Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Yang, Jihoon; Lee, Jaejin; Choi, Jinlyung; Ma, Lanying; Heaton, Emily A.; Howe, Adina

doi:10.1128/spectrum.02116-21

Title: Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Journal Article · Wed Feb 16 00:00:00 EST 2022 · Microbiology Spectrum

DOI:https://doi.org/10.1128/spectrum.02116-21· OSTI ID:1860636

^[1]; Lee, Jaejin ^[1]; Choi, Jinlyung ^[2]; Ma, Lanying ^[3]; Heaton, Emily A. ^[4];

^[1]

Iowa State Univ., Ames, IA (United States); Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States)
Iowa State Univ., Ames, IA (United States); Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); Second Genome Inc., Brisbane, CA (United States)
Iowa State Univ., Ames, IA (United States); Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); VastBiome Inc., Millbrae, CA (United States)
Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL (United States); Iowa State Univ., Ames, IA (United States)

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

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Research Organization:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018420

OSTI ID:: 1860636

Journal Information:: Microbiology Spectrum, Vol. 10, Issue 1; ISSN 2165-0497

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Miscanthus × giganteus
RNA
activity
nitrogen
soil microbiome

Title: Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

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