Insufficient sampling constrains our characterization of plant microbiomes

Abstract Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling...

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Autores principales:	Lorinda S. Bullington, Ylva Lekberg, Beau G. Larkin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9718367d27c7442aa9746c55cc8431cb
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spelling	oai:doaj.org-article:9718367d27c7442aa9746c55cc8431cb2021-12-02T14:11:29ZInsufficient sampling constrains our characterization of plant microbiomes10.1038/s41598-021-83153-92045-2322https://doaj.org/article/9718367d27c7442aa9746c55cc8431cb2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83153-9https://doaj.org/toc/2045-2322Abstract Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling (30 mg), and (2) homogenizing bulk tissue before subsampling (30 mg). We targeted bacteria, arbuscular mycorrhizal (AM) fungi and non-AM fungi in roots, and foliar fungal endophytes (FFE) in leaves. We further extracted DNA from all of the leaf tissue collected to determine the extent of undersampling of FFE, and sampled FFE twice across the season using strategy one to assess temporal dynamics. All microbial groups except AM fungi differed in composition between the two sampling strategies. Community overlap increased when rare taxa were removed, but FFE and bacterial communities still differed between strategies, with largely non-overlapping communities within individual plants. Increasing the extraction mass 10 × increased FFE richness ~ 10 ×, confirming the severe undersampling indicated in the sampling comparisons. Still, seasonal patterns in FFEs were apparent, suggesting that strong drivers are identified despite severe undersampling. Our findings highlight that current sampling practices poorly characterize many microbial groups, and increased sampling intensity is necessary for increase reproducibility and to identify subtler patterns in microbial distributions.Lorinda S. BullingtonYlva LekbergBeau G. LarkinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lorinda S. Bullington Ylva Lekberg Beau G. Larkin Insufficient sampling constrains our characterization of plant microbiomes
description	Abstract Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling (30 mg), and (2) homogenizing bulk tissue before subsampling (30 mg). We targeted bacteria, arbuscular mycorrhizal (AM) fungi and non-AM fungi in roots, and foliar fungal endophytes (FFE) in leaves. We further extracted DNA from all of the leaf tissue collected to determine the extent of undersampling of FFE, and sampled FFE twice across the season using strategy one to assess temporal dynamics. All microbial groups except AM fungi differed in composition between the two sampling strategies. Community overlap increased when rare taxa were removed, but FFE and bacterial communities still differed between strategies, with largely non-overlapping communities within individual plants. Increasing the extraction mass 10 × increased FFE richness ~ 10 ×, confirming the severe undersampling indicated in the sampling comparisons. Still, seasonal patterns in FFEs were apparent, suggesting that strong drivers are identified despite severe undersampling. Our findings highlight that current sampling practices poorly characterize many microbial groups, and increased sampling intensity is necessary for increase reproducibility and to identify subtler patterns in microbial distributions.
format	article
author	Lorinda S. Bullington Ylva Lekberg Beau G. Larkin
author_facet	Lorinda S. Bullington Ylva Lekberg Beau G. Larkin
author_sort	Lorinda S. Bullington
title	Insufficient sampling constrains our characterization of plant microbiomes
title_short	Insufficient sampling constrains our characterization of plant microbiomes
title_full	Insufficient sampling constrains our characterization of plant microbiomes
title_fullStr	Insufficient sampling constrains our characterization of plant microbiomes
title_full_unstemmed	Insufficient sampling constrains our characterization of plant microbiomes
title_sort	insufficient sampling constrains our characterization of plant microbiomes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9718367d27c7442aa9746c55cc8431cb
work_keys_str_mv	AT lorindasbullington insufficientsamplingconstrainsourcharacterizationofplantmicrobiomes AT ylvalekberg insufficientsamplingconstrainsourcharacterizationofplantmicrobiomes AT beauglarkin insufficientsamplingconstrainsourcharacterizationofplantmicrobiomes
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Insufficient sampling constrains our characterization of plant microbiomes

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