西溪湿地土壤病毒多样性及其碳代谢基因解析

doi:10.17520/biods.2025190

生物多样性 ›› 2025, Vol. 33 ›› Issue (9): 25190. DOI: 10.17520/biods.2025190

• 研究报告: 微生物多样性 • 上一篇下一篇

西溪湿地土壤病毒多样性及其碳代谢基因解析

洪欣艺¹, 蔡易朗¹, 方嘉乐¹, 姚可侃², 李佳乐³, 王懿祥⁴, 白尚斌¹, 王楠¹, 周秀梅¹^,^*()

1.浙江农林大学暨阳学院, 浙江诸暨 311800
2.杭州西溪国家湿地公园生态文化研究中心, 浙江西溪湿地生态系统定位观测研究站, 杭州 310030
3.南京师范大学数学科学学院, 南京 210023
4.浙江农林大学环境与资源学院、碳中和学院, 杭州 311300

收稿日期:2025-05-22 接受日期:2025-07-26 出版日期:2025-09-20 发布日期:2025-10-31
通讯作者: *E-mail: zhouxm0324@163.com
基金资助:
浙江省尖兵领雁项目(2022C02038);浙江省教育厅一般项目(Y202250349);浙江农林大学暨阳学院科研发展基金项目/人才启动项目(RC2021B05);浙江农林大学暨阳学院科研发展基金项目/人才启动项目(RQ2020B03)

Soil viral diversity and carbon metabolism genes profiling in Xixi Wetland

Xinyi Hong¹, Yilang Cai¹, Jiale Fang¹, Kekan Yao², Jiale Li³, Yixiang Wang⁴, Shangbin Bai¹, Nan Wang¹, Xiumei Zhou¹^,^*()

1 Jiyang College of Zhejiang A&F University, Zhuji, Zhejiang 311800, China
2 Hangzhou Xixi National Wetland Park Ecological and Cultural Research Center, Zhejiang Xixi Wetland Ecosystem Observation and Research Station, Zhejiang, Hangzhou 310030, China
3 School of Mathematical Sciences, Nanjing Normal University, Nanjing 210023, China
4 College of Environmental & Resource Science, College of Carbon Neutralization, Zhejiang A&F University, Hangzhou 311300, China

Received:2025-05-22 Accepted:2025-07-26 Online:2025-09-20 Published:2025-10-31
Contact: *E-mail: zhouxm0324@163.com
Supported by:
Zhejiang Province “Vanguard and Leading Goose” R&D Program(2022C02038);Research Project of Department of Education of Zhejiang Province(Y202250349);Research Foundation of Jiyang College of Zhejiang A&F University/Talent Project(RC2021B05);Research Foundation of Jiyang College of Zhejiang A&F University/Talent Project(RQ2020B03)

1. 附录.pdf(632KB)

摘要/Abstract

摘要：

湿地土壤病毒在有机碳循环中发挥关键作用, 其携带的碳水化合物活性酶(CAZymes)基因可辅助碳代谢过程。为揭示城市湿地土壤病毒多样性特征及其碳代谢功能, 本研究以杭州西溪国家湿地公园为研究对象, 选取乔灌草地、灌草地、芦苇(Phragmites australis)地、池塘和浅滩5种典型生境, 通过病毒宏基因组测序与生物信息学分析, 系统探究了不同湿地生境类型土壤中病毒的多样性特征及其碳代谢基因组成。研究结果显示, 5种生境的病毒丰富度、多样性存在显著差异(P < 0.05), 由高到低依次为灌草地 > 乔灌草地 > 芦苇地 > 浅滩 > 池塘; 结构方程模型分析表明, 该格局主要受土壤理化性质影响, 对病毒多样性效应值排序依次为pH > 土壤湿度 > 土壤有机碳(SOC) ≈ 全氮(TN) > 土壤温度, 对病毒宿主与病毒多样性的综合效应值贡献度依次为TN > SOC > 土壤温度, 病毒宿主对病毒多样性强显著(效应值 = 0.87); 研究共鉴定出158个独特的碳水化合物运输与代谢(G)基因, 包含13种碳水化合物活性酶基因。其中糖基转移酶占比最高(65.8%), 表明土壤病毒在湿地碳循环中可能发挥重要作用。病毒功能基因的表达与分布受SOC和TN含量的显著影响, 说明土壤养分状况与病毒生态功能有密切的联系。研究结果为深入理解碳循环的微生物调控机制提供了重要科学依据, 对湿地保护与管理具有重要实践意义。

关键词: 湿地, 病毒宏基因组测序, 土壤有机碳固持, 碳水化合物活性酶基因, 生态功能

Abstract

Aims: The purpose of this study is to systematically examine soil viral community composition and assess their carbon metabolic functional potential across urban wetland ecosystems.

Methods: We took five habitat types of sample plots, including trees, shrubs and grasslands, shrub grasslands, reed marshes, shoals and ponds, distributed widely in Hangzhou Xixi National Wetland Park, Zhejiang Province (Xixi Wetland) as the research objects. This study investigated soil viral diversity patterns and carbon metabolic gene composition across these five habitat types using virus metagenomic sequencing coupled with bioinformatics analysis.

Results: There were significant differences in viral richness and diversity among the five habitat types (P < 0.05), with hierarchical rankings as follows: shrub grasslands > trees, shrubs and grasslands > reed marshes > shoals > ponds; The structural equation modeling analysis showed that this spatial pattern was predominantly mainly driven by soil physicochemical properties, with the order of effect size was pH > soil moisture > SOC (soil organic carbon) ≈ TN (total nitrogen) > soil temperature. The contribution of comprehensive effect size of viral host and viral diversity was in the order of TN > SOC > soil temperature, and the direct effect of viral host on viral diversity was the strongest (effect size = 0.87); A total of 158 unique carbohydrate transport and metabolism (G) genes were identified, including 13 distinct carbohydrates active enzyme (CAZyme) families. Among these glycosyltransferases accounted for the highest proportion (65.8%), indicating that soil viruses may play an important role in wetland carbon cycling through glycosylation-mediated processes.

Conclusion: The diversity of soil viruses in Xixi Wetland exhibits significant spatial heterogeneity. This distribution pattern is closely linked to variations in soil physicochemical properties (especially the key factors such as SOC, TN and soil moisture). The CAZyme genes identified in five habitat types contribute to wetland carbon cycling processes through regulating the metabolic pathways of host microorganisms.

Key words: wetlands, viral metagenomic sequencing, soil organic carbon sequestration, CAZymes genes, ecological function

洪欣艺, 蔡易朗, 方嘉乐, 姚可侃, 李佳乐, 王懿祥, 白尚斌, 王楠, 周秀梅 (2025) 西溪湿地土壤病毒多样性及其碳代谢基因解析. 生物多样性, 33, 25190. DOI: 10.17520/biods.2025190.

Xinyi Hong, Yilang Cai, Jiale Fang, Kekan Yao, Jiale Li, Yixiang Wang, Shangbin Bai, Nan Wang, Xiumei Zhou (2025) Soil viral diversity and carbon metabolism genes profiling in Xixi Wetland. Biodiversity Science, 33, 25190. DOI: 10.17520/biods.2025190.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2025190

https://www.biodiversity-science.net/CN/Y2025/V33/I9/25190

图/表 10

表1 西溪湿地不同斑块类型的土壤理化性质。数据为平均值 ± 标准差。

Table 1 Soil physicochemical properties across different habitat types in Xixi Wetland. The data is the mean ± SD.

	土壤温度 Soil temperature (℃)	土壤湿度 Soil moisture (%)	pH	土壤有机碳 Soil organic carbon (g/kg)	土壤全氮 Total nitrogen (g/kg)
乔灌草地 Trees, shrubs and grasslands	9.1 ± 0.2^ab	32.60 ± 14.06^bc	6.84 ± 0.44^a	41.3 ± 24.5^a	3.4 ± 1.8^a
灌草地 Shrub grasslands	8.9 ± 1.4^b	25.29 ± 3.67^c	6.36 ± 0.50^a	30.8 ± 9.6^ab	2.8 ± 0.3^ab
芦苇地 Reed marshes	7.1 ± 0.3^c	39.24 ± 11.89^b	5.57 ± 0.41^b	26.0 ± 10.4^b	2.2 ± 0.8^b
池塘 Ponds	7.4 ± 0.1^c	51.70 ± 10.56^ab	6.56 ± 0.04^a	13.6 ± 0.8^c	1.1 ± 0.1^c
浅滩 Shoals	11.1 ± 0.5^a	74.13 ± 8.35^a	5.47 ± 0.12^b	16.2 ± 1.1^bc	1.4 ± 0.1^c

图1 西溪湿地不同斑块类型的contig长度分布图。A: 乔灌草地; B: 灌草地; C: 芦苇地; D: 池塘; E: 浅滩。

Fig. 1 The distribution of contig lengths for different habitat types in Xixi Wetland. A, Trees, shrubs and grasslands; B, Shrub grasslandes; C, Reed marshes; D, Ponds; E, Shoals.

表2 所预测的病毒宿主大于50条的数量及其在不同湿地斑块类型的分布

Table 2 Summary of the predicted viral hosts with over 50 sequence counts and their distribution across different habitat types

宿主属 Host genus	病毒序列数量 Number of viral sequences	占总预测病毒宿主序列数的比值 Proportion of predicted viral host sequences (%)	乔灌草地 Trees, shrubs and grasslands	灌草地 Shrub grasslands	芦苇地 Reed marshes	池塘 Ponds	浅滩 Shoals
不动杆菌属 Acinetobacter	76	1.23	57	69	12	2	2
伯克霍尔德氏菌属 Burkholderia	105	1.70	58	87	45	2	2
汉密尔顿菌属(暂定类群) Candidatus_Hamiltonella	76	1.23	33	64	6	0	0
蛭弧菌属 Bdellovibrio	1,939	31.38	1,372	1,563	99	4	2
柄杆菌属 Caulobacter	155	2.51	105	136	55	2	2
埃希氏菌属 Escherichia	375	6.07	257	320	62	6	1
地芽孢杆菌属 Geobacillus	63	1.02	39	52	4	0	0
螺杆菌属 Helicobacter	61	0.99	39	46	6	2	0
黏液乳杆菌属 Limosilactobacillus	104	1.68	55	82	14	1	0
李斯特菌属 Listeria	120	1.94	50	86	27	10	0
中慢生根瘤菌属 Mesorhizobium	76	1.23	52	60	21	0	0
分枝杆菌属 Mycolicibacterium	114	1.84	71	89	39	0	0
副拟杆菌属 Parabacteroides	68	1.10	51	54	8	0	0
土球腔菌属 Pedosphaera	50	0.81	31	47	12	0	0
普雷斯科特氏菌属 Prescottella	77	1.25	53	70	7	0	0
原绿球藻属 Prochlorococcus	50	0.81	39	32	3	0	0
假单胞菌属 Pseudomonas	203	3.28	109	173	34	2	2
红杆菌属 Rhodobacter	69	1.12	57	61	26	2	3
红育菌属 Rhodovulum	53	0.86	34	45	14	2	2
罗格氏菌属 Ruegeria	54	0.87	38	41	10	1	1
中华根瘤菌属 Sinorhizobium	57	0.92	40	42	32	1	1
弧菌属 Vibrio	129	2.09	84	102	26	4	2
未知 Unknown	266	4.30	161	213	105	3	2

表3 西溪湿地不同斑块类型的病毒Shannon指数、Simpson指数和Chao1指数

Table 3 Shannon index, Simpson index and Chao1 index of virus across different habitat types in Xixi Wetland

多样性指数 Diversity index	乔灌草地 Trees, shrubs and grasslands	灌草地 Shrub grasslands	芦苇地 Reed marshes	池塘 Ponds	浅滩 Shoals
Shannon指数 Shannon index	6.30^b	8.26^a	7.50^ab	3.88^c	5.83^bc
Simpson指数 Simpson index	0.95^a	0.96^a	0.88^b	0.84^b	0.86^b
Chao1指数 Chao1 index	15,357.66^ab	20,083.64^a	4,650.26^b	257.23^c	543.23^bc

图2 西溪湿地不同斑块类型的病毒群落结构。A: 乔灌草地; B: 灌草地; C: 芦苇地; D: 池塘; E: 浅滩。

Fig. 2 Viral community structure of different habitat types in Xixi Wetland. A, Trees, shrubs and grasslands; B, Shrub grasslands; C, Reed marshes; D, Ponds; E, Shoals.

图3 西溪湿地不同斑块病毒目水平群落结构组成。RPKM: 每百万条映射读数中每千碱基的读数。

Fig. 3 Composition of horizontal community structure of viral order level in different habitat types of Xixi Wetland. RPKM, Reads per Kilobase per Million mapped reads.

图4 西溪湿地病毒科水平与土壤理化性质的相关关系。* P < 0.05, ** P < 0.01。

Fig. 4 Correlation between viral families composition and soil physicochemical properties in Xixi Wetland. SWC, Soil water content; ST, Soil temperature; SOC, Soil organic carbon; TN, Total nitrogen. * P < 0.05, ** P < 0.01.

图5 土壤理化性质与病毒宿主结构方程模型。e为残差项; 单箭头为变量间的直接影响关系, 其正值代表正相关(越高相关性越大), 负值代表负相关(其绝对值越高相关性越大); 双箭头为拟合线, 其正值表示观察值大于模型预测值, 负值代表观察值小于模型预测值。

Fig. 5 The structural equation modeling of soil physicochemical properties and viral host. The e represents the residual term; The one-way arrow indicates the direct effect relationship between variables, where positive values indicate a positive correlation (the higher the value, the stronger the correlation) and negative values indicate a negative correlation (the larger the absolute value, the stronger the correlation); The double arrow indicates fitted lines, with positive values meaning observed values are greater than model-predicted values and negative values meaning observed values are less than model-predicted values.

图6 土壤理化性质与病毒多样性的结构方程模型。e为残差项; 单箭头为变量间的直接影响关系, 其正值代表正相关(越高相关性越大), 负值代表负相关(其绝对值越高相关性越大); 双箭头为拟合线, 其正值表示观察值大于模型预测值, 负值代表观察值小于模型预测值。

Fig. 6 The structural equation modeling of soil physicochemical properties and viral diversity. The e represents the residual term; The one-way arrow indicates the direct effect relationship between variables, where positive values indicate a positive correlation (the higher the value, the stronger the correlation) and negative values indicate a negative correlation (the larger the absolute value, the stronger the correlation); The double arrow indicates fitted lines, with positive values meaning observed values are greater than model-predicted values and negative values meaning observed values are less than model-predicted values.

图7 土壤理化性质-病毒宿主-病毒多样性的结构方程模型。绿实线单向箭头(指向观测变量)表示直接正相关, 绿虚线单向箭头表示间接相关性, 双箭头为拟合线, 实心红线表示直接负相关; 负值代表负面(抑制性效应), 正值则代表正面效应。Bdellovibrio: 蛭弧菌属; Vibrio: 弧菌属; Caulobacter: 柄杆菌属; Chao1: Chao1指数; Shannon: Shannon指数; SOC: 土壤有机碳; TN: 土壤全氮; Temp: 温度; Viral_diversity: 病毒多样性; Viral_host: 病毒宿主; Soil_Env: 土壤环境。

Fig. 7 The structural equation modeling of soil physicochemical properties-viral host-viral diversity. A solid green one-way arrow (pointing to the observed variable) indicates a direct positive correlation, while a dashed green one-way arrow indicates an indirect correlation, and the double arrow indicates the fitting line, the solid red line indicates a direct negative correlation. Negative values represent a negative (inhibitory) effect, while positive values represent a positive effect. Chao1, Chao1 index; Shannon, Shannon index; SOC, Soil organic carbon; TN, Total nitrogen; Temp, Temperature; Viral_diversity, Viral diversity; Viral_host, Viral host; Soil_Env, Soil environment.

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西溪湿地土壤病毒多样性及其碳代谢基因解析

Soil viral diversity and carbon metabolism genes profiling in Xixi Wetland

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