Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Paul Carini, Manuel Delgado-Baquerizo, Eve-Lyn S. Hinckley, Hannah Holland‐Moritz, Tess E. Brewer, Garrett Rue, Caihong Vanderburgh, Diane McKnight, Noah Fierer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	microbial seasonality soil microbial ecology microbial interactions soil bacterial and fungal communities hillslope aspect nitrogen cycling Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6a87ccfb46104e45926f91d53eaecdf3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:6a87ccfb46104e45926f91d53eaecdf3
record_format	dspace
spelling	oai:doaj.org-article:6a87ccfb46104e45926f91d53eaecdf32021-11-15T15:56:58ZEffects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities10.1128/mBio.02776-192150-7511https://doaj.org/article/6a87ccfb46104e45926f91d53eaecdf32020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02776-19https://doaj.org/toc/2150-7511ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.Paul CariniManuel Delgado-BaquerizoEve-Lyn S. HinckleyHannah Holland‐MoritzTess E. BrewerGarrett RueCaihong VanderburghDiane McKnightNoah FiererAmerican Society for Microbiologyarticlemicrobial seasonalitysoil microbial ecologymicrobial interactionssoil bacterial and fungal communitieshillslope aspectnitrogen cyclingMicrobiologyQR1-502ENmBio, Vol 11, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	microbial seasonality soil microbial ecology microbial interactions soil bacterial and fungal communities hillslope aspect nitrogen cycling Microbiology QR1-502
spellingShingle	microbial seasonality soil microbial ecology microbial interactions soil bacterial and fungal communities hillslope aspect nitrogen cycling Microbiology QR1-502 Paul Carini Manuel Delgado-Baquerizo Eve-Lyn S. Hinckley Hannah Holland‐Moritz Tess E. Brewer Garrett Rue Caihong Vanderburgh Diane McKnight Noah Fierer Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
description	ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.
format	article
author	Paul Carini Manuel Delgado-Baquerizo Eve-Lyn S. Hinckley Hannah Holland‐Moritz Tess E. Brewer Garrett Rue Caihong Vanderburgh Diane McKnight Noah Fierer
author_facet	Paul Carini Manuel Delgado-Baquerizo Eve-Lyn S. Hinckley Hannah Holland‐Moritz Tess E. Brewer Garrett Rue Caihong Vanderburgh Diane McKnight Noah Fierer
author_sort	Paul Carini
title	Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
title_short	Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
title_full	Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
title_fullStr	Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
title_full_unstemmed	Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities
title_sort	effects of spatial variability and relic dna removal on the detection of temporal dynamics in soil microbial communities
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/6a87ccfb46104e45926f91d53eaecdf3
work_keys_str_mv	AT paulcarini effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT manueldelgadobaquerizo effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT evelynshinckley effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT hannahhollandmoritz effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT tessebrewer effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT garrettrue effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT caihongvanderburgh effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT dianemcknight effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities AT noahfierer effectsofspatialvariabilityandrelicdnaremovalonthedetectionoftemporaldynamicsinsoilmicrobialcommunities
_version_	1718427093706997760

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Ejemplares similares