Composition and diversity of microbial communities in high-altitude karst soil
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摘要: 高寒岩溶是四川黄龙风景区独特的地质特征。为分析高寒岩溶区土壤微生物群落组成特征与土壤理化性质间的相关性，以黄龙风景区土壤为研究对象，对土壤细菌的16SrRNA基因序列和真菌ITS序列进行高通量测序。结果表明：不同岩溶区的土壤细菌多样性和丰富度具有显著差异，但土壤真菌差异不显著，且土壤细菌群落占主导地位；细菌群落以变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)为主；真菌群落以子囊菌门(Ascomycota)、担子菌门(Basidiomycota)为主，真菌在门和属水平的差异较大。冗余分析发现总磷和温度是黄龙风景区土壤微生物群落结构变化的重要环境因子，pH是第二重要的环境因子。Abstract:
As a World Natural Heritage Site, Huanglong Scenic Area, is located in the eastern part of the Qinghai–Tibet Plateau in Songpan county, Aba Tibetan and Qiang Autonomous Prefecture, Sichuan Province. Huanglong valley is 3.50 km long, with an altitude of 3,145–3,578 m. In the Huanglong Scenic Area, there is a six-month freezing period, with a minimum temperature of 3 ℃. The main vegetation types are coniferous and broad-leaved mixed forests and coniferous forests, belonging to a typical plateau temperate to subfrigid monsoon climate. This scenic area is renowned at home and abroad for its rare and colorful karst landscape. At present, there is still a research gap in the structure and function of soil microorganisms of high-altitude karst habitats. Therefore, in order to explore the characteristics of soil microbial communities in Huanglong Scenic Area—a high-altitude karst area, we compared the differences in soil microbial community structure and diversity between high-altitude karst and non-high-altitude karst areas, with typical primary karst in Guilin—a non-high-altitude karst area. By analyzing the structural characteristics of soil microbial communities and their correlation with environmental impact factors, we laid a theoretical foundation for the relationship between soil microbial communities and ecological environment in high-altitude karst areas. In this study, we collected and analyzed soil samples from Huanglong valley, the main scenic area of the Huanglong Scenic Area. A total of 27 (three replicates) samples were collected and compared with the samples from the typical primary karst area in Guilin. We collected data on environmental factor, such as Total Organic Carbon (TOC), Soil Organic Matter (SOM), Total Nitrogen (TN), Total Product (TP), Temperature (T), Soil Water Content (SWC), and pH. Meanwhile, we employed high-throughput sequencing techniques such as 16SrRNA and ITS gene sequencing to perform bioinformatics analysis on sequencing data, including species diversity and β diversity. Then, we identified the main driving factors affecting soil in the Huanglong Scenic Area through principal component analysis (PCA), and explored the relationship between environmental factors and soil microbial communities by Spearman correlation analysis and redundancy analysis (RDA). The results show that the soil pH at each sampling point in Huanglong valley indicates a neutral to alkaline property, with no significant difference. But there are significant temperature differences at various sampling points. Compared to the soil from slopes of the Yaji test site in the non-high-altitude karst area of Guilin, the SOC, SOM, and TN contents in soil at various points in the Huanglong Scenic Area are relatively higher. There are differences in the bacterial chao1 index and observed OTUs index between Guilin's primary karst area and Huanglong valley. Similarly, the ACE index of bacteria and fungi also shows differences. These results may be attributed to the influence of vegetation types, soil types, and topographical factors on the distribution of soil microorganisms. The diversity indices of Shannon and Chao1 at HJ.4 sampling point in Huanglong valley are higher than those of other sampling points, indicating the richest biodiversity in this sampling point. At a phylum level, the bacterial community is mainly composed of Proteobacteria and Acidobacteria. Ascomycota and Basidiomycota are the dominant microbial groups in the high-altitude karst habitat of the Huanglong area. At a subordinate level, the main dominant bacteria in Huanglong valley are Pseudomonas, RB41, and Candidatus_Udaeobacter, with an average abundance of 14.57%, 3.11%, and 2.29%, respectively. The most dominant group in the primary karst area of Guilin is Candidatus_Udaeobacter, with an abundance of 6%. At a genus level, the dominant fungi in Huanglong valley are Humicola (22%) and Mortierella (22%). The dominant groups of the primary karst area in Guilin are Staphylococcum (5%), Absidia (5%), and Fusarium (4%). The differences in fungi at the phylum and genus levels are greater than those in bacteria. In summary, the proportion of dominant microorganisms in the primary karst area is relatively low, and the community types differ significantly compared to those in Huanglong valley. Samples collected from nine sampling points (three replicates) in Huanglong valley and in the primary karst area of Guilin show varying degrees of dispersion. UPGMA clustering analysis shows a high degree of similarity in various eukaryotic communities in Huanglong valley, while there are certain differences in the composition of prokaryotes among them. Redundancy analysis indicates that in bacteria, TP is the most correlated factor with community distribution, while T is the second most important environmental factor. In fungi, TP is also the most correlated factor, while T and pH are the second most important environmental factors. Both soil TP and T have a significant impact on the distribution of fungal and bacterial communities. -
图 1 采样区位置图
注：HJ.1.迎宾池左; HJ.2.盆景池右; HJ.3.接仙桥左; HJ.4.黄龙古寺右; HY.1.迎宾池右; HY.2.盆景池左; HY.3.接仙桥右; HY.4.黄龙古寺左; YS.桂林原生岩溶（丫吉岩溶试验场）
Figure 1. Location of sampling points in Huanglong Scenic Area
Note: HJ.1. the left of Yingbin pool; HJ.2. the right of Penjing pool; HJ.3. the left of Jiexianqiao pool; HJ.4. the right of Huanglong ancient temple; HY.1. the right of Yingbin pool; HY.2. the left of Penjing pool; HY.3. the right of Jiexianqiao pool; HY.4. the left of Huanglong ancient temple; YS. primary karst (Yaji karst experimental site in Guilin, China).
图 2 土壤细菌和真菌基于OTUs的花瓣图
Figure 2. OTUs-based petaline diagram of soil fungi and bacteria
图 3 细菌门和属水平的物种丰度
注：①表示黄龙沟的物种丰度，②表示桂林原生岩溶物种丰度，并用红色虚框圈出。
Figure 3. Species abundance of bacteria at the phylum and genus levels
Note: ① indicates the species abundance of Huanglong valley; ② in a red dotted circle indicates abundance of native karst species in Guilin.
图 5 土壤微生物群落主坐标（PCoA）分析
Figure 5. Analysis of principal coordinate of soil microbial community (PCoA)
图 6 土壤微生物群落结构组成的非度量多维排序（NMDS）
Figure 6. Non-metric multidimensional scaling(NMDS) of soil microbial community structure
图 7 UPGMA聚类树与门水平优势细菌和真菌
Figure 7. UPGMA clustering tree and phylum level of dominant bacteria and fungi
图 8 环境因子与土壤细菌、真菌在门水平的冗余分析
Figure 8. Redundancy analysis of environmental factors and soil fungi and bacteria at the phylum level
图 9 环境因子与土壤细菌、真菌门水平组成的Spearman分析
Figure 9. Spearman analysis of environmental factors and the composition of soil bacteria and fungi at the phylum level
表 1 采样信息
Table 1. Information of sample points
采样区 样品 纬度 经度 海拔 迎宾池左 HJ.1 32°74′96″N 103°82′58″E 3 200.00 m 盆景池右 HJ.2 32°74′63″N 103°82′84″E 3 300.00 m 接仙桥左 HJ.3 32°73′42″N 103°83′39″E 3 400.00 m 黄龙古寺右 HJ.4 32°72′68″N 103°83′20″E 3 500.00 m 迎宾池右 HY.1 32°74′96″N 103°82′35″E 3 200.00 m 盆景池左 HY.2 32°74′64″N 103°82′95″E 3 300.00 m 接仙桥右 HY.3 32°73′71″N 103°83′04″E 3 400.00 m 黄龙古寺左 HY.4 32°72′77″N 103°83′40″E 3 500.00 m 桂林原生岩溶 YS 25°10′60″N 110°45′21″E 150 m 
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表 2 土壤环境因子分析
Table 2. Analysis of soil environmental factors
理化指标 HJ.1 HJ.2 HJ.3 HJ.4 HY.1 HY.2 HY.3 HY.4 YS T ℃ 13.07±1.01b 5.5±0.76ef 5.4±0.15f 10±0.15c 6.2±0.10ef 7.9±0.21d 6.8±0.25e 9.47±0.50c 26.55±0.66a pH 7.64±0.15ab 7.31±0.19bc 7.59±0.34ab 7.39±0.34bc 7.38±0.23bc 7.77±0.17ab 7.14±0.04bc 7.16±0.12bc 8.58±0.24a TP/mg·L−1 2.24±1.43d 4.18±0.73ab 2.94±0.56bcd 3.55±1.07abc 4.87±0.11a 2.78±1.06cd 5.47±0.26abc 2.55±0.27cd 2.65±0.13b TN/mg·L−1 0.96±0.14d 3.28±0.24b 1.65±0.06c 1.05±0.12d 0.13±0.19e 1.93±0.33c 0.33±0.16e 1.35±0.68cd 7.77±0.18a Ec/us 172.87±39.43abc 225.17±35.37a 223.60±27.58ab 160.57±19.86bc 168.70±49.62abc 180.27±18.07abc 126.50±36.00cd 86.40±10.92d 193.30±3.46b SOC/g·kg−1 26.48±5.84b 51.36±5.96a 17.21±1.99bc 28.21±11.47b 18.31±6.25bc 18.37±1.96bc 27.43±2.38b 20.83±1.88bc 10.23±5.24c SOM/g·kg1 45.66±10.06ab 29.79±3.46bc 29.66±3.43bc 64.46±28.11a 31.57±10.77bc 31.68±3.38bc 47.31±4.10ab 35.91±3.24bc 17.77±62c SWC/ % 21.77±0.40f 50±7.21bc 44.67±2.52cd 38.77±0.68de 54.67±3.06b 32.73±0.64e 48.33±2.08bc 63.37±4.15a 14.92±1.32b 注：表中数据为平均值±标准差，不同小写字母代表差异显著（P＜0.05）。
Note: Data in the Table 2 indicate mean ± standard deviation. Lowercase letters represent significant differences (P＜0.05).
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表 3 土壤微生物α多样性
Table 3. Alpha diversity of soil microorganism
样品 Chao1指数 Shannon指数 Simpson指数 Observed_OTUs指数 ACE指数 细菌 真菌 细菌 真菌 细菌 真菌 细菌 真菌 细菌 真菌 HJ.1 1199.54±326.40c 326.04±143.87b 6.66±0.91b 2.67±1.42c 0.90±0.04bc 0.51±0.22b 1195.33±326.76c 324.33±142.62c 2648.93±500.73e 787.50±305.84de HJ.2 1737.44±21.77ab 678.86±230.88ab 9.85±0.05a 4.93±1.02abc 1.00±0.00a 0.78±0.19a 1734.00±22.11ab 675.00±233.22abc 3961.61±155.55ab 1723.36±673.85abcd HJ.3 1839.00±63.00a 627.37±213.97ab 9.97±0.04a 4.65±1.14bc 1.00±0.00a 0.81±0.16a 1837.33±63.22a 624.67±214.15abc 3876.56±267.65ab 1535.09±638.65bcde HJ.4 2019.37±52.47a 975.64±153.96a 10.21±0.03a 7.3±0.61a 1.00±0.00a 0.98±0.01a 2017.33±52.00a 974.33±152.72a 4269.48±273.22a 2751.19±870.78a HY.1 1770.97±130.19a 971.38±160.10a 9.86±0.03a 7.39±0.50a 1.00±0.00a 0.98±0.01a 1769.33±129.33a 968.67±159.48a 3755.03±77.57bc 2490.57±633.04ab HY.2 1301.99±504.66bc 569.99±170.57ab 6.66±2.79b 5.15±1.47abc 0.84±0.14c 0.87±0.09a 1301.00±505.35bc 569.00±170.84abc 3059.07±134.61de 1319.98±479.86cde HY.3 1788.48±38.07a 769.33±97.95a 9.97±0.05a 6.17±0.77ab 1.00±0.00a 0.93±0.06a 1786.00±40.04a 766.33±95.97ab 4065.98±52.40ab 2062.51±219.78abc HY.4 1631.30±189.07abc 699.15±327.77ab 8.95±0.75a 5.35±2.24ab 0.98±0.03ab 0.87±0.09a 1630.00±188.75abc 694.67±331.24abc 3383.84±184.75cd 1409.53±405.28bcde YS 760.42±59.05d 545.08±297.01ab 5.94±0.03b 3.7±0.81bc 1.00±0.00a 0.89±0.07a 748.00±52.83d 522.67±280.45bc 761.43±304.62f 547.22±304.62e 注：表中数据为平均值±标准差，不同小写字母代表差异显著（P＜0.05）。
Note: Data in table indicate mean ± standard deviation. Lowercase letters represent significant differences (P＜0.05).
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