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Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Author

Listed:
  • Tami L. Swenson

    (Lawrence Berkeley National Laboratory)

  • Ulas Karaoz

    (Lawrence Berkeley National Laboratory)

  • Joel M. Swenson

    (Lawrence Berkeley National Laboratory)

  • Benjamin P. Bowen

    (Lawrence Berkeley National Laboratory
    DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek)

  • Trent R. Northen

    (Lawrence Berkeley National Laboratory
    DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek)

Abstract

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Suggested Citation

  • Tami L. Swenson & Ulas Karaoz & Joel M. Swenson & Benjamin P. Bowen & Trent R. Northen, 2018. "Linking soil biology and chemistry in biological soil crust using isolate exometabolomics," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02356-9
    DOI: 10.1038/s41467-017-02356-9
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    Cited by:

    1. Yi Liu & Yun Yang & Wendong Chen & Feng Shen & Linhai Xie & Yingying Zhang & Yuanjun Zhai & Fuchu He & Yunping Zhu & Cheng Chang, 2023. "DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Yaoben Lin & Yuanbo Wang & Xingjun Lv & Shuangyan Yue & Hongmei Liu & Guangyu Li & Jinghui Zhao, 2023. "How to Improve the Benefits of Short-Term Fallow on Soil Physicochemical and Microbial Properties: A Case Study from the Yellow River Delta," Land, MDPI, vol. 12(7), pages 1-15, July.
    3. Yichao Wu & Chengxia Fu & Caroline L. Peacock & Søren J. Sørensen & Marc A. Redmile-Gordon & Ke-Qing Xiao & Chunhui Gao & Jun Liu & Qiaoyun Huang & Zixue Li & Peiyi Song & Yongguan Zhu & Jizhong Zhou , 2023. "Cooperative microbial interactions drive spatial segregation in porous environments," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Stefanie Imminger & Dimitri V. Meier & Arno Schintlmeister & Anton Legin & Jörg Schnecker & Andreas Richter & Osnat Gillor & Stephanie A. Eichorst & Dagmar Woebken, 2024. "Survival and rapid resuscitation permit limited productivity in desert microbial communities," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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