Biotechnology Bulletin ›› 2022, Vol. 38 ›› Issue (6): 81-92.doi: 10.13560/j.cnki.biotech.bull.1985.2021-1102
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ZHONG Hui1,2(), LIU Ya-jun1,2, WANG Bin-hua1,2, HE Meng-jie1,2, WU Lan1,2()
Received:
2021-08-27
Online:
2022-06-26
Published:
2022-07-11
Contact:
WU Lan
E-mail:udaio@qq.com;ncusk724@hotmail.com
ZHONG Hui, LIU Ya-jun, WANG Bin-hua, HE Meng-jie, WU Lan. Effects of Analysis Methods on the Analyzed Results of 16S rRNA Gene Amplicon Sequencing in Bacterial Communities[J]. Biotechnology Bulletin, 2022, 38(6): 81-92.
样本 Sample | 样本类型 Sample type | 采样时间 Sampling time | 酸碱度 pH | 总有机碳 Total organic carbon(TOC)/(g·kg-1) | 总氮 Total nitrogen(TN)/(g·kg-1) | 总磷 Total phosphorus(TP)/(g·kg-1) | 氨态氮 NH4+ N/ (mg·kg-1) | 硝态氮 NO3- N/ (mg·kg-1) |
---|---|---|---|---|---|---|---|---|
FS1 | 森林土壤 | 2016年8月 | 4.57±0.24 | 48.07±1.17 | 3.98±0.26 | 0.49±0.09 | 9.01±0.64 | 45.14±11.26 |
FS2 | 森林土壤 | 2016年8月 | 4.64±0.1 | 58.29±9.12 | 3.86±0.62 | 0.68±0.17 | 46.73±4.21 | 12.19±2.08 |
FS3 | 森林土壤 | 2016年8月 | 4.70±0.12 | 55.17±4.91 | 3.93±0.83 | 0.56±0.11 | 13.24±1.48 | 27.90±3.41 |
FS4 | 森林土壤 | 2016年8月 | 5.35±0.67 | 22.96±0.86 | 2.68±0.54 | 0.80±0.14 | 9.06±1.05 | 32.48±7.65 |
WS1 | 湿地土壤 | 2015年1月 | 5.29±0.14 | 7.31±1.68 | 0.92±0.25 | 0.60±0.18 | 2.30±0.27 | 0.71±0.06 |
WS2 | 湿地土壤 | 2015年1月 | 4.95±0.58 | 6.89±1.78 | 0.97±0.26 | 0.64±0.19 | 2.85±0.42 | 0.42±0.04 |
WS3 | 湿地土壤 | 2015年1月 | 5.19±0.25 | 8.82±3.33 | 0.98±0.23 | 0.54±0.06 | 2.79±0.33 | 0.75±0.42 |
WS4 | 湿地土壤 | 2015年1月 | 5.72±0.39 | 6.64±2.81 | 1.02±0.24 | 0.41±0.06 | 2.65±0.47 | 1.07±0.36 |
CS1 | 农田土壤 | 2017年5月 | 4.71±0.54 | 36.60±4.66 | 3.95±0.15 | 0.45±0.19 | 0.91±0.11 | 2.54±1.18 |
CS2 | 农田土壤 | 2017年5月 | 5.22±0.02 | 66.34±3.13 | 7.86±1.15 | 0.55±0.09 | 1.05±0.11 | 5.81±0.25 |
CS3 | 农田土壤 | 2017年5月 | 5.17±0.17 | 41.11±1.62 | 4.13±0.36 | 0.26±0.01 | 0.87±0.12 | 3.37±0.80 |
CS4 | 农田土壤 | 2017年5月 | 5.06±0.07 | 44.49±2.11 | 4.97±0.13 | 0.52±0.13 | 0.96±0.08 | 6.52±0.32 |
LS1 | 湖泊沉积物 | 2018年5月 | 6.60±0.35 | 9.78±1.61 | 1.01±0.14 | 0.96±0.24 | 15.72±9.03 | 1.18±0.68 |
LS2 | 湖泊沉积物 | 2018年5月 | 7.30±0.22 | 9.97±5.50 | 14.40±2.07 | 1.15±0.16 | 22.10±7.40 | 1.75±0.57 |
LS3 | 湖泊沉积物 | 2018年5月 | 6.63±0.03 | 7.47±6.21 | 6.96±2.41 | 0.71±0.11 | 5.51±1.08 | 1.68±1.84 |
LS4 | 湖泊沉积物 | 2018年5月 | 8.08±0.08 | 5.32±3.72 | 14.37±8.57 | 0.90±0.22 | 16.83±2.47 | 1.79±1.04 |
Table1 Information and environmental parameters of soil and sediment samples
样本 Sample | 样本类型 Sample type | 采样时间 Sampling time | 酸碱度 pH | 总有机碳 Total organic carbon(TOC)/(g·kg-1) | 总氮 Total nitrogen(TN)/(g·kg-1) | 总磷 Total phosphorus(TP)/(g·kg-1) | 氨态氮 NH4+ N/ (mg·kg-1) | 硝态氮 NO3- N/ (mg·kg-1) |
---|---|---|---|---|---|---|---|---|
FS1 | 森林土壤 | 2016年8月 | 4.57±0.24 | 48.07±1.17 | 3.98±0.26 | 0.49±0.09 | 9.01±0.64 | 45.14±11.26 |
FS2 | 森林土壤 | 2016年8月 | 4.64±0.1 | 58.29±9.12 | 3.86±0.62 | 0.68±0.17 | 46.73±4.21 | 12.19±2.08 |
FS3 | 森林土壤 | 2016年8月 | 4.70±0.12 | 55.17±4.91 | 3.93±0.83 | 0.56±0.11 | 13.24±1.48 | 27.90±3.41 |
FS4 | 森林土壤 | 2016年8月 | 5.35±0.67 | 22.96±0.86 | 2.68±0.54 | 0.80±0.14 | 9.06±1.05 | 32.48±7.65 |
WS1 | 湿地土壤 | 2015年1月 | 5.29±0.14 | 7.31±1.68 | 0.92±0.25 | 0.60±0.18 | 2.30±0.27 | 0.71±0.06 |
WS2 | 湿地土壤 | 2015年1月 | 4.95±0.58 | 6.89±1.78 | 0.97±0.26 | 0.64±0.19 | 2.85±0.42 | 0.42±0.04 |
WS3 | 湿地土壤 | 2015年1月 | 5.19±0.25 | 8.82±3.33 | 0.98±0.23 | 0.54±0.06 | 2.79±0.33 | 0.75±0.42 |
WS4 | 湿地土壤 | 2015年1月 | 5.72±0.39 | 6.64±2.81 | 1.02±0.24 | 0.41±0.06 | 2.65±0.47 | 1.07±0.36 |
CS1 | 农田土壤 | 2017年5月 | 4.71±0.54 | 36.60±4.66 | 3.95±0.15 | 0.45±0.19 | 0.91±0.11 | 2.54±1.18 |
CS2 | 农田土壤 | 2017年5月 | 5.22±0.02 | 66.34±3.13 | 7.86±1.15 | 0.55±0.09 | 1.05±0.11 | 5.81±0.25 |
CS3 | 农田土壤 | 2017年5月 | 5.17±0.17 | 41.11±1.62 | 4.13±0.36 | 0.26±0.01 | 0.87±0.12 | 3.37±0.80 |
CS4 | 农田土壤 | 2017年5月 | 5.06±0.07 | 44.49±2.11 | 4.97±0.13 | 0.52±0.13 | 0.96±0.08 | 6.52±0.32 |
LS1 | 湖泊沉积物 | 2018年5月 | 6.60±0.35 | 9.78±1.61 | 1.01±0.14 | 0.96±0.24 | 15.72±9.03 | 1.18±0.68 |
LS2 | 湖泊沉积物 | 2018年5月 | 7.30±0.22 | 9.97±5.50 | 14.40±2.07 | 1.15±0.16 | 22.10±7.40 | 1.75±0.57 |
LS3 | 湖泊沉积物 | 2018年5月 | 6.63±0.03 | 7.47±6.21 | 6.96±2.41 | 0.71±0.11 | 5.51±1.08 | 1.68±1.84 |
LS4 | 湖泊沉积物 | 2018年5月 | 8.08±0.08 | 5.32±3.72 | 14.37±8.57 | 0.90±0.22 | 16.83±2.47 | 1.79±1.04 |
样本 Sample | 样本类型 Sample type | 采样时间 Sampling time | 酸碱度 pH | 总有机碳 TOC/(mg·kg-1) | 总氮 TN/(mg·kg-1) | 总磷 TP/(mg·kg-1) | 氨态氮 NH4+ N/(mg·kg-1) | 硝态氮 NO3--N/(mg·kg-1) |
---|---|---|---|---|---|---|---|---|
LW1 | 湖泊水体 | 2017年7月 | 7.87±0.50 | 16.39±6.93 | 2.40±0.66 | 0.13±0.03 | 0.26±0.10 | 0.66±0.12 |
LW2 | 湖泊水体 | 2017年7月 | 7.3±0.16 | 12.40±5.44 | 3.10±0.63 | 0.13±0.02 | 0.14±0.05 | 0.26±0.04 |
LW3 | 湖泊水体 | 2017年7月 | 6.79±0.41 | 11.09±5.51 | 1.38±0.36 | 0.11±0.04 | 0.34±0.15 | 0.48±0.04 |
LW4 | 湖泊水体 | 2017年7月 | 7.12±0.13 | 14.06±6.00 | 1.14±0.67 | 0.11±0.04 | 0.25±0.06 | 0.02±0.03 |
Table2 Water samples information and environmental parameters
样本 Sample | 样本类型 Sample type | 采样时间 Sampling time | 酸碱度 pH | 总有机碳 TOC/(mg·kg-1) | 总氮 TN/(mg·kg-1) | 总磷 TP/(mg·kg-1) | 氨态氮 NH4+ N/(mg·kg-1) | 硝态氮 NO3--N/(mg·kg-1) |
---|---|---|---|---|---|---|---|---|
LW1 | 湖泊水体 | 2017年7月 | 7.87±0.50 | 16.39±6.93 | 2.40±0.66 | 0.13±0.03 | 0.26±0.10 | 0.66±0.12 |
LW2 | 湖泊水体 | 2017年7月 | 7.3±0.16 | 12.40±5.44 | 3.10±0.63 | 0.13±0.02 | 0.14±0.05 | 0.26±0.04 |
LW3 | 湖泊水体 | 2017年7月 | 6.79±0.41 | 11.09±5.51 | 1.38±0.36 | 0.11±0.04 | 0.34±0.15 | 0.48±0.04 |
LW4 | 湖泊水体 | 2017年7月 | 7.12±0.13 | 14.06±6.00 | 1.14±0.67 | 0.11±0.04 | 0.25±0.06 | 0.02±0.03 |
群落生境 Biotope | 多样性指数 Diversity index | 97 OTU | 98 OTU | 99 OTU | 100 OTU | ASV | F | P |
---|---|---|---|---|---|---|---|---|
FS | Shannon | 8.89±0.59c | 9.44±0.57c | 10.06±0.53b | 11.35±0.34a | 9.36±0.36c | 3.76 | 0.01 |
Faith’s phylog-enetic diversity | 200.65±30.09a | 206.76±30.33a | 205.45±31.21a | 189.98±30.05a | 76.57±17.53b | 3.59 | 0.01 | |
Chao1 | 6 197.73±681.64d | 7 715.24±864.03c | 9 783.86±1121.87b | 15 783.82±1 896.16a | 1 348.3±250.55e | 64.05 | <0.01 | |
WS | Shannon | 9.15±0.44cd | 9.51±0.40c | 9.93±0.33b | 10.76±0.22a | 9.10±0.25d | 45.32 | <0.01 |
Faith’s phylog-enetic diversity | 131.82±20.02ab | 135.38±20.39a | 131.70±21.02ab | 112.17±17.56b | 59.95±11.00c | 46.78 | <0.01 | |
Chao1 | 3 432.91±489.63c | 4 119.94±523.16bc | 4 834.80±605.21b | 6 259.35±1 102.91a | 909.03±166.82d | 272.21 | <0.01 | |
CS | Shannon | 8.99±0.88b | 9.27±0.93b | 9.60±1.01ab | 10.40±1.00a | 9.42±0.92ab | 3.51 | 0.01 |
Faith’s phylog-enetic diversity | 180.30±33.33ab | 169.08±31.10ab | 202.30±38.74a | 199.45±36.96a | 159.09±30.77b | 1.1 | 0.37 | |
Chao1 | 3 672.12±892.42c | 4 271.85±1 029.13bc | 4 993.04±1 280.13b | 9 069.09±1 554.95a | 2 186.44±570.72d | 51.61 | <0.01 | |
LS | Shannon | 6.82±1.06b | 6.96±1.15b | 7.21±1.24ab | 8.32±1.09a | 7.20±0.90ab | 49.53 | <0.01 |
Faith’s phylog-enetic diversity | 97.39±35.21a | 97.87±34.88a | 99.98±35.44a | 110.06±32.85a | 83.22±15.54a | 35.66 | <0.01 | |
Chao1 | 1 429.92±867.84bc | 1 646.30±1 010.35bc | 1 916.62±1 242.16b | 5 343.72±481.48a | 934.21±263.76c | 110.54 | <0.01 | |
LW | Shannon | 6.71±1.12b | 6.98±1.14b | 7.36±1.10b | 9.04±0.71a | 7.50±0.80b | 10.01 | <0.01 |
Faith’s phylog-enetic diversity | 79.77±30.70a | 88.65±32.64a | 91.25±32.18a | 85.25±24.93a | 59.01±18.95a | 2.48 | 0.05 | |
Chao1 | 1 709.26±868.06bc | 2 043.13±914.34bc | 2 674.50±1 066.06b | 8 847.05±1 696.64a | 837.88±332.8c | 108.4 | <0.01 |
Table 3 Alpha diversity of bacterial community
群落生境 Biotope | 多样性指数 Diversity index | 97 OTU | 98 OTU | 99 OTU | 100 OTU | ASV | F | P |
---|---|---|---|---|---|---|---|---|
FS | Shannon | 8.89±0.59c | 9.44±0.57c | 10.06±0.53b | 11.35±0.34a | 9.36±0.36c | 3.76 | 0.01 |
Faith’s phylog-enetic diversity | 200.65±30.09a | 206.76±30.33a | 205.45±31.21a | 189.98±30.05a | 76.57±17.53b | 3.59 | 0.01 | |
Chao1 | 6 197.73±681.64d | 7 715.24±864.03c | 9 783.86±1121.87b | 15 783.82±1 896.16a | 1 348.3±250.55e | 64.05 | <0.01 | |
WS | Shannon | 9.15±0.44cd | 9.51±0.40c | 9.93±0.33b | 10.76±0.22a | 9.10±0.25d | 45.32 | <0.01 |
Faith’s phylog-enetic diversity | 131.82±20.02ab | 135.38±20.39a | 131.70±21.02ab | 112.17±17.56b | 59.95±11.00c | 46.78 | <0.01 | |
Chao1 | 3 432.91±489.63c | 4 119.94±523.16bc | 4 834.80±605.21b | 6 259.35±1 102.91a | 909.03±166.82d | 272.21 | <0.01 | |
CS | Shannon | 8.99±0.88b | 9.27±0.93b | 9.60±1.01ab | 10.40±1.00a | 9.42±0.92ab | 3.51 | 0.01 |
Faith’s phylog-enetic diversity | 180.30±33.33ab | 169.08±31.10ab | 202.30±38.74a | 199.45±36.96a | 159.09±30.77b | 1.1 | 0.37 | |
Chao1 | 3 672.12±892.42c | 4 271.85±1 029.13bc | 4 993.04±1 280.13b | 9 069.09±1 554.95a | 2 186.44±570.72d | 51.61 | <0.01 | |
LS | Shannon | 6.82±1.06b | 6.96±1.15b | 7.21±1.24ab | 8.32±1.09a | 7.20±0.90ab | 49.53 | <0.01 |
Faith’s phylog-enetic diversity | 97.39±35.21a | 97.87±34.88a | 99.98±35.44a | 110.06±32.85a | 83.22±15.54a | 35.66 | <0.01 | |
Chao1 | 1 429.92±867.84bc | 1 646.30±1 010.35bc | 1 916.62±1 242.16b | 5 343.72±481.48a | 934.21±263.76c | 110.54 | <0.01 | |
LW | Shannon | 6.71±1.12b | 6.98±1.14b | 7.36±1.10b | 9.04±0.71a | 7.50±0.80b | 10.01 | <0.01 |
Faith’s phylog-enetic diversity | 79.77±30.70a | 88.65±32.64a | 91.25±32.18a | 85.25±24.93a | 59.01±18.95a | 2.48 | 0.05 | |
Chao1 | 1 709.26±868.06bc | 2 043.13±914.34bc | 2 674.50±1 066.06b | 8 847.05±1 696.64a | 837.88±332.8c | 108.4 | <0.01 |
样地 Sampling site | 门总数 Number of phyla | 差异门 Differential phylum | 差异门丰度Abundance of differential phylum/% | 属总数 Number of genera | 差异属 Differential genus | 差异属丰度Abundance of differential genus/% |
---|---|---|---|---|---|---|
FS | 40 | 2 | 3.7 | 888 | 75 | 2.9 |
WS | 52 | 0 | 0 | 854 | 30 | 0.35 |
CS | 58 | 0 | 0 | 1 227 | 38 | 3.21 |
LS | 54 | 0 | 0 | 1 304 | 15 | 14.9 |
LW | 51 | 0 | 0 | 1 179 | 18 | 1.32 |
Table 4 Effects of the minimum taxonomy unit division method on the abundances of bacterial community phylum and genus
样地 Sampling site | 门总数 Number of phyla | 差异门 Differential phylum | 差异门丰度Abundance of differential phylum/% | 属总数 Number of genera | 差异属 Differential genus | 差异属丰度Abundance of differential genus/% |
---|---|---|---|---|---|---|
FS | 40 | 2 | 3.7 | 888 | 75 | 2.9 |
WS | 52 | 0 | 0 | 854 | 30 | 0.35 |
CS | 58 | 0 | 0 | 1 227 | 38 | 3.21 |
LS | 54 | 0 | 0 | 1 304 | 15 | 14.9 |
LW | 51 | 0 | 0 | 1 179 | 18 | 1.32 |
Fig.2 Analysis of β diversity based on the bacterial community(genus level)bray-curtis dissimility A:Cluster analysis. B:Principal co-ordinates analysis(PCoA). C:Differences in beta-diversity among the division methods
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