Liu Qian, Chen Yuhao, Xu Xue-Wei
Donghai Laboratory, Zhoushan, Zhejiang, China.
Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China.
Front Microbiol. 2023 Dec 13;14:1273211. doi: 10.3389/fmicb.2023.1273211. eCollection 2023.
Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: and , AOB: , and NOB and comammox: and ) accompanied by urease genes . The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter ( and ) and degradation () genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes and in AOA evolved independently from bacteria during the transition from to AOA, while in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes and / detected only in a terrestrial AOA Nitrsosphaera gargensis Ga9.2 could be gained synchronously with of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.
氨氧化古菌（AOA）和细菌（AOB）、亚硝酸盐氧化细菌（NOB）以及全程氨氧化菌（comammox）在自然界中负责硝化作用；然而，据报道一些菌群利用不稳定溶解有机氮（LDON）来满足氮需求。为了解它们LDON代谢能力的普遍性，我们从典型环境中收集了70个AOA、AOB、NOB和comammox的完整基因组，以探索它们对代表性LDON（尿素、多胺、氰酸盐、牛磺酸、甘氨酸甜菜碱和甲胺）的代谢潜力。基因组分析表明，尿素是硝化菌最常用的LDON。每个菌群都含有独特的尿素转运蛋白基因（AOA： 和 ，AOB： ，NOB和comammox： 和 ）以及脲酶基因 。这些转运蛋白底物亲和力的差异暗示了硝化菌中尿素利用效率的差异，这可能驱使它们进入不同的生态位。氰酸盐转运蛋白（ 和 ）和降解（ ）基因大多在NOB中检测到，表明它们偏好多种氮底物以满足高氮需求。大多数硝化菌中缺乏参与多胺、牛磺酸、甘氨酸甜菜碱和甲胺代谢的基因，这表明只有如先前报道的那样在细胞外被降解或氧化时，它们才能作为铵的来源。系统发育分析结合硝化菌靶基因与全基因组之间的GC%和密码子适应指数比较表明，AOA中的尿素代谢基因 和 在从 向AOA转变过程中与细菌独立进化，而陆地AOA中的 是通过横向基因转移（LGT）从细菌获得的。仅在陆地AOA 嗜盐碱球菌Ga9.2中检测到的氰酸盐转运蛋白基因 和 / 可能通过古老的LGT与NOB的 同步获得。我们的结果表明，LDON利用是硝化菌的一个共同特征，但不同硝化菌的代谢潜力不同，这可能与它们的生态位、生存策略和进化密切相关。
