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Microorganisms
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Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition
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Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 5822

Special Issue Editor

Prof. Dr. John Crawford

E-Mail Website
Guest Editor
Adam Smith Business School, University of Glasgow, Glasgow, UK
Interests: soil systems science; theoretical biology; modelling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, entitled “Restoring the Integrated Behaviour of the Soil-Plant-Microbe System”

The world is facing an existential threat from climate change, biodiversity collapse, and food and water insecurity. The restoration of global soil health mitigates the risk from all of these challenges. Whilst we have sufficient knowledge to get started, there remain substantial challenges to transforming the health of the world’s soils. Central to these challenges is understanding how carbon impacts microbial function and how this leads to changes in the physical and biological properties that underpin natural fertility. This Special Issue will pull together the leading thinkers in the integrated behaviour of the soil-plant-microbe system to suggest a way forward to fill these knowledge gaps, whilst simultaneously delivering impact in the ground at the scale and pace required. This perspective will be combined with the views of leaders from the agricultural, finance, and technology sectors to propose a self-sustaining systems approach.

I look forward to receiving your contributions.

Prof. Dr. John Crawford
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Microorganisms is an international peer-reviewed open access monthly 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

  • food security
  • agriculture
  • technology
  • plant
  • soil
  • microbe

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Published Papers (6 papers)

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Research

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18 pages, 2398 KiB  
Article
Short-Term Fertilization with the Nitrogen-Fixing Bacterium (NFB) Kosakonia radicincitans GXGL-4A Agent Can Modify the Transcriptome Expression Profiling of Cucumber (Cucumis sativus L.) Root
by Baoyun Feng, Erxing Wang, Yating Zhang, Lurong Xu, Yanwen Xue and Yunpeng Chen
Microorganisms 2025, 13(3), 506; https://doi.org/10.3390/microorganisms13030506 - 25 Feb 2025
Viewed by 436
Abstract
The application of nitrogen-fixing bacteria (NFB) as a biofertilizer can greatly reduce or even avoid environmental pollution caused by the excessive use of chemical nitrogen fertilizers. To explore the effect of short-term fertilization of GXGL-4A on the expression of functional genes in the [...] Read more.
The application of nitrogen-fixing bacteria (NFB) as a biofertilizer can greatly reduce or even avoid environmental pollution caused by the excessive use of chemical nitrogen fertilizers. To explore the effect of short-term fertilization of GXGL-4A on the expression of functional genes in the roots of the cucumber (Cucumis sativus L.) cultivar “Xintaimici”, this study used transcriptome sequencing technology combined with fluorescent quantitative RT-PCR (qRT-PCR) verification to compare the gene transcription profiles of GXGL-4A-treated and control (sterile-water-treated) groups. A total of 418 differentially expressed genes (DEGs) were detected. The transcription levels of genes Csa5G161290 and Csa3G027720, which encode nitrate transporters, showed significant up-regulation (3.04- and 2.27-fold, respectively) in roots inoculated with GXGL-4A. The genes CsaV3_5G006200, encoding cytokinin dehydrogenase involved in the biosynthesis of zeatin, CsaV3_1G011730, encoding a wound-responsive protein, and CsaV3_6G015610, encoding a heat stress transcription factor, were significantly up-regulated at the transcriptional level (p < 0.05). However, the transcription of nitrogen cycling functional genes CsaV3_3G036500, CsaV3_1g008910, and CsaV3_3G018610, which encode nitrate reductase, high-affinity nitrate transporter (NRT), and ferredoxin-nitrite reductase, respectively, showed significant down-regulation (p < 0.05). Only the KEGG pathway of phenylpropanoid biosynthesis reached a significant level (p < 0.05). This study contributes to a deeper understanding of the interaction between NFB and plants and provides theoretical guidance for the development of GXGL-4A as a mature biological agent for sustainable agricultural production under drought stress. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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16 pages, 2852 KiB  
Article
Effects of Different Nitrogen Fertilizer Application Rates on Soil Microbial Structure in Paddy Soil When Combined with Rice Straw Return
by Xiannan Zeng, Qi Wang, Qiulai Song, Quanxi Liang, Yu Sun and Fuqiang Song
Microorganisms 2025, 13(1), 79; https://doi.org/10.3390/microorganisms13010079 - 3 Jan 2025
Cited by 1 | Viewed by 1030
Abstract
Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China’s black paddy soil used for rice production. Here, [...] Read more.
Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China’s black paddy soil used for rice production. Here, we investigated changes in the composition, diversity, and structure of soil microbial communities in the soil treated with four amounts of nitrogen fertilizers (53, 93, 133, and 173 kg/ha) applied to the soil under a constant straw return of 7500 kg/ha, with a control not receiving N. The relationships between soil microbial community structure and soil physical and chemical properties were determined. The results showed that the available K content of the soil significantly (p < 0.05) increased in soil receiving the lowest N-fertilizer dose. When applied at high amounts, N-fertilizer changed the Chao1 and ACE indices of the soil microorganisms (p < 0.05), and the treatments resulted in significant differences in the β-diversity of the soil microorganisms. By NMDS analysis it was demonstrated that the treatment significantly affected the structure of the soil microbial communities. Redundancy analysis showed that the main physicochemical drivers behind these differences were total nitrogen, total potassium, ammonium nitrogen, total phosphorus, and available potassium. The soil microbial communities in the control treatment were negatively correlated with nitrate and ammonium nitrogen; the lowest N-fertilizer treatment produced positive correlations with total nitrogen, total potassium, and total phosphorus and negative correlations with ammonium nitrogen; the highest dose negatively correlated with total nitrogen, available potassium, available phosphorus, total phosphorus, and pH. This study showed that moderate N fertilizer application is an effective way to increase soil microbial diversity and improve soil quality. This experiment provides technical support for the application of the alternative fertilizer technology of straw return to the field and provides a theoretical basis for rational fertilization of paddy fields in a cold climate. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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17 pages, 12899 KiB  
Article
The Sweet Cherry Tree Genotype Restricts the Aggressiveness of the Wood Decay Fungi Cytospora sorbicola and Calosphaeria pulchella
by Claudio Osorio-Navarro, Constanza Saez, Felipe Durán, Mauricio Rubilar, Paula Reyes-Bravo, Madelaine Azócar, Verónica Estrada, Marcela Esterio and Jaime Auger
Microorganisms 2024, 12(12), 2456; https://doi.org/10.3390/microorganisms12122456 - 29 Nov 2024
Viewed by 895
Abstract
The wood decay fungi Cytospora sorbicola and Calosphaeria pulchella severely threaten the worldwide cultivation of sweet cherry trees (Prunus avium L.). Both fungi cause similar symptoms, including vascular necrosis, which leads to branch and twig dieback. In advanced stages of the disease, [...] Read more.
The wood decay fungi Cytospora sorbicola and Calosphaeria pulchella severely threaten the worldwide cultivation of sweet cherry trees (Prunus avium L.). Both fungi cause similar symptoms, including vascular necrosis, which leads to branch and twig dieback. In advanced stages of the disease, cankers are visible on tree branches and trunks. The sweet cherry is the most widely planted fruit tree in Chile, with 74,000 hectares in 2023. According to the planted surface, the predominant sweet cherry varieties are Lapins, Santina, Regina, and Bing. Variety-dependent susceptibility studies on Cyt. sorbicola and Cal. pulchella are lacking. The main entry points for wood necrosis-causing fungi are pruning wounds; therefore, we evaluated the aggressiveness of Cyt. sorbicola and Cal. pulchella in one-year-old sweet cherry plants. Santina and Lapins showed the lowest necrotic lesion caused by Cyt. sorbicola (13.6 and 14.31 mm, respectively), followed by Bing (19.51 mm) and Regina (26.14 mm). All plants infected by Cyt. sorbicola showed shoot blight regardless of the variety. In addition, there was a varying susceptibility to Cal. pulchella, with Lapins (21.6 mm), Bing (22.83 mm), Santina (27.62 mm), and Regina (30.8 mm) showing increasing levels of observed necrosis. The lesion caused by Cal. pulchella was more significant than that observed for Cyt. sorbicola, regardless of the cherry tree genotype. We identified each fungal growth from the wood necrosis progression area using two independent novel PCR-HRM strategies based on the ITS fungal region, which allowed us to differentiate each pathogen of interest individually or simultaneously. This study demonstrates different levels of susceptibility of sweet cherry tree genotypes to wood-degrading pathogens, emphasizing the need to include these factors in phytosanitary management programs. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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14 pages, 1194 KiB  
Article
Agricultural Soil as a Reservoir of Pseudomonas aeruginosa with Potential Risk to Public Health
by Jessica I. Licea-Herrera, Abraham Guerrero, Maribel Mireles-Martínez, Yuridia Rodríguez-González, Guadalupe Aguilera-Arreola, Araceli Contreras-Rodríguez, Susana Fernandez-Davila, Rocío Requena-Castro, Gildardo Rivera, Virgilio Bocanegra-García and Ana Verónica Martínez-Vázquez
Microorganisms 2024, 12(11), 2181; https://doi.org/10.3390/microorganisms12112181 - 30 Oct 2024
Cited by 1 | Viewed by 1759
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen with a high capacity to adapt to different factors. The aim of this study is to analyze the pathogenicity in P. aeruginosa strains and their resistance to heavy metals and antibiotics, in agricultural soil of the state [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen with a high capacity to adapt to different factors. The aim of this study is to analyze the pathogenicity in P. aeruginosa strains and their resistance to heavy metals and antibiotics, in agricultural soil of the state of Tamaulipas, Mexico. Susceptibility to 16 antibiotics was tested using the Kirby-Bauer method (CLSI). Eight virulence factors (FV) and six genes associated with heavy metal resistance were detected by PCR. As a result, P. aeruginosa was detected in 55% of the samples. The eight virulence factors were identified in ≥80% of the strains. The strains showed some level of resistance to only three antibiotics: 32.8% to ticarcillin, 40.8% to ticarcillin/clavulanic acid and 2.4% to aztreonam. The most frequent heavy metal resistance genes were arsC (92.8%) and copA (90.4%). However, copB and arsB genes were also identified in a percentage greater than 80%, and the least frequent genes were merA in 14.4% and czcA in 7.2%. Although P. aeruginosa strains showed a high percentage of factor virulence (potential ability to cause infections), their high levels of susceptibility to antibiotics lead to the assumption that infections are easily curable. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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11 pages, 1995 KiB  
Article
Are Changes Occurring in Bacterial Taxa Community and Diversity with the Utilization of Different Substrates within SIR Measurements?
by Yosef Steinberger, Tirza Doniger, Itaii Applebaum and Chen Sherman
Microorganisms 2024, 12(10), 2034; https://doi.org/10.3390/microorganisms12102034 - 9 Oct 2024
Cited by 1 | Viewed by 910
Abstract
This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The [...] Read more.
This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The study observed gradual changes in bacterial diversity in response to the addition of different substrate-induced respiration (SIR) substrates. Understanding the structure, dynamics, and functions of soil microbial communities is essential for assessing soil quality in sustainable agriculture. The preference for carbon sources among bacterial phyla is largely influenced by their life history and trophic strategies. Bacterial phyla like Proteobacteria, Bacteroidetes, and Actinobacteria, which thrive in nutrient-rich environments, preferentially utilize glucose. On the other hand, oligotrophic bacterial phyla such as Acidobacteria or Chloroflexi, which are found in lower numbers, have a lower ability to utilize labile C. The main difference between the two lies in their substrate utilization strategies. Understanding these distinct strategies is crucial for uncovering the bacterial functional traits involved in soil organic carbon turnover. Additionally, adding organic matter can promote the growth of copiotrophic bacteria, thus enhancing soil fertility. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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Review

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18 pages, 607 KiB  
Review
Fungi in Mangrove: Ecological Importance, Climate Change Impacts, and the Role in Environmental Remediation
by Juliana Britto Martins de Oliveira, Dario Corrêa Junior, Cláudio Ernesto Taveira Parente and Susana Frases
Microorganisms 2025, 13(4), 878; https://doi.org/10.3390/microorganisms13040878 - 11 Apr 2025
Viewed by 376
Abstract
Mangroves are coastal ecosystems of great ecological importance, located in transition areas between marine and terrestrial environments, predominantly found in tropical and subtropical regions. In Brazil, these biomes are present along the entire coastline, playing essential environmental roles such as sediment stabilization, coastal [...] Read more.
Mangroves are coastal ecosystems of great ecological importance, located in transition areas between marine and terrestrial environments, predominantly found in tropical and subtropical regions. In Brazil, these biomes are present along the entire coastline, playing essential environmental roles such as sediment stabilization, coastal erosion control, and the filtration of nutrients and pollutants. The unique structure of the roots of some mangrove tree species facilitates sediment deposition and organic matter retention, creating favorable conditions for the development of rich and specialized biodiversity, including fungi, bacteria, and other life forms. Furthermore, mangroves serve as important nurseries for many species of fish, crustaceans, and birds, being fundamental to maintaining trophic networks and the local economy, which relies on fishing resources. However, these ecosystems have been significantly impacted by anthropogenic pressures and global climate change. In recent years, the increase in average global temperatures, rising sea levels, changes in precipitation patterns, and ocean acidification have contributed to the degradation of mangroves. Additionally, human activities such as domestic sewage discharge, pollution from organic and inorganic compounds, and alterations in hydrological regimes have accelerated this degradation process. These factors directly affect the biodiversity present in mangrove sediments, including the fungal community, which plays a crucial role in the decomposition of organic matter and nutrient cycling. Fungi, which include various taxonomic groups such as Ascomycota, Basidiomycota, and Zygomycota, are sensitive to changes in environmental conditions, making the study of their diversity and distribution relevant for understanding the impacts of climate change and pollution. In particular, fungal bioremediation has gained significant attention as an effective strategy for mitigating pollution in these sensitive ecosystems. Fungi possess unique abilities to degrade or detoxify environmental pollutants, including heavy metals and organic contaminants, through processes such as biosorption, bioaccumulation, and enzymatic degradation. This bioremediation potential can help restore the ecological balance of mangrove ecosystems and protect their biodiversity from the adverse effects of pollution. Recent studies suggest that changes in temperature, salinity, and the chemical composition of sediments can drastically modify microbial and fungal communities in these environments, influencing the resilience of the ecosystem. The objective of this narrative synthesis is to point out the diversity of fungi present in mangrove sediments, emphasizing how the impacts of climate change and anthropogenic pollution influence the composition and functionality of these communities. By exploring these interactions, including the role of fungal bioremediation in ecosystem restoration, it is expected that this study would provide a solid scientific basis for the conservation of mangroves and the development of strategies to mitigate the environmental impacts on these valuable ecosystems. Full article
(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)
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