Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices

Abstract

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.

Changes in Structural and Functional Responses of Bacterial Communities under Different Levels of Long-Term Compost Application in Paddy Soils

“…Relative abundance of bacterial community (Fig. 1B) at phylum level showed dominant groups (> 1%) across all the soil samples were Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Nitrospira, Actinobacteria, Chlorobi, Firmicutes, Planctomycetes, Cyanobacteria, Gemmatimonadetes, Armatimonadetes, Verrucomicrobia and TM7, which falls in line with earlier studies [13,14]. The most dominant phylum observed in the current study was Proteobacteria, which agrees with the earlier reports [15].…”

Soil microbial community and activity are affected by integrated agricultural practices in China

“…In the seven dominant bacterial phyla, Proteobacteria was the most abundant bacterial phylum, which accords with the results of Ahn et al . () and Lei et al . ().…”

“…Proteobacteria are thought to be adapted to conditions with a high nutrient status, and their relative abundance increased in soils with large amounts of available organic matter and a large rate of mineralization (Ahn et al ., ). Sphingomonas was the most abundance genus of Proteobacteria in this study, and their relative abundance was larger in IP topsoil than CP topsoil, which can probably be attributed to the large amount of crop residues returned to the soil under IP.…”

“…In general, intensive and conventional practices reduced soil microbial community and activity, whereas sustainable and conservation practices increased them. Previous studies found that the abundance, activity and diversity of microbes were enhanced with the return of crop straw to soil (Ahn et al ., ; Lei et al ., ). The effects of different agricultural practices on the structure and properties of the soil microbial community have been controversial, from beneficial to none or negative (Spedding et al ., ; Zhang et al, ).…”

Continental-Scale Paddy Soil Bacterial Community Structure, Function and Biotic Interaction

“…Paddy soil was also enriched for Desulfuromonadaceae (including Geobacter and Anaeromyxobacter, Figure 2 and Additional le 1: Figure S2),, which perform acetate metabolism and can compete with methanogens via dissimilatory Fe (III)-reduction [26]. Also enriched was the genus Sideroxydans which is a chemoautotroph using iron or sulfur as energy sources [27]. Harboring these enriched bacteria suggests why paddy soil metagenomes were enriched for fermentation, organic metabolism, and elemental (such as iron and sulfur) cycling genes, compared with non-paddy soils ( Figure 2C).…”