The soil microbiome influences grapevine-associated microbiota

Zarraonaindia, Iratxe; Owens, Sarah M.; Weisenhorn, Pamela; West, Kristin; Hampton-Marcell, Jarrad; Lax, Simon; Bokulich, Nicholas A.; Mills, David A.; Martin, Gilles; Taghavi, Safiyh; van der Lelie, Daniel; Gilbert, Jack A.

doi:10.1128/mBio.02527-14

Title: The soil microbiome influences grapevine-associated microbiota

Journal Article · Tue Mar 24 00:00:00 EDT 2015 · mBio (Online)

DOI:https://doi.org/10.1128/mBio.02527-14· OSTI ID:1214587

Zarraonaindia, Iratxe ^[1]; Owens, Sarah M. ^[2]; Weisenhorn, Pamela ^[3]; West, Kristin ^[4]; Hampton-Marcell, Jarrad ^[2]; Lax, Simon ^[3]; Bokulich, Nicholas A. ^[5]; Mills, David A. ^[5]; Martin, Gilles ^[6]; Taghavi, Safiyh ^[4]; van der Lelie, Daniel ^[4]; Gilbert, Jack A. ^[7]

Argonne National Lab. (ANL), Argonne, IL (United States); Basque Foundation for Science, Bilbao (Spain)
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
Univ. of Chicago, Chicago, IL (United States)
FMC Corporation, Research Triangle Park, NC (United States)
Univ. of California, Davis, CA (United States)
Sparkling Pointe, Southold, NY (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States); Marine Biological Lab., Woods Hole, MA (United States); Zhejiang Univ., Hangzhou (China)

Grapevine is a well-studied, economically relevant crop, whose associated bacteria could influence its organoleptic properties. In this study, the spatial and temporal dynamics of the bacterial communities associated with grapevine organs (leaves, flowers, grapes, and roots) and soils were characterized over two growing seasons to determine the influence of vine cultivar, edaphic parameters, vine developmental stage (dormancy, flowering, preharvest), and vineyard. Belowground bacterial communities differed significantly from those aboveground, and yet the communities associated with leaves, flowers, and grapes shared a greater proportion of taxa with soil communities than with each other, suggesting that soil may serve as a bacterial reservoir. A subset of soil microorganisms, including root colonizers significantly enriched in plant growth-promoting bacteria and related functional genes, were selected by the grapevine. In addition to plant selective pressure, the structure of soil and root microbiota was significantly influenced by soil pH and C:N ratio, and changes in leaf- and grape-associated microbiota were correlated with soil carbon and showed interannual variation even at small spatial scales. Diazotrophic bacteria, e.g., Rhizobiaceae and Bradyrhizobium spp., were significantly more abundant in soil samples and root samples of specific vineyards. Vine-associated microbial assemblages were influenced by myriad factors that shape their composition and structure, but the majority of organ-associated taxa originated in the soil, and their distribution reflected the influence of highly localized biogeographic factors and vineyard management.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1214587

Journal Information:: mBio (Online), Vol. 6, Issue 2; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 559 works

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Geographical Origin Has a Greater Impact on Grape Berry Fungal Community than Grape Variety and Maturation State Kioroglou, Dimitrios; Kraeva-Deloire, Elena; Schmidtke, Leigh M. Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120669	journal	December 2019
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Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies: Microbiome structure and function in fungal fruiting-bodies Pent, Mari; Hiltunen, Markus; Põldmaa, Kadri Environmental Microbiology, Vol. 20, Issue 5 https://doi.org/10.1111/1462-2920.14069	journal	March 2018
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Species abundance information improves sequence taxonomy classification accuracy Kaehler, Benjamin D.; Bokulich, Nicholas A.; McDonald, Daniel ETH Zurich https://doi.org/10.3929/ethz-b-000431166	text	January 2019
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Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum Splivallo, Richard; Vahdatzadeh, Maryam; Maciá-Vicente, Jose G. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01437	journal	June 2019
Soil Biological Quality Assessment to Improve Decision Support in the Wine Sector Ghiglieno, Isabella; Simonetto, Anna; Donna, Pierluigi Agronomy, Vol. 9, Issue 10 https://doi.org/10.3390/agronomy9100593	journal	September 2019
Microbial Community Analyses Associated with Nine Varieties of Wine Grape Carposphere Based on High-Throughput Sequencing Zhang, Shiwei; Chen, Xi; Zhong, Qiding Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120668	journal	December 2019
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming Hartman, Kyle; Van Der Heijden, Marcel G. A.; Wittwer, Raphaël A. ETH Zurich https://doi.org/10.3929/ethz-b-000237418	text	January 2018
Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard Mandl, Karin; Cantelmo, Clemens; Gruber, Edith Bulletin of Environmental Contamination and Toxicology, Vol. 101, Issue 5 https://doi.org/10.1007/s00128-018-2438-x	journal	September 2018
Species abundance information improves sequence taxonomy classification accuracy Kaehler, Benjamin D.; Bokulich, Nicholas A.; McDonald, Daniel Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12669-6	journal	October 2019
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming Hartman, Kyle; Van Der Heijden, Marcel G. A.; Wittwer, Raphaël A. BioMed Central https://doi.org/10.5167/uzh-168385	text	January 2018
The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ Wei, Na; Ashman, Tia-Lynn bioRxiv https://doi.org/10.1101/225755	posted_content	November 2017
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing Song, Luyang; Xie, Kabin Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00859-0	journal	June 2020

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