Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation

Yushan Zhan,Youzhi Feng,Evangelos Petropoulos,Jianwei Zhang,Xiangui Lin,Wenjing Liu,Zhongpei Li,Yuanyuan Bao

doi:10.1038/s41598-018-26375-8

Yushan Zhan, Youzhi Feng + Show 6 more

Open Access

https://doi.org/10.1038/s41598-018-26375-8

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Abstract

Straw, mainly dry stalks of crops, is an agricultural byproduct. Its incorporation to soils via microbial redistribution is an environment-friendly way to increase fertility. Fertilization influences soil microorganisms and straw degradation. However, our up to date knowledge on the responses of the straw decomposers to fertilization remains elusive. To this end, inoculated with paddy soils with 26-year applications of chemical fertilizers, organic amendments or controls without fertilization, microcosms were anoxically incubated with 13C-labelled rice straw amendment. DNA-based stable isotope probing and molecular ecological network analysis were conducted to unravel how straw degrading bacterial species shift in responses to fertilizations, as well as evaluate what their roles/links in the microbiome are. It was found that only a small percentage of the community ecotypes was participating into straw degradation under both fertilizations. Fertilization, especially with organic amendments decreased the predominance of Firmicutes- and Acidobacteria-like straw decomposers but increased those of the copiotrophs, such as β-Proteobacteria and Bacteroidetes due to increased soil fertility. For the same reason, fertilization shifted the hub species towards those of high degrading potential and created a more stable and efficient microbial consortium. These findings indicate that fertilization shapes a well-organized community of decomposers for accelerated straw degradation.

Highlights

Rice production is expected to significantly increase in the near future to meet the demand of the rising human population
After 25 days it was shown that fertilized soils had a higher net C mineralization ratio over the total C from the amended straw compared to those achieved by the Control soils (Fig. 1C)
Fungi are mainly involved in decomposition of straw in oxic soils, at anoxic conditions bacterial species are the predominant decomposers, especially in paddy soils[31]

Summary

Introduction

Rice production is expected to significantly increase in the near future to meet the demand of the rising human population. The importance of the Clostridia classes, followed by Acidobacteria, Bacteroidetes and Proteobacteria were reported by Lee et al.[20] who used DNA-SIP in anoxic rice callus treated microcosms Molecular ecological network analysis was widely used to understand the potential biotic interactions between habitat affinities and shared physiologies[26,27] This new statistical approach offers novel insights into the understanding of the microbiome and the significance of specific members in the community[26,28]. Bioinformatics analysis on fractionated and non-fractionated DNAs was conducted to (i) identify the bacterial taxa associated with the assimilation of 13C derived from 13C-labled rice straw; (ii) unravel the influence of different fertilization regimes on the paddy straw degrading species and their hub roles in the associated molecular ecological networks

Methods

Results

Conclusion