title: The soil microbiome influences grapevine-associated microbiota.
abstract: 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.
  
  
  OBJECTIVE
  Vine-associated bacterial communities may play specific roles in the productivity and disease resistance of their host plant. Also, the bacterial communities on grapes have the potential to influence the organoleptic properties of the wine, contributing to a regional terroir. Understanding that factors that influence these bacteria may provide insights into management practices to shape and craft individual wine properties. We show that soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native grapevine microbiome preharvest.
authors: Iratxe
authors: I
authors: Zarraonaindia
authors: Sarah M
authors: SM
authors: Owens
authors: Computation Institute, University of Chicago, Chicago, Illinois, USA.
authors: Pamela
authors: P
authors: Weisenhorn
authors: Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA.
authors: Kristin
authors: K
authors: West
authors: Jarrad
authors: J
authors: Hampton-Marcell
authors: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
authors: Simon
authors: S
authors: Lax
authors: Departments of Viticulture and Enology; Food Science and Technology; Foods for Health Institute, University of California, Davis, California, USA.
authors: Nicholas A
authors: NA
authors: Bokulich
authors: Departments of Viticulture and Enology; Food Science and Technology; Foods for Health Institute, University of California, Davis, California, USA.
authors: David A
authors: DA
authors: Mills
authors: Sparkling Pointe, Southold, New York, USA.
authors: Gilles
authors: G
authors: Martin
authors: Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA.
authors: Safiyh
authors: S
authors: Taghavi
authors: Center of Excellence for Agricultural Biosolutions, FMC Corporation, Research Triangle Park, North Carolina, USA.
authors: Daniel
authors: D
authors: van der Lelie
authors: gilbertjack@anl.gov.
authors: Jack A
authors: JA
authors: Gilbert
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D058448:Biota; D002244:Carbon / Q000032:analysis; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000032:analysis; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D062211:Spatio-Temporal Analysis; D027843:Vitis / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012987:Soil; D002244:Carbon; D009584:Nitrogen