Different types of agricultural land use drive distinct soil bacterial communities

Shin Ae Lee,Jaekyeong Song,Jae-Hyung Ahn,Jeong Myeong Kim,Yiseul Kim,Seong-Soo Kang,Jae-Ho Joa,Mincheol Kim,Hang-Yeon Weon

doi:10.1038/s41598-020-74193-8

Abstract

Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Highlights

Agricultural management such as fertilization, irrigation, and tillage are important factors that affect the biodiversity and function of terrestrial ecosystems and can lead to soil ecosystem d egradation[9,10,11,12,13]
We obtained a total of 3,616,347 high-quality sequence reads by 16S rRNA gene pyrosequencing and identified 68,528 operational taxonomic units (OTUs) based on 97% sequence identity across all samples
The variation in bacterial community structures was visualized with a nonmetric multidimensional scale (NMDS) plot based on Bray–Curtis distance

Summary

Introduction

Agricultural management such as fertilization, irrigation, and tillage are important factors that affect the biodiversity and function of terrestrial ecosystems and can lead to soil ecosystem d egradation[9,10,11,12,13]. A recent study by Hermans et al showed that microbial communities across diverse New Zealand soil types (e.g., indigenous forest, exotic forest, horticulture, and dairy) are more sensitive to changing soil environments than to variation in climate or increased geographical h eterogeneity[26]. They observed certain dominant taxa to be significantly related to specific soil parameters. The co-occurrence networks of soil bacterial communities in different types of agricultural land use have not been explored using a large number of samples. The specific objectives of this study were to characterize bacterial communities in different agricultural land-use types through analyses of bacterial community diversity, composition, indicator species, and co-occurrence patterns

Objectives

Methods

Results

Discussion

Conclusion