Management-associated soil chemistry shapes bacterial communities in Mediterranean vineyards: A comparison of wild, organic, and conventional systems

Diversity of small terrestrial mammals under different organic farming management in Mediterranean and Continental agriculture ecosystems

Sustained tillage and continual applications of phytopharmaceutical and fertilizers using heavy machineries frequently give rise to soil erosion, loss of soil organic matter (SOM) and contamination phenomena in Mediterranean vineyards. Because of their distinctive properties, applying natural zeolites to vineyard soils can conceivably affect the efficient use of fertilizers and reduce nutrient leaching losses. This work assesses the impact of zeolite amendment at differing rates (0, 5 and 10 t/ha) on the chemical and biochemical soil properties of three vineyard soils after 6 months from initial treatments. In particular, chemical properties usually related to soil fertility were evaluated along with more sensitive indicators of soil functionality and indicators of chemical–structural characteristics of SOM. The vineyard soils amended with zeolite showed higher nutrient availability and dehydrogenase activity if compared with the control soils. In addition, even though total organic carbon (TOC) content was unchanged, a decrease in humic substances was observed in the zeolite‐treated soils. These results suggested that the stimulation of soil microbial processes by adding zeolite triggered a microbial mineralization process of soil organic carbon stocks. In addition, the modification in the chemical–structural composition of soil organic matter in zeolite‐treated soils was shown by the pyrolysis–gas chromatography (Py‐GC) results. Py‐CG of soil organic matter clearly demonstrated an increase in the labile aliphatic compound furfural and a decline in the more stable aromatic pyrolytic fragments in zeolite‐treated soils in contrast with the control soils, thus indicating the higher extent of decomposition of the SOM more stable pool.

BackgroundThe importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil.MethodologyOur organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic.ResultsWe observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and β- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields.ConclusionDifferent organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.

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This study was conducted over the period 2017–2019 in Czesławice (central Lublin region, Poland). The aim of the present study was to compare chemical soil quality parameters (soil pH, available P and K, organic carbon, and total nitrogen content) and soil enzymatic activity (dehydrogenase, acid phosphatase, alkaline phosphatase, urease, protease) in organic and conventional farming systems. The experimental design included two crop rotations (organic and conventional) in which identical plant species were grown: sugar beet-spring barley-red clover-winter wheat-oats. The loess soil on which the experiment was conducted was characterized by the grain size distribution of silt loam, and this soil was categorized as good wheat soil complex (soil class II). The experiment was set up as a split-plot design in triplicate in plots with an area of 40 m2. Soil sampling was carried out using a soil auger within an area of 0.20 m2 (from the 0 to 20 cm layer) in each plot during the autumn period. Over the 3-year study period, it was found that the organic system contributed to an increased soil content of organic carbon and total nitrogen. Moreover, a significantly higher soil pH value and a favorable narrow C/N ratio were found under the organic system (regardless of the crop species). Under the conventional system, in turn, a higher soil phosphorus and potassium content was observed. Enzymatic tests of the soil in the five-field crop rotation proved significantly higher activity of all the enzymes studied (in particular that of dehydrogenase, protease, and urease) in the organic system relative to the conventional one, regardless of the crop plant. Among the plants grown in crop rotation, sugar beet, and red clover had the most beneficial effect on the activity of the soil enzymes, followed by oats (especially under the organic system). The activity of the studied enzymes in the organic system was positively correlated (statistically significantly) with favorable soil pH, a higher content of organic C, and total N, and C/N ratio.

This study investigated the effects of four rice-based cropping systems (rice-vegetable pea + coriander; rice-chickpea + coriander; rice-potato and rice-wheat) cultivated in long-term organic, integrated and conventional production systems on system productivity (SP), soil organic carbon (SOC) sequestration and soil properties. The experiment was laid out in a split plot design with the production system assigned to the main plots and the cropping system to sub-plots. The results revealed that SP, SOC content and SOC sequestration in the organic system were significantly higher than in the conventional counterpart (17.1%, 59.4% and 165.9% higher, respectively). The fractions of total organic carbon followed the order: very labile carbon > non-labile carbon > labile carbon > less labile carbon. The soil in the organic system had, in general, the most improved physical (water holding capacity, bulk density), chemical (available N, P, K and S, and DTPA-extractable Fe, Mn, Cu and Zn) and biological properties (dehydrogenase and acid and alkaline phosphatase activity), especially when compared with the conventional system. The legume-based cropping systems (rice-chickpea + coriander and rice-vegetable pea + coriander) enhanced the SP, SOC content and SOC sequestration by 22.6% and 46.5%, 16.3% and 11.9% and 47.5% and 29.4%, respectively, compared with the rice-wheat cropping system, with improvements also in different physical, chemical and biological soil properties. Thus, organic system with legume-based cropping (rice-chickpea + coriander and/or rice-vegetable pea + coriander) was concluded to sustain crop productivity and have greater soil carbon sequestration potential in the longer term.

In agriculture, the farming system significantly affects chemical soil properties. The organic system, which is based among others on the use of natural (organic) fertilizers, promotes increased soil contents of humus, organic C, and micronutrients. The conventional system, in turn, may cause soil acidification if high rates of mineral (particularly nitrogen) fertilization are used. The crop plant species also modifies soil chemistry by providing different (quantitatively and qualitatively) crop residues. The study was conducted over the period 2013–2016 in Czesławice (Lublin Region, Poland). The aim of this study was to determine the content of some chemical components determining the quality of loess soil on which four plant species were grown under organic and conventional farming systems. This research involved the determination of some parameters of the chemical composition of the soil: soil pH, total sorption capacity, humus content, macronutrient (P, K, Mg) and micronutrient (B, Cu, Mn, Zn) content, organic carbon, and total nitrogen content. The content of different forms of nitrogen, N-NO3 and N-NH4, was also determined. The experimental design included two crop rotations (organic and conventional) in which identical plant species were grown: potato—winter wheat—field bean—spring barley. The experiment was established on loess soil with the grain size distribution of silt loam and classified as good wheat soil complex (soil class II). It was carried out as a split-plot design in three replicates, and the area of a single plot was 80 m2. Soil samples were taken using a soil sampling tube from an area of 0.20 m2 (from the 0–25 cm layer) in each plot at the end of the growing season of the specific crops grown. Over the four year study period, it was found that the organic system contributed to an increased soil content of magnesium, boron, copper, manganese, zinc, organic carbon, and total nitrogen. Moreover, organic cropping promoted more favorable soil pH and higher soil humus content. Organic cropping significantly improved the total sorption capacity of the soil compared to conventional cultivation. Moreover, the organic system contributed to a higher soil content of nitrogen in the form of N-NH4 and its lower content in the form of N-NO3. Under the conventional system, in turn, a higher soil phosphorus and potassium content was observed. To sum up, the study confirmed the assumed hypothesis that the organic farming system would contribute to an improvement in the chemical quality indicators of loess soil. Regardless of the cropping system, potato and field bean had the most beneficial effect on soil chemistry, whereas cereal crops showed the weakest effect. Winter wheat and spring barley had an effect on significantly lower total sorption capacity of the soil and a significantly lower soil content of N-NO3 and N-NH4.

Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system

​Soil microbiota is central to agroecosystem sustainability, influencing fertility, plant health, and resilience. Agricultural practices shape these communities in distinct ways: conventional systems, with intensive chemical inputs, often promote microbial homogeneity, whereas organic systems, with higher organic matter inputs and reduced disturbance, tend to sustain functionally diverse microbiomes. Yet, the extent of these effects remains poorly understood, particularly when taxonomic, functional, and machine-learning-based indicators are evaluated jointly across different cropping systems. To address this gap, we compared the taxonomic and functional diversity of soil microbiota in organic and conventional fields cultivated with common bean (Phaseolus vulgaris) and grapevine (Vitis vinifera) in Brazil. Microbial communities were profiled using 16S rRNA and ITS sequencing, with analyses spanning diversity metrics, taxonomic composition, functional inference, and machine-learning-based biomarker identification. Bacterial diversity was greater under conventional management, while fungal diversity did not differ between systems. Machine-learning approaches identified Bradyrhizobium and Roseococcus (bacteria) and Lecythophora (fungus) as consistent biomarkers of organic soils. Functional predictions pointed to enhanced nitrogen fixation and carbon cycling in organic fields, whereas sulfur cycling was more prominent in conventional ones. Microbial community structure clearly separated by management and correlated strongly with soil chemistry, and Venn analysis revealed more unique bacterial and fungal operational taxonomic units (OTUs) in organic soils. Together, these results highlight how agricultural management acts as a strong ecological filter of soil microbiota. Conventional farming favored broader bacterial diversity. In contrast, organic systems fostered distinct microbial biomarkers and enhanced functional potential, particularly for nitrogen and carbon pathways.

Understanding interactions that emerge in complex ecological networks is fundamental to developing a more sustainable agriculture. We studied three agricultural farms in subtropical Brazil, consisting of conventional citrus (Cconv), organic citrus (Corg) and citrus in agroforestry system (Cagr), and two forest areas, one 40-years old (F40) and the other 200-years old (F200). We determined Pfeiffer’s circular chromatography (PCC) analyses and soil chemical, physical, and biological properties in different soil layers. The PCC expressed soil properties in an integrated manner and improved our understanding of the relation of chromatography patterns with soil physical properties (soil density, porosity, aggregate stability, total organic carbon, and FDA hydrolysis). Forest areas and citrus orchards under different managements were also distinguished by chromatography. Thus, chromatography is an important tool for assessing soil quality/health in citrus and forest systems. The best options to maintain soil quality in citrus orchards are the agroforestry and organic systems. These two cropping systems have greater spontaneous coverage (Margalef index, occurrence, and richness) and soil pH, soil organic carbon, porosity, and Pfeiffer chromatography parameters. Permanent soil cover, mowing, composting, biofertilizers, and minimum machinery traffic contribute to improving soil quality.

The cacao plantations in Sulawesi Island, Indonesia are responsible for a great part of the local economy; however, their soils still need to be deeply explored. Our study focused on evaluation of the microbial communities in cacao soils according to their location and applied management system. Four soil samples were taken from six cacao farms under two kinds of systems (conventional and organic). 16S and ITS rDNA amplicon sequencing analyses of soils were also performed to identify bacteria and fungi, respectively, whereby their relative abundance and diversity were determined. In general view, the bacterial and fungal communities were affected by management system at the local and general levels. Bacterial analyses indicated that the number of operational taxonomic units and bacterial diversity were higher under the organic system in Kulawi, Palolo, and Poso farms. The composition and biodiversity of fungi were clearly different between organic and conventional systems and between different places (coastal and inland). The effect of agricultural management was observed in each location individually and in general.

Chapter 8 - Redesigning soil–water management with sustainable resilience strategies in almond orchards in a Mediterranean environment

Long-term impacts of organic and conventional farming on the soil microbiome in boreal arable soil

Microbial immobilization of ammonium and nitrate in relation to ammonification and nitrification rates in organic and conventional cropping systems

Invader-resident relatedness and soil management history shape patterns of invasion of compost microbial populations into agricultural soils