High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, <i>amoA</i>-Based Functional Gene Array

Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.微生物生态学研究的进展往往受限于现有方法论的性能局限。好氧自养硝化作用（aerobic autotrophic nitrification）是陆地与水生生态系统中最重要且研究最为深入的微生物过程之一。本研究开发并验证了一款基于氨单加氧酶亚基A（ammonia-monooxygenase subunit A, amoA）基因的微生物诊断微阵列，可用于深入解析细菌与古菌氨氧化菌的群落结构。该amoA基因微阵列已成功应用于海洋、河口、土壤及污水处理厂环境中的硝化菌多样性分析。该微阵列的人力与耗材成本适中，单人每周即可完成数百份环境DNA或RNA样本的分析工作。该阵列已通过多组单一及复合靶标（分别对应amoA克隆与环境样本）完成全面验证，并结合传统测序方法开展平行对照分析。该微阵列适中的成本与高通量特性，使得针对微生物氨氧化生态学的更广泛研究问题得以充分开展——这类问题往往需要大量样本量与高精度的群落组成解析能力。