Intrator Naomi, Jayakumar Amal, Ward Bess B
Department of Geosciences, Princeton University, Princeton, NJ, United States.
Front Microbiol. 2024 May 21;15:1407573. doi: 10.3389/fmicb.2024.1407573. eCollection 2024.
Nitrous oxide (NO) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric NO originates in aquatic environments. Reduction of NO to dinitrogen gas (N) requires the nitrous oxide reductase enzyme, which is encoded by the gene . Organisms that contain are the only known biological sinks of NO and are found in diverse genera and a wide range of environments. The two clades of (Clade I and II) contain great diversity, making it challenging to study the population structure and distribution of containing organisms in the environment. A database of over 11,000 sequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where NO levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade I genes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade I genes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that the gene displays regional and environmental separation. This study expands the known diversity of genes and provides a clearer picture of how the clades and phylogeny of organisms are distributed across diverse environments.
一氧化二氮（NO）是一种强效温室气体，也是臭氧消耗的主要原因。大气中三分之一的NO源自水生环境。将NO还原为氮气（N₂）需要一氧化二氮还原酶，该酶由 基因编码。含有该基因的生物是已知唯一的NO生物汇，存在于不同的属和广泛的环境中。该基因的两个进化枝（进化枝I和II）具有高度多样性，这使得研究环境中含该基因生物的种群结构和分布具有挑战性。从NCBI（代表不同的水生环境）以及未发表的序列和宏基因组（主要来自氧含量极低的区域，即OMZ，那里的NO水平通常较高）中编译了一个包含超过11000个该基因序列的数据库。根据DNA和氨基酸序列同一性将序列聚类为原型，并确定它们的进化枝、系统发育和环境来源。对序列的来源和环境分布进行的进一步分析表明，进化枝和系统发育之间存在强烈的栖息地分离。尽管汇编中进化枝I的该基因更多，但进化枝II在系统发育上更加多样化，并且在环境来源中的分布更广。另一方面，进化枝I的该基因主要存在于海洋沉积物中，主要来自假单胞菌门。从海洋OMZ分析的大多数序列代表了不同OMZ之间不同的系统发育型，这表明该基因表现出区域和环境分离。这项研究扩展了已知的该基因多样性，并更清楚地描绘了含该基因生物的进化枝和系统发育如何分布在不同环境中。
