Organic and IPM apples differ in soil life, yields and fruit quality

A three-year comparison of two long-term apple orchards in Estonia found that the integrated pest management (IPM) orchard produced higher total and fresh-market yields for two of three cultivars, while the organic orchard had darker, more intensely coloured apples on average. The results also revealed contrasting patterns in soil biology: the IPM orchard contained more earthworms overall, but the organic orchard consistently supported a larger proportion of anecic earthworms, including the deep-burrowing species Aporrectodea longa. Springtail abundance did not differ significantly between the systems. Fruit taste and antioxidant traits, by contrast, were shaped more consistently by cultivar and year than by cultivation system.

The study was conducted from 2022 to 2024 at the Polli Horticultural Research Centre in southern Estonia. The adjacent orchards shared the same Albic Luvisol soil type, MM106 rootstock, standard-spindle training system, planting density and ground-cover management, and were separated by about 300 metres. The organic orchard had been managed under its system since 2008 and the IPM orchard since 2010, giving the sites 14 and 12 years of management history when observations began. The study examined the Estonian cultivars “Katre” and “Krista” and the Belarusian cultivar “Alesja,” assessing yield, fruit chemistry, peel colour, firmness, soil chemistry, earthworms and springtails. These were orchard-level observations from two specific sites rather than a randomized comparison of many independent orchards.

The orchards differed chiefly in crop protection and fertilisation. Neither used herbicides. The IPM orchard received registered synthetic insecticides, including deltamethrin and flonicamid, and fungicides including cyprodinil, difenoconazole and dithianon. The organic orchard relied on products permitted in organic production, including azadirachtin and Bacillus thuringiensis, and no fungicides were applied there. In the fertilised years, nitrogen inputs were substantially higher in the IPM orchard: a compound fertiliser in 2022 supplied 36.4 kg N per hectare, while ammonium nitrate in 2024 supplied 41.4 kg N per hectare. The organic orchard received poultry manure-based fertiliser supplying 11.8 kg N per hectare per application. No fertiliser was applied in either orchard in 2023. Because management history, crop protection and fertiliser inputs were not independently manipulated, their separate effects could not be determined.

Yield was evaluated in 2022, the only year for which a representative crop could be compared. Severe frosts in early May 2023 destroyed the crop, and frost during flowering in 2024 produced non-representative crop loads, so yield was not assessed in those years. Total yield was significantly higher under IPM management for “Katre” and “Alesja,” while no significant system difference occurred for “Krista.” Averaged across cultivars, total yield was 42.1 ± 9.1 kg per tree in the IPM orchard and 32.1 ± 18.4 kg per tree in the organic orchard. Fresh-market yield was also higher overall under IPM, at 28.1 ± 7.2 versus 19.7 ± 12.6 kg per tree, but the proportion classified as fresh-market fruit did not differ consistently between systems. The higher fresh-market output therefore reflected greater total production rather than a universal improvement in marketability. “Alesja” was an exception: only 49.3% of organically grown fruit met fresh-market standards, compared with 72.8% under IPM, largely because of greater codling moth damage in the organic orchard.

Because fertilisation was not experimentally separated from the production systems, the study could not determine whether nutrient supply or another aspect of management caused the observed differences. The IPM orchard nevertheless produced fruit with higher average nitrogen concentrations in 2024, while organic apples had higher average phosphorus and potassium. Fruit firmness ranged from 52 to 82 N in 2022 and 40 to 58 N in 2024, but did not differ significantly between cultivation systems for any cultivar in either year. Colour, measured only in 2024, showed a clearer system-level pattern. Averaged across cultivars, organic apples had lower lightness, higher redness and chroma, and lower hue angle, indicating darker, redder and more intensely coloured peel. Cultivar-specific differences were less consistent, with organic “Alesja” showing significantly greater chroma than its IPM counterpart while several other within-cultivar comparisons were not significant. The study associated these patterns with the different nutrient regimes, but it did not establish nitrogen availability as the cause.

Taste-related measures followed no single management pattern. Soluble solids content was lower in IPM-grown “Katre” and “Krista” in 2022, but the reverse occurred for “Alesja”; in 2024, soluble solids were again lower in IPM “Katre” while “Alesja” was lower. Titratable acidity was higher in organic “Katre” and “Alesja” in both sampled years, but the overall ratio of soluble solids to titratable acids was higher under IPM when averaged across cultivars. Some contrasts reached levels that consumers could potentially perceive: the study cited thresholds of more than 1 °Brix for soluble solids and more than 0.08% for titratable acidity. These included 1.1 °Brix for “Krista” in 2022 and acidity differences of 0.10–0.17% for “Katre.” Individual sugars did not show a consistent system effect, and the authors noted that genotype and weather appeared to influence fruit composition more strongly than management history.

Antioxidant measurements produced a similar cultivar-dependent pattern. Organic “Katre” had significantly higher total polyphenol content in both 2022 and 2024, but the same difference was not detected for “Krista” or “Alesja.” “Alesja” had the highest total polyphenol and anthocyanin concentrations regardless of cultivation system, supporting the importance of genotype. Anthocyanins averaged higher in organic fruit in 2022, but the management effect disappeared in 2024, and there was no significant overall difference in ascorbic acid content. The contrast between years coincided with contrasting weather: a cool spring and dry June preceded a warm August in 2022, whereas 2024 brought exceptionally dry May conditions followed by above-average temperatures and wetter late-season conditions. The researchers said these climatic differences could alter pigment and vitamin C accumulation, making it inappropriate to treat the two years as equivalent tests of a stable management effect.

Soil chemistry showed significant differences between the orchards. Organic orchard soil had higher pH, phosphorus and calcium in each sampling year. Its pH in KCl ranged from 5.84 to 6.27, compared with 4.94 to 5.24 in the IPM orchard. Total phosphorus was 109–122 mg per kilogram in the organic soil and 47–55 mg per kilogram in the IPM soil, while calcium ranged from 969 to 1,050 versus 658 to 726 mg per kilogram. Magnesium, total nitrogen and total potassium did not differ significantly. The different fertiliser sources were plausibly involved: the organic orchard’s poultry manure product supplied calcium and organic matter, but fertiliser type could not be isolated from the orchards’ longer management histories or site-specific conditions.

Earthworm results showed contrasting patterns between total abundance and community composition. Six species were recorded in both systems, but total abundance was significantly higher in the IPM orchard in 2024, with mean abundance across the three years reported as 148.0 ± 28.5 individuals per square metre, compared with 96.4 ± 9.1 in the organic orchard. The pattern was not explained by permanent dominance of one ecological group. Instead, the organic orchard consistently had a higher share of anecic earthworms, which occupy deep permanent burrows and feed at the surface, including A. longa. Exploratory ordination associated organic samples with higher pH, phosphorus, calcium, magnesium and microbial-activity indices, while IPM samples were positioned closer to precipitation, moisture and temperature variables. These were visual associations rather than formal causal tests: the analysis used only six orchard-year combinations, and soil microbial respiration and biomass lacked independent within-orchard replication.

Springtails did not show a significant overall abundance response to management. Across the study, total abundance was not significantly affected by year, cultivation system or their interaction, although the organic orchard numerically exceeded IPM in 2022 and 2023 before the order reversed in 2024. Ecological life form did matter: euedaphic springtails living within the soil matrix were significantly more abundant than hemiedaphic forms. The organic orchard generally recorded more species, including 20, 22 and 21 in the three years, compared with 18, 23 and 17 under IPM, while the IPM orchard had a higher share of euedaphic forms in two years. Exploratory correlations linked community differences to soil moisture, precipitation, nitrogen, pH and phosphorus rather than demonstrating a direct effect of cultivation system.

Together, the results offer a nuanced picture of long-term apple production under Nordic and Baltic conditions. IPM management was associated with greater productivity for two cultivars, and organic management with more intense peel colour, higher soil pH, more phosphorus and calcium, and a larger proportion of anecic earthworms. Neither system consistently produced sweeter, more acidic or more antioxidant-rich fruit across cultivars and years. The study’s strongest limitation is also its most important caution: each system was represented by only one orchard, so cultivation method was confounded with orchard identity, microclimate and management history. Trees and soil sampling points were subsamples rather than independent orchard-level replicates. Replicated comparisons across multiple orchards would be needed before these site-specific patterns could be generalized to organic and IPM production systems.

Subject of Research: Comparison of apple quality and soil biological diversity in long-term organic and integrated pest management orchards

Article Title: Apple quality and soil biological diversity in long-term organic and IPM apple orchards

Article References: Moor, U., Kuu, A., Kahu, K., Põldma, P., & Rätsep, R. (2026). Apple quality and soil biological diversity in long-term organic and IPM apple orchards. Frontiers in Sustainable Food Systems, 10, Article 1943487. https://doi.org/10.3389/fsufs.2026.1943487

Image Credits: AI Generated

DOI: 10.3389/fsufs.2026.1943487

Keywords: apple orchards, organic farming, integrated pest management, soil biodiversity, earthworms, springtails, fruit quality, peel colour, antioxidants, Estonia, Apple, quality