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Applied Microbiology
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Microbiome in Ecosystem, 3rd Edition
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Microbiome in Ecosystem, 3rd Edition

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 30 June 2025 | Viewed by 7791

Special Issue Editor

Dr. Bong-Soo Kim

E-Mail Website
Guest Editor
Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
Interests: microbiome; metagenomics; homeostasis; disease; ecosystem
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue “Microbiome in Ecosystem” and “Microbiome in Ecosystem 2.0”.

The microbiome consists of complex microbes and related molecules. Recently, the microbiome has been applied to various fields in order to develop a novel way for maintaining homeostasis or the balance of ecosystems. The understanding of the microbiome’s interaction with its habitats including its host is still limited. This Special Issue is devoted to publishing original research and review articles on various aspects of the microbiome in ecosystems. Topics of interest include, but are not restricted to, novel methods for understanding the microbiome, the role of the microbiome in ecosystems, microbe–microbe interactions in the microbiome, microbe–host interactions, and microbe–environment interactions in various ecosystems.

Dr. Bong-Soo Kim
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. Applied Microbiology is an international peer-reviewed open access quarterly 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 1000 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

  • microbiome
  • metagenomics
  • ecosystem

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Related Special Issues

Published Papers (6 papers)

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Research

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16 pages, 2329 KiB  
Article
Carbon Metabolic Profiling as a Response to Previous Plant Mycotrophy and Soil Disturbance in Wheat Growth
by Taiana Conceição, Galdino Andrade and Isabel Brito
Appl. Microbiol. 2024, 4(4), 1661-1676; https://doi.org/10.3390/applmicrobiol4040113 - 11 Dec 2024
Viewed by 274
Abstract
Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat [...] Read more.
Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat microbiomes metabolism. Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ Ecoplates. The results of average well color development (AWCD) showed that the degree of mycotrophy of preceding crop and soil disturbance affected the soil microbiome, although no impact on Shannon Evenness Index was observed during the experiment. The Shannon–Wiener Diversity Index showed variations among the different preceding plants, but not in wheat analysis. The pattern of the C sources metabolism also changed differentially regarding plant type and soil disturbance during the experiment, being also different within the highly mycotrophic plants (legume and grass). In the legume, an increase in the metabolism of amine/amides and phenolic acids was observed, whilst in the grass, an increase in the metabolism of phosphate-carbons (P carbon) and carbohydrates was more evident. Principal component analysis showed that a grouping in the distinct phases of the experiment correlated with the widening of the metabolism of amino acids, carboxylic acids, and carbohydrates. The results indicate that soil functional community structure reflects soil agricultural practice conditions. Previous plant types and soil disturbance impacted the soil microbiome metabolic response (AWCD) in wheat, generating different patterns of carbon metabolism related to previous plant mycotrophy. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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16 pages, 3988 KiB  
Article
Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes
by Zachary L. McAdams, Susheel Bhanu Busi, Kevin L. Gustafson, Nathan Bivens, Craig L. Franklin, Paul Wilmes and Aaron C. Ericsson
Appl. Microbiol. 2024, 4(4), 1600-1615; https://doi.org/10.3390/applmicrobiol4040109 - 30 Nov 2024
Viewed by 566
Abstract
Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well [...] Read more.
Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on targeted-amplicon sequencing data, and functional differences between these communities remain poorly defined. We applied a multi-omic (metagenomic and metatranscriptomic) approach to biomolecules extracted from murine feces representative of two U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes, frequently containing genomic content unique to each supplier. Transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier including carbohydrate, fatty acid, and sulfite metabolism. These data provide a detailed characterization of the baseline differences in the fecal metagenome of mice from two U.S. commercial suppliers, suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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15 pages, 1266 KiB  
Article
Addition of Chicken Litter Compost Changes Bacteriobiome in Fallow Soil
by Natalia Naumova, Pavel Barsukov, Olga Baturina, Olga Rusalimova and Marsel Kabilov
Appl. Microbiol. 2024, 4(3), 1268-1282; https://doi.org/10.3390/applmicrobiol4030087 - 3 Sep 2024
Viewed by 763
Abstract
Composting is an environmentally friendly process, turning animal waste into fertilizer. Chicken litter compost (CLC) improves soil properties, increasing crop yields. However, the CLC effect on the soil microbiome is understudied. This study aimed to compare bacteriobiome diversity in fallow arable Chernozem with [...] Read more.
Composting is an environmentally friendly process, turning animal waste into fertilizer. Chicken litter compost (CLC) improves soil properties, increasing crop yields. However, the CLC effect on the soil microbiome is understudied. This study aimed to compare bacteriobiome diversity in fallow arable Chernozem with and without CLC addition in a field experiment in the Novosibirsk region, Russia, using 16S rRNA gene metabarcoding. Pseudomonadota, Actinomycetota and Acidobacteriota were the most OTU-rich phyla, together accounting for >50% of the total number of sequence reads. CLC-related shifts in the bacteriobiome structure occurred at all taxonomic levels: the Bacillota abundance was 10-fold increased due to increased Bacilli, both being indicator taxa for the CLC-soil. The main Actinomycetota classes were the indicators for the CLC-soil (Actinobacteria) and no-CLC soil (Thermoleophilia, represented Gaiella). Both Bacillota and Actinomycetota phyla were the ultimate constituents of the CLC added, persisting in the soil for five months of fallowing. The no-CLC soil indicator phyla were Acidobacteriota (represented by Acidobacteria_Group3) and Verrucomicrobiota. Future metabarcoding studies of chicken litter application in agricultural soils, including cropped studies, should address the soil microbiome at the species/strain levels in more detail, as well as how it is affected by specific crops, preferably accompanied by a direct methodology revealing the microbiota functions. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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11 pages, 1567 KiB  
Article
Predicting Microbiome Growth Dynamics under Environmental Perturbations
by George Sun and Yi-Hui Zhou
Appl. Microbiol. 2024, 4(2), 948-958; https://doi.org/10.3390/applmicrobiol4020064 - 10 Jun 2024
Viewed by 1226
Abstract
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a [...] Read more.
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabilities of MicroGrowthPredictor, which include the integration of LSTM modeling with a novel confidence interval estimation technique. The LSTM network captures the complex temporal dynamics of microbiome systems, while the novel confidence intervals provide a robust measure of prediction uncertainty. We include two examples—one illustrating the human gut microbiota composition and diversity due to recurrent antibiotic treatment and the other demonstrating the application of MicroGrowthPredictor on an artificial gut dataset. The results demonstrate the enhanced accuracy and reliability of the LSTM-based predictions facilitated by MicroGrowthPredictor. The inclusion of specific metrics, such as the mean square error, validates the model’s predictive performance. Our model holds immense potential for applications in environmental sciences, healthcare, and biotechnology, fostering advancements in microbiome research and analysis. Moreover, it is noteworthy that MicroGrowthPredictor is applicable to real data with small sample sizes and temporal observations under environmental perturbations, thus ensuring its practical utility across various domains. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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Review

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19 pages, 1575 KiB  
Review
Soil Symphony: A Comprehensive Overview of Plant–Microbe Interactions in Agricultural Systems
by Arpitha Chatchatnahalli Tharanath, Raje Siddiraju Upendra and Karthik Rajendra
Appl. Microbiol. 2024, 4(4), 1549-1567; https://doi.org/10.3390/applmicrobiol4040106 - 27 Nov 2024
Viewed by 918
Abstract
The rhizosphere, a narrow region of soil surrounding plant roots, is an environment rich in microbial diversity that profoundly influences plants’ health, growth, and agricultural productivity. This microbial community, known as the rhizosphere microbiome, consists of a complex array of bacteria, fungi, archaea, [...] Read more.
The rhizosphere, a narrow region of soil surrounding plant roots, is an environment rich in microbial diversity that profoundly influences plants’ health, growth, and agricultural productivity. This microbial community, known as the rhizosphere microbiome, consists of a complex array of bacteria, fungi, archaea, and other microorganisms that engage in complex interactions with plant roots. These microorganisms contribute to nutrient cycling, mineral uptake facilitation, and protection against soil-borne pathogens, thereby promoting plant growth and resilience towards biotic and abiotic stresses. Additionally, microbial signaling molecules, including phytohormones such as auxins, cytokinin, gibberellins, ethylene, and abscisic acid, play a pivotal role in regulating these interactions by modulating plants’ responses to environmental stressors. Recent advancements in microbiomics have enabled a deeper understanding of the rhizosphere’s diversity, composition, and functions, paving the way for more sustainable agricultural practices. By harnessing the potential of the rhizosphere microbiome, innovative strategies can be developed to reduce dependency on synthetic agrochemicals, enhance soil fertility, and increase crop yields. This review discusses the diversity and mechanisms of plant–microbe interactions, focusing on the role of microbial signaling molecules, and explores their applications in promoting agricultural sustainability. The insights gained from microbiomics studies can revolutionize farming practices by reducing dependency on chemical inputs, enhancing crop productivity, and nurturing soil health and environmental sustainability. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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15 pages, 1563 KiB  
Review
Reassessing Gout Management through the Lens of Gut Microbiota
by Jean Demarquoy and Oumaima Dehmej
Appl. Microbiol. 2024, 4(2), 824-838; https://doi.org/10.3390/applmicrobiol4020057 - 22 May 2024
Viewed by 2282
Abstract
Gout, recognized as the most common form of inflammatory arthritis, arises from the accumulation of uric acid crystals, leading to intense pain, particularly in the big toe. This condition has traditionally been associated with the overproduction or reduced clearance of uric acid. Recent [...] Read more.
Gout, recognized as the most common form of inflammatory arthritis, arises from the accumulation of uric acid crystals, leading to intense pain, particularly in the big toe. This condition has traditionally been associated with the overproduction or reduced clearance of uric acid. Recent studies, however, have underscored the significant role of the gut microbiota in uric acid metabolism, impacting both its production and elimination. This emerging understanding suggests that maintaining gut health could offer innovative approaches to treating gout, complementing traditional dietary and pharmacological interventions. It highlights the potential of probiotics or microbiome-based therapies, indicating a future where treatments are tailored to an individual’s microbiome. This offers a fresh perspective on gout management and underscores the broader influence of the microbiota on health and disease. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem, 3rd Edition)
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