Soil–Plant–Microbe Interactions: The Role of Biostimulants and Agro-Environmental Implications

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: 30 October 2025 | Viewed by 4059

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Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA) Finca El Encín, Autovía A-2. Km. 38,200, 28805 Alcalá de Henares, Spain
Interests: soil–plant–microbe system; chickpea culture; biostimulants; edaphic organisms; ciliates; protists
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Special Issue Information

Dear Colleagues,

This Special Issue, edited by Dr. Regina Gabilondo and Dr. Zhang, will continue with the topic initiated by the preceding Special Issue on the "Effect of Biostimulants in the Soil–Plant–Microbe System" and will delve into the mechanisms of action of biostimulants and the interactions and processes of the soil–plant–microbe system. Regulation (EU) 2019/1009 defines the term biostimulant as “an EU fertilizer product whose function is to stimulate the nutritional processes of plants regardless of the nutrient content of the product, with the sole objective of improving one or more of the following plant characteristics and its rhizosphere: efficiency in the use of nutrients, tolerance to abiotic stress, quality characteristics or availability of nutrients immobilized in the soil and the rhizosphere”. There are different types of biostimulants, including those based on beneficial microorganisms (bacteria and fungi), algae, and chitosan products. Those belonging to the group called “plant growth-promoting rhizobacteria” (PGPR) are among the most commonly used treatments in plant cultures. Most of the beneficial organisms used as biostimulants for plants live in the rhizosphere, a region around the plant roots with intense microbial and faunal activity, where the plant nutrient absorption, a process that is still not fully understood, takes place. Plants secrete large amounts of molecules, called exudates, into the soil through their roots and which stimulate microbial activity in the rhizosphere. These exudates provide carbon to the soil microorganisms, mainly fast-growing bacteria, that are strongly carbon-limited and are thereby increased together with microfaunal grazers such as bacterial-feeding protozoa and free-living nematodes. The exudate carbon comes from the total net fixed carbon by plants, representing some 10–20% of it. Another 10–20% is consumed by microbial symbionts, such as mycorrhizae or N2-fixing microorganisms. Supporting microbial interactions in the rhizosphere is of great importance for plants because the availability of mineral nutrients to plants is strongly enhanced via the microbial loop. Bacteria feed on the soil nutrients in different ways, liberating them through microfaunal grazing and increasing their bioavailability for plants. Biostimulants provide beneficial microorganisms, nutrients, vitamins, and other compounds that interact with the soil and the rhizosphere of plants, with the aim of promoting their growth and yield.

In this Special Issue, research advances will be presented to aid understanding of the role of biostimulants, soil–plant–microbe interactions, ecology and biochemistry, biostimulant mechanisms of action, and agro-environmental implications.

Dr. Regina Gabilondo
Prof. Dr. Ling Zhang
Guest Editors

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Keywords

  • soil–plant–microbe system
  • biostimulants
  • rhizosphere
  • fertilizers
  • availability of mineral nutrients
  • microfaunal grazing
  • protozoa
  • nematode
  • mycorrhizae
  • microbial loop

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Published Papers (3 papers)

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Research

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21 pages, 4788 KiB  
Article
Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach
by Angela Maffia, Riccardo Scotti, Thomas Wood, Adele Muscolo, Alessandra Lepore, Elisabetta Acocella and Giuseppe Celano
Life 2024, 14(12), 1633; https://doi.org/10.3390/life14121633 - 9 Dec 2024
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Abstract
Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a [...] Read more.
Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity. Full article
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16 pages, 1323 KiB  
Article
Significant Differences in Microbial Soil Properties, Stoichiometry and Tree Growth Occurred within 15 Years after Afforestation on Different Parent Material
by Emre Babur
Life 2024, 14(9), 1139; https://doi.org/10.3390/life14091139 - 9 Sep 2024
Cited by 2 | Viewed by 1265
Abstract
The mineralogical composition of the parent material, together with plant species and soil microorganisms, constitutes the foundational components of an ecosystem’s energy cycle. Afforestation in arid-semi arid regions plays a crucial role in preventing erosion and enhancing soil quality, offering significant economic and [...] Read more.
The mineralogical composition of the parent material, together with plant species and soil microorganisms, constitutes the foundational components of an ecosystem’s energy cycle. Afforestation in arid-semi arid regions plays a crucial role in preventing erosion and enhancing soil quality, offering significant economic and ecological benefits. This study evaluated the effects of afforestation and different parent materials on the physicochemical and microbiological properties of soils, including microbial basal respiration (MR), as well as how these changes in soil properties after 15 years influence plant growth. For this purpose, various soil physicochemical parameters, MR, soil microbial biomass carbon (Cmic), stoichiometry (microbial quotient = Cmic/Corg = qMic and metabolic quotient = MR/Cmic = qCO2), and tree growth metrics such as height and diameter were measured. The results indicated that when the physicochemical and microbiological properties of soils from different bedrock types, along with the average values of tree growth parameters, were analyzed, afforestation areas with limestone bedrock performed better than those with andesite bedrock. Notably, sensitive microbial properties, such as Cmic, MR, and qMic, were positively influenced by afforestation. The highest values of Cmic (323 μg C g−1) and MR (1.3 CO2–C g−1 h−1) were recorded in soils derived from limestone. In contrast, the highest qCO2 was observed in the control plots of soils with andesite parent material (7.14). Considering all the measured soil properties, the samples can be ranked in the following order: limestone sample (LS) > andesite sample (AS) > limestone control (LC) > andesite control (AC). Similarly, considering measured plant growth parameters were ranked as LS > AS. As a result, the higher plant growth capacity and carbon retention of limestone soil indicate that it has high microbial biomass and microbial activity. This study emphasizes the importance of selecting suitable parent material and understanding soil properties to optimize future afforestation efforts on bare lands. Full article
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Review

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27 pages, 1050 KiB  
Review
A Review of Biochar from Biomass and Its Interaction with Microbes: Enhancing Soil Quality and Crop Yield in Brassica Cultivation
by Kritsana Jatuwong, Worawoot Aiduang, Tanongkiat Kiatsiriroat, Wassana Kamopas and Saisamorn Lumyong
Life 2025, 15(2), 284; https://doi.org/10.3390/life15020284 - 12 Feb 2025
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Abstract
Biochar, produced from biomass, has become recognized as a sustainable soil amendment that has the potential to improve soil quality and agricultural production. This review focuses on production processes and properties of biochar derived from different types of biomass, including the synergistic interactions [...] Read more.
Biochar, produced from biomass, has become recognized as a sustainable soil amendment that has the potential to improve soil quality and agricultural production. This review focuses on production processes and properties of biochar derived from different types of biomass, including the synergistic interactions between biochar and soil microorganisms, emphasizing their influence on overall soil quality and crop production, particularly in cultivation of Brassica crops. It additionally addresses the potential benefits and limitations of biochar and microbial application. Biomass is a renewable and abundant resource and can be converted through pyrolysis into biochar, which has high porosity, abundant surface functionalities, and the capacity to retain nutrients. These characteristics provide optimal conditions for beneficial microbial communities that increase nutrient cycling, reduce pathogens, and improve soil structure. The information indicates that the use of biochar in Brassica crops can result in improved plant growth, yield, nutrient uptake, and stress mitigation. This review includes information about biochar properties such as pH, elemental composition, ash content, and yield, which can be affected by the different types of biomass used as well as pyrolysis conditions like temperature. Understanding these variables is essential for optimizing biochar for agricultural use. Moreover, the information on the limitations of biochar and microbes emphasizes the importance of their benefits with potential constraints. Therefore, sustainable agriculture methods can possibly be achieved by integrating biochar with microbial management measurements, resulting in higher productivity and adaptability in Brassica or other plant crop cultivation systems. This review aims to provide a comprehensive understanding of biochar’s role in supporting sustainable Brassica farming and its potential to address contemporary agricultural challenges. Full article
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