Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines

From winery by-product to soil improver? - A comprehensive review of grape pomace in agriculture and its effects on soil properties and functions

Grape pomace (GP), a by-product of winemaking, is rich in organic carbon and nutrients, offering potential as an alternative to synthetic soil amendments. However, its broader use in agriculture remains limited due to uncertainties about long-term environmental and agronomic impacts. This review assesses the potential of GP as a soil amendment, highlighting its ability to enhance soil organic matter, nutrient availability, and soil physicochemical properties. At the same time, concerns remain regarding its acidic nature, wide carbon-to‑nitrogen (C/N) ratio, and bioactive compounds, such as mycotoxins and (poly)phenols, which could negatively impact soil microbial communities and nutrient cycling. Furthermore, residual contaminants such as pesticides and heavy metals in GP may pose ecotoxicological risks, potentially disrupting soil ecosystem functions and contaminating surrounding environments. Besides these challenges, research on the efficiency, fate and mobility of GP in soil, particularly in relation to soil type, climate, and agricultural practices, is limited. Furthermore, the effects of various (pre)treatments (e.g., composting, fermentation) on GP properties and soil interactions require more systematic investigation. Future research should focus on long-term field trials, advanced analytical methods, and effective monitoring frameworks. It is essential to refine regulatory guidance based on comprehensive risk assessments to ensure safe application and maximize GP's agronomic and environmental benefits. Overcoming these challenges could transform GP into a valuable resource for sustainable agriculture, contributing to soil health, climate resilience, and a circular economy.

Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota

The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.

Effects of Coffea canephora genotypes on the microbial community of soil and fruit

In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.

The changes of rhizosphere microbial communities in pepper varieties with different capsaicinoids

Capsaicinoids are produced uniquely in pepper fruits, and its level determines the commercial quality and health-promoting properties of pepper. So, it is particularly important to increase capsaicinoids content in pepper. Rhizosphere microbiota is critical to plant growth and performance, and affected by plant varieties. However, the impact of pepper varieties with different capsaicinoids yields on the rhizosphere microbiota is poorly understood. Using high-throughput sequencing of the 16S rRNA and internal transcribed spacer (ITS) region, we investigated the rhizosphere microbial community among five pepper varieties containing different capsaicinoids. Our results demonstrated that pepper variety significantly influenced the diversity and structure of rhizosphere microbial community. Bacterial diversity in varieties with high capsaicinoids content was significantly higher than in varieties with low capsaicinoids content, while fungal diversity was opposite to bacterial diversity. The correlation analysis revealed that 19 dominant bacterial genera (e.g., Chujaibacter, Rhodanobacter, and Gemmatimonas) were significantly correlated with capsaicinoids content, and nine of them were also significantly associated with soil nutrients, whereas only one fungal genus (Podospora) was significantly correlated with capsaicinoids content. Additionally, almost all genera which significantly correlated to capsaicinoids content were biomarkers of the five pepper varieties and the correlation was well corresponding to the capsaicinoids content. Overall, our results confirmed that the variety of pepper significantly affected the rhizosphere microbial community in the fields, and bacteria and fungi responded differently to capsaicinoids, which may affect the biosynthesis of capsaicinoids and contribute to further improvement of capsaicinoids production in pepper fruits.

The rootstock modifies the arbuscular mycorrhizal community of the root system, while the influence of the scion is limited in grapevines

Understanding the effects of grapevine rootstock and scion genotypes on arbuscular mycorrhizal fungi (AMF), as well as the roles of these fungi in plant development, could provide new avenues for adapting viticulture to climate change and reducing agrochemical inputs. The root colonization of 10 rootstock/scion combinations was studied using microscopy and metabarcoding approaches and linked to plant development phenotypes. The AMF communities were analysed using 18S rRNA gene sequencing. The 28S rRNA gene was also sequenced for some combinations to evaluate whether the method changed the results. Root colonization indexes measured by microscopy were not significantly different between genotypes. Metabarcoding analyses showed an effect of the rootstock genotype on the β-diversity and the enrichment of several taxa with both target genes, as well as an effect on the Chao1 index with the 18S rRNA gene. We confirm that rootstocks recruit different AMF communities when subjected to the same pedoclimatic conditions, while the scion has little or no effect. Significant correlations were observed between AMF community composition and grapevine development, suggesting that AMF have a positive effect on plant growth. Given these results, it will be important to define consensus methods for studying the role of these beneficial micro-organisms in vineyards.

Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil

Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact

BACKGROUND

Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence host health. In response to environmental stresses, the plant roots exude specific molecules influencing the composition and functioning of the rhizospheric and root microbiomes. This response is host genotype-dependent and is affected by the soil microbiological and chemical properties. It is essential to unravel the influence of grapevine rootstock and scion genotypes on the composition of this microbiome, and to investigate this relationship with plant growth and adaptation to its environment. Here, the composition and the predicted functions of the microbiome of the root system were studied using metabarcoding on ten grapevine scion-rootstock combinations, in addition to plant growth and nutrition measurements.

RESULTS

The rootstock genotype significantly influenced the diversity and the structure of the bacterial and fungal microbiome, as well as its predicted functioning in rhizosphere and root compartments when grafted with the same scion cultivar. Based on β-diversity analyses, 1103P rootstock showed distinct bacterial and fungal communities compared to the five others (RGM, SO4, 41B, 3309 C and Nemadex). The influence of the scion genotype was more variable depending on the community and the investigated compartment. Its contribution was primarily observed on the β-diversity measured for bacteria and fungi in both root system compartments, as well as for the arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Significant correlations were established between microbial variables and the plant phenotype, as well as with the plant mineral status measured in the petioles and the roots.

CONCLUSION

These results shed light on the capacity of grapevine rootstock and scion genotypes to recruit different functional communities of microorganisms, which affect host growth and adaptation to the environment. Selecting rootstocks capable of associating with positive symbiotic microorganisms is an adaptation tool that can facilitate the move towards sustainable viticulture and help cope with environmental constraints.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

Species-level resolution for the vaginal microbiota with short amplicons

Specific bacterial species have been found to play important roles in human vagina. Achieving high species-level resolution is vital for analyzing vaginal microbiota data. However, contradictory conclusions were yielded from different methodological studies. More comprehensive evaluation is needed for determining an optimal pipeline for vaginal microbiota. Based on the sequences of vaginal bacterial species downloaded from NCBI, we conducted simulated amplification with various primer sets targeting different 16S regions as well as taxonomic classification on the amplicons applying different combinations of algorithms (BLAST+, VSEARCH, and Sklearn) and reference databases (Greengenes2, SILVA, and RDP). Vaginal swabs were collected from participants with different vaginal microecology to construct 16S full-length sequenced mock communities. Both computational and experimental amplifications were performed on the mock samples. Classification accuracy of each pipeline was determined. Microbial profiles were compared between the full-length and partial 16S sequencing samples. The optimal pipeline was further validated in a multicenter cohort against the PCR results of common STI pathogens. Pipeline V1-V3_Sklearn_Combined had the highest accuracy for classifying the amplicons generated from both the NCBI downloaded data (84.20% ± 2.39%) and the full-length sequencing data (95.65% ± 3.04%). Vaginal samples amplified and sequenced targeting the V1-V3 region but merely employing the forward reads (223 bp) and classified using the optimal pipeline, resembled the mock communities the most. The pipeline demonstrated high F1-scores for detecting STI pathogens within the validation cohort. We have determined an optimal pipeline to achieve high species-level resolution for vaginal microbiota with short amplicons, which will facilitate future studies.IMPORTANCEFor vaginal microbiota studies, diverse 16S rRNA gene regions were applied for amplification and sequencing, which affect the comparability between different studies as well as the species-level resolution of taxonomic classification. We conducted comprehensive evaluation on the methods which influence the accuracy for the taxonomic classification and established an optimal pipeline to achieve high species-level resolution for vaginal microbiota with short amplicons, which will facilitate future studies.

Vitislactone, a non-canonical strigolactone exudated by grapevine rootstocks in response to nitrogen starvation

Strigolactones are compounds produced by plant roots in response to nutrient deficiency, acting both as local and systemic signals to control development and nutrition. Strigolactones are exuded in the rhizosphere to positively influence interactions with beneficial microbes. LC-MS/MS analysis shows that two genetically distinct grapevine rootstocks exudate one or two non-canonical strigolactones when subjected to low nitrogen conditions. Gene expression profiles and orobanche seed germination assays confirm that the biosynthesis and exudation of non-canonical compounds is the preferred pathway. The first compound, corresponding to heliolactone or 6-epi-heliolactone, is only exuded by the rootstock showing lower shoot branching and a higher level of mycorrhization with arbuscular mycorrhizal fungi. The structure of the second compound exuded by both rootstocks was identified by NMR and LC-MS/MS analysis. It is a non-canonical strigolactone, which has never been identified in another species. This first identification of a natural compound with the potential to stimulate beneficial root-microbe interactions in grapevines opens new perspectives in viticulture.

The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina

The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.