Effects of different management regimes on microbial biodiversity in vineyard soils

Yeasts, arthropods, and environmental matrix: a triad to disentangle the multi-level definition of biodiversity

Our understanding of the spread of yeasts in natural ecosystems remains somewhat limited. The recent momentum of yeast ecology research has unveiled novel habitats and vectors that, alongside human activities, impact yeast communities in their natural environments. Yeasts, as non-airborne microorganisms, rely on animal vectors, predominantly insects. However, the overlooked actor in this interplay is the environmental matrix, a player potentially influencing yeast populations and their vectors. This study aims to delve deeper into the intricate, multi-layered connections between yeast populations and ecosystems, focusing on the interactions between the attributes of the environmental matrix, arthropod diversity, and the mycobiota within a renowned yeast-inhabited framework: the vineyard. To investigate these relationships, we sampled both invertebrate and yeast diversity in six organic and conventional vineyards described in terms of management and landscape composition. We identified 80 different invertebrate taxa and isolated 170 yeast strains belonging to 18 species. Notably, new species-specific yeast-insect associations were observed, including the exclusive association between Candida orthopsilosis and Hymenoptera and between Metschnikowia pulcherrima and Coleoptera. These newly identified potential associations provide valuable insights into insect and yeast physiology, hence holding the promise of enhancing our understanding of yeast and arthropod ecology and their collective impact on overall ecosystem health.

Soil Microbial Communities and Wine Terroir: Research Gaps and Data Needs

Microbes found in soil can have a significant impact on the taste and quality of wine, also referred to as wine terroir. To date, wine terroir has been thought to be associated with the physical and chemical characteristics of the soil. However, there is a fragmented understanding of the contribution of vineyard soil microbes to wine terroir. Additionally, vineyards can play an important role in carbon sequestration since the promotion of healthy soil and microbial communities directly impacts greenhouse gas emissions in the atmosphere. We review 24 studies that explore the role of soil microbial communities in vineyards and their influence on grapevine health, grape composition, and wine quality. Studies spanning 2015 to 2018 laid a foundation by exploring soil microbial biogeography in vineyards, vineyard management effects, and the reservoir function of soil microbes for grape-associated microbiota. On the other hand, studies spanning 2019 to 2023 appear to have a more specific and targeted approach, delving into the relationships between soil microbes and grape metabolites, the microbial distribution at different soil depths, and microbial influences on wine flavor and composition. Next, we identify research gaps and make recommendations for future work. Specifically, most of the studies utilize targeted sequencing (16S, 26S, ITS), which only reveals community composition. Utilizing high-throughput omics approaches such as shotgun sequencing (to infer function) and transcriptomics (for actual function) is vital to determining the specific mechanisms by which soil microbes influence grape chemistry. Going forward, understanding the long-term effects of vineyard management practices and climate change on soil microbiology, grapevine trunk diseases, and the role of bacteriophages in vineyard soil and wine-making would be a fruitful investigation. Overall, the studies presented shed light on the importance of soil microbiomes and their interactions with grapevines in shaping wine production. However, there are still many aspects of this complex ecosystem that require further exploration and understanding to support sustainable viticulture and enhance wine quality.

Soil and bark biodiversity forms discrete islands between vineyards that are not affected by distance or management regime

Within geographic regions, the existing data suggest that physical habitat (bark, soil, etc.) is the strongest factor determining agroecosystem microbial community assemblage, followed by geographic location (site), and then management regime (organic, conventional, etc.). The data also suggest community similarities decay with increasing geographic distance. However, integrated hypotheses for these observations have not been developed. We formalized and tested such hypotheses by sequencing 3.8 million bacterial 16S, fungal ITS2 and non-fungal eukaryotic COI barcodes deriving from 108 samples across two habitats (soil and bark) from six vineyards sites under conventional or conservation management. We found both habitat and site significantly affected community assemblage, with habitat the stronger for bacteria only, but there was no effect of management. There was no evidence for community similarity distance-decay within sites within each habitat. While communities significantly differed between vineyard sites, there was no evidence for between site community similarity distance-decay apart from bark bacterial communities, and no correlations with soil and bark pH apart from soil bacterial communities. Thus, within habitats, vineyard sites represent discrete biodiversity islands, and while bacterial, fungal and non-fungal eukaryotic biodiversity mostly differs between sites, the distance by which they are separated does not define how different they are.

Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a 'Red Jonaprince' apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches.

Soil management affects carbon and nitrogen concentrations and stable isotope ratios in vine products

Weeds reduce vineyard productivity and affect grape quality by competing with grapevines (Vitis vinifera L.) for water and nutrients. The increased banning of herbicides has prompted the evaluation of alternative soil management strategies. Cover cropping seems to be the best alternative for weed management. However, it may impact vine growth, grape yield, and quality. Quantitative studies on these changes are scarce. Our study aimed to investigate the combined effect of grass cover and water availability on vines of three cultivars, the white Chasselas and Petite Arvine and the red Pinot noir field-grown under identical climatic and pedological conditions and grafted onto the same rootstock. Soil management and irrigation experiments were performed during the 2020-2021 seasons. Two extreme soil management practices were established in the vineyard, based on 100 % bare soil (BS) by the application of herbicides with glufosinate or glyphosate as active ingredients and 100 % grass-covered soil (GS) by cover cropping with a mixture of plant species. Two water statuses were imposed by drip irrigation (DI) and no irrigation (NI). The level of vine-weed competition for water and nitrogen (N) was assessed in the vine, must, and wine solid residues (WSRs) by comparing measurements, i.e., the yeast assimilable N content, C/N_WSR, carbon and N isotope ratios (δ¹³C_grape-sugars, δ¹³C_WSR, and δ¹⁵N_WSR) among the different treatments (BS-DI, BS-NI, GS-DI, GS-NI). The increase in the δ¹³C_grape-sugars and δ¹³C_WSR values with increasing plant water deficit mimicked the observations in irrigation experiments on BS. The N_WSR content and δ¹⁵N_WSR values decreased with water stress and much more strongly in vines on GS. The dramatic N deficit in rainfed vines on GS could be alleviated with irrigation. The present study provides insights from chemical and stable isotope analyses into the potential impact of cover cropping in vineyards in the context of the banning of herbicides in a time of global water scarcity due to climate change.

Identifying candidates for the phytoremediation of copper in viticultural soils: A systematic review

For many years, copper-based fungicides have been used in viticulture and have contributed to increasing concentrations in soils. Today, it is not uncommon to find vineyard soils with total copper topsoil concentrations above 100 mg kg^-1, which may have consequences for both the environment and human health. Phytoremediation, the use of plants to remove heavy metals from soils, is a promising and environmentally-friendly method to extract copper from soils. The objectives of this study were to review and synthesise the current knowledge on copper phytoremediation in vineyard soils and identify future applications. A systematic literature search in Web of Science was conducted on 19 July 2022 and resulted in twenty-seven papers meeting the inclusion criteria. Approximately one third of the papers were from Brazil and most of the experiments had been carried out in pots. In some studies, the addition of bacteria or chelators was also evaluated. Some species, such as Plantago lanceolata L. or Ricinus communis L., can accumulate copper in their tissues at concentrations above 1000 mg kg^-1. Addition of bacteria and chelators to the soil can also increase the copper uptake capacity by plants. However, most of the species evaluated accumulate copper in the roots, rather than in the shoots, thus limiting the implementation of this method in practice. Further studies are thus needed to find other hyperaccumulator plants. Future research should focus primarily on the ability of plants to accumulate copper in their aerial parts, their ability to transfer copper from roots to shoots, and their biomass production under high soil copper concentrations. Longer-term experiments and more in situ testing are also needed to evaluate the potential for development and use of copper phytoremediation in vineyards. To conclude, species of the Poaceae and Lamiaceae families are the most promising so far for phytoremediation. Identifying plants able to translocate copper from the roots to the aerial parts will be an important factor in the success of this method.

Natural and sustainable wine: a review

With the awakening of consumers' awareness of sustainable development issues and demand for terroir wines, natural wines provide opportunities for the future development of the wine industry. Microbiomes are integral to viticulture and winemaking, where various microorganisms can exert positive and negative effects on grape health and wine quality. Communities of microorganisms associated with the vineyard play an important role in soil productivity as well as disease resistance developed by the vine. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. In this review, we first examined that mimicking natural ecological cultivation to improve microbial diversity can enhance vineyard ecological services and reduce external inputs; then we examined that grape berries naturally possess all the elements of winemaking, including the nutrients for microbial growth, driving forces for the microbiota succession, and the enzymatic system for biochemical reactions; finally, we examined food safety, stability, specific interventions, and sustainability of natural wine industry-scale practices.

The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases

Grapevine trunk diseases (GTDs) are one of the most devastating pathologies that threaten the survival and profitability of vineyards around the world. Progressive banning of chemical pesticides and their withdrawal from the market has increased interest in the development of effective biocontrol agents (BCAs) for GTD treatment. In recent years, considerable progress has been made regarding the characterization of the grapevine microbiome, including the aerial part microbiome (flowers, berries and leaves), the wood microbiome, the root environment and vineyard soil microbiomes. In this work, we review these advances especially in relation to the etiology and the understanding of the composition of microbial populations in plants affected by GTDs. We also discuss how the grapevine microbiome is becoming a source for the isolation and characterization of new, more promising BCAs that, in the near future, could become effective tools for controlling these pathologies.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.

Diversity of soil fungi in the vineyards of Changli region in China

This study aimed to elucidate the fungal diversity in Changli vineyard soil in China. High-throughput sequencing technology was used to investigate the diversity and composition of soil fungi in five vineyards at different geographical locations of Changli. Although the five vineyards had similar fungal communities, diversity, the composition and distribution of high-abundance species differed. Ascomycota, Basidiomycota and Mortierellomycota were the dominant phyla. Among the14 high-abundance genera of fungi, Odiodendron, Pleotrichocladium and Plectosephalella were rarely reported in other vineyards and are the unique species from Changli region. In addition, Solicoccozyma aeria and Solicoccozyma terrea were the dominant species in five vineyards and were rarely reported in domestic vineyards. Additionally, Rhizophagus, Wardomyces, Mortierella, Volutella and Cryptococcus were significantly different in the five vineyard soils. Among these species, Mortierella was highly abundant in each vineyard, but its contents were significantly different across vineyards. These findings enriched the information on the composition and diversity of soil fungi in the vineyard of Changli region, which helped to explore the regional or distinctive sensorial attributes of wine from the perspective of microbial biogeography.

The microbiota of the grapevine holobiont: A key component of plant health

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Grapevine interacts different microbiota living around and within its tissues

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Addition of microbial genes to plant genome gives supplementary functions to the holobiont

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The composition of grapevine microbiota varies according to endogenous and exogenous factors

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Microbiota variations can lead to perturbations of grapevine metabolism

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The link between symptom emergence of dieback and microbial imbalance is currently studied

Background

Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions.

Aim of review

The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed.

Key scientific concepts of review

This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.

The effect of plant domestication on host control of the microbiota

Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.

Features of Bacterial Microbiota in the Wild Habitat of Pulsatilla tongkangensis, the Endangered "Long-Sepal Donggang Pasque-Flower Plant," Endemic to Karst Topography of Korea

Microbes associated with plants significantly influence the development and health of the plants. The diversity and function of microbiomes associated with the long-sepal Donggang pasque-flower (DPF) plant, an endemic and endangered species in karst ecosystems, remain unexplored. In this study, we investigated the features of bacterial communities associated with the rhizosphere and roots of DPF plants and their functions in plant growth promotion. The DPF plants were collected from natural and cultivated habitats, and their 16S rDNA was sequenced to assess the bacterial community structures. The bacterial microbiota was more diverse in wild than in cultivated plants. The core bacterial microbiota commonly functioned as endophytes in both wild and cultivated DPF plants, although there were some differences. The identified bacterial strains benefited plants through nitrogen fixation, phosphate solubilization, or phytohormone production, inducing measurable growth differences in Arabidopsis thaliana. To the best of our knowledge, this study is the first to report the bacterial community structures associated with the rhizosphere soil and roots of DPF plants in karst ecosystems. The bacterial strains isolated in this study could be used to aid sustainable growth and restoration of rare plants in karst ecosystems. Our systematic research on the microbiomes associated with these endangered plants will contribute to their conservation as well as development of better cultivation.

Copper Content and Export in European Vineyard Soils Influenced by Climate and Soil Properties

Copper-based fungicides (Cu_f) are used in European (EU) vineyards to prevent fungal diseases. Soil physicochemical properties locally govern the variation of the total copper content (Cu_t) in EU vineyards. However, variables controlling Cu_t distribution at a larger scale are poorly known. Here, machine learning techniques were used to identify governing variables and to predict the Cu_t distribution in EU vineyards. Precipitation, aridity and soil organic carbon are key variables explaining together 45% of Cu_t distribution across EU vineyards. This underlines the effect of both climate and soil properties on Cu_t distribution. The average net export of Cu at the EU scale is 0.29 kg Cu ha^-1, which is 2 orders of magnitude less than the net accumulation of Cu (24.8 kg Cu ha^-1). Four scenarios of Cu_f application were compared. The current EU regulation with a maximum of 4 kg Cu ha^-1 year^-1 may increase by 2% of the EU vineyard area, exceeding the predicted no-effect concentration (PNEC) in soil in the next 100 years. Overall, our results highlight the vineyard areas requiring specific remediation measures and strategies of Cu_f use to manage a trade-off between pest control and soil and water contamination.

Rootstocks Shape Their Microbiome-Bacterial Communities in the Rhizosphere of Different Grapevine Rootstocks

The microbiota associated with the rhizosphere is responsible for crucial processes. Understanding how the plant and its bacterial community interact is of great importance to face the upcoming agricultural and viticultural challenges. The composition of the bacterial communities associated with the rhizosphere of grapevines is the result of the interaction between many drivers: biogeography, edaphic factors, soil management and plant genotype. The experimental design of this study aimed to reduce the variability resulting from all factors except the genotype of the rootstock. This was made possible by investigating four ungrafted grapevine rootstock varieties of the same age, grown on the same soil under the same climatic conditions and managed identically. The bacterial communities associated with the rhizosphere of the rootstocks 1103 Paulsen, 140 Ruggeri, 161-49 Couderc and Kober 5BB were characterized with the amplicon based sequencing technique, targeting regions V4–V5 of 16S rRNA gene. Linear discriminant analysis effect Size (LEfSe) analysis was performed to determine differential abundant taxa. The four rootstocks showed similarities concerning the structure of the bacteria assemblage (richness and evenness). Nonetheless, differences were detected in the composition of the bacterial communities. Indeed, all investigated rootstocks recruited communities with distinguishable traits, thus confirming the role of rootstock genotype as driver of the bacteria composition.

Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol - BA and Abruptic Luvisol - AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms - FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.

Spatial Differentiation of Physical and Chemical Soil Parameters under Integrated, Organic, and Biodynamic Viticulture

Vineyard soils show an increased risk of degradation due to being intensively cultivated. The preservation of soil integrity and fertility is a key concept of organic and biodynamic farming. However, both systems are also subject to criticism due to their higher amount of plant protection products used and their increased traffic intensity compared to integrated viticulture, both detrimental to soil quality. The aim of this study was therefore to assess long-term effects of these three management systems on chemical and physical soil quality parameters. For this purpose, topsoil samples were taken in a long-term field trial vineyard at different positions and examined for bulk density, available water capacity (AWC), soil organic carbon (SOC), N, pH, and for total and bioavailable copper (Cu) concentrations. Biodynamic plots had a lower bulk density and higher SOC concentration than the integrated ones, which is probably due to the species-rich cover crop mixture used in the inter-row. However, organic and biodynamic farming showed an accumulation of copper in the under-vine area and in the tractor track, which is problematic for soil fertility in the long-term. Therefore, alternatives for copper in plant protection are necessary to ensure sustainable soil quality through organic and biodynamic viticulture.

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

Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.

The establishment of a fungal consortium in a new winery

The biodiversity and evolution of fungal communities were monitored over a period of 3 vintages in a new winery. Samples were collected before grape receipt and 3 months after fermentation from 3 different wine related environments (WRE): floor, walls and equipment and analyzed using Illumina Mi-Seq. Genera of mold and filamentous fungi (294), non-enological (10) and wine-associated yeasts (25) were detected on all WREs before the arrival of the first harvest. Among them, genera like Alternaria and Aureobasidium persisted during two vintages. Therefore, these genera are not specific to winery environment and appear to be adapted to natural or anthropic environments due to their ubiquitous character. Some genera like Candida were also detected before the first harvest but only on one WREs, whereas, on the other WREs they were found after the harvest. The ubiquitous character and phenotypic traits of these fungal genera can explain their dynamics. After the first harvest and during 3 vintages the initial consortium was enriched by oenological genera like Starmerella introduced either by harvest or by potential transfers between the different WREs. However, these establishing genera, including Saccharomyces, do not appear to persist due to their low adaptation to the stressful conditions of winery environment.

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

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.

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

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.

Organic and biodynamic wines quality and characteristics: A review

This review collates the scientific literature regarding organic and biodynamic wines. It concerns techniques that allow organic or biodynamic wines to be distinguished from conventional products. Other aspects of the organic wines addressed include the antioxidant capacities and the content of compounds potentially toxic to human health, like metals, such as copper, deriving from treatments in the vineyard, or ochratoxin A and biogenic amines. Organic wines, in which, unlike non-organic wines, the SO₂ must be lower or absent, may undergo premature ageing and present high levels of oxidation compounds. Some authors used selected indigenous yeasts to reduce the production of these molecules and improve the organoleptic quality of the wine. Also, the effects of biodynamic viticulture practices on the chemical and sensory characteristics of wines are compared with other conventional or organic products. With the growing market interest, differences among conventional, organic and, moreover, biodynamic wines, require more in-depth analysis.

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

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Microbiota are important for plant growth, health and stress resilience.

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Inoculation with key microbiota members can improve plant traits.

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Tailored selection and delivery of microbial strains or consortia is required.

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Microbiome improvement may be achieved by appropriate agro-management practices.

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Plant breeding for improved interaction with microbiota will be of benefit.

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. On the one hand microbial strains or strain combinations can be applied, however, field success is often variable and improvement is urgently required. Smart, knowledge-driven selection of microorganisms is needed as well as the use of suitable delivery approaches and formulations. On the other hand, farming practices or the plant genotype can influence plant microbiota and thus functioning. Therefore, selection of appropriate farming practices and plant breeding leading to improved plant-microbiome interactions are avenues to increase the benefit of plant microbiota. In conclusion, different avenues making use of a new generation of inoculants as well as the application of microbiome-based agro-management practices and improved plant lines could lead to a better use of the plant microbiome. This paper reviews the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plant-associated bacteria.

Molecular fungal community and its decomposition activity in sapwood and heartwood of 13 temperate European tree species

Deadwood is an important structural component in forest ecosystems and plays a significant role in global carbon and nutrient cycling. Relatively little is known about the formation and decomposition of CWD by microbial communities in situ and about the factors controlling the associated processes. In this study, we intensively analyzed the molecular fungal community composition and species richness in relation to extracellular enzyme activity and differences in decomposing sapwood and heartwood of 13 temperate tree species (four coniferous and nine deciduous species, log diameter 30–40 cm and 4 m long) in an artificial experiment involving placing the logs on the forest soil for six years. We observed strong differences in the molecular fungal community composition and richness among the 13 tree species, and specifically between deciduous and coniferous wood, but unexpectedly no difference was found between sapwood and heartwood. Fungal species richness correlated positively with wood extractives and negatively with fungal biomass. A distinct fungal community secreting lignocellulolytic key enzymes seemed to dominate the decomposition of the logs in this specific phase. In particular, the relative sequence abundance of basidiomycetous species of the Meruliaceae (e.g. Bjerkandera adusta) correlated with ligninolytic manganese peroxidase activity. Moreover, this study reveals abundant white-rot causing Basidiomycota and soft-rot causing Ascomycota during this phase of wood decomposition.

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity

In recent years, the concept of “microbial terroir” has been introduced in the frame of the more renowned notion of “vitivinicultural terroir,’ since several studies demonstrated that wine characteristics are related to regional microbial community compositions. Most of the existing research focused on grape berries microbiota, since it can directly impact wine quality. In this work we studied, for the first time through next-generation sequencing, the epiphytic bacterial community of vine bark and its relationships with grape microbiota. The study was carried out in two Italian wine appellations (situated in different regions) to explore the impact of biogeography, and the influence of two agronomical practices (biodynamic and conventional) was evaluated as well. Overall, our results show that grapevine bark harbors a rich epiphytic microbiota and displays a higher microbial biodiversity than grape berry. Moreover, this study suggests that geographic and anthropogenic factors impact both bark and grape bacteriomes, but to a different extent. The evidence of a “microbial terroir” seems to be even more marked in bark than in berries, possibly due to its permanence over time and to its physical proximity with soil. The importance of vine trunk bark, as potential source of inoculum for grapes and as interesting bacterial diversity habitat, is evidenced. This opens new fields of investigation, not only for researchers that aim at describing this little-known habitat within the vineyard, but also for stakeholders from the wine industry that want to understand the roles of microorganisms on the entire winemaking process, from vineyard to cellar.

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

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.