Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels

doi:10.1016/S2095-3119(20)63364-0

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (10): 2797-2806.DOI: 10.1016/S2095-3119(20)63364-0

所属专题：农业生态环境-土壤微生物合辑Agro-ecosystem & Environment—Soil microbe

收稿日期:2020-04-08 出版日期:2021-10-01 发布日期:2021-08-09

Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels

MA Xin-ling^{1, 2*}, LIU Jia^3*, CHEN Xiao-fen³, LI Wei-tao⁴, JIANG Chun-yu^{1, 2}, WU Meng^{1, 2}, LIU Ming^{1, 2}, LI Zhong-pei^{1, 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

Received:2020-04-08 Online:2021-10-01 Published:2021-08-09
Contact: Correspondence LIU Ming, Tel: +86-25-86881337, E-mail: mliu@issas.ac.cn; LI Zhong-pei, Tel: +86-25-86881323, E-mail: zhpli@issas.ac.cn
About author:MA Xin-ling, E-mail: maxl-scu@qq.com; LIU Jia, E-mail: liujia422@126.com; * These authors contributed equally to this study.
Supported by:
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).

摘要/Abstract

摘要：

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。

Abstract:

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.

Key words: microorganisms , soil biodiversity , soil fertility , soil texture , soil nutrients

. [J]. Journal of Integrative Agriculture, 2021, 20(10): 2797-2806.

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[J]. Journal of Integrative Agriculture, 2021, 20(10): 2797-2806.

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Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels

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