Effects of different management regimes on microbial biodiversity in vineyard soils

Hendgen, Maximilian; Hoppe, Björn; Döring, Johanna; Friedel, Matthias; Kauer, Randolf; Frisch, Matthias; Dahl, Andreas; Kellner, Harald

doi:10.1038/s41598-018-27743-0

Cited by 80 publications

(62 citation statements)

References 51 publications

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“…PCR genomic DNA amplicon libraries of the targeted microorganisms (bacteria and fungi) were produced from the genomic DNA templates. The bacterial 16S and fungal ITS2 within the rDNA region were amplified using a modified primer mix: P5_8N_515F + P5_7N_515F (forward) together with P7_2N_806R + P7_1N_806R (Caporaso et al, 2012;Moll et al, 2018) for the bacteria, and P5-5N-ITS4 (Gardes and Bruns, 1993;Leonhardt et al, 2019)/P7-4N-fITS7 (Ihrmark et al, 2012;Leonhardt et al, 2019) for the fungi, all containing the Illumina adapter sequences (see Supplementary Table S2 for an overview of the utilized primer sequences according to Hendgen et al, 2018). All PCRs were conducted using the proofreading KAPA Hifi polymerase (Kapa Biosystems, Boston, MA, United States).…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

et al. 2020

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Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

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Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

et al. 2020

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“…Such unclear patterns of herbicide effects on the microbial soil communities have also been reported by others (Kopčáková et al 2016 ; Newman et al 2016 ). However, a clear difference in soil bacterial and fungal composition in vineyards was reported between herbicide treated and untreated grapevine rows (Chou et al 2018 ; Hendgen et al 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard

Mandl

Cantelmo

Gruber

et al. 2018

Bull Environ Contam Toxicol

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In a vineyard we examined the effects of broad-spectrum herbicides with three different active ingredients (glyphosate, glufosinate, flazasulfuron) on soil microorganisms. Mechanical weeding served as control treatment. Treatments were applied within grapevine rows and soil samples taken from there in 10–20 cm depth 77 days after application. Fungi were analyzed using classical sequencing technology and bacteria using next-generation sequencing. The number of colony-forming units (CFU) comprising bacteria, yeasts and molds was higher under flazasulfuron compared to all other treatments which had similar CFU levels. Abundance of the fungus Mucor was higher under flazasulfuron than glufosinate and mechanical weeding; Mucor was absent under glyphosate. Several other fungi taxa were exclusively found under a specific treatment. Up to 160 different bacteria species were found – some of them for the first time in vineyard soils. Total bacterial counts under herbicides were on average 260% higher than under mechanical weeding; however due to high variability this was not statistically significant. We suggest that herbicide-induced alterations of soil microorganisms could have knock-on effects on other parts of the grapevine system.

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“…While Loranger‐Merciris et al . focused on microbial functions, Hendgen et al . studied the diversity of the microbial community underneath different crops.…”

Section: Discussionmentioning

confidence: 99%

“…But in our case, the main reason for the differences in soil chemical conditions lies most probably in the different physiologies of lucerne versus ryegrass. While Loranger-Merciris et al 21 focused on microbial functions, Hendgen et al 2 studied the diversity of the microbial community underneath different crops. They did not observe the microbial diversity change under different cover crop regimes.…”

Section: Discussionmentioning

confidence: 99%

Species‐dependent effect of cover cropping on trace elements and nutrients in vineyard soil and Vitis

et al. 2019

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BACKGROUND The research focused on the evaluation of the impact of cover cropping on trace metals (Fe, Mn, Cu, Zn, Pb, Co and Cd) and nutrients in vineyard soils and Vitis vinifera L. For this purpose, two types of cover crops (Lolium perenne L. and Medicago sativa L.) and their mixture were planted between vine rows of Muscat white in the vineyard in South Crimea. Trace elements, nutrients and other parameters were analyzed in the soil layers, leaves and grapevines of control and cover cropped plots. RESULTS The effect of cover cropping was dependent on applied plant species. Ryegrass (L. perenne L.) seems to compete with V. vinifera L. for nutrients – these were lower in the soil and vines of the treated plot. In parallel, lead (Pb) bioconcentration in grapevines was reduced. In contrast, under lucerne (M. sativa L.), nitrogen in the soil and vines, and trace metal bioconcentration (Fe, Pb and Co) were higher. CONCLUSIONS Our results indicate that cover cropping can influence the chemical composition of soil and vines. This should be considered when selecting cover crops. © 2019 Society of Chemical Industry

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Effects of different management regimes on microbial biodiversity in vineyard soils

Cited by 80 publications

References 51 publications

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard

Species‐dependent effect of cover cropping on trace elements and nutrients in vineyard soil and Vitis

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