Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry. We find that on average 25% of deep-sea cells assimilated urea-derived N (60% of detectably active cells), and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrososphaeria (syn., Thaumarchaeota; likely for nitrification) as well as members of thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes estimated ureC within 10–46% of deep-sea cells around the world, with higher prevalence below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.

中文翻译：

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尿素同化和氧化支持黑暗海洋系统发育多样化的微生物群落的活性


尿素被认为是深海微生物氮和化学能的重要来源;然而，缺乏尿素在上层海洋以下使用的直接证据。在这里，我们使用宏基因组学、硝化速率和纳米级二次离子质谱法的单细胞稳定同位素摄取测量来探索东北太平洋 50 至 4000 米深处的尿素利用。我们发现平均 25% 的深海细胞同化了尿素衍生的 N （60% 的可检测活性细胞），并且尿素的细胞特异性氮掺入率高于铵态氮。尿素浓度和相对于铵态氮的同化率通常都在真光区以下增加。我们在分析的两个地点之一检测到所有深度的基于氨和尿素的硝化作用，证明了它们有可能支持中上层和深海区域的化学自养。使用新生成的宏基因组，我们发现编码脲酶催化亚基的 ureC 基因存在于该区域 39% 的深海细胞中，包括 Nitrososphaeria（同义词，Thaumarchaeota;可能用于硝化）以及其他 13 个门的成员，如变形菌门、疣微菌门、Plantomycetota、Nitrospinota 和 Chloroflexota（可能用于同化）。对公共宏基因组的分析估计，全球 10-46% 的深海细胞中存在尿素，光区以下的患病率更高，这表明尿素在全球范围内的深海微生物组中广泛可用。我们的结果表明，尿素是黑暗海洋中丰富多样微生物的氮源，也是深海硝化的重要贡献者，因此是化学自养的燃料。