潮滩湿地硝化螺菌的代谢潜力和环境适应机制

doi:10.3969/j.issn.1000-5641.2023.03.012

摘要/Abstract

摘要：

为了揭示硝化螺菌(Nitrospira)在潮滩湿地中的代谢潜力和环境适应机制, 本研究使用宏基因组学拼接与组装的方法, 从中国沿岸的5个潮滩湿地构建了14个较高质量的Nitrospira基因组. 系统发育分析结果表明, 在这些基因组中, 3个属于全程氨氧化细菌(complete ammonia oxidizer, Comammox); 9个为硝化螺菌世系Ⅱ和Ⅳ; 2个属于至今未见报道的世系Ⅲ型. 这表明, 潮滩湿地富含多样化的硝化螺菌类群. 代谢分析表明, 潮滩湿地Comammox和典型的Nitrospira含有氰酸酶、脲酶以及参与腈类、酰胺类化合物分解的酶, 暗示着它们能够与氨氧化微生物耦合利用有机氮作为能源. 此外, Nitrospira有着多重压力抵抗、病毒防御和渗透压调控策略. 这些结果深化了对Nitrospira 在潮滩湿地的多样性、生态功能潜力和环境适应机制上的认识.

关键词: 硝化螺菌, 系统发育, 代谢潜力, 环境适应, 潮滩湿地

Abstract:

To understand the metabolic potential and environmental adaptation mechanisms of Nitrospira in tidal flat wetlands, 14 high-quality Nitrospira genomes were constructed from five tidal flat wetlands along the coast of China using metagenomic binning and assembly methods. Phylogenetic analysis showed that among these genomes, three belonged to Comammox (complete ammonia oxidizer), nine belonged to lineage II and IV of Nitrospira, and two belonged to lineage III, which has yet to be discovered; taken together, this data suggests that abundant and diverse Nitrospira are present in China’s tidal flat wetlands. Metabolic reconstruction revealed that these Comammox and Nitrospira contained cyanase, urease, and other enzymes involved in the degradation of nitrile compounds and amide compounds; hence, they may utilize the organic nitrogen as energy by coupling with ammonia-oxidizing microorganisms. In addition, Nitrospira possessed flexible strategies to resist environmental stresses such as viral attack and osmotic changes. These results provide insights on the diversity, ecological function, and environmental adaptation mechanisms of Nitrospira from tidal wetlands.

Key words: Nitrospira, phylogeny, metabolic potential, environmental adaptation, tidal flat wetland

中图分类号:

Q938.1

陈国浩, 毛铁墙, 董宏坡, 欧亚飞, 张家伟. 潮滩湿地硝化螺菌的代谢潜力和环境适应机制[J]. 华东师范大学学报（自然科学版）, 2023, 2023(3): 118-131.

Guohao CHEN, Tieqiang MAO, Hongpo DONG, Yafei OU, Jiawei ZHANG. Metabolic potential and environmental adaptation mechanisms of Nitrospira in tidal flat wetlands[J]. Journal of East China Normal University(Natural Science), 2023, 2023(3): 118-131.

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样品	站位	位置	深度/cm	盐度/‰	温度/℃	pH 值	采样时间	来源
CM01s	CM01	31°30′N, 121°58′E	15~20	0.9	9.3	8.16	2018年11月	崇明东滩湿地 (上海市)
CM01m	CM01	31°30′N, 121°58′E	55~60	1.0	9.3	8.10	2018年11月	崇明东滩湿地 (上海市)
CM01b	CM01	31°30′N, 121°58′E	95~100	1.1	9.3	8.22	2018年11月	崇明东滩湿地 (上海市)
CM02s	CM02	31°30′N, 121°58′E	15~20	1.2	9.2	7.99	2018年11月	崇明东滩湿地 (上海市)
CM02m	CM02	31°30′N, 121°58′E	55~60	0.9	9.2	8.36	2018年11月	崇明东滩湿地 (上海市)
CM02b	CM02	31°30′N, 121°58′E	95~100	0.9	9.2	8.37	2018年11月	崇明东滩湿地 (上海市)
QMs	QM	18°13′N, 109°37′E	0~5	9.0	23.5	7.17	2020年11月	青梅港红树林自然保护区 (海南省, 三亚)
QMm	QM	18°13′N, 109°37′E	10~15	11.0	23.5	7.43	2020年11月	青梅港红树林自然保护区 (海南省, 三亚)
QMb	QM	18°13′N, 109°37′E	25-30	12.0	23.5	7.54	2020年11月	青梅港红树林自然保护区 (海南省, 三亚)
LH01	LH01	40°47′N, 121°56′E	0~5	27.0	14.3	8.15	2019年03月	辽河口盐沼湿地 (辽宁省)
LH02	LH02	40°51′N, 121°56′E	0~5	26.0	12.0	7.93	2019年03月	辽河口盐沼湿地 (辽宁省)
ZN01	ZN01	24°20′N, 117°45′E					2015年09月	紫泥红树林自然保护区 (福建省, 龙海) ^[33]
ZN02	ZN02	24°20′N, 117°45′E					2015年09月	紫泥红树林自然保护区 (福建省, 龙海) ^[33]
YD	YD	37°49′N, 119°07′E					2017年12月	黄河三角洲湿地 (山东省)

基因组名称	序列数	基因组大小/Mb	GC含量/%	编码基因数	完整度/%	污染度/%
QMm6	86	3.34	64.94	3169	93.18	2.27
QMm125	437	3.29	51.51	3459	93.53	0
QMm174	409	3.16	49.78	3228	76.53	0.91
QMb135	78	3.30	64.94	3087	96.82	2.27
QMb347	295	4.20	50.36	4065	95.85	0.30
ZN01_bin277	601	3.64	55.70	3993	95.40	2.16
ZN02_bin95	568	3.66	55.78	4023	97.37	4.99
ZN02_bin129	407	3.49	49.77	3557	92.85	2.12
CM01m262	247	4.30	55.30	4495	77.04	0.91
CM01s42	677	3.05	55.63	3529	71.65	0.81
CM02s178	624	3.69	56.05	4084	80.30	1.75
CM02m401	591	3.47	55.53	3875	86.30	0.91
YD_bin17	653	2.16	57.60	2620	72.60	0.36
LH01_bin68	697	3.33	47.95	3659	81.20	2.73

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