Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer

Ryan V Trexler, Terrence H Bell

Research output: Contribution to journalArticle

Abstract

Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through 1) direct soil transfer at two dilutions, and 2) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events, and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.

Original languageEnglish (US)
JournalFEMS Microbiology Letters
DOIs
StateE-pub ahead of print - Nov 15 2019
Externally publishedYes

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title = "Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer",
abstract = "Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through 1) direct soil transfer at two dilutions, and 2) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events, and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.",
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N2 - Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through 1) direct soil transfer at two dilutions, and 2) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events, and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.

AB - Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through 1) direct soil transfer at two dilutions, and 2) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events, and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.

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