Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity

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.

Long‐term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro‐ecosystems across the globe

“…Microbial diversity is a fundamental property of soil ecosystems as microorganisms play critical roles in nutrient cycling, soil structure maintenance, and crop production (Madigan, Martinko, Dunlap, & Clark, ). Although bacterial diversity is critical for the maintenance of soil health and quality (Garbeva, van Veen, & van Elsas, ), uncertainties still remain across the literature regarding the long‐term effect of N fertilization on bacterial diversity, e.g., negative effects (Ling et al., ; Niu et al., ; Zhou et al., ) and no/positive effects (Ramirez et al., ; Wang et al., ; Yuan et al., ). These results can probably be attributed to the great heterogeneity in soil properties, rate of fertilization, water management regimes, and other biotic and abiotic factors.…”

DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization

“…Mineral, in contrast to organic, inputs alter the general balance of soil stoichiometry, thereby resulting in adaptative selection of a resident population of oligotrophic taxa (high C use efficiency, slow growing) instead of more copiotrophic taxa (low C use efficiency, fast growing). Wang et al (41) reported that the application of organic fertilizers increased the abundance of generally copiotrophic bacterial groups, while application of mineral fertilizers increased the abundance of oligotrophic groups. Thus, we hypothesized that there will be a shift in dominance and response strategies of specific microbial groups involved in residue assimilation in soils after manuring compared to these strategies after only mineral fertilization.…”

Rapid production of organic fertilizer from degradable waste by thermochemical processing

“…The soil root zone, especially the rhizosphere, is the active zone of microbial and root activity (Lagos et al 2015). The pH of the rhizosphere zone is, therefore, critical in deciding microbial activity (Wang et al 2016), which in turn regulates the innumerable chemical reactions involved in nutrient transformations and uptake by plant roots. The ideal pH range for active growth and development of plants and microbes is 6.5-7.5.…”