Bacterial diversity exploring and functional prediction in ancient rice original-producing regions of Wannian County, China
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摘要: 为探讨我国古稻原产区独特的土壤微生态环境, 本研究以江西省万年县古稻原产区及临近区域稻田为研究对象, 采用16S rDNA高通量测序技术和FAPROTAX功能预测分析了细菌群落结构及功能, 并探究影响细菌群落结构与功能特性的关键土壤理化因子。结果显示, 古稻原产区土壤除了包含更高含量的有效氮和Cu, 其他理化因子与临近区域并未表现出明显的差异。古稻原产区的细菌群落特征与其他区域的差异性主要体现在种群组成上, 而不是细菌丰度(基于16S rDNA 荧光定量PCR技术)和Alpha多样性。与临近区域相比, 古稻原产区土壤中包含更高相对丰度的厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidota), 酸杆菌门(Acidobacteriota)和硝化螺旋菌门(Nitrospirota)则相反。此外, 古稻原产区细菌类群表现出更强的碳代谢(包括甲醇氧化、发酵、纤维素分解和碳氢化合物降解等)能力和更弱的氮(包括硝化作用和N2O反硝化等)、硫代谢潜力。进一步的分析发现, 细菌的群落和功能潜力特征除了受土壤营养元素的影响, 还受pH和多种重金属元素(如Cd、Cu、Hg、Ni)的影响。本研究解析了古稻原产区微生态环境的特异性, 明确了其稻田土壤拥有更高的碳周转和氮储能力, 为未来推广优质水稻种植和改善农田生态系统提供了理论参考。Abstract: Rice (genus Oryza) is the world’s largest food crop, and China has a very long history of rice cultivation, with widespread rice distribution. This study investigated the unique soil microecological environment of ancient rice-producing regions in China by examining rice-producing areas around Wannian County. The study analyzed the structure and function of bacterial communities using 16S rDNA high-throughput sequencing technology and FAPROTAX function prediction while exploring the critical factors affecting them. The results showed that while there were no significant differences in physicochemical parameters (including pH, cation exchange capacity, organic matter, total phosphorus, available potassium, available phosphorus, Cr, Pb, Hg, Ni and As) between the ancient rice-producing area and the neighboring regions, this area had higher levels of total nitrogen (2.42 g∙kg−1), available nitrogen (289.57 mg∙kg−1) and copper (57.60 mg∙kg−1). The bacteria community characteristics were primarily different in composition rather than abundance (based on 16S rDNA fluorescence quantitative PCR technology) and Alpha diversities (including ACE index, Chao1index, Shannon index, Simpson index, and PD_whole_tree index), with 51 bacterial phyla found in the study area, and Proteobacteria (22.17%), Chloroflexi (19.31%), Acidobacteriota (16.95%), and Actinobacteria (13.46%) being the most abundant. Specifically, soils in the original rice-producing area contained a higher relative abundance of Firmicutes (5.80%) and Bacteroidota (2.98%), while Acidobacteriota (13.83%) and Nitrospirota(2.24%) were opposite. For the dominant bacterial genus (>1%), soils in the original rice-producing area had a higher relative abundance of Xanthobacteraceae_unclassified (3.44%), Conexibacter (1.79%) and Methylocystis (1.83%), while Acidobacteriales_norank (3.09%), Thermofovibrionia_norank (1.37%), Candidatus_Solibacter(0.08%), Bryobacter(0.88%) and Holophagae_Subgroup_7_norank (0.88%) were low (not significant, P>0.05). In addition, the bacterial taxa in the ancient rice-producing area displayed a higher capacity for carbon metabolism (including methanol oxidation, fermentation, cellulolysis, methanotrophy, hydrocarbon degradation, and methylotrophy) but a weaker potential for nitrogen (such as denitrification, nitrous oxide denitrification, nitrite denitrification, nitrate denitrification, nitrite respiration, nitrate respiration, nitrogen respiration) and sulfur metabolism (such as anoxygenic photoautotrophy sulfur-oxidizing and dark oxidation of sulfur compounds). Further analysis revealed that both soil nutrient elements (e.g., cation exchange capacity, organic matter, total nitrogen, available nitrogen, available potassium, and available phosphorus) and pH, as well as heavy metal elements (e.g., Cd, Cu, Hg, and Ni), influenced the characteristics and functional potential of the bacterial community. In conclusion, the distinctiveness of the soil environment in the ancient rice-producing area primarily stemmed from a higher availability of nitrogen and Cu, with the bacterial community showing a higher potential for carbon metabolism than nitrogen metabolism. Our study found that not only were the physical and chemical environments of paddy soil in ancient rice original-producing regions different from those in other study areas but that the microorganisms enriched there had higher carbon turnover and nitrogen storage capacity. These factors together constitute the unique soil microecological environment in the ancient rice original-producing regions. This study provides a valuable theoretical reference for high-quality rice cultivation and environmentally friendly field management practices.
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Key words:
- Ancient rice /
- Paddy soil /
- High-throughput sequencing /
- Bacterial community /
- Functional prediction
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图 2 不同区域细菌群落的基于OTU水平的主坐标分析(a)、基于Adonis的组间差异分析(b)和基于Bray-curtis距离的物种组内差异分析(c)
ZTN: 珠田北; ZTS: 珠田南; SFE: 上坊东; SFW: 上坊西; PME: 裴梅东; PMW: 裴梅西。ZTN: north of Zhutian Township; ZTS: south of Zhutian Township; SFE: east of Shangfang Township; SFW: west of Shangfang Township; PME: west of Peimei Township; PMW: east of Peimei Township.
Figure 2. (a) ordination of soil bacterial communities via principal coordinate analysis (PCoA) of bacterial communities at the OTU level; (b) analysis of differences between groups based on Adonis; (c) analysis of differences within species groups based on Bray-curtis distances.
图 3 不同区域水稻土壤优势(>1%)细菌门(a)和属(b)水平的相对丰度
ZTN: 珠田北; ZTS: 珠田南; SFE: 上坊东; SFW: 上坊西; PME: 裴梅东; PMW: 裴梅西。ZTN: north of Zhutian Township; ZTS: south of Zhutian Township; SFE: east of Shangfang Township; SFW: west of Shangfang Township; PME: west of Peimei Township; PMW: east of Peimei Township.
Figure 3. Relative abundances of the soil bacterial communities of paddy in different areas at the dominant (>1%) phylum (a) and genus (b)
图 4 不同研究区土壤微生物菌群预测功能分组
ZTN: 珠田北; ZTS: 珠田南; SFE: 上坊东; SFW: 上坊西; PME: 裴梅东; PMW: 裴梅西。ZTN: north of Zhutian Township; ZTS: south of Zhutian Township; SFE: east of Shangfang Township; SFW: west of Shangfang Township; PME: west of Peimei Township; PMW: east of Peimei Township.
Figure 4. Functional prediction of the microbial flora in different study areas.
图 5 细菌群落结构、功能与土壤性质的关系
Clay: 黏粒; Silt: 粉粒; Sand: 砂粒; CEC: 阳离子交换量; OM: 有机质; TN: 总氮; TP: 总磷; AN: 有效氮; AK: 有效钾; AP: 有效磷。CEC: cation exchange capacity; OM: organic matter; TN: total nitrogen; TP: total phosphorus; AN: available nitrogen; AK: available potassium; AP: available phosphorus.
Figure 5. Relationship between bacterial communities, functional and soil properties
表 1 不同研究区域土壤理化指标
Table 1. Physicochemical parameters of soil samples from different areas
指标
Index附近普通稻产区
Normal rice growing regions nearby古稻原产区
Ancient rice original
producing regionZTN (珠田北) ZTS (珠田南) SFE (上坊东) SFW (上坊西) PME (裴梅东) PMW (裴梅西) 黏粒 Clay (%) 5.45±2.93b 2.75±1.75b 4.57±1.79b 0.69±0.62b 31.36±15.55a 2.1±1.39b 粉粒 Silt (%) 59.52±8.10a 63.02±10.02a 62.02±8.44a 61.62±10.66a 50.85±11.32a 69.3±4.6a 砂粒 Sand (%) 35.03±9.57a 34.23±9.66a 33.41±7.64a 37.69±11.12a 17.79±5.32a 28.6±5.08a pH 5.45±0.29a 5.4±0.14a 5.14±0.07a 5.22±0.08a 5.24±0.07a 5.13±0.07a 阳离子交换量
Cation exchange capacity (cmol∙kg−1)8.21±0.36a 9.65±1.33a 7.34±0.39a 7.49±0.30a 8.06±0.63a 9.40±0.35a 有机质 Organic matter (g∙kg−1) 24.79±6.32a 37.74±5.35a 28.67±4.44a 34.58±3.36a 32.05±8.21a 31.10±3.85a 总氮 Total nitrogen (g∙kg−1) 1.19±0.18a 1.99±0.35a 1.67±0.28a 2.17±0.13a 1.95±0.53a 2.41±0.20a 总磷 Total phosphorus (g∙kg−1) 0.56±0.07a 0.58±0.06a 0.54±0.04a 0.46±0.06a 0.44±0.07a 0.51±0.05a 有效氮 Available nitrogen (mg∙kg−1) 106.93±16.53b 160.85±23.00b 137.87±22.56b 177.82±7.00b 154.19±37.94b 289.57±41.24a 有效钾 Available potassium (mg∙kg−1) 114.70±27.33a 93.38±27.86a 105.92±19.84a 112.58±19.74a 113.45±12.21a 109.79±16.04a 有效磷 Available phosphorus (mg∙kg−1) 21.77±2.46a 16.78±2.96a 13.59±1.10a 18.41±3.98a 16.15±2.70a 15.69±1.19a 镉 Cd (mg∙kg−1) 0.27±0.02a 0.17±0.01b 0.15±0.01ab 0.27±0.05a 0.17±0.02ab 0.16±0.01ab 铬 Cr (mg∙kg−1) 44.4±5.66a 43.2±5.43a 45.6±4.18a 42.0±1.26a 58.6±3.17a 44.2±3.01a 铅 Pb (mg∙kg−1) 27.82±3.54a 30.34±5.71a 33.00±5.32a 32.40±2.96a 32.00±4.53a 32.40±3.64a 锌 Zn (mg∙kg−1) 80.2±9.3ab 97.6±5.31ab 83.6±6.72ab 103.2±11.00a 80.6±10.64ab 64.6±3.89b 铜 Cu (mg∙kg−1) 26.0±5.19b 34.8±5.81b 40.8±5.03ab 45.0± 4.44ab 41.8±5.95ab 57.6±5.37a 汞 Hg (mg∙kg−1) 0.14±0.04a 0.07±0.01a 0.08±0.01a 0.08±0.01a 0.08±0.01a 0.08±0.01a 镍 Ni (mg∙kg−1) 30.8±6.19a 41.4±3.19a 36.8±2.82a 45.4±1.44a 31.8±1.85a 32.4±3.31a 砷 As (mg∙kg−1) 2.79±0.74a 2.43±0.81a 2.36±1.07a 1.72±0.26a 1.78±0.28a 1.86±0.3a 数据为平均值±标准误, 同行不同字母表示差异显著(P<0.05)。Values are mean±SD. Different lowercase letters in each row are significantly different (P<0.05). 
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表 2 不同研究区域细菌群落丰度及多样性
Table 2. Bacterial community abundance and diversity of soil samples from different areas
指标
Index附近普通稻产区
Normal rice growing regions nearby古稻原产区
Ancient rice original
producing regionZTN (珠田北) ZTS (珠田南) SFE (上坊东) SFW (上坊西) PME (裴梅东) PMW (裴梅西) 细菌丰度
Bacterial abundance (1010 copies∙g−1)1.91±0.36a 3.22±0.56a 2.22±0.46a 2.62±0.48a 1.84±0.53a 2.51±0.19a 物种丰富度指数
ACE index5042.44±759.8a 5268.53±374.29a 6168.65±266.56a 6256.8±126.56a 5529.5±140.48a 6055.51±182.27a 物种丰富度指数
Chao1 index4995.17±739.35a 5238.03±380.39a 6048.62±278.81a 6147.41±117.5a 5486.65±128.56a 5938.04±193.99a 香农-威纳指数
Shannon index6.91±0.27a 7.12±0.06a 7.34±0.09a 7.27±0.04a 7.24±0.04a 7.28±0.05a 辛普森指数
Simpson index0.0041±0.0013a 0.0023±0.0001a 0.002±0.0003a 0.0022±0.0002a 0.002±0.0001a 0.0024±0.0001a 谱系多样性指数
PD_whole_tree index190.17±24.76a 205.71±10.91a 230.53±7.39a 233.82±4.48a 215.89±4.44a 233.64±5.76a 数据为平均值±标准误, 同行不同小写字母表示差异显著(P<0.05)。Values are mean±SD. Different lowercase letters in each row are significantly different (P<0.05).
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