Plant, Soil, and Microbial Interactions Under Climate Change: Responses, Consequences, and Perspectives

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

Deadline for manuscript submissions: 31 December 2026 | Viewed by 2225

Special Issue Editors


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Institute for Agriculture and Forestry Systems in the Mediterranean, National Research Council, P.le E. Fermi 1, 80055 Portici, Italy
Interests: plant ecophysiology; soil microbial ecology; soil GHGs emission; plant–microbe interactions
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Guest Editor
Institute of Biosciences and Bioresources, National Research Council, Research Division Portici, Via Università 133, 80055 Portici, Italy
Interests: salinity; irrigation; environment sustainability; crop production
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Guest Editor

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Guest Editor Assistant
1. Higher Institute of Water Sciences and Techniques of Gabès, University of Gabès, Gabès, Tunisia
2. Laboratory of Eremology and Combating Desertification, Institute of Arid Regions, Medenine, Tunisia
Interests: soil and water conservation; hydrological modelling; irrigation management; crop modelling; agricultural resilience under arid and semi-arid conditions

Special Issue Information

Dear Colleagues,

Plant–soil–microbial interactions, consisting of biological, physical, and chemical processes that occur at the interface between plant roots and soil, are significantly affected by climate change. These interactions are fundamental for nutrient cycling, plant productivity, and ecosystem stability, and they involve complex mechanisms that facilitate relationships between plants and soil microorganisms. These mechanisms imply signalling molecules, released by both plants and microbes, that active physiological responses able to modulate the plant growth and development, to activate defence responses, and to promote symbiotic relationships. Through complex physiological mechanisms involving plant growth-promoting molecules or by stimulating systemic resistance mechanisms such as systemic acquired resistance (SAR) or induced systemic resistance (ISR) through the production of active compounds, among those VOCs, the soil microbes promote growth and development of plants and confer them tolerance to environmental stress (i.e., salinity, drought, pests, etc.). Plant–microorganism interactions play also a critical role in promoting soil stability through an increased soil aggregation and stabilization that promote soil resilience. All this occurs through the secretion of substances that facilitate the aggregation of soil particles, thus forming stable aggregates that improve soil structure and in turn their water holding.

Climate change significantly affects the complex plant–soil–microbial interactions. Changes in temperature and precipitation directly impact soil microbial communities, affecting their structure and composition and, in turn, activities. On the end of the spectrum, plant physiology is also altered under climate change, and this might modify the signalling pathways with the microbial communities in the rhizosphere. Climate change-induced shifts in these interactions alter nutrient cycling, soil health, and ecosystem stability impacting ecosystem resilience. 

This Special Issue aims to explore the complex dynamics between plants, soil, and microbes as well as the consequences of climate change on these interactions, filling knowledge gaps, proposing new concepts, and making recommendations to guide future research. A full understanding of plant–soil–microbe relationships will aid in developing management and policy tools to improve the ecosystems’ resilience.

The Special Issue topic will cover, but is not restricted to, the following subjects:

  • Rhizospheric soil, plant, and microbial interactions.
  • Soil structure.
  • Soil water availability and distribution.
  • Soil nutrient concentration and availability.
  • Rhizosphere microbiome.
  • Mechanisms of soil, plant, and microbe interactions, including signalling compounds and biological nitrification inhibitors.
  • Beneficial microbes-induced plants’ resilience to environmental stress, including abiotic and biotic factors.
  • Recommendations for improving ecosystems’ resilience to climate change.

Dr. Luca Vitale
Dr. Anna Tedeschi
Dr. Francisco Garcia-Sanchez
Guest Editors

Dr. Fatma Wassar
Guest Editor Assistant

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

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

  • rhizosphere
  • soil ecology
  • soil conservation
  • plant physiology
  • signalling compounds
  • soil resilience
  • beneficial microbes
  • climate change

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Published Papers (4 papers)

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Research

18 pages, 2136 KB  
Article
Responses of Soil Fungal Community Structure, Co-Occurrence Networks, and Functions to Different Oak-Dominated Mixed Plantations
by Yanfang Wang, Xiaoqiu Yuan, Zhichao Li, Zhengyang Yan, Yage Li and Ling Liu
Plants 2026, 15(9), 1399; https://doi.org/10.3390/plants15091399 - 2 May 2026
Viewed by 194
Abstract
Quercus variabilis is one of the primary species for plantation regeneration across China’s warm-temperate and subtropical zones. However, its long-term monoculture leads to ecosystem instability. Soil fungi are essential for nutrient cycling and ecosystem functioning, yet their responses to oak-dominated mixed plantations remain [...] Read more.
Quercus variabilis is one of the primary species for plantation regeneration across China’s warm-temperate and subtropical zones. However, its long-term monoculture leads to ecosystem instability. Soil fungi are essential for nutrient cycling and ecosystem functioning, yet their responses to oak-dominated mixed plantations remain insufficiently understood. This study investigated the soil fungal communities among Q. variabilis monoculture (QV), mixed plantations of Q. variabilis and Platycladus orientalis (PO), Q. variabilis and Pinus tabuliformis (PT), and Q. variabilis, P. orientalis and P. tabuliformis (PPQ). The results showed that PO and PPQ plantations contained significantly higher concentrations of SOC, TN, and TP compared to QV monoculture. Ascomycota and Basidiomycota were identified as the dominant fungal phyla across four plantation types, with PO exhibiting the highest relative abundance of Ascomycota (60.85%) and fungal alpha diversity. The soil fungal communities across all plantations were predominantly saprotrophic, followed by mixotrophic modes. The relative abundance of saprotrophic fungi was significantly greater in the mixed plantations, peaking in PO at 44.69%. The soil fungal communities in both PO and PPQ plantations exhibited higher network interaction density. The SOC, TN, TP, water content, zinc, and β-glucosidase activity served as key environmental drivers of fungal community composition. Overall, the mixed plantation of Q. variabilis and P. orientalis most effectively improved soil fertility, enhanced fungal diversity, and increased network complexity, suggesting its potential as a sustainable afforestation strategy for oak-dominated ecosystems in the low hilly regions of western Henan. However, these findings are based on a single sampling period, and long-term monitoring is required to confirm its sustained ecological benefits. Full article
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17 pages, 2801 KB  
Article
Climate Variability Under ENSO Reshapes the Coffea arabica Rhizosphere Microbiome While Preserving a Conserved Bacterial Core
by Jorge A. Rueda Foronda, Juan S. Ríos López, Luisa María Múnera Porras and Nancy J. Pino Rodriguez
Plants 2026, 15(8), 1259; https://doi.org/10.3390/plants15081259 - 20 Apr 2026
Viewed by 359
Abstract
Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño–Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica [...] Read more.
Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño–Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11–17% of β-diversity, exceeding the contribution of intra-annual seasonality (6–12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems. Full article
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12 pages, 1697 KB  
Article
The Role of Root and Shoot Structures in CH4 Transport and Release in Wetland Plants
by Mengyu Ge and Yang Qiu
Plants 2026, 15(7), 1049; https://doi.org/10.3390/plants15071049 - 29 Mar 2026
Viewed by 457
Abstract
Plant-mediated CH4 transport can enhance ecosystem CH4 emission by transporting soil-produced CH4. This pathway can exceed diffusion and ebullition as the dominant CH4 emission route. However, limited studies have investigated the morphological and anatomical factors influencing CH4 [...] Read more.
Plant-mediated CH4 transport can enhance ecosystem CH4 emission by transporting soil-produced CH4. This pathway can exceed diffusion and ebullition as the dominant CH4 emission route. However, limited studies have investigated the morphological and anatomical factors influencing CH4 transport in plants. Through a series of manipulative experiments on the shoots and roots, this study examines the role of root and shoot structures in CH4 transport and release in six widespread wetland species: Carex rostrata Stokes, Carex lasiocarpa Ehrh., Carex aquatilis Wahlenb., Iris pseudacorus L., Juncus effusus L., and Alocasia odora (Lodd.) Spach. CH4 flux from all investigated species dropped significantly after clipping fine roots, while it did not change significantly after removing coarse roots. Shoot clipping and sealing significantly decreased CH4 flux from the investigated Carex species, but not from the other species. Our results demonstrate the important role of fine roots in controlling CH4 flux, whereas coarse roots play a minor role. Leaf blades are the major release site of CH4 from Carex species, while micropores at the shoot base are the primary release site of CH4 from the other species. Our study suggests that integrating plant-specific anatomical and morphological characteristics into global methane models is crucial to better predict and mitigate climate change impacts. Full article
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15 pages, 3265 KB  
Article
Plant Roots and Phenology Drive the Spatio-Temporal Variability of Boreal Forest Floor Respiration
by Quan Zhou, Zonghua Wang and Meilian Chen
Plants 2026, 15(4), 538; https://doi.org/10.3390/plants15040538 - 9 Feb 2026
Viewed by 594
Abstract
Understanding the drivers of soil carbon efflux is critical for predicting forest carbon cycles under climate change. This study investigates how plant roots and phenology govern the spatio-temporal variability of boreal forest floor respiration (Rf) in an ectomycorrhizal-dominated forest. By analyzing stabilized soil [...] Read more.
Understanding the drivers of soil carbon efflux is critical for predicting forest carbon cycles under climate change. This study investigates how plant roots and phenology govern the spatio-temporal variability of boreal forest floor respiration (Rf) in an ectomycorrhizal-dominated forest. By analyzing stabilized soil carbon fluxes (NEE, Ra, and Rh) one year after root exclusion in northern Sweden, we challenge the passive physicochemical paradigm. Results show that the spatial distribution and magnitude of Rf are primarily driven by plant roots, with Ra accounting for >60% of total efflux. The collapse of respiration in trenched plots confirms the mycorrhizal bridge as the essential conduit for these spatial patterns. Regarding temporal variability, we identified a biological pulse driven by plant phenology. After temperature-normalization, Ra maintained a strong seasonal peak in July and August. Notably, static drivers like fine root biomass failed to explain spatial variation (R < 0.3, p > 0.05), whereas dynamic NEE showed significant positive correlations (R = 0.52, p < 0.0001). This holistic perspective suggests that the forest floor operates as an integrated metabolic continuum, where root activity and phenological pump are the main regulating factors on carbon release. Future models should reposition plant–fungal phenology as the primary engine of soil metabolism. Full article
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