Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, P.O. Box 1663, Los Alamos, NM, 87545, USA.
Department of Biochemistry, Mississippi State University, Starkville, MS, USA.
Microb Ecol. 2019 Apr;77(3):597-606. doi: 10.1007/s00248-018-1239-4. Epub 2018 Aug 13.
Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.
尽管宏基因组测序数据呈爆炸式增长，但利用组学数据来预测环境生物地球化学仍然是一个挑战。元组学数据中通常使用感兴趣代谢途径中的一个或几个基因（称为标记基因）来表示生物地球化学反应的普遍性。这种方法通常不能证明基因丰度与生态系统过程速率之间存在一致的关系。出现这种情况的一个原因是，如果标记基因不是完整途径的良好代表。在这里，我们使用整合微生物基因组数据库（Integrated Microbial Genomes database）在 6000 多个完整的细菌和古菌基因组中绘制了 11 种氮（N）循环途径的存在情况。在所调查的古菌和细菌物种中，有 39%存在不完全的 N 循环途径，这表明当前的标记基因分析存在弱点。此外，我们发现大多数生物体在多种氧化态下利用无机 N 的能力有限。这表明无机 N 化合物在生物体之间的交换很常见，这突出了群落组成和空间结构在确定生态系统中回收与损失程度方面的重要性。
