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Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China

Cite this dataset

Wang, Hang et al. (2021). Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China [Dataset]. Dryad.


This dataset contains data from 257 sites in four typical rice-growing regions across a 4,000-km transect in China, including geographic location data and environment factors data.

The study was conducted across a 4,000-km transect of China’s rice-growing areas, from Heilong Jiang province to Yunnan province (100°55′ E to 134°08′° E, 22°46′ N to 48°02′ N, Table S1). Four typical rice-growing regions were selected along this transect: Sanjiang Plain (modern mechanical farming), Taihu Plain (mechanical plus minor manual farming), Lianghu Plain (manual plus minor mechanical farming), and Hani Terrace (traditional manual farming).

Field sampling was conducted during July and August in 2014 and 2015. Soil samples were collected from 178 flooded paddy fields and 79 surrounding non-paddy areas across four typical rice-growing regions of China. At each site, one homogenized sample was obtained, which was then separated into two parts. One part, which was obtained for DNA extraction, was placed into a sterile plastic tube then immediately placed in liquid nitrogen for short-term transportation. After shipping to the laboratory, these tubes were stored at −80 °C. The second part of the soil sample was placed into a plastic bag and stored at 4.0 °C for determining the soil physicochemical properties.

Main results of the experiments are that: (1) Distance–decay patterns of bacterial communities in paddy fields revealed reduced β-diversity compared to surrounding natural habitats. (2) Modern rice farming practices (plowing with machines) caused stronger homogenization of soil bacterial communities than traditional farming (plowing by hand). Among the four paddy regions, plowing by hand retained the highest soil bacterial β-diversity. (3) Moreover, a significant inverse correlation was observed between bacterial β-diversity and the agricultural mechanization level. (4) Among multiple environmental factors, dramatic spatial homogenization of soil physicochemical properties, particularly soil nutrient contents, and reduced dispersal limitation caused by modern farming activities both strongly predict a reduction of bacterial β-diversity in modern paddy fields.


Across a 4000 km transect of China, we collected a total of 257 samples from four typical rice-growing regions. These regions follow a rice cultivation management gradient from modern mechanical to traditional manual practices. We examined distance decay patterns of soil bacterial communities regionally and continentally. With more than 50 environmental factors determined, we then used multiple statistical tools to unveil mechanisms underlying such patterns.

Usage notes

Sample ID and geographic location.xlsx

The longitude (long) and latitude (lat) coordinates for a total of 257 soil samples taken across four rice-growing regions, China. 


Studied environmental factors.xlsx

All studied environmental variables and their measured/determined values, including 19 climate variables, 26 plant-soil variables, and 9 landscape/topography variables.

Long: longitude

Lat: latitude

AMT: Annual mean temperature

MDR: Mean diurnal range

ISO: Isothermal sex

TSEA: Temperature Seasonality

MAXTWM: Max Temperature of Warmest Month

MINTCM: Min Temperature of Coldest Month

TRANGE: Temperature Annual Range

TWETQ: Mean Temperature of Wettest Quarter

TDQ: Mean Temperature of Driest Quarter

TWARQ: Mean Temperature of Warmest Quarter

TCQ: Mean Temperature of Coldest Quarter

AP: Annual Precipitation

PWETM: Precipitation of Wettest Month

PDM: Precipitation of Driest Month

PSEA: Precipitation Seasonality

PWETQ: Precipitation of Wettest Quarter

PDQ: Precipitation of Driest Quarter

PWARQ: Precipitation of Warmest Quarter

PCQ: Precipitation of Coldest Quarter

TC: Total carbon

TN: Total nitrogen

TP: Total phosphorus

Olsen-P: Olsen-phosphorus

C_N: Ratio of carbon and nitrogen

C_P: Ratio of carbon and phosphorus

N_P: Ratio of nitrogen and phosphorus

TK: Total potassium

Ca: Total calcium

Mg: Total magnesium

S: Sulfur

Fe: Iron

Mn: Manganese

K+: exchangeable potassium

Ca2+: exchangeable calcium

Mg2+: exchangeable magnesium


National Natural Science Foundation of China, Award: 41673081

Joint Agricultural Projects of Yunnan Province, Award: Grant No. 2017FG001-018

National Natural Science Foundation of China, Award: 41877346

National Natural Science Foundation of China, Award: 41373074