Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China

Abstract

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Figure 1

Abundance of bacteria as indicated by the numbers of 16S rDNA copies measured using quantitative PCR. sCK, sN₁ and sN₂ indicate different N treatments in the soybean season; wCK, wN₁ and wN₂ indicate different N treatments in the wheat season. The ‘r’ indicates Pearson’s correlation coefficient between N added and 16S rDNA copies (**P < 0.01, *P < 0.05).

Figure 2

Differences in bacterial community diversity and richness between different N fertilizer regimes. (A) Community diversity between different N fertilizer regimes (both wheat and soybean seasons). (B) Community richness between different N fertilizer regimes (both wheat and soybean seasons). Asterisks show significant differences between samples (**P < 0.01, *P < 0.05, Tukey r-test). sCK, sN₁ and sN₂ indicate different N treatments in the soybean season; wCK, wN₁ and wN₂ indicate different N treatments in the wheat season.

Figure 3

Bacterial compositions of different N fertilizer regimes. Each bar represents the average relative abundance of each bacterial taxon within a group. The top 20 abundant phyla are shown (relative abundance >0.01%). sCK, sN₁ and sN₂ indicate different N treatments in the soybean season; wCK, wN₁ and wN₂ indicate different N treatments in the wheat season.

Figure 4

Changes in the relative abundances of bacterial genera across the N gradients in the wheat (A) and soybean (B) seasons. Only shown are those classes correlated with N added (Spearman’s r-values). Bars indicate one standard deviation. Asterisks show significant correlations (**P < 0.01, *P < 0.05). sCK, sN₁ and sN₂ indicate different N treatments in the soybean season; wCK, wN₁ and wN₂ indicate different N treatments in the wheat season.

Figure 5

Principal coordinate analysis of pyrosequencing reads obtained from soils subjected to different fertilization regimes based on the weighted Fast UniFrac metric. The first three axes are shown and the percent of variance explained by each axis is given.