TY - JOUR
T1 - Field to Greenhouse
T2 - How Stable Is the Soil Microbiome after Removal from the Field?
AU - Kushwaha, Priyanka
AU - Soto Velázquez, Ana L.
AU - McMahan, Colleen
AU - Neilson, Julia W.
N1 - Publisher Copyright:
© 2024 by the authors.
PY - 2024/1
Y1 - 2024/1
N2 - Plant-soil feedback (PSF) processes impact plant productivity and ecosystem function, but they are poorly understood because PSFs vary significantly with plant and soil type, plant growth stage, and environmental conditions. Controlled greenhouse studies are essential to unravel the mechanisms associating PSFs with plant productivity; however, successful implementation of these controlled experiments is constrained by our understanding of the persistence of the soil microbiome during the transition from field to greenhouse. This study evaluates the preservation potential of a field soil microbiome when stored in the laboratory under field temperature and moisture levels. Soil microbial diversity, taxonomic composition, and functional potential were evaluated via amplicon sequencing at the start of storage (W0), week 3 (W3), week 6 (W6), and week 9 (W9) to determine the effect of storage time on soil microbiome integrity. Though microbial richness remained stable, Shannon diversity indices decreased significantly at W6 for bacteria/archaea and W3 for fungi. Bacterial/archaeal community composition also remained stable, whereas the fungal community changed significantly during the first 3 weeks. Functional predictions revealed increased capacity for chemoheterotrophy for bacteria/archaea and decreased relative proportions of arbuscular mycorrhizal and ectomycorrhizal fungi. We show that preservation of the field soil microbiome must be a fundamental component of experimental design. Either greenhouse experiments should be initiated within 3 weeks of field soil collection, or a preliminary incubation study should be conducted to determine the time and storage conditions required to sustain the integrity of the specific field soil microbiome being studied.
AB - Plant-soil feedback (PSF) processes impact plant productivity and ecosystem function, but they are poorly understood because PSFs vary significantly with plant and soil type, plant growth stage, and environmental conditions. Controlled greenhouse studies are essential to unravel the mechanisms associating PSFs with plant productivity; however, successful implementation of these controlled experiments is constrained by our understanding of the persistence of the soil microbiome during the transition from field to greenhouse. This study evaluates the preservation potential of a field soil microbiome when stored in the laboratory under field temperature and moisture levels. Soil microbial diversity, taxonomic composition, and functional potential were evaluated via amplicon sequencing at the start of storage (W0), week 3 (W3), week 6 (W6), and week 9 (W9) to determine the effect of storage time on soil microbiome integrity. Though microbial richness remained stable, Shannon diversity indices decreased significantly at W6 for bacteria/archaea and W3 for fungi. Bacterial/archaeal community composition also remained stable, whereas the fungal community changed significantly during the first 3 weeks. Functional predictions revealed increased capacity for chemoheterotrophy for bacteria/archaea and decreased relative proportions of arbuscular mycorrhizal and ectomycorrhizal fungi. We show that preservation of the field soil microbiome must be a fundamental component of experimental design. Either greenhouse experiments should be initiated within 3 weeks of field soil collection, or a preliminary incubation study should be conducted to determine the time and storage conditions required to sustain the integrity of the specific field soil microbiome being studied.
KW - plant–soil feedbacks
KW - soil legacy
KW - soil microbiome stability
KW - soil storage
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U2 - 10.3390/microorganisms12010110
DO - 10.3390/microorganisms12010110
M3 - Article
AN - SCOPUS:85183605194
SN - 2076-2607
VL - 12
JO - Microorganisms
JF - Microorganisms
IS - 1
M1 - 110
ER -