Dissertation Research: Assessing the vulnerability of salt marsh carbon storage to nutrient enrichment using an integrated meta-omics framework

随着人口的增加，对食物的需求也会增加。氮肥生产有助于满足这一需求。然而，添加过量的氮会极大地改变自然栖息地，如盐沼和其他作为陆地径流接收水的栖息地。沿海湿地提供多种生态系统服务，包括鱼类和鸟类的苗圃栖息地、风暴潮保护和营养过滤。先前的研究表明，过量的氮可能会增加这些沉积物中的分解，导致复杂有机物更快地降解为二氧化碳。是什么控制了这些过程，以及负责这些过程的微生物还没有被很好地理解。这一博士论文改进项目将使用受控实验室实验来研究添加氮素对有机物分解影响背后的机理。这项研究将深入分析盐沼微生物群落的成员及其在沼泽沉积物中的活动。数据将深入了解盐沼对氮肥径流的反应，这些信息对于沿海湿地系统的适应性管理及其对环境变化的反应至关重要。本博士论文改进项目将利用反应器系统中的可控流动来研究硝酸盐对盐沼沉积物有机质微生物分解的机理影响。我们假设，由于硝酸盐在异养微生物呼吸中是一个有利的电子受体，它可以促进有机物的氧化，否则这些有机物将保持未处理状态。目前的生物地球化学数据表明，由于硝酸盐的添加，微生物呼吸作用，特别是反硝化作用显著增加，其中在150至200年前的深层沉积物中影响最明显。这一点意义重大，因为这种深度的有机物通常被认为更耐微生物降解，这意味着盐沼储存碳的能力可能会随着富营养化而减弱。为了进一步评估这些结果，我们需要更好地了解负责有机物分解的微生物联合体。微生物活动在控制碳分解的多少方面起着关键作用；尽管我们对盐沼沉积物微生物群的结构和功能知之甚少，以及它可能如何随着硝酸盐的添加而改变。因此，这篇论文的改进拨款将通过采用集成的“元组学”方法来为现有数据做出贡献。为了补充反应器实验的流程，将使用元基因组学研究营养丰富条件下有机物分解的微生物遗传基础，并通过测量微生物转录组的表达来评估这些微生物参与者的代谢活性。这些数据有可能揭示深盐沼沉积物中新的微生物谱系，并得出微生物基因表达模式与有机碳质量变化之间的独特联系。成功地将这些荟萃组学方法与现有的地球化学速率测量相结合，将极大地提高我们对微生物在有机物分解中的作用的理解，并可能使我们能够更好地预测性地理解盐沼中的碳储存能力将如何响应未来的氮负荷。

As human populations increase, so will the demand for food. Nitrogen fertilizer production helps meet this need. However, adding excess nitrogen drastically alters natural habitats such as salt marshes and others that receive water as runoff from land. Coastal wetlands provide several ecosystem services, including nursery habitat for fish and birds, storm surge protection, and nutrient filtration. Prior studies suggest that excess nitrogen may increase decomposition in these sediments, resulting in faster degradation of complex organic matter to carbon dioxide. What controls these processes, and the micro-organisms responsible for them is not well understood. This doctoral dissertation improvement project will use controlled laboratory experiments to investigate the mechanisms behind the effect of added nitrogen on organic matter decomposition. This research will provide an in-depth analysis of the members of the salt marsh microbiome and their activities in marsh sediments. Data will provide insight into how salt marshes are responding to nitrogen fertilizer runoff, information that is essential for the adaptive management of coastal wetland systems and their response to environmental change. This doctoral dissertation improvement project will use controlled flow through reactor systems to investigate the mechanistic effect of nitrate on microbial decomposition of salt marsh sediment organic matter. We hypothesize that, because nitrate is a favorable electron acceptor in heterotrophic, microbial respiration, it can promote oxidation of organic matter that would otherwise remain unprocessed. Current biogeochemical data indicate a significant increase in microbial respiration, particularly denitrification, in response to nitrate addition, with the most pronounced effect in deep sediments ranging from 150 to 200 years old. This is significant, because organic matter at this depth is typically thought to be more resistant to microbial degradation, which means that the capacity of salt marshes to store carbon may lessen with eutrophication. To further assess these results, we need to gain a better understanding of the microbial consortia responsible for organic matter decomposition. Microbial activity plays a critical role in controlling how much carbon is decomposed; though we know little about salt marsh sediment microbiome structure and function, and how it may change in response to nitrate addition. Accordingly, this dissertation improvement grant will contribute to existing data by taking an integrated 'meta-omics' approach. To complement flow through reactor experiments, the microbial genetic underpinnings of organic matter decomposition under conditions of nutrient enrichment will be investigated using metagenomics, and the metabolic activity of these microbial players will be assessed by measuring the expression of the microbial metatranscriptome. These data have the potential to reveal novel microbial lineages from deep salt marsh sediment, and draw unique linkages between microbial gene expression patterns and changes in organic carbon quality. Successful integration of these meta-omics approaches with existing geochemical rate measurements will vastly improve our understanding of the role of microbes in organic matter decomposition, and potentially allow for a better predictive understanding for how carbon storage capacity in salt marshes will respond to future nitrogen loading.