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

Tami L Swenson,Joel M Swenson,Ulas Karaoz,Benjamin P Bowen,Trent R Northen

doi:10.1038/s41467-017-02356-9

Tami L Swenson, Joel M Swenson + Show 3 more

Open Access

https://doi.org/10.1038/s41467-017-02356-9

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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.

Highlights

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; linking these data to exogenous metabolites that microorganisms process and produce remains challenging
It is thought that the organic matter that is cycled by soil microbes is a complex mixture of microbial metabolites[15,16] that can be characterized in detail using soil metabolomics[17,18]
We compared our current results with previous laboratory-derived knowledge of substrate preferences for four dominant microorganisms by relating the abundance of these bacteria to soil metabolites measured in the intact biocrust system (Fig. 1b)

Summary

Introduction

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. It is predicted that the aridity of drylands will increase, reducing SOM and microbial community diversity, and that this will impact ecosystem productivity[7,11] This strong coupling between soil moisture, SOM and community structure is especially important in the arid land topsoil microbial communities known as biological soil crusts (biocrusts), which cover a large fraction of arid regions and are critical in nutrient cycling[12]. Exometabolomics enables direct examination of how microbes transform the small molecule metabolites within their environment, providing new insights into resource competition and cross-feeding[21] For this approach, microbes (typically isolates) are cultured in an environmentally-relevant mixture of metabolites and spent media is profiled to determine the uptake and release of metabolites. As microorganisms from diverse taxa continue to be cultivated and examined, this approach holds substantial potential to provide valuable phenotypic information that can link community structure to SOM composition

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