Distinct soil bacterial communities in response to the cropping system in a Mollisol of northeast China

- Bacterial communities shifted in response to cropping system in both bulk and rhizosphere soils.
- Bacterial abundance and diversity were higher in rotation than those in monoculture.
- The variation induce by cropping system in rhizosphere was greater than in bulk soil.
- Soil pH is a primary factor in determining bacterial community composition.

Cropping systems such as monoculture and rotation can affect soil microbial communities, however, the mechanisms of how bacterial community are affected and the possible links between these effects and cropping systems remain unclear. To address this question, we comparatively investigated the bacterial abundance, diversity and structure in the bulk and rhizosphere soils of soybean grown in two cropping systems, i.e., continuous cropping of soybean (CC) and cropping rotation with maize (CR) using real-time PCR and Illumina Miseq sequencing methods The results showed that soil pH, total N, total P, and available nutrients such as N, P and K were significantly higher in the bulk soil of CR than in CC. No significant variation of bulk soil total C content was detected between the two cropping systems. The bacterial abundance and diversity were higher in the bulk and rhizosphere soils of CR than in corresponding soil samples of CC. In addition, higher abundance and lower diversity of bacterial communities were observed in rhizosphere soil than in bulk soil within each cropping system. Compared with CC treatment, 12 and 17 bacterial phyla/classes were significantly increased for CR in bulk soil and rhizosphere, respectively. Among the altered bacterial phyla/classes, Betaproteobacteria, Acidobacteria, Actinobacteria and Alphaproteobacteria were the most important taxa contributing to the variation between the two crop systems in both bulk and rhizosphere soils. The results of principal coordinate analysis (PCoA) and three nonparametric multivariate statistical tests revealed that the bacterial communities were distinctly separated between CC and CR both in the bulk and rhizosphere soils; the variation of Bray-Curtis difference in rhizosphere soil was greater than in bulk soil. Furthermore, the composition and diversity of the soil bacterial communities in bulk soil were affected by soil pH, total nitrogen (TN), total phosphorus (TP) and soil available potassium, nitrogen and phosphorus (AK, AN and AP), and the effect of soil pH was a primary factor in determining bacterial community composition.