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Microorganisms
Special Issues
Microbial Interactions in Soil 2.0
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Microbial Interactions in Soil 2.0

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 8357

Special Issue Editor

Prof. Dr. Volker Brozel

E-Mail Website
Guest Editor
Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
Interests: diazotroph; nitrogen fixation; soil; biofilm
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue "Microbial Interactions in Soil".

Soils are inhabited by a rich diversity of microorganisms that impact their chemical composition, structure, and water retention, among others. Importantly, soil microorganisms influence plant phenotype and growth, impacting food production. Members of the soil microbiota affect each other through a range of beneficial and deleterious interactions, thereby affecting the soil ecosystem. The development of next-generation sequencing technologies has expanded our view on the diversity and distribution of soil microbiota, but less is known on how these organisms affect each other.

This Special Issue will provide a collection of articles that showcase new findings on how microorganisms interact in the soil environment. I invite you to submit research articles, review articles, and short communications related to microbial interactions in the soil environment.

Prof. Dr. Volker Brozel
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

  • soil
  • bacteria
  • rhizosphere
  • endophyte
  • biofilm
  • signaling
  • mutualism
  • syntrophy/syntrophism
  • commensalism
  • competition
  • antagonism/amensalism
  • predation

Published Papers (5 papers)

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Editorial

Jump to: Research

3 pages, 187 KiB  
Editorial
Microbial Interactions in Soil
by Volker S. Brözel
Microorganisms 2022, 10(10), 1939; https://doi.org/10.3390/microorganisms10101939 - 29 Sep 2022
Cited by 1 | Viewed by 1776
Abstract
Our view on the diversity and distribution of soil microbiota has expanded and continues to do so, driven by high-throughput sequencing technologies, but comparatively little is known about how these organisms affect each other [...] Full article
(This article belongs to the Special Issue Microbial Interactions in Soil 2.0)

Research

Jump to: Editorial

17 pages, 3124 KiB  
Article
High Ammonium Addition Changes the Diversity and Structure of Bacterial Communities in Temperate Wetland Soils of Northeastern China
by Xiaohong Weng, Mingyu Wang, Xin Sui, Beat Frey, Yingnan Liu, Rongtao Zhang, Hongwei Ni and Maihe Li
Microorganisms 2023, 11(8), 2033; https://doi.org/10.3390/microorganisms11082033 - 8 Aug 2023
Cited by 6 | Viewed by 1367
Abstract
The soil microbiome is an important component of wetland ecosystems and plays a pivotal role in nutrient cycling and climate regulation. Nitrogen (N) addition influences the soil’s microbial diversity, composition, and function by affecting the soil’s nutrient status. The change in soil bacterial [...] Read more.
The soil microbiome is an important component of wetland ecosystems and plays a pivotal role in nutrient cycling and climate regulation. Nitrogen (N) addition influences the soil’s microbial diversity, composition, and function by affecting the soil’s nutrient status. The change in soil bacterial diversity and composition in temperate wetland ecosystems in response to high ammonium nitrogen additions remains unclear. In this study, we used high-throughput sequencing technology to study the changes of soil bacterial diversity and community structure with increasing ammonium concentrations [CK (control, 0 kg ha−1 a−1), LN (low nitrogen addition, 40 kg ha−1 a−1), and HN (high nitrogen addition, 80 kg ha−1 a−1)] at a field experimental site in the Sanjiang Plain wetland, China. Our results showed that except for soil organic carbon (SOC), other soil physicochemical parameters, i.e., soil moisture content (SMC), dissolved organic nitrogen (DON), total nitrogen (TN), pH, ammonium nitrogen (NH4+), and dissolved organic carbon (DOC), changed significantly among three ammonium nitrogen addition concentrations (p < 0.05). Compared to CK, LN did not change soil bacterial α-diversity (p > 0.05), and HN only decreased the Shannon (p < 0.05) and did not change the Chao (p > 0.05) indices of soil bacterial community. Ammonium nitrogen addition did not significantly affect the soil’s bacterial community structure based on non-metric multidimensional scaling (NMDS) and PERMANOVA (ADONIS) analyses. Acidobacteriota (24.96–31.11%), Proteobacteria (16.82–26.78%), Chloroflexi (10.34–18.09%), Verrucomicrobiota (5.23–11.56%), and Actinobacteriota (5.63–8.75%) were the most abundant bacterial phyla in the soils. Nitrogen addition changed the complexity and stability of the bacterial network. SMC, NO3−, and pH were the main drivers of the bacterial community structure. These findings indicate that enhanced atmospheric nitrogen addition may have an impact on bacterial communities in soil, and this study will allow us to better understand the response of the soil microbiome in wetland ecosystems in the framework of increasing nitrogen deposition. Full article
(This article belongs to the Special Issue Microbial Interactions in Soil 2.0)
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14 pages, 2135 KiB  
Article
Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum
by Gitanjali NandaKafle, Lane A. Blasius, Tarren Seale and Volker S. Brözel
Microorganisms 2023, 11(6), 1457; https://doi.org/10.3390/microorganisms11061457 - 31 May 2023
Viewed by 1339
Abstract
Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, [...] Read more.
Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, suggesting that other biological factors play a role in controlling E. coli populations in soil. Free-living protozoa can affect the bacterial population by grazing. We hypothesized that E. coli strains capable of surviving in non-sterile soil possess mechanisms to protect themselves from amoeba predation. We determined the grazing rate of E. coli pasture isolates by using Dictyostelium discoideum. Bacterial suspensions applied to lactose agar as lines were allowed to grow for 24 h, when 4 μL of D. discoideum culture was inoculated in the center of each bacterial line. Grazing distances were measured after 4 days. The genomes of five grazing-susceptible and five grazing-resistant isolates were sequenced and compared. Grazing distance varied among isolates, which indicated that some E. coli are more susceptible to grazing by protozoa than others. When presented with a choice between grazing-susceptible and grazing-resistant isolates, D. discoideum grazed only on the susceptible strain. Grazing susceptibility phenotype did not align with the phylogroup, with both B1 and E strains found in both grazing groups. They also did not align by core genome phylogeny. Whole genome comparisons revealed that the five most highly grazed strains had 389 shared genes not found in the five least grazed strains. Conversely, the five least grazed strains shared 130 unique genes. The results indicate that long-term persistence of E. coli in soil is due at least in part to resistance to grazing by soil amoeba. Full article
(This article belongs to the Special Issue Microbial Interactions in Soil 2.0)
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22 pages, 2285 KiB  
Article
Nonlinear Effects Induced by Interactions among Functional Groups of Bacteria and Fungi Regulate the Priming Effect in Malagasy Soils
by Benoît Jaillard, Kanto Razanamalala, Cyrille Violle and Laetitia Bernard
Microorganisms 2023, 11(5), 1106; https://doi.org/10.3390/microorganisms11051106 - 23 Apr 2023
Viewed by 1222
Abstract
The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition [...] Read more.
The priming effect (PE) occurs when fresh organic matter (FOM) supplied to soil alters the rate of decomposition of older soil organic matter (SOM). The PE can be generated by different mechanisms driven by interactions between microorganisms with different live strategies and decomposition abilities. Among those, stoichiometric decomposition results from FOM decomposition, which induces the decomposition of SOM by the release of exoenzymes by FOM-decomposers. Nutrient mining results from the co-metabolism of energy-rich FOM with nutrient-rich SOM by SOM-decomposers. While existing statistical approaches enable measurement of the effect of community composition (linear effect) on the PE, the effect of interactions among co-occurring populations (non-linear effect) is more difficult to grasp. We compare a non-linear, clustering approach with a strictly linear approach to separately and comprehensively capture all linear and non-linear effects induced by soil microbial populations on the PE and to identify the species involved. We used an already published data set, acquired from two climatic transects of Madagascar Highlands, in which the high-throughput sequencing of soil samples was applied parallel to the analysis of the potential capacity of microbial communities to generate PE following a 13C-labeled wheat straw input. The linear and clustering approaches highlight two different aspects of the effects of microbial biodiversity on SOM decomposition. The comparison of the results enabled identification of bacterial and fungal families, and combinations of families, inducing either a linear, a non-linear, or no effect on PE after incubation. Bacterial families mainly favoured a PE proportional to their relative abundances in soil (linear effect). Inversely, fungal families induced strong non-linear effects resulting from interactions among them and with bacteria. Our findings suggest that bacteria support stoichiometric decomposition in the first days of incubation, while fungi support mainly the nutrient mining of soil’s organic matter several weeks after the beginning of incubation. Used together, the clustering and linear approaches therefore enable the estimation of the relative importance of linear effects related to microbial relative abundances, and non-linear effects related to interactions among microbial populations on soil properties. Both approaches also enable the identification of key microbial families that mainly regulate soil properties. Full article
(This article belongs to the Special Issue Microbial Interactions in Soil 2.0)
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20 pages, 5465 KiB  
Article
Metabarcoding and Metabolomics Reveal the Effect of the Invasive Alien Tree Miconia calvescens DC. on Soil Diversity on the Tropical Island of Mo’orea (French Polynesia)
by Camille Clerissi, Slimane Chaïb, Delphine Raviglione, Benoit Espiau, Cédric Bertrand and Jean-Yves Meyer
Microorganisms 2023, 11(4), 832; https://doi.org/10.3390/microorganisms11040832 - 24 Mar 2023
Cited by 3 | Viewed by 1941
Abstract
Miconia calvescens is a dominant invasive alien tree species that threatens several endemic plants in French Polynesia (South Pacific). While most analyses have been performed at the scale of plant communities, the effects on the rhizosphere have not been described so far. However, [...] Read more.
Miconia calvescens is a dominant invasive alien tree species that threatens several endemic plants in French Polynesia (South Pacific). While most analyses have been performed at the scale of plant communities, the effects on the rhizosphere have not been described so far. However, this compartment can be involved in plant fitness through inhibitory activities, nutritive exchanges, and communication with other organisms. In particular, it was not known whether M. calvescens forms specific associations with soil organisms or has a specific chemical composition of secondary metabolites. To tackle these issues, the rhizosphere of six plant species was sampled on the tropical island of Mo’orea in French Polynesia at both the seedling and tree stages. The diversity of soil organisms (bacteria, microeukaryotes, and metazoa) and of secondary metabolites was studied using high-throughput technologies (metabarcoding and metabolomics, respectively). We found that trees had higher effects on soil diversity than seedlings. Moreover, M. calvescens showed a specific association with microeukaryotes of the Cryptomycota family at the tree stage. This family was positively correlated with the terpenoids found in the soil. Many terpenoids were also found within the roots of M. calvescens, suggesting that these molecules were probably produced by the plant and favored the presence of Cryptomycota. Both terpenoids and Cryptomycota were thus specific chemicals and biomarkers of M. calvescens. Additional studies must be performed in the future to better understand if they contribute to the success of this invasive tree. Full article
(This article belongs to the Special Issue Microbial Interactions in Soil 2.0)
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