Moisture effects on the active prokaryotic communities in a saline soil unraveled by 18 O-informed metagenomics
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SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE
Moisture effects on the active prokaryotic communities in a saline soil unraveled by 18O-informed metagenomics Yeliang Dai 1 & Yanshuo Pan 1,2 & Yue Sun 1 & Jun Zeng 1 & Guangming Liu 3 & Wenhui Zhong 4 & Xuanzhen Li 2 & Yucheng Wu 1 & Xiangui Lin 1 Received: 23 April 2020 / Accepted: 30 August 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Purpose Water availability influences soil ecosystem functioning by shaping soil microbial community composition and regulating metabolic rate. These moisture effects are mirrored in taxonomic and functional attributes of actively growing microorganisms. Methods Stable isotope probing (SIP) technique with 18O-H2O as the labeling substrate was used to capture the active microbiome in a saline soil under different moisture conditions. The SIP microcosms were adjusted to 20%, 60%, or 100% of the soil water holding capacity (WHC) with 18O- or 16O-H2O and were incubated for 4 weeks. The bacterial communities in these microcosms were examined by amplicon sequencing of 16S rRNA genes. The 18O-labeled DNA was recovered by ultracentrifugation and fractionation. Shotgun metagenomic sequencing was performed with the labeled DNA to explore the moisture effects on functional attributes of these active microbes. Results Isotopes (16O and 18O) had a negligible effect on soil bacterial communities compared with soil moisture. Taxonomic alignment of both total and 18O-labeled microbiomes revealed contrasting tendencies for Actinobacteria and Proteobacteria along the moisture gradient. Archaeal components became more abundant at 60% WHC and were dominated by Euryarchaeota. Functional annotation of the active microbiomes revealed broad responses in genes associated with osmotic regulation, membrane transport, cell motility, iron acquisition, phages and prophages to moisture manipulation. In particular, the considerable changes in protein biosynthesis genes suggested an altered reproductive strategy of the dominant taxa at different WHC levels. Conclusion These findings indicate taxonomic and functional effects of soil moisture on active prokaryotes in a saline soil, and demonstrate the potential of combined 18O-water SIP and metagenomics in achieving a holistic understanding of the active soil microbiome. Keywords Bacteria . Archaea . Taxonomic composition . Functional potential . Stable isotope probing
Yeliang Dai and Yanshuo Pan contributed equally to this work. Responsible editor: Jizheng He Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11368-020-02771-4) contains supplementary material, which is available to authorized users. * Xuanzhen Li [email protected]
2
College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
* Yucheng Wu [email protected]
3
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
1
4
Jiangsu Provincial Key Laboratory of Material
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