农业生态环境-土壤微生物合辑Agro-ecosystem & Environment—Soil microbe
|Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels
MA Xin-ling1, 2*, LIU Jia3*, CHEN Xiao-fen3, LI Wei-tao4, JIANG Chun-yu1, 2, WU Meng1, 2, LIU Ming1, 2, LI Zhong-pei1, 2
1 State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, P.R.China
2 University of Chinese Academy of Sciences, Beijing 100049, P.R.China
3 Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, P.R.China
4 CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, P.R.China
一方面，中国亚热带红壤区水稻土母质和肥力水平多变；另一方面，细菌多样性和群落组成在土壤生态系统过程和功能中发挥关键作用。但是水稻土的母质和肥力对细菌多样性和群落组成的影响如何仍不清楚，不同母质和肥力水平条件下驱动水稻土细菌多样性、群落组成和特异微生物种群变化的关键因素尚不明确。因此，本研究采集亚热带红壤区具有不同母质（第四纪红黏土或第三纪红砂岩）和不同肥力水平（高肥力或低肥力）的典型样地水稻土样品，通过454高通量测序测定细菌16S rRNA基因的V4−V5区，分析细菌多样性指数和群落组成变化。采用two-way ANOVA和two-way PERMANOVA探明母质和肥力对细菌多样性和群落组成的影响；主坐标分析（PCoA）、冗余分析（RDA）和多元回归树分析（MRT）明确细菌群落的变化，以及驱动该变化的关键土壤因子；共现网络分析阐明属水平特异细菌种群和关键土壤因子的关系；宏基因组差异分析工具（STAMP）确定不同土壤样品间差异物种。结果显示，母质和肥力对水稻土细菌多样性指数变化的贡献相似。但是肥力水平对细菌群落组成的影响要远大于母质。土壤因子，特别是土壤质地与细菌多样性指数密切相关。RDA分析发现土壤有机碳（SOC）是影响细菌群落组成的首要因素，并且25.5 g kg−1有机碳含量是驱动高肥力和低肥力土壤细菌群落组成分异的关键阈值。共现网络分析暗示高肥力水平下，由于土壤环境的改善，细菌趋向于合作关系，并且富营养型细菌占主导地位。STAMP分析发现高肥力水稻土中Massilia和Rhodanobacter等富营养型细菌大量富集；而低肥力土壤中Anaerolinea等贫营养型细菌占主导。研究结果表明，不同母质和肥力水稻土中，土壤质地影响细菌多样性指数变化；而养分水平，特别是有机碳水平决定细菌群落组成的变化。
Parent materials and the fertility levels of paddy soils are highly variable in subtropical China. Bacterial diversity and community composition play pivotal roles in soil ecosystem processes and functions. However, the effects of parent material and fertility on bacterial diversity and community composition in paddy soils are unclear. The key soil factors driving the changes in bacterial diversity, community composition, and the specific bacterial species in soils that are derived from different parent materials and have differing fertility levels are unknown. Soil samples were collected from paddy fields in two areas with different parent materials (quaternary red clay or tertiary sandstone) and two levels of fertility (high or low). The variations in bacterial diversity indices and communities were evaluated by 454 pyrosequencing which targeted the V4–V5 region of the 16S rRNA gene. The effects of parent material and fertility on bacterial diversity and community composition were clarified by a two-way ANOVA and a two-way PERMANOVA. A principal coordinate analysis (PCoA), a redundancy analysis (RDA), and multivariate regression trees (MRT) were used to assess changes in the studied variables and identify the factors affecting bacterial community composition. Co-occurrence network analysis was performed to find correlations between bacterial genera and specific soil properties, and a statistical analysis of metagenomic profiles (STAMP) was used to determine bacterial genus abundance differences between the soil samples. The contributions made by parent material and soil fertility to changes in the bacterial diversity indices were comparable, but soil fertility accounted for a larger part of the shift in bacterial community composition than the parent material. Soil properties, especially soil texture, were strongly associated with bacterial diversity. The RDA showed that soil organic carbon (SOC) was the primary factor influencing bacterial community composition. A key threshold for SOC (25.5 g kg–1) separated low fertility soils from high fertility soils. The network analysis implied that bacterial interactions tended towards cooperation and that copiotrophic bacteria became dominant when the soil environment improved. The STAMP revealed that copiotrophic bacteria, such as Massilia and Rhodanobacter, were more abundant in the high fertility soils, while oligotrophic bacteria, such as Anaerolinea, were dominant in low fertility soils. The results showed that soil texture played a role in bacterial diversity, but nutrients, especially SOC, shaped bacterial community composition in paddy soils with different parent materials and fertility levels.
Received: 08 April 2020
|Fund: This work was supported by the National Key Research and Development Program of China (2018YFD0301104-01), the National Natural Science Foundation of China (41201242 and 41907041), the Major Research and Development Program for Science and Technology of Jiangxi Province, China (20182ABC28006), and the “135” Plan and the Field Frontier Project, China (ISSASIP1642).
Correspondence LIU Ming, Tel: +86-25-86881337, E-mail: firstname.lastname@example.org; LI Zhong-pei, Tel: +86-25-86881323, E-mail: email@example.com
|About author: MA Xin-ling, E-mail: firstname.lastname@example.org; LIU Jia, E-mail: email@example.com; * These authors contributed equally to this study.
Cite this article:
MA Xin-ling, LIU Jia, CHEN Xiao-fen, LI Wei-tao, JIANG Chun-yu, WU Meng, LIU Ming, LI Zhong-pei.
Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels. Journal of Integrative Agriculture, 20(10): 2797-2806.
| Bhat A K. 2013. Preserving microbial diversity of soil ecosystem: A key to sustainable productivity. International Journal of Current Microbiology and Applied Sciences, 2, 85–101.
Brussaard L, Ruiter P, Brown G. 2007. Soil biodiversity for agricultural sustainability. Agriculture Ecosystems & Environment, 121, 233–244.
Cao Y, Li Y, Li C, Huang G, Lu G. 2016. Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures. Applied Soil Ecology, 103, 93–100.
Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Pena A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, Muegge B D, Pirrung M, Reeder J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335–336.
Carson J K, Gonzalez-Quiñones V, Murphy D V, Hinz C, Shaw J A, Gleeson D B. 2010. Low pore connectivity increases bacterial diversity in soil. Applied and Environmental Microbiology, 76, 3936–3942.
Cederlund H, Wessén E, Enwall K, Jones C M, Juhanson J, Pell M, Philippot L, Hallin S. 2014. Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla. Applied Soil Ecology, 84, 62–68.
Chau J F, Bagtzoglou A C, Willig M R. 2011. The effect of soil texture on richness and diversity of bacterial communities. Environmental Forensics, 12, 333–341.
Chen H, Xia Q, Yang T, Shi W. 2018. Eighteen-year farming management moderately shapes the soil microbial community structure but promotes habitat-specific taxa. Frontiers in Microbiology, 9, 1776.
Chen X F, Liu M, Kuzyakov Y, Li W T, Liu J, Jiang C Y, Wu M, Li Z P. 2018. Incorporation of rice straw carbon into dissolved organic matter and microbial biomass along a 100-year paddy soil chronosequence. Applied Soil Ecology, 130, 84–90.
Chodak M, Niklinska M. 2010. Effect of texture and tree species on microbial properties of mine soils. Applied Soil Ecology, 46, 268–275.
Conway E J. 1948. Microdiffusion analysis and volumetric error. Nature, 161, 583.
De’Ath G. 2002. Multivariate regression trees: A new technique for modeling species–environment relationships. Ecology, 83, 1105–1117.
Deng H, Yu Y J, Sun J E, Zhang J B, Cai Z C, Guo G X, Zhong W H. 2015. Parent materials have stronger effects than land use types on microbial biomass, activity and diversity in red soil in subtropical China. Pedobiologia, 58, 73–79.
Dickman S R, Bray R H. 1940. Colorimetric determination of phosphate. Industrial and Engineering Chemistry, Analytical Edition, 11, 665–668.
Edgar R C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.
Faoro H, Alves A C, Souza E M, Rigo L U, Cruz L M, Al-Janabi S M, Monteiro R A, Baura V A, Pedrosa F O. 2010. Influence of soil characteristics on the diversity of bacteria in the southern Brazilian Atlantic Forest. Applied and Environmental Microbiology, 76, 4744–4749.
Feng K, Zhang Z J, Cai W W, Liu W Z, Xu M Y, Yin H Q, Wang A J, He Z L, Deng Y. 2017. Biodiversity and species competition regulate the resilience of microbial biofilm community. Molecular Ecology, 26, 6170–6182.
Fierer N, Jackson R B. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103, 626–631.
García-Orenes F, Roldán A, Morugán-Coronado A, Linares C, Cerdà A, Caravaca F. 2016. Organic fertilization in traditional mediterranean grapevine orchards mediates changes in soil microbial community structure and enhances soil fertility. Land Degradation & Development, 27, 1622–1628.
Griffiths R I, Thomson B C, James P, Bell T, Bailey M, Whiteley A S. 2011. The bacterial biogeography of British soils. Environmental Microbiology, 13, 1642–1654.
Guo H C, Wang W B, Luo X H, Wu X P. 2013. Variations in rhizosphere microbial communities of rubber plantations in Hainan Island, China. Journal of Rubber Research, 16, 243–256.
Guo H C, Wang W B, Luo X H, Wu X P. 2015. Characteristics of rhizosphere and bulk soil microbial communities in rubber plantations in Hainan island, China. Journal of Tropical Forest Science, 27, 202–212.
Hammer Ø, Harper D A T, Ryan P D. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron, 4, 1–9.
Heijden M G A V D, Bardgett R D, Straalen N M V. 2008. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11, 296–310.
Ibekwe A, Kennedy A, Frohne P, Papiernik S, Yang C H, Crowley D. 2002. Microbial diversity along a transect of agronomic zones. FEMS Microbiology Ecology, 39, 183–191.
Jia J, Li Z, Liu M, Che Y. 2010. Effect of glucose addition on N transformations in paddy soils with a gradient of organic C content in subtropical China. Agricultural Sciences in China, 9, 1309–1316.
Johnson M J, Lee K Y, Scow K M. 2003. DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities. Geoderma, 114, 279–303.
Józefowska A, Pietrzykowski M, Wo? B, Cajthaml T, Frouz J. 2017. Relationships between respiration, chemical and microbial properties of afforested mine soils with different soil texture and tree species: Does the time of incubation matter. European Journal of Soil Biology, 80, 102–109.
Kjeldahl J. 1883. Neue méthode zur bestimmung des stickstoffs in organischen Körpern. Zeitschrift für Analytische Chemie, 22, 366−382. (in German)
Kuramae E E, Yergeau E, Wong L C, Pijl A S, Veen J, Kowalchu G A. 2012. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiology Ecology, 79, 12–24.
Lauber C L, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology, 75, 5111–5120.
Li P F, Liu M, Ma X Y, Wu M, Jiang C Y, Liu K, Liu J, Li Z P. 2020. Responses of microbial communities to a gradient of pig manure amendment in red paddy soils. Science of the Total Environment, 705, 135884.
Li W T, Liu M, Wu M, Jiang C Y, Kuzyakov Y, Gavrichkova O, Feng Y Z, Dong Y H, Li Z P. 2019. Bacterial community succession in paddy soil depending on rice fertilization. Applied Soil Ecology, 144, 92−97.
Liu M, Liu J, Chen X F, Jiang C H, Wu M, Li Z P. 2018. Shifts in bacterial and fungal diversity in a paddy soil faced with phosphorus surplus. Biology and Fertility of Soils, 54, 259–267.
Madhaiyan M, Poonguzhali S, Saravanan V S, Kwon S W. 2014. Rhodanobacter glycinis sp. nov., a yellow-pigmented gamma proteobacterium isolated from the rhizoplane of field-grown soybean. International Journal of Systematic and Evolutionary Microbiology, 64, 2023−2028.
Mebius L J. 1960. A rapid method for the determination of organic carbon in soil. Analytica Chimica Acta, 22, 120−124.
Melero S, Madejon E, Herencia J F, Ruiz J C. 2007. Biochemical properties of two different textured soils (loam and clay) after the addition of two different composts during conversion to organic farming. Spanish Journal of Agricultural Research, 5, 593–604.
Meriles J M, Vargas G S, Conforto C, Figoni G, Lovera E, March G J, Guamán C A. 2009. Soil microbial communities under different soybean cropping systems: characterization of microbial population dynamics, soil microbial activity, microbial biomass, and fatty acid profiles. Soil & Tillage Research, 103, 271–281.
Müller T, Höper H. 2004. Soil organic matter turnover as a function of the soil clay content: Consequences for model applications. Soil Biology & Biochemistry, 36, 877–888.
Naveed M, Herath L, Moldrup P, Arthur E, Nicolaisen M, Norgaard T, Ferre T P A, Jonge L W. 2016. Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field. Applied Soil Ecology, 103, 44–55.
Pansu M, Gautheyrou J. 2006. Handbook of Soil Analysis: Mineralogical, Organic and Inorganic Methods. Springer, Berlin Heidelberg, Berlin.
Parks D H, Tyson G W, Hugenholtz P, Beiko R G. 2014. STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics, 30, 3123–3124.
R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. [2019-09-10]. http://www.R-project.org/
Ramirez K S, Lauber C L, Knight R, Bradford M A, Fierer N. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology, 91, 3463–3470.
Ramírez M, López-Piñeiro A, Peña D, Nunes J R, Albarrán Á, Muñoz A, Gama J, Loures L. 2017. Seasonal and interannual fluctuation of the microbial soil community in a maize field under long-term conservation agriculture management. Sustainability, 9, 778.
Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.
Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X, Liang W, Chu H. 2013. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biology & Biochemistry, 57, 204–211.
Sheng R, Qin H, O’Donnell A G, Huang S, Wu J, Wei W. 2015. Bacterial succession in paddy soils derived from different parent materials. Journal of Soils and Sediments, 15, 982–992.
Sun L, Xun W, Huang T, Zhang G, Gao J, Ran W, Li D, Shen Q, Zhang R. 2016. Alteration of the soil bacterial community during parent material maturation driven by different fertilization treatments. Soil Biology & Biochemistry, 96, 207–215.
Sun R, Zhang X X, Guo X, Wang D, Chu H. 2015. Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biology & Biochemistry, 88, 9–18.
Ulrich A, Becker R. 2006. Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiology Ecology, 56, 430–443.
Wagai R, Kitayama K, Satomura T, Fujinuma R, Balser T. 2011. Interactive influences of climate and parent material on soil microbial community structure in Bornean tropical forest ecosystems. Ecological Research, 26, 627–636.
Wang Q, Garrity G M, Tiedje J M, Cole J R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261–5267.
Won K, Singh H, Ngo H T T, Son H M, Kook M C, Kim K Y, Yi T H. 2015. Rhodanobacter koreensis sp. nov., a bacterium isolated from tomato rhizosphere. International Journal of Systematic and Evolutionary Microbiology, 65, 1180−1185.
Xia Y, Wang Y B, Wang Y, Chin F Y L, Zhang T. 2016. Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation. Biotechnology for Biofuels, 9, 111.
Xie L, Zhang Q J, Cao J L, Liu X F, Xiong D C, Kong Q, Yang Y S. 2019. Effects of warming and nitrogen addition on the soil bacterial community in a subtropical Chinese fir plantation. Forest, 10, 861.
Xu Y B, Cai Z C. 2007. Denitrification characteristics of subtropical soils in China affected by soil parent material and land use. European Journal of Soil Science, 58, 1293–1303.
Zhang W W, Wang C, Xue R, Wang L J. 2019. Effects of salinity on the soil microbial community and soil fertility. Journal of Integrative Agriculture, 18, 1360–1368.
Zhang Y, Li Q, Chen Y L, Dai Q G, Hu J. 2019. Dynamic change in enzyme activity and bacterial community with long-term rice cultivation in mudflats. Current Microbiology, 76, 361−369.
Zhou S M, Zhang M, Zhang K K, Yang X W, He D X, Yin J, Wang C Y. 2020. Effects of reduced nitrogen and suitable soil moisture on wheat (Triticum aestivum L.) rhizosphere soil microbiological, biochemical properties and yield in the Huanghuai Plain, China. Journal of Integrative Agriculture, 19, 234–250.
Zul D, Wanner G, Overmann J. 2008. Massilia brevitalea sp. nov., a novel beta proteobacterium isolated from lysimeter soil. International Journal of Systematic and Evolutionary Microbiology, 58, 1245−1251.
|No Suggested Reading articles found!