法，了解不同微生物相互作用在驱动土壤碳循环过程中的作用。不同土地利用强度梯度的微生物密度和多样性的差异将被用来研究微生物物种的共生，这是微生物相互作用的一个标志。这些将通过实验室中胚层实验进行进一步测试。不同微生物密度和多样性的群落将被接种到无微生物模式土壤中。将在组装的群落中进行物种共生的时间分辨网络分析，并将这些分析与C循环速率联系起来，以推断生态系统影响。将进行进一步的实验室实验，使用不同的培养微生物组合来研究共同底物上的相互作用和有机物分解的速度。研究方法和培训：将使用扩增和鸟枪元基因组测序来测量田间和实验土壤中微生物群落结构和功能的变化。将使用已建立的管道进行分类和功能分类。生物信息学支持将通过导师提供给学生。13C标记的植物有机质将被用作实验室实验的底物，以监测分解速度。在野外和实验室实验中，基因组测序和同位素方法的这种结合将使学生获得一系列独特的技术技能。

- Soils harbour an immense diversity of microorganisms that are critical to ecosystem functioning. Microbial communities in soil are significant drivers of soil carbon cycling - they control the fate of recent plant carbon inputs and determine the stability of assimilated carbon. Our work has shown that higher microbial growth yield, with a greater proportion of substrate allocated to biosynthesis, increases the ability of communities to store carbon in soils1. We also know that soil abiotic factors such as moisture levels and resource availability can affect microbial growth yield and hence carbon sequestration. However, the role of biotic interactions within microbial communities in determining carbon cycling rates has not been explored.Land use has a big impact on microbial diversity and functioning in soil. In lower land use intensity soils, higher water holding capacity and greater availability of resources leads to higher microbial density, higher functional diversity and greater microbial biomass. With the greater connectivity of microbial habitats there is a greater probability of microbial interactions in less intensive soil communities than in those from higher intensity land use. Biotic interactions among individuals can range from defence, antagonism and competition, to cell signalling, co-metabolism and symbiosis. On the contrary, resource limitation and higher turnover in communities in high intensity land use may lead to competition and antagonism between community members. How these interactions influence community dynamics and ecosystem processes has not been understood2.Project aims: The project aims to understand the role of different microbial interactions in driving carbon cycling processes in soils using a combination of field assessment and targeted lab experiments. The differences in microbial density and diversity across land use intensity gradients will be used to study co-occurrence of microbial species which is an indication of microbial interactions. These will be further tested using lab mesocosm experiments. Communities with different microbial density and diversity3 will be inoculated into microbe-free model soil. Time-resolved network analysis of species co-occurrence will be performed in the assembled communities and these will be linked to C cycling rates to infer ecosystem implications. Further lab experiments will be performed which will use different combinations of cultured microbes to study interactions on common substrates and rates of organic matter decomposition.Research methods and training:Changes in microbial community structure and functions in field and experimental soils will be measured using amplicon and shotgun metagenomic sequencing. Taxonomic and functional classification will be performed using established pipelines. Bioinformatics support will be available to the student through the supervisors. 13C-labelled plant organic matter will be used as a substrate in lab experiments to monitor decomposition rates. Such a combination of genomic sequencing and isotopic approaches in field and lab experiments will allow the student gain a range of unique technical skills.