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Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems
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Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant–Soil Interactions".

Deadline for manuscript submissions: 31 March 2027 | Viewed by 5243

Special Issue Editors

Prof. Dr. Weijun Fu

E-Mail Website
Guest Editor
National Key Laboratory for Development and Utilization of Forest Food Resources, Zhejiang A&F University, Hangzhou 311300, China
Interests: soil nutrient cycling; element transfer in plant–soil systems; soil health assessment; soil organic carbon; carbon cycling in forest ecosystems; soil microbes
Dr. Jizi Wu

E-Mail Website
Guest Editor
Key Laboratory of Soil Remediation and Quality Improvement in Zhejiang Province, Zhejiang A&F University, Lin'an 311300, China
Interests: soil pollution remediation; soil microbe interactions with soil pollutants; pollutant transfer in soil–plant–microbe systems

Special Issue Information

Dear Colleagues, 

Agroforest ecosystems are important for global biodiversity, carbon sequestration, and sustainable agriculture. The intricate interactions between plants, soils, and microbial communities form the foundation of ecosystem health, influencing nutrient cycling, disease suppression, and resilience to environmental stresses. Understanding these dynamic relationships is critical for advancing ecological management, restoring degraded lands, and promoting climate-smart practices. This Special Issue explores interesting research on plant–soil–microbe interactions and their roles in maintaining agroforest ecosystem health. Research topics of this Special Issue could include microbiome-driven nutrient mobilization and plant growth promotion; soil biodiversity as a regulator of ecosystem services; climate change adaptation through plants and soil; sustainable agroforestry practices leveraging microbial symbioses; soil remediation through the interaction of plant and soil microbes; the response of soil microbes in soil remediation; soil microbe interactions with soil pollutants; and pollutant transfer in soil–plant–microbe systems. We welcome original studies, reviews, and perspectives that bridge theory and practice, offering innovative solutions for resilient agroforest ecosystems.

Prof. Dr. Weijun Fu
Dr. Jizi Wu
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • agroforest ecosystems
  • plant and soil
  • soil microbes
  • biodiversity
  • soil health

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Published Papers (6 papers)

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Research

20 pages, 1595 KB  
Article
Host-Mediated Selection Shapes Conserved Root Bacterial Microbiomes Across Geographically Separated Thismia Species
by Phuwadon Udompongpaiboon, Nuttapol Noirungsee, Sahassawat Chailungka, Ponsit Sathapondecha, Sahut Chantanaorrapint and Lompong Klinnawee
Plants 2026, 15(9), 1316; https://doi.org/10.3390/plants15091316 (registering DOI) - 25 Apr 2026
Abstract
Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica [...] Read more.
Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
17 pages, 1213 KB  
Article
Mycorrhizal Fungi Funneliformis mosseae Mitigates Cadmium Bioavailability in Pepper Rhizosphere via Glomalin Production and pH Elevation
by Yanlong Jia, Peng Zhou, Dehui Tu, Xiaolong Lan, Wenjie Lin, Dan Xing and Zengping Ning
Plants 2026, 15(6), 952; https://doi.org/10.3390/plants15060952 - 20 Mar 2026
Viewed by 393
Abstract
Cadmium (Cd) contamination in agricultural soils, especially in regions with a naturally high geochemical background such as Southwest China, poses a serious threat to food safety and the health of terrestrial ecosystems. Although arbuscular mycorrhizal fungi (AMFs) are known to enhance plant tolerance [...] Read more.
Cadmium (Cd) contamination in agricultural soils, especially in regions with a naturally high geochemical background such as Southwest China, poses a serious threat to food safety and the health of terrestrial ecosystems. Although arbuscular mycorrhizal fungi (AMFs) are known to enhance plant tolerance to heavy metals, the specific mechanisms by which dominant AMF species in karst soils—such as Funneliformis mosseae (Fm) and Rhizophagus intraradices (Ri)—immobilize Cd are not yet fully understood. In this study, a pot experiment with pepper plants was conducted to investigate the effects of Fm and Ri inoculation on Cd geochemistry in both the rhizosphere and bulk soil. Key results showed that AMF inoculation, especially with Fm, significantly reduced total Cd (by up to 33.8%) and bioavailable Cd (by up to 36.3%) concentrations in the soil, with a more pronounced effect within the rhizosphere. Accordingly, Cd content in pepper shoots was reduced by up to 15.0%. Inoculation also increased soil pH, organic matter, available phosphorus, and glomalin-related soil protein (GRSP) content. Redundancy analysis identified soil pH and total extractable GRSP as primary factors negatively correlated with Cd bioavailability. The study concludes that AMFs, particularly Fm, represent a potent bioremediation strategy by effectively immobilizing Cd in contaminated soils through mechanisms linked to GRSP production and pH elevation, thereby reducing its phytoavailability and translocation to edible plant parts. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
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21 pages, 5701 KB  
Article
Amendment Bridges Habitat-Driven Quality Gaps in Tetrastigma hemsleyanum Through Coordinated Regulation of Soil Enzymes and Fungal Communities
by Su’e Zhang, Chaodu Wu, Peikun Jiang, Yinxiu Liu and Chengpeng Huang
Plants 2026, 15(6), 872; https://doi.org/10.3390/plants15060872 - 11 Mar 2026
Viewed by 340
Abstract
Tetrastigma hemsleyanum is a valuable medicinal plant whose dryland cultivation typically yields 30–35% lower flavonoid concentration than forest understory systems due to soil and microbial deficiencies. We investigated whether biochar amendment could bridge this quality gap through rhizosphere microecological regulation. Using a split-plot [...] Read more.
Tetrastigma hemsleyanum is a valuable medicinal plant whose dryland cultivation typically yields 30–35% lower flavonoid concentration than forest understory systems due to soil and microbial deficiencies. We investigated whether biochar amendment could bridge this quality gap through rhizosphere microecological regulation. Using a split-plot pot experiment with in situ soils from a bamboo forest and a vegetable field, we applied biochar at 2%. Biochar in bamboo forest (MBBC) achieved the highest flavonoid concentrations, exceeding unamended forest and vegetable controls by 22% and 35%, respectively. Biochar effects were habitat-specific. In acidic forest soils (pH 4.95), it raised the pH to 5.61, while in vegetable fields, it boosted leucine aminopeptidase by 159%. Partial least squares path modeling revealed biochar exerted its effects indirectly (indirect effect = 0.88), with soil extracellular enzymes mediating between soil conditions and plant biosynthetic enzymes (PAL, CHS, CHI). Fungal composition was positively associated with biosynthesis (β = 1.68, p < 0.01), particularly Mortierellomycetes, whereas bacterial diversity unexpectedly exhibited a significant negative correlation with it (β = −0.79, p < 0.05). Biochar disrupted Eurotiomycetes dominance in forest soils (from 85% to 39%), creating functionally diverse niches that were associated with enhanced flavonoid accumulation. These findings demonstrate biochar functions as an ecological niche regulator, providing a sustainable strategy for high-quality medicinal plant production in non-native habitats. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
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20 pages, 1763 KB  
Article
Soil Stoichiometry-Regulated Microbial Carbon Use Efficiency Between Rhizosphere and Bulk Soils in the Temperate Forests of Northeastern China
by Beixing Duan and Ruihan Xiao
Plants 2026, 15(4), 652; https://doi.org/10.3390/plants15040652 - 20 Feb 2026
Viewed by 801
Abstract
In forest ecosystems, rhizodeposition can lead to significant differences in the availability of soil carbon (C), nitrogen (N), and phosphorus (P) between rhizosphere and bulk soils. Soil stoichiometry affects microbial and enzyme nutrient content and determines the abundance and composition of microbes and [...] Read more.
In forest ecosystems, rhizodeposition can lead to significant differences in the availability of soil carbon (C), nitrogen (N), and phosphorus (P) between rhizosphere and bulk soils. Soil stoichiometry affects microbial and enzyme nutrient content and determines the abundance and composition of microbes and thus regulates microbial carbon use efficiency (CUE). However, how soil stoichiometry—particularly its variation between the rhizosphere and bulk soil—regulates microbial CUE by shaping microbial biomass, extracellular enzyme stoichiometry, and community composition remains insufficiently quantified. Here, through the C:N, C:P, and N:P ratios for available soil nutrients, microbial biomass, and extracellular enzyme activities—(β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminodase (NAG), leucine aminopeptidase (LAP), and acid phosphatase (ACP))—and the composition and activity of microbial communities (based on sequencing of bacterial 16S rRNA and fungal ITS genes) in the rhizosphere and bulk soils of five temperate forest ecosystems in northeastern China, we aimed to unravel their integrated effects on microbial CUE. Results indicated that soil C, N, and P and their stoichiometry, microbial community composition, and microbial CUE were significantly different between rhizosphere and bulk soils among all tree species. The disproportionate variation in soil nutrient pools between the rhizosphere and non-rhizosphere regions has led to a stoichiometric imbalance. There was higher microbial CUE in the rhizosphere soil than that in the bulk soil among all tree species. However, the effect pathways of tree species on microbial CUE in the rhizosphere and bulk soils differed. The structural equation model (SEM) further suggested that tree species affected microbial CUE through distinct pathways in different soil compartments. In the rhizosphere, the effect was directly driven by available nutrient stoichiometry. In bulk soil, it was jointly mediated by both available nutrients and microbial biomass stoichiometry. These findings demonstrate that root rhizodeposition shapes microbial carbon cycling by altering soil stoichiometric imbalances, which can strengthen the current understanding of plant–microbe–soil interactions in temperate forests. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
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20 pages, 20102 KB  
Article
Influence of Alpine Forest Types on Soil Microbial Diversity and Soil Quality
by Shuang Ji, Xunxun Qiu, Huichun Xie, Zhiqiang Dong and Hongye Li
Plants 2026, 15(2), 315; https://doi.org/10.3390/plants15020315 - 21 Jan 2026
Viewed by 398
Abstract
Alpine forests are key regulators of soil biogeochemical cycles, yet the extent to which forest type constrains soil microbial diversity and soil quality in high-elevation regions remains insufficiently resolved. Here, we assessed how contrasting alpine forest types influence the taxonomic composition and diversity [...] Read more.
Alpine forests are key regulators of soil biogeochemical cycles, yet the extent to which forest type constrains soil microbial diversity and soil quality in high-elevation regions remains insufficiently resolved. Here, we assessed how contrasting alpine forest types influence the taxonomic composition and diversity of soil microbial communities, identified the dominant environmental drivers, and evaluated soil quality along the southern slope of the Qilian Mountains. Six forest types were examined, including four monospecific stands (Picea crassifolia, QQ; Betula spp., HS; Juniperus przewalskii, YB; and Pinus tabuliformis, YS) and two mixed formations (mixed conifer–broadleaf, ZKHJ; and mixed broadleaved, KKHJ). Bacterial and fungal communities were characterized using Illumina high-throughput sequencing, while structural equation modeling (SEM) was used to identify primary drivers of diversity and principal component analysis (PCA) was applied to construct the minimum data set (MDS) for soil quality evaluation. Mixed forests consistently exhibited higher bacterial and fungal alpha diversity than pure stands. Environmental gradients were the strongest positive drivers of microbial diversity, whereas soil chemical properties and vegetation-related biotic factors exerted partially negative effects. Soil quality index (SQI) values ranked as follows: KKHJ (0.55) > ZKHJ (0.49) > YB (0.48) > HS (0.46) > YS (0.44) > QQ (0.43). The mixed broadleaved forest reached Grade IV (upper-intermediate level) soil quality, whereas the other forest types were classified as Grade III (intermediate). Mixed forests showed stronger capacities for organic matter accumulation and nutrient retention. These findings indicate that promoting mixed forest stands is critical for improving soil structure, nutrient retention, and microbial diversity in this alpine region. Accordingly, forest management should prioritize the development of mixed forests to enhance overall soil quality. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
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15 pages, 3212 KB  
Article
Soil Microbial Communities Significantly Changed Along Stand Ages in Masson Pine (Pinus massoniana Lamb.) Plantation
by Weijun Fu, Bingyi Wang, Dunzhu Li and Yong Zhang
Plants 2025, 14(19), 3004; https://doi.org/10.3390/plants14193004 - 28 Sep 2025
Viewed by 897
Abstract
Soil microbial communities are important for nutrient cycling regulation in forest ecosystems. However, limited knowledge exists regarding the characteristics of these microbial communities in Masson pine (Pinus massoniana Lamb.) plantations of different stand ages. In this study, four planted Masson pine stands [...] Read more.
Soil microbial communities are important for nutrient cycling regulation in forest ecosystems. However, limited knowledge exists regarding the characteristics of these microbial communities in Masson pine (Pinus massoniana Lamb.) plantations of different stand ages. In this study, four planted Masson pine stands (8-year-old, 12-year-old, 22-year-old, and 38-year-old stands) and one natural broadleaved forest stand (as a control) with three replications, were selected in the Laoshan Forest Farm, Qiandao Lake Town, Zhejiang Province, China. Soil physicochemical properties were measured and their effects on soil microbial communities were studied. Amplicon-based high-throughput sequencing was employed to process raw sequence data for soil microbes. It is worth noting that significant differences (p < 0.05) in soil bacterial genera were observed among different stand age groups. Total nitrogen (TN), total phosphorus (TP), total potassium (TK), available potassium (AK), soil organic carbon (SOC), and soil bulk density (BD) were identified as the primary factors influencing bacterial community distribution (p < 0.05). Available nitrogen (AN), SOC, TN, and TK showed significant correlations with soil fungal communities (p < 0.05). These findings underscore the crucial role of soil physicochemical properties in shaping soil microbial community composition in Masson pine plantations. Full article
(This article belongs to the Special Issue Plant-Soil-Microbe Interactions for the Health of Agroforest Ecosystems)
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