The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Sites
2.2. Soil Sample Collection
2.3. Physicochemical Analysis
2.4. DNA Extraction
2.5. Bioinformatic Analysis and Statistical Analysis
3. Results
3.1. Soil Physicochemical Parameters with Land Use Changes
3.2. Soil Bacterial Community Structure and Diversity
3.3. The Relationship between Soil Physicochemical Parameters and Soil Bacteria
4. Discussion
4.1. The Characteristics of the Soil Physicochemical Properties
4.2. Distribution of Bacterial Diversity Compositions
4.3. Relationships of Bacterial Communities with Basic Soil Parameters
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Yao, L.S. The formation mechanism and model of faulted karst basins in Yunnan province. Carsol. Sin. 1984, 3, 48–55. (In Chinese) [Google Scholar]
- Wang, Y.; Zhang, H.; Zhang, G.; Wang, B.; Peng, S.H.; He, R.S.; Zhou, C.Q. Zoning of environmental geology and functions in karst fault-depression basins. Carsol. Sin. 2017, 36, 283–295. [Google Scholar] [CrossRef]
- Deng, L.; Zhou, P.; Guan, S.; Li, R. Effects of the grain-for-green program on soil erosion in China. Int. J. Sediment. Res. 2012, 27, 120–127. [Google Scholar] [CrossRef]
- Yang, J. Yunnan Natural Forest Resources Conservation Project Phase II Started in an All-round Way. Yunnan For. 2011, 32, 24. (In Chinese) [Google Scholar]
- Bai, C.L. Deepening Reform and Accelerating Development Creating a New Situation of Natural Forest Protection Project Construction in Yunnan Province. Yunnan For. 2007, 28, 4–7. (In Chinese) [Google Scholar]
- Xu, H.J.; Wang, X.H.; Li, H.; Yao, H.Y.; Su, J.Q.; Zhu, Y.G. Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape. Environ. Sci. Technol. 2014, 48, 9391–9399. [Google Scholar] [CrossRef]
- Zhang, Y.; Du, B.H.; Jin, Z.G.; Li, Z.H.; Song, H.N.; Ding, Y.Q. Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages. Plant. Soil 2011, 339, 447–455. [Google Scholar] [CrossRef]
- McCann, K.S. The diversity-stability debate. Nature 2000, 405, 228–233. [Google Scholar] [CrossRef]
- Suleiman, A.K.A.; Manoeli, L.; Boldo, J.T.; Pereira, M.G.; Roesch, L.F.W. Shifts in soil bacterial community after eight years of land-use change. Syst. Appl. Microbiol. 2013, 36, 137–144. [Google Scholar] [CrossRef]
- Song, M.; Zou, D.S.; Du, H.; Peng, W.X.; Zeng, F.P.; Tan, Q.J.; Fan, F.J. Characteristics of soil microbial populations in depressions between karst hills under different land use patterns. Chin. J. Appl. Ecol. 2013, 24, 2471–2478. [Google Scholar] [CrossRef]
- Edarson, D.C.J.; Terence, L.M.; James, M.T.; Fatima, M.D.S.M. Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J. 2009, 3, 1004–1011. [Google Scholar] [CrossRef]
- Bremner, J.M.; Jenkinson, D.S. Determination of organic carbon in soil. I. Oxidation by dichromate of organic matter in soil and plant materials. Eur. J. Soil Sci. 2010, 11, 394–402. [Google Scholar] [CrossRef]
- Parkinson, J.A.; Allen, S.E. A wet oxidation procedure suitable for determination of nitrogen and mineral nutrients in biological material. Commun. Soil Sci. Plant Anal. 1975, 6, 1–11. [Google Scholar] [CrossRef]
- Carson, P.L. Recommended potassium test. In Recommended Chemical Soil Test Procedures for the North Central Region; Dahnke, W.C., Ed.; North Dakota Agricultural Experiment Station: Fargo, ND, USA, 1980; Volume 499, pp. 17–18. [Google Scholar]
- Wilke, B.M. Determination of chemical and physical soil properties. In Monitoring and Assessing Soil Bioremediation; Springer: Heidelberg/Berlin, Germany, 2005. [Google Scholar] [CrossRef]
- Li, Q.; Hu, Q.; Zhang, C.; Müller, W.E.G.; Schröder, H.C.; Li, Z. The effect of toxicity of heavy metals contained in tailing sands on the organic carbon metabolic activity of soil microorganisms from different land use types in the karst region. Environ. Earth Sci. 2015, 74, 6747–6756. [Google Scholar] [CrossRef]
- Chan, C.O.; Yang, X.D.; Fu, Y.; Feng, Z.L.; Sha, L.Q.; Peter, C.; Zou, X.M. 16S rRNA gene analyses of bacterial community structures in the soils of evergreen broad-leaved forests in south-west China. FEMS Microbiol. Ecol. 2006, 58, 247–259. [Google Scholar] [CrossRef] [Green Version]
- Magoč, T.; Salzberg, S.L. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011, 27, 2957–2963. [Google Scholar] [CrossRef]
- Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011, 17, 10–12. [Google Scholar] [CrossRef]
- Quast, C.; Pruesse, E.; Yilmaz, P.; Gerken, J.; Schweer, T.; Yarza, P.; Peplies, J.; Glöckner, F.O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucl. Acids Res. 2013, 41, D590–D596. [Google Scholar] [CrossRef]
- Edgar, R.C.; Haas, B.J.; Clemente, J.C.; Quince, C.; Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27, 2194–2200. [Google Scholar] [CrossRef] [Green Version]
- Edgar, R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26, 2460–2461. [Google Scholar] [CrossRef] [Green Version]
- Caporaso, J.G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F.D.; Costello, E.K.; Fierer, N.; Goodrich, J.K.; Gordon, J.I.; Huttley, G.A.; et al. QIIME allows analysis of highthroughput community sequencing data. Nat. Methods 2010, 7, 335–336. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zuur, A.F.; Ieno, E.N.; Smith, G.M. Analysing Ecological Data; Springer: New York, NY, USA, 2007. [Google Scholar]
- R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2014; Available online: http://www.R-project.org/ (accessed on 15 July 2019).
- Anderson, M.J.; Willis, T.J. Canonical analysis of principal coordinates: A useful method of constrained ordination for ecology. Ecology 2003, 84, 511–525. [Google Scholar] [CrossRef]
- Bastian, M.; Heymann, S.; Gephi, M.J. An open source software for exploring and manipulating networks. In Proceedings of the Third International Conference on Weblogs and Social Media, ICWSM 2009, San Jose, CA, USA, 17–20 May 2009. [Google Scholar] [CrossRef]
- Oberson, A.; Friesen, D.K.; Rao, I.M.; Bühler, S.; Frossard, E. Phosphorus Transformations in an Oxisol under contrasting land-use systems: The role of the soil microbial biomass. Plant Soil 2001, 237, 197–210. [Google Scholar] [CrossRef]
- Batlle-Aguilar, J.; Brovelli, A.; Porporato, A.; Barry, D.A. Modelling soil carbon and nitrogen cycles during land use change-A review. Agron. Sustain. Dev. 2011, 31, 251–274. [Google Scholar] [CrossRef] [Green Version]
- Liu, Y.P.; Lu, M.X.; Zhang, X.W.; Sun, Q.B.; Liu, R.L.; Lian, B. Shift of the microbial communities from exposed sandstone rocks to forest soils during pedogenesis. Int. Biodeter. Biodegr. 2019, 140, 21–28. [Google Scholar] [CrossRef]
- Huang, X.F.; Zhou, Y.C.; Zhang, Z.M. Distribution characteristics of soil organic carbon under different land use in a karst rocky desertification area. J. Soil Water Conserv. 2017, 31, 215–221. [Google Scholar] [CrossRef]
- Tong, J.H.; Hu, Y.C.; Du, Z.L.; Zou, Y.Q.; Li, Y.Y. Effects of land use change on soil organic carbon and total nitrogen storage in karst immigration regions of Guanxi Province, China. Chin. J. Appl. Ecol. 2018, 29, 2890–2896. [Google Scholar] [CrossRef]
- Li, L.; Qin, F.C.; Jiang, L.N.; Yao, X.L. Vertical distribution of soil organic carbon content and its influenceing factors in Aaohan, Chifeng. Acta Ecol. Sin. 2019, 39, 345–354. [Google Scholar] [CrossRef]
- Chaplot, V.; Bouahom, B.; Valentin, C. Soil organic carbon stocks in Laos: Spatial variations and controlling factors. Glob. Chang. Biol. 2010, 16, 1380–1393. [Google Scholar] [CrossRef]
- Kuang, W.N.; Qian, J.Q.; Ma, Q.; Liu, Z.M. Vertical distribution of soil organic carbon content and its relation to root distribution in five desert shrub communities. Chin. J. Ecol. 2016, 35, 275–281. [Google Scholar] [CrossRef]
- Wang, D.; Geng, Z.C.; She, D.; He, W.X.; Hou, L. Soil organic carbon storage and vertical distribution of carbon and nitrogen across different forest types in the Qinling Mountains. Acta Ecol. Sin. 2015, 35, 5421–5429. [Google Scholar] [CrossRef] [Green Version]
- Daniel, C.S.; Matthew, G.B.; James, M.B.; Linda, L.K. Plant community richness and microbial interactions structure bacterial communities in soil. Ecology 2015, 96, 134–142. [Google Scholar] [CrossRef] [Green Version]
- Kinkel, L.L.; Bakker, M.G.; Schlatter, D.C. A coevolutionary framework for managing disease-suppressive soils. Annu. Rev. Phytopathol. 2011, 49, 47–67. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhang, C.; Li, J.; Wang, J.; Liua, G.B.; Wang, G.L.; Guo, L.; Peng, S.Z. Decreased temporary turnover of bacterial communities along soil depth gradient during a 35-year grazing exclusion period in a semiarid grassland. Geoderma 2019, 351, 49–58. [Google Scholar] [CrossRef]
- He, S.B.; Guo, L.X.; Niu, M.Y.; Miao, F.H.; Jiao, S.; Hu, T.M.; Long, M.X. Ecological diversity and cooccurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation. Sci. Rep. 2017, 3608, 7. [Google Scholar] [CrossRef]
- Cheng, J.M.; Guanghua Jing, G.H.; Wei, L.; Jing, Z.B. Long-term grazing exclusion effects on vegetation characteristics, soil properties and bacterial communities in the semiarid grasslands of China. Ecol. Eng. 2016, 97, 170–178. [Google Scholar] [CrossRef]
- Wang, S.X.; Wang, X.A.; Guo, H. Change patterns of β-diversity in the succession process of plant communities on Loess Plateau of Northwest China. Chin. J. Ecol. 2013, 32, 1135–1140. [Google Scholar] [CrossRef]
- Tian, Q.; Taniguchi, T.; Shi, W.Y.; Li, G.Q.; Yamanaka, N.; Du, S. Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China. Sci. Rep. 2017, 7, 45289. [Google Scholar] [CrossRef] [Green Version]
- Bru, D.; Ramette, A.; Saby, N.P.A.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.; Philippot, L. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J. 2011, 5, 532–542. [Google Scholar] [CrossRef] [Green Version]
- Adria, L.F.; Craig, C.S.; Donald, L.W.; Christopher, S.; Trevor, J.G.; Michael, J.S. Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment. Sci. Total Environ. 2016, 566, 949–959. [Google Scholar] [CrossRef] [Green Version]
- Manuel, D.B.; Angela, M.O.; Tess, E.B.; Alberto, B.G.; David, J.E.; Richard, D.B.; Fernando, T.M.; Brajesh, K.S.; Noah, F. A global atlas of the dominant bacteria found in soil. Science 2018, 359, 320–325. [Google Scholar] [CrossRef] [Green Version]
- Zhou, J.; Guan, D.W.; Zhou, B.K.; Zhao, B.S.; Ma, M.C.; Qin, J.; Jiang, X.; Chen, S.F.; Cao, F.M.; Shen, D.L.; et al. Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China. Soil Biol. Biochem. 2015, 90, 42–51. [Google Scholar] [CrossRef]
- Griffiths, B.S.; Philippot, L. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol. Rev. 2013, 37, 112–129. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Anna, K.; Jorge, L.M.R.; Eiko, E.K.; Patrick, S.G.C.; Johannes, A.V.V.; George, A.K. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol. Ecol. 2010, 71, 23–33. [Google Scholar] [CrossRef]
- David, C.W.; Susan, D.S.; David, B.R. The genus Sphingomonas: Physiology and ecology. Curr. Opin. Biotechnol. 1996, 7, 301–306. [Google Scholar] [CrossRef]
- David, V.; Kendra, R.M.; Erick, C.; Cameron, R.S.; Steven, J.H.; William, W.M. Non-symbiotic Bradyrhizobium ecotypes dominateNorth American forest soils. ISME J. 2015, 9, 2435–2441. [Google Scholar] [CrossRef] [Green Version]
- Heinz, S.; Cheryl, J.; Jamest, S. The phylum Verrucomicrobia: A phylogenetically heterogeneous bacterial group. Prokaryotes 2006, 7, 881–896. [Google Scholar] [CrossRef]
- Wagner, M.; Horn, M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 2006, 17, 241–249. [Google Scholar] [CrossRef]
- Noll, M.; Diethart, M.; Frenzel, P.; Manigee, D.; Liesack, W. Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ. Microbiol. 2005, 7, 382–395. [Google Scholar] [CrossRef]
- Fierer, N.; Ladau, J.; Clementei, J.C.; Leff, J.W.; Owens, S.M.; Katherine, S.P.; Knight, R.; Gilbert, J.A.; McCulley, R.L. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 2013, 342, 621–624. [Google Scholar] [CrossRef] [Green Version]
- Janssen, P.H.; Yates, P.S.; Grinton, B.E.; Taylor, P.M.; Sait, M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microb. 2002, 68, 2391–2396. [Google Scholar] [CrossRef] [Green Version]
- Stefan, S.; Boyke, B.; Cathrin, S.; Peter, S.; Manfred, R.; Brian, J.T.; Hans, P.K. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME J. 2016, 10, 2801–2816. [Google Scholar] [CrossRef] [Green Version]
- Wang, P.; Chen, B.; Zhang, H. High throughput sequencing analysis of bacterial communities in soils of a typical Poyang Lake wetland. Acta Ecol. Sin. 2017, 37, 1650–1658. [Google Scholar] [CrossRef] [Green Version]
- Zhang, Y.G.; Cong, J.; Lu, H.; Li, G.L.; Qu, Y.Y.; Su, X.J.; Zhou, J.Z.; Li, D.Q. Community structure and elevational diversity patterns of soil Acidobacteria. J. Environ. Sci. 2014, 26, 171–1724. [Google Scholar] [CrossRef]
Name | Land Use Pattern | TP | TN | SOC | AK | pH | Moisture | T | EC | E-Ca | E-Mg |
---|---|---|---|---|---|---|---|---|---|---|---|
(g/kg) | (g/kg) | (g/kg) | (g/kg) | (%) | (°C) | (ms.m−1) | (cmol/kg) | (cmol/kg) | |||
WLA | woodland | 0.828 ± 0.020 ab | 5.09 ± 0.24 a | 61.00 ± 1.96 a | 128.47 ± 5.78 b | 6.21 ± 0.11 b | 37.47 ± 5.04 a | 8.60 ± 0.21 c | 68.33 ± 4.10 b | 5.14 ± 1.15 a | 26.82 ± 0.65 c |
SLA | Shrubland | 0.734 ± 0.025 b | 4.11 ± 0.16 b | 47.00 ± 2.5 b | 124.03 ± 14.05 b | 6.72 ± 0.09 a | 42.85 ± 2.56 a | 11.60 ± 1.12 b | 64.33 ± 2.03 b | 6.91 ± 0.09 a | 36.18 ± 3.48 b |
GLA | Grassland | 0.941 ± 0.059 a | 2.97 ± 0.14 c | 33.00 ± 1.47 c | 262.17 ± 44.37 a | 6.68 ± 0.08 a | 40.00 ± 1.42 a | 16.53 ± 0.74 a | 84.67 ± 2.03 a | 6.87 ± 0.08 a | 51.56 ± 2.32 a |
WLB | woodland | 0.640 ± 0.037 a | 3.16 ± 0.49 a | 35.79 ± 5.32 a | 40.40 ± 2.14 b | 6.46 ± 0.10 a | 36.53 ± 2.98 a | 9.37 ± 0.09 c | 70.33 ± 6.64 ab | 6.64 ± 0.11 a | 29.21 ± 0.28 c |
SLB | Shrubland | 0.595 ± 0.025 a | 2.32 ± 0.12 a | 24.53 ± 2.13 ab | 38.40 ± 3.98 b | 6.66 ± 0.08 a | 33.07 ± 1.91 a | 10.97 ± 0.33 b | 56.00 ± 3.00 b | 6.85 ± 0.08 a | 34.20 ± 1.02 b |
GLB | Grassland | 0.762 ± 0.084 a | 2.34 ± 0.37 a | 20.46 ± 3.71 b | 127.27 ± 15.21 a | 6.55 ± 0.03 a | 32.70 ± 1.16 a | 12.77 ± 0.34 a | 79.33 ± 5.70 a | 6.73 ± 0.03 a | 39.82 ± 1.05 a |
Name | Land Use Pattern | Chao1 | Shannon | Simpson | Observed OTUs |
---|---|---|---|---|---|
WLA | Woodland | 1656 ± 69 b | 8.01 ± 0.23 b | 0.985 ± 0.004 a | 1162 ± 45 b |
SLA | Shrubland | 1640 ± 70 b | 7.69 ± 0.17 b | 0.977 ± 0.004 b | 1103 ± 48 b |
GLA | Grassland | 1935 ± 75 a | 8.85 ± 0.10 a | 0.993 ± 0.001 a | 1409 ± 25 a |
WLB | Woodland | 1582 ± 89 a | 7.80 ± 0.31 a | 0.981 ± 0.005 b | 1115 ± 67 a |
SLB | Shrubland | 1565 ± 62 a | 7.70 ± 0.07 a | 0.982 ± 0.002 a | 1030 ± 24 a |
GLB | Grassland | 1693 ± 119 a | 8.54 ± 0.37 a | 0.993 ± 0.003 a | 1212 ± 106 a |
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Qiu, J.; Cao, J.; Lan, G.; Liang, Y.; Wang, H.; Li, Q. The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China. Forests 2020, 11, 51. https://doi.org/10.3390/f11010051
Qiu J, Cao J, Lan G, Liang Y, Wang H, Li Q. The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China. Forests. 2020; 11(1):51. https://doi.org/10.3390/f11010051
Chicago/Turabian StyleQiu, Jiangmei, Jianhua Cao, Gaoyong Lan, Yueming Liang, Hua Wang, and Qiang Li. 2020. "The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China" Forests 11, no. 1: 51. https://doi.org/10.3390/f11010051
APA StyleQiu, J., Cao, J., Lan, G., Liang, Y., Wang, H., & Li, Q. (2020). The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China. Forests, 11(1), 51. https://doi.org/10.3390/f11010051