Abstract
Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.
Highlights
Winter wheat (Triticum aestivum L.) and summer rice (Oryza sativa L.) cultivation rotations, with two crops per year, has been practiced for thousands of years in Asia
3.4 Mha is under this system in the Yangtse River Basin in China, representing critical source for food security and livelihood of several hundreds of millions people in the region
The results revealed that across all stages of the wheat-rice rotation, the nitrogen fertilizer (NNF) treatment resulted in significantly higher (P < 0.05) relative abundances (RA) of the Cyanobacteria phylum, Cyanobacteria class and Cyanobacteria order, while the chemical fertilizer (CF) treatment had a higher RA of Acidobacteria_GP1
Summary
Winter wheat (Triticum aestivum L.) and summer rice (Oryza sativa L.) cultivation rotations, with two crops per year, has been practiced for thousands of years in Asia. The wheat-rice rotation is one of the highest yielding production systems (Timsina and Connor, 2001). This agricultural ecosystem is associated with serious environmental and ecological problems due to overly intensive farming, especially excessive CFs inputs (Yang et al, 2016). Soil microbes can be sensitive to environmental stress and play important roles in the nutrient transformation of fertilizers (Paul, 2014; Zhang et al, 2015), and soil-borne microbial communities are known to be impacted by fertilization management scheme (Geisseler and Scow, 2014). How soil bacterial communities respond to different fertilization practices is likely to be complex, especially in the ricewheat rotation system where soil undergoes alternate aerobic and anaerobic conditions
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