Microbial Diversity
Posted: 28 Oct 2022, 12:13
Effects of different management regimes on microbial biodiversity in vineyard soils
Maximilian Hendgen, Björn Hoppe, Johanna Döring, Matthias Friedel, Randolf Kauer, Matthias Frisch, Andreas Dahl & Harald Kellner
Abstract
An active and diverse soil biota is important for maintaining crop productivity and quality, and preservation of these traits is a major goal of sustainable farming. This study aimed at unravelling the impact of different management practices on soil fungal and bacterial biodiversity in vineyards as a model for permanent crops. Species diversity was assessed using an amplicon sequencing approach in a long-term field experiment in the Rheingau wine region of Germany where integrated, organic and biodynamic management practices had been in place for 10 years. Fungal community composition under integrated management differed significantly from organic and biodynamic management, whereas fungal species richness remained unaffected. Soil under integrated management had a significantly reduced bacterial species richness compared to organic, but community composition was similar to organically and biodynamically managed soils. Highest fungal richness was obtained under cover crop between rows in topsoil, arising from cover cropping and organic carbon supply.
Introduction
The microbiome of a soil impacts on organic matter decomposition1, nutrient cycling and buffering2, soil structure3, redox balance2 and the degradation of pollutants4. Furthermore, it influences plant health and growth through positive benefits for processes such as or mycorrhization5, symbiotic interaction6 and resistance induction7, or negatively through pathogenic infection8. Thus, the microbiota can be considered as a key player in soil functionality, ensuring soil productivity and product quality in agricultural production systems9. Despite the fact that little is known about the importance of single organisms for ecosystem functionality and about redundancy between organisms10, it is commonly agreed upon that high biodiversity can ensure vital and productive soils and buffers negative impacts11,12,13.
In viticulture, soils can be subjected to intensive cultivation over long-term time scales as part of cover cropping, soil water and weed management practices. Viticulture soils also receive frequent application of herbicides and fertilizers, and may accumulate copper or other fungicides following foliar applications for disease control14,15. However, integrated management may differ substantially from organic and biodynamic management systems concerning cultivation practices and chemical inputs, and this may influence the vitality and composition of soil organisms. Furthermore, vineyard sites are often established on less fertile and shallow soils, characterized by low water holding capacity, high sun exposure and low nitrogen availability, and are therefore regarded as sensitive ecosystems. Hence, viticulture in general, and integrated farming in particular, is often considered to reduce soil biodiversity and to drive soil biota extinction by the use of soil-destructive farming practices16, resulting in depleted grounds17. Nevertheless, vineyard soils are of major interest as they are an important determinant of grape and wine quality, a common basis for the classification of vineyard sites and part of the so called “terroir” of wines18,19.
In agriculture, organic farming is a constantly booming sector, exhibiting a total area of 57.8 million hectares worldwide and a growth rate of 420% since 1999 (standing 2016)20. Grape production is following this trend as well; comprising 380,000 ha worldwide that account for 5.3% of the total crop area, and of which 90% are located in Europe20. This rapid increase of organically farmed land, driven by political will and consumer demand, has sparked increasing scientific interest in the comparison of farming systems. Most studies focused on soil fertility, yield, crop quality and plant physiology; however, results are somewhat inconsistent21. So far, publications about the impact of management regimes on soil microbial diversity are only available for arable farming22,23, whereas results for viticultural land use are lacking. In this respect, traditional cultivation methods and phospholipid fatty acid (PLFA) profiling face a range of difficulties in evaluating the complete diversity of soil microflora24, as substantial amounts of microbial organisms and their ecology still need to be investigated. In addition, former studies on viticulture mostly focused on the impact of a single factor like copper contamination, or were conducted under artificial circumstances, on a small soil scale or in a short time frame25,26,27. Therefore, interaction effects like within the combined application of pesticides and herbicides or long-term effects like extinction debt could scarcely be detected16. To overcome these constraints, and to improve future agricultural management towards the preservation of edaphic biodiversity, the goals of this study were
1.
to explore differences in fungal and bacterial populations between soils under integrated, organic and biodynamic vineyard management in a long-term field experiment,
2.
to gain novel insights into the microbial biodiversity in a long-term vineyard soil in the Rheingau region in Western Germany, and
3.
to relate differences of the microbiome among management systems to specific management practices and resulting soil factors (in order to improve the sustainability of vineyard management).
To reach these goals, soil samples were taken at a long-term field trial, and biodiversity of soil fungi and bacteria was determined using a barcoding approach28,29,30. Furthermore, chemical and physical parameters of the soil samples were examined to screen for correlations with fungal and bacterial richness and community composition.
Results
Soil analysis
Altogether, soil analyses revealed largely homogenous ground conditions (Supplementary Table 1). However, some minor yet significant differences were detected according to the three investigated factors: Soil organic carbon, soil moisture content and potassium varied significantly in relation to management practice, position and depth (α = 0.05). With an average value of 1.25%, soil organic carbon content was highest in in-row topsoil, whereas values for subsoil samples were decreased by about 0.3%. Soil moisture content was rather low due to a previous drought period (~8.5%) with slightly lower values in topsoil compared to subsoil and in-row compared to under-vine (Supplementary Fig. 1). The only parameter exhibiting distinct differences solely according to the management system was magnesium; however, mean values ranged only between 12.81 mg 100 g−1 (org = highest) and 10.75 mg 100 g−1 soil (biodyn = lowest). Nitrogen (mean 0.086%) and pH (mean 7.35) differed slightly in comparison of top- and subsoil (Supplementary Fig. 1). Besides this, soil from the biodynamical farmed parcels showed increased total amounts of the heavy metals iron (about 23.8 g kg−1 vs. ~22.5 g kg−1), manganese (about 700 mg kg−1 vs. ~628 mg kg−1) and zinc (about 105 mg kg−1 vs. ~95 mg kg−1) compared to the integrated and organic farming.
Maximilian Hendgen, Björn Hoppe, Johanna Döring, Matthias Friedel, Randolf Kauer, Matthias Frisch, Andreas Dahl & Harald Kellner
Abstract
An active and diverse soil biota is important for maintaining crop productivity and quality, and preservation of these traits is a major goal of sustainable farming. This study aimed at unravelling the impact of different management practices on soil fungal and bacterial biodiversity in vineyards as a model for permanent crops. Species diversity was assessed using an amplicon sequencing approach in a long-term field experiment in the Rheingau wine region of Germany where integrated, organic and biodynamic management practices had been in place for 10 years. Fungal community composition under integrated management differed significantly from organic and biodynamic management, whereas fungal species richness remained unaffected. Soil under integrated management had a significantly reduced bacterial species richness compared to organic, but community composition was similar to organically and biodynamically managed soils. Highest fungal richness was obtained under cover crop between rows in topsoil, arising from cover cropping and organic carbon supply.
Introduction
The microbiome of a soil impacts on organic matter decomposition1, nutrient cycling and buffering2, soil structure3, redox balance2 and the degradation of pollutants4. Furthermore, it influences plant health and growth through positive benefits for processes such as or mycorrhization5, symbiotic interaction6 and resistance induction7, or negatively through pathogenic infection8. Thus, the microbiota can be considered as a key player in soil functionality, ensuring soil productivity and product quality in agricultural production systems9. Despite the fact that little is known about the importance of single organisms for ecosystem functionality and about redundancy between organisms10, it is commonly agreed upon that high biodiversity can ensure vital and productive soils and buffers negative impacts11,12,13.
In viticulture, soils can be subjected to intensive cultivation over long-term time scales as part of cover cropping, soil water and weed management practices. Viticulture soils also receive frequent application of herbicides and fertilizers, and may accumulate copper or other fungicides following foliar applications for disease control14,15. However, integrated management may differ substantially from organic and biodynamic management systems concerning cultivation practices and chemical inputs, and this may influence the vitality and composition of soil organisms. Furthermore, vineyard sites are often established on less fertile and shallow soils, characterized by low water holding capacity, high sun exposure and low nitrogen availability, and are therefore regarded as sensitive ecosystems. Hence, viticulture in general, and integrated farming in particular, is often considered to reduce soil biodiversity and to drive soil biota extinction by the use of soil-destructive farming practices16, resulting in depleted grounds17. Nevertheless, vineyard soils are of major interest as they are an important determinant of grape and wine quality, a common basis for the classification of vineyard sites and part of the so called “terroir” of wines18,19.
In agriculture, organic farming is a constantly booming sector, exhibiting a total area of 57.8 million hectares worldwide and a growth rate of 420% since 1999 (standing 2016)20. Grape production is following this trend as well; comprising 380,000 ha worldwide that account for 5.3% of the total crop area, and of which 90% are located in Europe20. This rapid increase of organically farmed land, driven by political will and consumer demand, has sparked increasing scientific interest in the comparison of farming systems. Most studies focused on soil fertility, yield, crop quality and plant physiology; however, results are somewhat inconsistent21. So far, publications about the impact of management regimes on soil microbial diversity are only available for arable farming22,23, whereas results for viticultural land use are lacking. In this respect, traditional cultivation methods and phospholipid fatty acid (PLFA) profiling face a range of difficulties in evaluating the complete diversity of soil microflora24, as substantial amounts of microbial organisms and their ecology still need to be investigated. In addition, former studies on viticulture mostly focused on the impact of a single factor like copper contamination, or were conducted under artificial circumstances, on a small soil scale or in a short time frame25,26,27. Therefore, interaction effects like within the combined application of pesticides and herbicides or long-term effects like extinction debt could scarcely be detected16. To overcome these constraints, and to improve future agricultural management towards the preservation of edaphic biodiversity, the goals of this study were
1.
to explore differences in fungal and bacterial populations between soils under integrated, organic and biodynamic vineyard management in a long-term field experiment,
2.
to gain novel insights into the microbial biodiversity in a long-term vineyard soil in the Rheingau region in Western Germany, and
3.
to relate differences of the microbiome among management systems to specific management practices and resulting soil factors (in order to improve the sustainability of vineyard management).
To reach these goals, soil samples were taken at a long-term field trial, and biodiversity of soil fungi and bacteria was determined using a barcoding approach28,29,30. Furthermore, chemical and physical parameters of the soil samples were examined to screen for correlations with fungal and bacterial richness and community composition.
Results
Soil analysis
Altogether, soil analyses revealed largely homogenous ground conditions (Supplementary Table 1). However, some minor yet significant differences were detected according to the three investigated factors: Soil organic carbon, soil moisture content and potassium varied significantly in relation to management practice, position and depth (α = 0.05). With an average value of 1.25%, soil organic carbon content was highest in in-row topsoil, whereas values for subsoil samples were decreased by about 0.3%. Soil moisture content was rather low due to a previous drought period (~8.5%) with slightly lower values in topsoil compared to subsoil and in-row compared to under-vine (Supplementary Fig. 1). The only parameter exhibiting distinct differences solely according to the management system was magnesium; however, mean values ranged only between 12.81 mg 100 g−1 (org = highest) and 10.75 mg 100 g−1 soil (biodyn = lowest). Nitrogen (mean 0.086%) and pH (mean 7.35) differed slightly in comparison of top- and subsoil (Supplementary Fig. 1). Besides this, soil from the biodynamical farmed parcels showed increased total amounts of the heavy metals iron (about 23.8 g kg−1 vs. ~22.5 g kg−1), manganese (about 700 mg kg−1 vs. ~628 mg kg−1) and zinc (about 105 mg kg−1 vs. ~95 mg kg−1) compared to the integrated and organic farming.