The Soil Microbiome Influences Grapevine-Associated Microbiota

By Iratxe Zarraonaindia, S. Owens, Pamela Weisenhorn, Kristi L. West, Jarrad T. Hampton-Marcell, S. Lax, Nicholas A. Bokulich, David A. Mills, Gilles Martin, S. Taghavi and 2 more. mBio, 2015

842 citations recorded by the source corpus.

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. IMPORTANCE 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. 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.

Subfields: Food Science, Plant Science

View Paper: https://www.semanticscholar.org/paper/b1666e1b1cf53833cafb3ad01d9d3f4fc6266622

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Citations in the corpus

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, background): “A number of recent microbial community surveys have described the root microbiomes of Arabidopsis thaliana [23, 24], clover [25], maize [26], rice [27], sugarcane [28], and grapevine [29] and reported significant effects of soil type on root microbiome composition.”
Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China (2019, methodology): “The highthroughput pyrosequencing of the 16S rRNA gene was conducted on the Illumina HiSeq platform to determine soil microbial community composition as per previous studies (Cao et al. 2015; Zarraonaindia et al. 2015; Xu et al. 2017).”
The Plant Microbiota: Systems-Level Insights and Perspectives. (2016, background): “For root or rhizosphere communities, genes relating to chemotaxis and motility have been identified as enriched categories in the metagenomes of the respective microbiota of wheat and cucumber (88) and grapevine (157) as well as in the metaproteome of rice (64).”
Rhizosphere-associated bacterial network structure and spatial distribution differ significantly from bulk soil in wheat crop fields (2017, background): “In grapevines, the root and plant-tissue associated communities have been shown to be a subset of the bulk soil community (Zarraonaindia et al., 2015).”
Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species (2015, background): “Similarly, the increased abundance of Proteobacteria and decreased presence of Acidobacteria in the plant-associated samples with respect to the surrounding soil has been observed for other plant hosts (Edwards et al., 2015; Zarraonaindia et al., 2015).”
The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion (2020, background): “…colors denote the direction of effects and asterisks above the bars indicate the significance levels (*, p < 0.05) Delmont et al. 2014; Setlow 2007; Zarraonaindia et al. 2015), the presence of microbes in the inoculant accounted for the majority of the total variation in rhizosphere microbiome…”
Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications (2020, background): “Normally, soil type, plant genotype and species, immune systemof the plant, age, climatic condition, and the geographic region are the factors forcing the bacterial community assembly (Leff et al. 2015; Zarraonaindia et al. 2015; Copeland et al. 2015).”
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application (2019, background): “It has been reported that phyllosphere bacteria also derive from the soil environment and are driven by the plant and by environmental parameters, however, the latter having a more profound effect [2,23,30].”
Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features (2015, background): “Zarraonaindia et al. (2015) recently demonstrated that a ‘native’ microbial fingerprint, relatively constant even with respect to other edaphic factors, exists between the microorganisms of the wine grape must, grapevine vegetative structures and fruit, and the microorganisms of the vine row soil.”
Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation (2016, background): “Indeed, colonization of the phyllosphere and rhizosphere has been suggested to proceed with an ordered effect of inocula distribution followed by species sorting [12,49].”
Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management (2016, background): “Recent work has shown that climate, region, soil type, and wine grape variety can play strong roles in structuring microbial communities in vineyard soil, the vine phyllosphere, must and wine, and that soil microbial activities and wine metabolome are correlated with microbial community structure (B”
Microbial interactions within the plant holobiont (2018, positive): “thaliana [30, 31, 34, 55, 56], and the reciprocal relocation between root- and leafassociated bacterial communities has been further validated using microbiota reconstitution experiments with germ-free A.”