Ammonia-oxidizing Bacteria Community in Rhizosphere Soils of Minjiang Estuary Wetlands
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摘要:
目的 研究闽江河口湿地不同植物根际土壤中氨氧化细菌群落多样性及结构组成，为阐明湿地植物根际土壤脱氮功能微生物类群研究提供科学数据。 方法 多点混合采样法采集不同季节不同土层闽江河口湿地芦苇、互花米草和红树林根际的土壤样品共24个，通过高通量测序技术测定样品氨单加氧酶编码基因amoA序列，生物信息学方法分析土壤样品氨氧化细菌的群落结构及多样性。 结果 24个样品中共检测到300 527条有效序列，2 794个OTU。多样性分析结果表明，芦苇、互花米草和红树林根际土壤样品Chao指数差别不大，Shannon指数平均值表现为红树林＞芦苇＞互花米草；芦苇和红树林根际土壤样品Chao指数和Shannon指数均表现为春季最低；不同土层芦苇、互花米草和红树林根际土壤样品Chao指数和Shannon指数均未呈现出明显的变化趋势。群落结构分析结果表明，闽江河口湿地土壤样品中存在着较多分类地位未确定的氨氧化细菌，而分类地位确定的氨氧化细菌中，优势菌门为变形菌门（Proteobacteria），优势菌属包括亚硝化单胞菌属（Nitrosomonas）、硫杆菌属（Thiobacillus）、Caldimonas属等。 结论 闽江河口湿地植物根际土壤中氨氧化细菌的主要优势菌群大多是亚硝化单胞菌属（Nitrosomonas），硫杆菌属（Thiobacillus）和Caldimonas属为个别样品的优势菌群。 Abstract:Objective Community and diversity of ammonia-oxidizing bacteria in rhizosphere soils of reeds, smooth cordgrasses, and mangroves on the wetlands at Minjiang estuaries were studied. Method Twenty-four rhizosphere soil specimens in different layers on the wetlands were collected in 4 seasons with the multi-point mixed sampling method. Sequence of amoA gene in the specimens was determined by the high-throughput sequencing technology for a bioinformatic analysis on the ammonia-oxidizing bacteria community at the sites. Result A total of 300 527 final tags and 2 794 OTUs were detected in the collected specimens. The OTU-based diversity analysis showed little difference on the Chao index among the reed, smooth cordgrass, and mangrove rhizosphere soils. The Shannon index of the mangrove soil was higher than that of the reed soil, while that of the smooth cordgrass soil being the lowest. The Chao and Shannon indices of the reed and mangrove soils were lowest in spring. There was no apparent pattern on the Chao or Shannon index of the soils in different depths. The taxonomy of many of the ammonia-oxidizing bacteria could not be clearly classified. The dominant phylum of the microbes identified in the soils was Proteobacteria, and Nitrosomonas, Thiobacillus, and Caldimonas being the predominant genera. Conclusion Nitrosomonas presented in most of the rhizosphere soils at the Minjiang estuary wetlands, but Thiobacillus and Caldimonas were dominant in individual soil specimens. -
图 1 闽江河口湿地植物根际土壤氨氧化细菌OTUs Venn图
注：样品名称中的LW代表芦苇，HHMC代表互花米草，HSL代表红树林；数字1、2、3、4分别代表春、夏、秋、冬4个季节。
Figure 1. OTUs Venn diagrams of ammonia-oxidizing bacteria in rhizosphere soils of Minjiang estuary wetlands
Note: LW, HHMC, and HSL are soil specimens collected from rhizosphere of reeds, smooth cordgrasses, and mangroves, respectively. Numbers 1, 2, 3, and 4 represent spring, summer, autumn, and winter, respectively.
图 2 门水平氨氧化细菌群落的相对丰度
Figure 2. Relative abundance of ammonia-oxidizing bacteria community at phylum level
图 3 属水平Top 20优势氨氧化细菌群落的相对丰度
Figure 3. Relative abundance of top 20 ammonia-oxidizing bacteria community at genus level
表 1 高通量测序有效数据统计
Table 1. Filtered valid data from high-throughput sequencing
样品名称
Samples原始序列
Raw tags/条优质序列
Clean tags/条最终序列
Final tags/条OTUs/
个LW1a 23 148 6 290 5 446 163 LW1b 41257 26130 24864 315 LW2a 32053 14607 12276 539 LW2b 36627 17348 15295 556 LW3a 40246 17897 15598 474 LW3b 41435 10144 8707 406 LW4a 38718 19722 17352 524 LW4b 36911 12376 10754 499 HHMC1a 40228 17800 15776 429 HHMC1b 35002 13091 11649 404 HHMC2a 36520 10868 9459 470 HHMC2b 38414 16536 14322 536 HHMC3a 39430 11740 10271 468 HHMC3b 37391 12534 11365 362 HHMC4a 44997 43330 40818 90 HHMC4b 37943 12801 11441 535 HSL1a 36184 11429 10253 115 HSL1b 32530 11192 9682 289 HSL2a 33604 8413 4422 454 HSL2b 34211 13402 11695 328 HSL3a 26488 3697 2282 259 HSL3b 33368 11522 10244 498 HSL4a 34230 8480 7061 460 HSL4b 36005 10866 9495 481 注：下机数据去除barcode和primer并拼接后得到原始序列，再经进一步去除嵌合体、短序列后得到优质序列；最终序列指OTU表中每个样本对应的序列数目；OTUs为每个样本最终得到的OTU数目。表中，LW代表芦苇，HHMC代表互花米草，HSL代表红树林；数字1、2、3、4分别代表春、夏、秋、冬四个季节；字母a和b分别代表0～20 cm土层和20～40 cm土层。表2同。
Note: Raw tags are results after filtering low-quality fastq data and splicing; clean tags, after further removing chimeric and short sequences; final tags, sequence corresponding to OTUs of individual sample; and, OTUs, final OTUs of individual sample. LW, HHMC, and HSL are soil specimens collected from rhizosphere of reeds, smooth cordgrasses, and mangroves, respectively. Numbers 1, 2, 3, and 4 represent spring, summer, autumn, and winter, respectively. “a” after name of specimen indicates soil sampled at depth from 0 to 20cm; and, “b” from 20 to 40cm. Same for below.
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表 2 土壤样品氨氧化细菌的Alpha多样性指数
Table 2. Alpha diversity indices of ammonia-oxidizing bacteria in soil specimens
样品名称
Samples观测到的OTU数
Observed species覆盖率
Coverage/%Chao Shannon LW1a 113 97.61 171.27 3.20 LW1b 108 97.39 193.64 3.04 LW2a 247 94.23 416.68 5.71 LW2b 275 93.74 449.41 5.89 LW3a 251 94.70 379.34 5.66 LW3b 243 95.15 352.09 5.77 LW4a 257 94.15 411.49 5.83 LW4b 290 94.06 418.03 6.15 HHMC1a 219 95.74 327.27 5.64 HHMC1b 206 95.48 330.74 4.77 HHMC2a 267 93.71 446.53 5.50 HHMC2b 233 93.99 422.84 4.93 HHMC3a 256 94.05 419.28 5.36 HHMC3b 222 96.04 301.32 5.79 HHMC4a 20 99.52 31.96 0.31 HHMC4b 271 93.48 459.07 5.74 HSL1a 68 99.02 104.45 4.24 HSL1b 191 96.43 269.71 4.88 HSL2a 380 94.49 477.93 7.42 HSL2b 200 96.35 276.89 5.36 HSL3a 251 95.99 329.87 5.53 HSL3b 263 94.02 428.09 5.78 HSL4a 323 93.90 452.82 6.50 HSL4b 287 94.33 417.08 5.98
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