Frontiers in Plant Science · 2025
Soybean green manure intercropping improves citrus quality by improving soil quality and altering microbial communities
Deng, S., Huang, B., Zeng, B., Cao, S., Gong, B., Liao, W., Zhang, W., Luo, S., Yang, S.
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Soybean green manure intercropping improves citrus quality b…
Abstract
Introduction Intercropping leguminous green manure in orchards represents a widely adopted agroecological practice that concurrently influences soil physicochemical properties, microbial communities, and crop performance. However, the temporal mechanisms by which different durations of soybean green manure (SGM) intercropping regulate soil-plant-microbe interactions remain insufficiently understood. This study elucidates the impact of SGM intercropping duration on ecosystem functionality in citrus orchards. Methods A multi-year field experiment compared SGM intercropping durations (0-, 1-, and 2-year treatments). We assessed citrus fruit quality parameters (total soluble solids, TSS; sugar-acid ratio, TSS/TA) and soil properties (pH, available nitrogen, total nitrogen, available phosphorus, available potassium, and organic matter). Microbial community structure was analyzed via high-throughput sequencing. Spearman correlation analysis (| ρ | ≥ 0.8, p < 0.05) delineated networks among intercropping duration, soil parameters, keystone microbial taxa (e.g., Proteobacteria, Acidobacteriota, Ascomycota), and fruit quality indicators. Results The two-year intercropping treatment (T2) significantly enhanced fruit quality: TSS increased by 11.66% and the sugar-acid ratio (TSS/TA) by 41.95% ( p < 0.05). Soil properties improved markedly: pH rose by 0.42 units, while AN, TN, AP, AK, and OM increased by 41.80%, 9.15%, 16.78%, 100.50%, and 79.53%, respectively ( p < 0.05). Microbial communities underwent structural reorganization, exhibiting increased α-diversity, enhanced network complexity, and selective enrichment of beneficial taxa including Actinobacteria, Mortierellales, and Ascomycota. Correlation networks revealed significant associations among intercropping duration, soil parameters, keystone microbes, and fruit quality. Discussion This study demonstrates that SGM intercropping enhances fruit quality through dual mechanisms: (1) amelioration of soil properties (pH elevation and improved nutrient availability), and (2) functional restructuring of microbial communities. Notably, specific taxa such as Actinobacteria play pivotal roles in nutrient cycling. Our findings provide empirical evidence for microbiome-mediated optimization of soil functionality, offering a sustainable rehabilitation strategy for degraded orchards and reinforcing the scientific value of ecological intensification in perennial cropping systems.
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Introduction Intercropping leguminous green manure in orchards represents a widely adopted agroecological practice that concurrently influences soil physicochemical properties, microbial communities, and crop performance. However, the temporal mechanisms by which different durations of soybean green manure (SGM) intercropping regulate soil-plant-microbe interactions remain insufficiently understood. This study elucidates the impact of SGM intercropping duration on ecosystem functionality in citrus orchards. Methods A multi-year field experiment compared SGM intercropping durations (0-, 1-, and 2-year treatments). We assessed citrus fruit quality parameters (total soluble solids, TSS; sugar-acid ratio, TSS/TA) and soil properties (pH, available nitrogen, total nitrogen, available phosphorus, available potassium, and organic matter). Microbial community structure was analyzed via high-throughput sequencing. Spearman correlation analysis (| ρ | ≥ 0.8, p < 0.05) delineated networks among intercropping duration, soil parameters, keystone microbial taxa (e.g., Proteobacteria, Acidobacteriota, Ascomycota), and fruit quality indicators. Results The two-year intercropping treatment (T2) significantly enhanced fruit quality: TSS increased by 11.66% and the sugar-acid ratio (TSS/TA) by 41.95% ( p < 0.05). Soil properties improved markedly: pH rose by 0.42 units, while AN, TN, AP, AK, and OM increased by 41.80%, 9.15%, 16.78%, 100.50%, and 79.53%, respectively ( p < 0.05). Microbial communities underwent structural reorganization, exhibiting increased α-diversity, enhanced network complexity, and selective enrichment of beneficial taxa including Actinobacteria, Mortierellales, and Ascomycota. Correlation networks revealed significant associations among intercropping duration, soil parameters, keystone microbes, and fruit quality. Discussion This study demonstrates that SGM intercropping enhances fruit quality through dual mechanisms: (1) amelioration of soil properties (pH elevation and improved nutrient availability), and (2) functional restructuring of microbial communities. Notably, specific taxa such as Actinobacteria play pivotal roles in nutrient cycling. Our findings provide empirical evidence for microbiome-mediated optimization of soil functionality, offering a sustainable rehabilitation strategy for degraded orchards and reinforcing the scientific value of ecological intensification in perennial cropping systems.
Introduction Intercropping leguminous green manure in orchards represents a widely adopted agroecological practice that concurrently influences soil physicochemical properties, microbial communities, and crop performance. However, the temporal mechanisms by which different durations of soybean green manure (SGM) intercropping regulate soil-plant-microbe interactions remain insufficiently understood. This study elucidates the impact of SGM intercropping duration on ecosystem functionality in citrus orchards. Methods A multi-year field experiment compared SGM intercropping durations (0-, 1-, and 2-year treatments). We assessed citrus fruit quality parameters (total soluble solids, TSS; sugar-acid ratio, TSS/TA) and soil properties (pH, available nitrogen, total nitrogen, available phosphorus, available potassium, and organic matter). Microbial community structure was analyzed via high-throughput sequencing. Spearman correlation analysis (| ρ | ≥ 0.8, p < 0.05) delineated networks among intercropping duration, soil parameters, keystone microbial taxa (e.g., Proteobacteria, Acidobacteriota, Ascomycota), and fruit quality indicators. Results The two-year intercropping treatment (T2) significantly enhanced fruit quality: TSS increased by 11.66% and the sugar-acid ratio (TSS/TA) by 41.95% ( p < 0.05). Soil properties improved markedly: pH rose by 0.42 units, while AN, TN, AP, AK, and OM increased by 41.80%, 9.15%, 16.78%, 100.50%, and 79.53%, respectively ( p < 0.05). Microbial communities underwent structural reorganization, exhibiting increased α-diversity, enhanced network complexity, and selective enrichment of beneficial taxa including Actinobacteria, Mortierellales, and Ascomycota. Correlation networks revealed significant associations among intercropping duration, soil parameters, keystone microbes, and fruit quality. Discussion This study demonstrates that SGM intercropping enhances fruit quality through dual mechanisms: (1) amelioration of soil properties (pH elevation and improved nutrient availability), and (2) functional restructuring of microbial communities. Notably, specific taxa such as Actinobacteria play pivotal roles in nutrient cycling. Our findings provide empirical evidence for microbiome-mediated optimization of soil functionality, offering a sustainable rehabilitation strategy for degraded orchards and reinforcing the scientific value of ecological intensification in perennial cropping systems.
Findings
What changed what, as the paper reports it. Grouped by the measured property. The largest groups are open; open the others as you need them.
total nitrogen
↑ 1= 12
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm; T2 only; T1ab shares controlb.
Numbers
- treatment 1.67 vs. control 1.53 g/kg (+9.15 %)
Source · p. 5 “the T2 treatment significantly improved the soil pH (+0.42 units), AN (+41.80%), total nitrogen (N, +9.15%), AP (+16.78%), AK (+100.50%), and OM (+79.53%) compared with the control (T0)”
- no effect
T1 one-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagenot significant · 5–15 cm · 12 November 2022 · Houjiawan Village citrus orchard · One-yearT1 package versusT0 only; time-duration variant has a different outcome from represented two-yearTN increase. Original Table2 ab/b shared letters at Duncan alpha0.05; five soil plots per treatment.
Numbers
- treatment 1.6 vs. control 1.53 g/kg (+4.575 %)
Source · p. 11 “1-year SGM intercropping significantly enhanced most soil physicochemical properties, with the exception of total N, P, and K content.”
fruit total soluble solids (TSS)
↑ 11
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 12 November2022 fruit harvest · Houjiawan Village citrus orchard · Two-year package; fruit methods specify four plots despite general five-plot design.
Numbers
- treatment 13.37 vs. control 11.97 % (+11.7 %)
Source · p. 4 “fruit TSS increased by 11.66% from 11.97% (T0) to 13.37% (T2)”
soil pH
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm; agreeing T1/T2 control pairs (b/a versusc).
Numbers
- treatment 5.37 vs. control 5.11 (+5.088 %) · T1
- treatment 5.53 vs. control 5.11 (+8.219 %) · T2
Source · p. 5 “significant enhancements (p \< 0.05) were observed in soil pH, available nitrogen (AN), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and organic matter (OM) content”
available nitrogen (alkali hydrolyzable)
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm; T1/T2 agreeing individual comparisons.
Numbers
- treatment 114.6 vs. control 97.6 mg/kg (+17.42 %) · T1
- treatment 138.4 vs. control 97.6 mg/kg (+41.8 %) · T2
Source · p. 5 “significant enhancements (p \< 0.05) were observed in soil pH, available nitrogen (AN), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and organic matter (OM) content”
available phosphorus
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 each vscontrol, botha versusb.
Numbers
- treatment 32.77 vs. control 28.78 mg/kg (+13.86 %) · T1
- treatment 33.61 vs. control 28.78 mg/kg (+16.78 %) · T2
Source · p. 5 “significant enhancements (p \< 0.05) were observed in soil pH, available nitrogen (AN), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and organic matter (OM) content”
available potassium
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 each vscontrol.
Numbers
- treatment 130.2 vs. control 80 mg/kg (+62.75 %) · T1
- treatment 160.4 vs. control 80 mg/kg (+100.5 %) · T2
Source · p. 5 “significant enhancements (p \< 0.05) were observed in soil pH, available nitrogen (AN), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and organic matter (OM) content”
organic matter
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 each vscontrol. ControlOM20.86±2.7 visiblePDF/Tablegrid but absentpages.md, so observations use printed textual percentage changes instead.
Numbers
- percent_change 28.52 · T1 versusT0
- percent_change 79.53 · T2 versusT0
Source · p. 5 “significant enhancements (p \< 0.05) were observed in soil pH, available nitrogen (AN), total nitrogen (TN), available phosphorus (AP), available potassium (AK), and organic matter (OM) content”
bacterial Chao1 richness
↑ 11
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;Fig1c bacterialChao1a versusb;T1ab excluded.
Source · p. 6 “theT2treatment(2-year intercropping) induced significant elevations (p \< 0.05) in both Chao1 and Shannon indices for soil bacterial and fungal communities.”
fungal Chao1 richness
↑ 11
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;fungalChao1a versusb;T1ab excluded.
Source · p. 6 “theT2treatment(2-year intercropping) induced significant elevations (p \< 0.05) in both Chao1 and Shannon indices for soil bacterial and fungal communities.”
bacterial Shannon diversity
↑ 11
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;Fig1c bacterialShannonT1/T2a versusT0b, despite prose emphasizingonlyT2.
Source · p. 6 “Analyses of a-diversity indices (Chao1, observed species, Simpson, and Shannon) for soil bacterial and fungal communities revealed consistent increases under SGM intercropping treatments (T1, T2) compared to the monoculture control (T0)”
Source · p. 6 “Soil bacteria (Bac) and fungal (Fun) communities of the top 10 phyla: relative abundance (a), Veen analysis (b), principal coordinate analysis (c), and alpha-diversity (d).”
fungal Shannon diversity
↑ 11
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;Fig1c fungalShannona versusb;T1b sharescontrol.
Source · p. 6 “theT2treatment(2-year intercropping) induced significant elevations (p \< 0.05) in both Chao1 and Shannon indices for soil bacterial and fungal communities.”
Actinobacteriota relative abundance
1
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T2Actinobacteriota enrichment. LEfSe groupdiscrimination LDA≥4, no explicit T2/T0pairtest; bars have no pairmarks.
Source · p. 6 “Actinobacteriota (the phylum) and Burkholderiales (from family to genus) were significantly enriched in T2 treatment.”
Proteobacteria relative abundance
1
- increase
T1 one-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1Proteobacteria enrichment. LEfSe multigroupbiomarker, no explicit pairtest; do not inferT2enrichment from conclusion.
Source · p. 6 “Acidobacteria (from phylum to genus) and Proteobacteria (from phylum to genus) were significantly enriched in T0 and T1 treatments, respectively.”
Acidobacteriota relative abundance
1
- decrease
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 lowerrelativeabundance thanT0;Fig1bars/Fig2T0 biomarker, no individualpairp.
Source · p. 11 “increased Actinobacteria and decreased Acidobacteria in bacterial communities”
Source · p. 6 “Acidobacteria (from phylum to genus) and Proteobacteria (from phylum to genus) were significantly enriched in T0 and T1 treatments, respectively.”
Mortierellales relative abundance
1
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T2Mortierellales biomarker;Fig2d, no explicit T2/T0pairtest. Higherphyla/group repeats merged.
Source · p. 7 “Fusarium solani (species taxon) in T1, and Mortierellales (order taxon) in T2.”
Source · p. 6 “Mortierellomycota (from phylum to genus) and Dothideomycetes (the class and its family Lophiostomataceae) were significantly enriched in T2 treatment.”
Ascomycota relative abundance
1
- decrease
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;Fig1a/Fig2d andresults showT0enrichment, T1/T2decrease. Overridesabstract/conclusionincreaseclaim. LEfSe overall, no specificpairp.
Source · p. 11 “elevated Mortierellomycota and reduced Ascomycota abundance in fungal populations”
Source · p. 6 “Ascomycota (the phylum and its order Sordariomycetes)andRutstroemiaceae (from family to species) were significantly enriched in T0 treatment.”
bacterial network complexity
1
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 bacterialnetworkcomplexity;Fig3increasednodes/links. Networkedgecorrelationp not a testoftreatmentpair. No scalarindex invented.
Source · p. 7 “The co-occurrence networks of soil bacterial and fungal communities exhibited increased node counts, link numbers, and structural complexity with extended intercropping duration (years) with SGM.”
fungal network complexity
1
- increase
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagesignificance not stated · 5–15 cm · 12 November2022 · Houjiawan Village citrus orchard · 5–15cm;T1/T2 fungalnetworkcomplexity;Fig3increasednodes/links. No treatmentpairtest; networkedgep not copied.
Source · p. 7 “The co-occurrence networks of soil bacterial and fungal communities exhibited increased node counts, link numbers, and structural complexity with extended intercropping duration (years) with SGM.”
fruit sugar-acid ratio (TSS/TA)
↑ 11
- increase
T2 two-year SGM intercropping/incorporation/tillage vs. T0 noSGM intercropping or tillagesignificant · 12 November2022 fruit harvest · Houjiawan Village citrus orchard · Two-year SGM package; Table 1 Duncan .05: T2 22.12 a vs T0 15.59 b; T1 18.23 b not different from T0
Source · p. 4 “41.95% from 15.59 (T0) to 22.12 (T2)”
Source · p. 5 “22.12 ± 3.79 a”
citrus yield per tree (YPT)
= 11
- no effect
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagenot significant · 12 November 2022 fruit harvest · Houjiawan Village citrus orchard · T1 one-year and T2 two-year soybean intercrop/residue-incorporation/rotary-tillage packages each versusT0. Yield per tree; four fruit plots per treatment per Methods pp3-4, distinguished from general five soil plots. Table1 all a at Duncan alpha0.05.
Numbers
- treatment 28.9 vs. control 27.79 kg (+3.994 %) · T1 versusT0; kg per tree
- treatment 29.98 vs. control 27.79 kg (+7.881 %) · T2 versusT0; kg per tree
Source · p. 4 “Although the YPT, SFW, and TA showed favorable directional changes (increases for YPT/SFW, decrease for TA), these alterations failed to reach statistical significance.”
single fruit weight (SFW)
= 11
- no effect
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagenot significant · 12 November 2022 fruit harvest · Houjiawan Village citrus orchard · T1/T2 packages each versusT0; single fresh-fruit mass, distinct from yield per tree; four fruit plots per treatment. Original Table1 all a at Duncan alpha0.05.
Numbers
- treatment 164.6 vs. control 158.9 g (+3.568 %) · T1 versusT0
- treatment 167.8 vs. control 158.9 g (+5.588 %) · T2 versusT0
Source · p. 4 “Although the YPT, SFW, and TA showed favorable directional changes (increases for YPT/SFW, decrease for TA), these alterations failed to reach statistical significance.”
total soil phosphorus (TP)
= 11
- no effect
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagenot significant · 5–15 cm · 12 November 2022 · Houjiawan Village citrus orchard · T1/T2 packages each versusT0; total soil P, distinct from availableP increase. Original Table2 all a at Duncan alpha0.05; five soil plots per treatment.
Numbers
- treatment 2.1 vs. control 2.11 g/kg (-0.4739 %) · T1 versusT0
- treatment 2.14 vs. control 2.11 g/kg (+1.422 %) · T2 versusT0
Source · p. 5 “However, no significant differences occurred in total phosphorus (TP) or total potassium (TK).”
total soil potassium (TK)
= 11
- no effect
T1/T2 agreeing SGM variants vs. T0 noSGM intercropping or tillagenot significant · 5–15 cm · 12 November 2022 · Houjiawan Village citrus orchard · T1/T2 packages each versusT0; total soil K, distinct from availableK increase. Original Table2 all a at Duncan alpha0.05; five soil plots per treatment.
Numbers
- treatment 12.92 vs. control 13.2 g/kg (-2.121 %) · T1 versusT0
- treatment 13.86 vs. control 13.2 g/kg (+5 %) · T2 versusT0
Source · p. 5 “However, no significant differences occurred in total phosphorus (TP) or total potassium (TK).”
Set-up
Treatments
- soybean green manure intercropping durationIntercropping
- T0 noSGM intercropping or tillageNo cover cropT1 one-year SGM intercropping/incorporation/tillageIntercroppingT2 two-year SGM intercropping/incorporation/tillageIntercroppingT1/T2 agreeing SGM variantsIntercropping
Measured
- fruit total soluble solids (TSS)Crop quality
- Unit
- %
- Method
- handheld refractometer
- soil pHpH
- Method
- 1:2.5 soil:deionized water
- available nitrogen (alkali hydrolyzable)Hydrolysable nitrogen
- Unit
- mg/kg
- Method
- alkaline hydrolysis diffusion
- total nitrogen
- Unit
- g/kg
- available phosphorus
- Unit
- mg/kg
- available potassiumExchangeable/available potassium
- Unit
- mg/kg
- organic matterSoil organic matter
- Unit
- g/kg
- Method
- potassium dichromate–sulfuric acid oxidation
- bacterial Chao1 richnessSpecies richness
- fungal Chao1 richnessSpecies richness
- bacterial Shannon diversityShannon index
- fungal Shannon diversityShannon index
- bacterial Simpson indexSimpson index
- Actinobacteriota relative abundanceActinomycetes/Actinobacteria
- Method
- 16S sequencing, LEfSe LDA≥4
- Proteobacteria relative abundanceProteobacteria
- Method
- 16S sequencing, LEfSe LDA≥4
- Acidobacteriota relative abundanceAcidobacteriota
- Method
- 16S sequencing, LEfSe LDA≥4
- Mortierellales relative abundanceMortierellomycota
- Method
- ITS sequencing, LEfSe LDA≥4
- Ascomycota relative abundanceAscomycota
- Method
- ITS sequencing, LEfSe LDA≥4
- bacterial network complexityMicrobial network complexity
- Method
- ASV cooccurrence networks; inferred by nodes and edges, not a scalar index
- fungal network complexityMicrobial network complexity
- Method
- ASV cooccurrence networks; inferred by nodes and edges, not a scalar index
- fruit sugar-acid ratio (TSS/TA)Crop quality
- citrus yield per tree (YPT)Yield
- Unit
- kg
- Method
- Mean single fruit weight multiplied by field-recorded total fruit count per tree; November12 harvest
- single fruit weight (SFW)Plant biomass
- Unit
- g
- Method
- Fresh single-fruit mass using electronic balance; catalogue plant biomass includes average single fruit weight
- total soil phosphorus (TP)Total Phosphorus
- Unit
- g/kg
- Method
- Molybdenum blue colorimetry
- total soil potassium (TK)Total Potassium/Total K
- Unit
- g/kg
- Method
- Flame photometry
Sites
Houjiawan Village citrus orchard
- Location
- Houjiawan Village, Yongding District, Zhangjiajie City, Hunan Province, China29.18° N, 110.70° E
- Climate
- 17 °C mean annual temperature1,400 mm annual precipitation
- Soil
- brown soil · Chinese
- Land use
- citrus orchardFruit trees
- Management on the whole site
- annual organic fertilizerOrganic fertilizer, compound NPK fertilizerNPK fertilizer
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