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Microorganisms
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Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem...
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Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (15 May 2024) | Viewed by 8027

Special Issue Editors

Prof. Dr. Nelson Marmiroli

E-Mail Website
Guest Editor
Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
Interests: environmental biotechnology; microbial ecology
Special Issues, Collections and Topics in MDPI journals
Dr. Luca Pagano

E-Mail Website
Guest Editor
Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
Interests: nanomaterials; genomics; transcriptomicis; abiotic stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil microorganisms are the hidden architects of terrestrial ecosystems, orchestrating vital processes that sustain life on our planet. Their intricate interactions with plants and the surrounding environment play a pivotal role in shaping ecosystem dynamics and providing essential services to humanity. We are pleased to introduce this Special Issue of Microorganisms.

The power of soil microorganisms: Soil microorganisms, including bacteria, fungi, archaea and viruses, constitute a diverse and dynamic community that inhabits the rhizosphere, soil and even the plant endosphere. These microbial communities engage in complex networks of interactions with plants, forming symbiotic relationships that influence plant health, growth and nutrient acquisition. Moreover, they are fundamental drivers of essential ecosystem processes, such as nutrient cycling, carbon sequestration and soil structure formation.

Themes of the Special Issue: This Special Issue seeks to explore the multifaceted world of soil microorganisms and their interactions with plants and the broader ecosystem. We invite original research articles, reviews and perspectives on a wide range of topics, including:

  • Plant–microbe interactions: investigating the molecular and ecological mechanisms governing the plant–soil microbial interactions and their implications for plant health and productivity;
  • Microbial diversity and community dynamics: exploring the factors that shape the microbial community structure in soil and how these communities respond to environmental changes;
  • Ecosystem services: assessing the contributions of soil microorganisms to ecosystem services, including nutrient cycling, disease suppression and soil fertility;
  • Emerging technologies: highlighting innovative technologies and approaches for studying soil microorganisms and their roles in ecosystem functioning.

We invite researchers, scientists, ecologists and microbiologists to contribute to this Special Issue and help unravel the mysteries of soil microorganisms, their intricate relationships with plants and profound impact on ecosystem services. We eagerly await your contributions and the opportunity to collaborate in advancing our knowledge of this vital aspect of ecology.

Prof. Dr. Nelson Marmiroli
Dr. Luca Pagano
Guest Editors

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

  • soil microorganisms
  • ecosystems
  • plant–microbe interactions
  • microbial diversity
  • ecosystem services
  • emerging technologies

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

15 pages, 1523 KiB  
Article
Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils
by Ilenia Iosa, Caterina Agrimonti and Nelson Marmiroli
Microorganisms 2024, 12(5), 1002; https://doi.org/10.3390/microorganisms12051002 - 16 May 2024
Cited by 3 | Viewed by 1928
Abstract
To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time [...] Read more.
To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery. Full article
(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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22 pages, 6554 KiB  
Article
Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems
by Bing Yang, Wanju Feng, Wenjia Zhou, Ke He and Zhisong Yang
Microorganisms 2024, 12(4), 728; https://doi.org/10.3390/microorganisms12040728 - 3 Apr 2024
Cited by 5 | Viewed by 2073
Abstract
Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to [...] Read more.
Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray–Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes. Full article
(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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17 pages, 13202 KiB  
Article
The Bacterial and Fungal Compositions in the Rhizosphere of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. in a Typical Planting Region
by Fuqi Wang, Zilu Zhao, Yangyang Han, Shiying Li, Xinhua Bi, Shumeng Ren, Yingni Pan, Dongmei Wang and Xiaoqiu Liu
Microorganisms 2024, 12(4), 692; https://doi.org/10.3390/microorganisms12040692 - 29 Mar 2024
Viewed by 1478
Abstract
Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During [...] Read more.
Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During four cropping years and collecting months, we used ITS rRNA gene amplicon and sequencing to assess the population, diversity, and predominant kinds of bacteria and fungus in the rhizosphere of Asarum. HPLC was used to determine the three bioactive ingredients, namely asarinin, aristolochic acid I, and volatile oil. The mainly secondary metabolites of Asarum, relationships between microbial communities, soil physicochemical parameters, and possible influences on microbial communities owing to various cropping years and collecting months were all statistically examined. The cropping years and collecting months affected the abundance and diversity of rhizosphere bacteria and fungi, but the cropping year had a significant impact on the structures and compositions of the bacterial communities. The rhizosphere microorganisms were influenced by both the soil physicochemical properties and enzyme activities. Additionally, this study revealed that Trichoderma was positively correlated with the three bioactive ingredients of Asarum, while Tausonia showed entirely opposite results. Gibberella and Leptosphaeria demonstrated a significantly negative correlation with asarinin and violate oil, but they were weakly correlated with the aristolochic acid I content. This study revealed variations in the Asarum rhizosphere microorganism population, diversity, and dominant types across four cropping years and collecting months. The relationship between Asarum secondary metabolites, the soil physicochemical properties, enzyme activities, and rhizosphere microorganisms was discussed. Our results will guide the exploration of the soil characteristics and rhizosphere microorganisms’ structures by regulating the microbial community to enhance Asarum quality. Full article
(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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12 pages, 1865 KiB  
Article
Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants
by Katherine V. Weigh, Bruna D. Batista, Huong Hoang and Paul G. Dennis
Microorganisms 2023, 11(12), 2984; https://doi.org/10.3390/microorganisms11122984 - 14 Dec 2023
Cited by 2 | Viewed by 1790
Abstract
The ability to sense and direct movement along chemical gradients is known as ‘chemotaxis’ and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change [...] Read more.
The ability to sense and direct movement along chemical gradients is known as ‘chemotaxis’ and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress. Full article
(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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