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Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale

  • Microbial Ecology and Environmental Microbiology
  • Published:
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Abstract

Microbial communities in the rhizosphere play a crucial role in determining plant growth and crop yield. A few studies have been performed to evaluate the diversity and co-occurrence patterns of rhizosphere microbiomes in soybean (Glycine max) at a regional scale. Here, we used a culture-independent method to compare the bacterial communities of the soybean rhizosphere between Nebraska (NE), a high-yield state, and Oklahoma (OK), a low-yield state. It is well known that the rhizosphere microbiome is a subset of microbes that ultimately get colonized by microbial communities from the surrounding bulk soil. Therefore, we hypothesized that differences in the soybean yield are attributed to the variations in the rhizosphere microbes at taxonomic, functional, and community levels. In addition, soil physicochemical properties were also evaluated from each sampling site for comparative study. Our result showed that distinct clusters were formed between NE and OK in terms of their soil physicochemical property. Among 3 primary nutrients (i.e., nitrogen, phosphorus, and potassium), potassium is more positively correlated with the high-yield state NE samples. We also attempted to identify keystone communities that significantly affected the soybean yield using co-occurrence network patterns. Network analysis revealed that communities formed distinct clusters in which members of modules having significantly positive correlations with the soybean yield were more abundant in NE than OK. In addition, we identified the most influential bacteria for the soybean yield in the identified modules. For instance, included are class Anaerolineae, family Micromonosporaceae, genus Plantomyces, and genus Nitrospira in the most complex module (ME9) and genus Rhizobium in ME23. This research would help to further identify a way to increase soybean yield in low-yield states in the U.S. as well as worldwide by reconstructing the microbial communities in the rhizosphere.

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Data Availability

The complete 16S rRNA gene sequencing data in this study are available in the National Center for Biotechnology Information (NCBI) database under the BioProject accession number PRJNA873129 associated with the accession numbers of 12 BioSamples (SAMN30489248 - SAMN30489259).

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Acknowledgements

We thank the Genomic Sequencing and Analysis Facility (GSAF) at the University of Texas at Austin for sequencing.

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  1. Sarbjeet Niraula

    Present address: Division of Vascular Surgery, Department of Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA

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  1. Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA

    Sarbjeet Niraula, Meaghan Rose & Woo-Suk Chang

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Niraula, S., Rose, M. & Chang, WS. Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale. J Microbiol. 60, 986–997 (2022). https://doi.org/10.1007/s12275-022-2363-x

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