Department of Geosciences, Princeton University, Princeton, NJ 08544, United States.
Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, United States.
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae160.
Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean's oxygen minimum zones (OMZs), challenging the current understanding of OMZ nitrogen cycling. Previous attempts to determine whether nitrite-oxidizing bacteria in the anoxic layer differ from known nitrite oxidizers in the open ocean were limited by cultivation difficulties and sequencing depth. Here, we construct 31 draft genomes of nitrite-oxidizing bacteria from global OMZs. The distribution of nitrite oxidation rates, abundance and expression of nitrite oxidoreductase genes, and relative abundance of nitrite-oxidizing bacterial draft genomes from the same samples all show peaks in the core of the oxygen-depleted zone (ODZ) and are all highly correlated in depth profiles within the major ocean oxygen minimum zones. The ODZ nitrite oxidizers are not found in the Tara Oceans global dataset (the most complete oxic ocean dataset), and the major nitrite oxidizers found in the oxygenated ocean do not occur in ODZ waters. A pangenomic analysis shows the ODZ nitrite oxidizers have distinct gene clusters compared to oxic nitrite oxidizers and are microaerophilic. These findings all indicate the existence of nitrite oxidizers whose niche is oxygen-deficient seawater. Thus, specialist nitrite-oxidizing bacteria are responsible for fixed nitrogen retention in marine oxygen minimum zones, with implications for control of the ocean's fixed nitrogen inventory.
亚硝酸盐是氮循环中的核心分子，因为亚硝酸盐氧化为硝酸盐（有氧过程）将固定氮保留在系统中，而其还原为氮气（无氧）则减少了固定氮的储量。尽管亚硝酸盐氧化需要氧气，但在海洋氧气最小区（OMZ）缺氧层中观察到亚硝酸盐氧化，这挑战了当前对 OMZ 氮循环的理解。以前试图确定缺氧层中的亚硝酸盐氧化细菌是否与开阔海洋中的已知亚硝酸盐氧化剂不同，受到培养困难和测序深度的限制。在这里，我们从全球 OMZ 构建了 31 个亚硝酸盐氧化细菌的草图基因组。从相同样本中获得的亚硝酸盐氧化速率分布、亚硝酸盐氧化还原酶基因的丰度和表达以及亚硝酸盐氧化细菌草图基因组的相对丰度均在缺氧区（ODZ）核心处呈现峰值，并且在主要海洋氧气最小区的深度剖面中均具有高度相关性。ODZ 中的硝化细菌在 Tara Oceans 全球数据集（最完整的氧化海洋数据集）中未被发现，而在含氧海洋中发现的主要硝化细菌在 ODZ 水域中并未出现。全基因组分析表明，与有氧硝化细菌相比，ODZ 硝化细菌具有独特的基因簇，并且是微需氧的。这些发现均表明存在专门的亚硝酸盐氧化细菌，其生态位是缺氧海水。因此，海洋氧气最小区中固定氮的保留是由专门的亚硝酸盐氧化细菌负责的，这对控制海洋的固定氮储量具有重要意义。
