Shared and unique features of bacterial communities in native forest and vineyard phyllosphere

Abstract

Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus‐level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii

“…www.nature.com/scientificreports/ Numerous environmental and anthropogenic factors have been shown to influence the composition of microbial communities found in soil or associated with plant material. These include season for communities in subtropical low mountain forest soils 46 or vintage for grape vines 26,47 ; physical characteristics of the soil, including carbon and nitrogen content 48 ; vine vegetative cycle 42 ; topological characteristics of the land 49 ; application of chemical fungicides and fertilizers 47,50,51 ; agricultural management practices in crop plantations and vineyards [52][53][54] ; land-use change 55 ; and erosion in farmlands 56 . Although none of these factors were investigated here, it is likely that several parameters, including climatic conditions, rainfall and soil nutrient availability, or combinations of these factors, shape the microbial populations associated with E. gunnii.…”

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

“…For stem and leaf material, the primer set 799f/1115r [ 53 ] can be selected, as recommended in previous works [ 69 , 70 ]. These chloroplast 16S rRNA gene-discriminating primers are commonly utilized for the identification of phyllosphere associated Bacteria [ 71 , 72 , 73 ] because these primers do not amplify host-plant nor cyanobacterial DNA; cyanobacteria are known to be rare in the phyllosphere [ 74 , 75 ].…”

Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China

“…Biogeographical patterns of shared and unique bacterial taxa in different habitats have been under-researched compared with the abundant and rare bacterial taxa in lakes and reservoirs (Baltar et al, 2015;Wu et al, 2016;Xue et al, 2018). Shared taxa are species that exist in every habitat within a certain boundary, which means that they have a stronger diffusion level and adaptability (Miura et al, 2019). Unique taxa are more restricted in habitat range, and their distribution is strongly affected by habitat conditions and distance between habitats (Mckenzie et al, 2012;Miura et al, 2019).…”

“…Shared taxa are species that exist in every habitat within a certain boundary, which means that they have a stronger diffusion level and adaptability (Miura et al, 2019). Unique taxa are more restricted in habitat range, and their distribution is strongly affected by habitat conditions and distance between habitats (Mckenzie et al, 2012;Miura et al, 2019). It seems that both rare and unique taxa are mainly affected by environmental factors, but unique taxa have strict habitat specificity.…”

“…Microbes display diverse biogeographical patterns, ranging from cosmopolitanism to provincialism (Hanson et al, 2012), but the underlying mechanisms that generate and maintain those patterns at a distinct range of spatial scales and habitats remain largely under explored (Meyer et al, 2013). Only a few studies have shown significant differences in the bacterial community structure of shared and unique taxa in the phyllosphere of forest, vineyard, and accompanying weed plants in local and regional areas (Samad et al, 2017;Miura et al, 2019). Those studies also showed the important influence of the environment on the structure and composition of a microbial community.…”