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Microorganisms
Special Issues
Microbiome Research for Animal, Plant and Environmental Health: Second Edition
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Microbiome Research for Animal, Plant and Environmental Health: Second Edition

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 4857

Special Issue Editors

Dr. Alex Galanis

E-Mail Website
Guest Editor
Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: probiotics; microbiota; microbiome; beneficial microbes; multi-omics; lactic acid bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Aglaia Pappa

E-Mail Website
Guest Editor
Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: natural products; probiotics; microbiome; rhizobiome; cellular stress responses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Microbiome Research for Animal, Plant and Environmental Health” (https://www.mdpi.com/si/195604).

Microbial communities play an integral role in the homeostasis and physiology of macro- and micro-ecosystems. Accumulating evidence demonstrates the critical impact of human microbiota on health and disease. In this context, it is recognized that the host microbiota contributes to crucial processes, such as nutrient synthesis and digestion, immunomodulation, intestinal barrier integrity, and protection against pathogenic insults, while exerting extraintestinal and systemic effects. By extension, microbiota research is of great interest because of its potential applications in the field of agriculture and animal husbandry. Indeed, the soil microbiome, as well as the plant microbiome and the rhizosphere microbiome (rhizobiome), can influence plant health, nutritional value, and the ability of plants to adapt to and withstand extreme environmental conditions, thus having major ecological and economic implications. In addition, the correlation between microbiota composition and the spread of pathogens to animals and the food chain is gaining increasing attention in the context of the “One Health” approach. Manipulating the composition of microbiota in these ecosystems can have a significant impact on human and animal health whilst also contributing to sustainable agriculture.

As Guest Editors of this Special Issue, we would like to invite you to submit original research articles, review articles, and short communications on various aspects of animal, plant, environmental, or soil microbiome research, new mechanistic insights into host–microbe interactions, methods of microbiome manipulation, and innovative technologies for sustainable livestock and agri-food production.

Dr. Alex Galanis
Dr. Aglaia Pappa
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 250 words) can be sent to the Editorial Office for assessment.

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

  • environmental microbiome
  • soil microbiome
  • rhizobiome
  • host–microbe interactions
  • microbiome manipulation
  • sustainable agriculture

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Published Papers (4 papers)

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Research

16 pages, 1929 KB  
Article
Combined Micronutrient and Microbial Inoculant Application Improves Bur Clover Yield and Quality While Reshaping Rhizosphere Microbial Communities Under Greenhouse Conditions
by Guiliang Wang, Yao Liu, Chen Zhao, Haitao Zhao, Xiaoqing Qian and Juanjuan Wang
Microorganisms 2026, 14(5), 1010; https://doi.org/10.3390/microorganisms14051010 - 30 Apr 2026
Viewed by 277
Abstract
Micronutrient limitation and rhizosphere imbalance often constrain the productivity and quality of leafy vegetables in intensively managed greenhouse soils. This study evaluated the effects of conventional fertilization (CK), micronutrient supplementation (Mi), and micronutrient supplementation combined with a compound microbial inoculant (MM) on bur [...] Read more.
Micronutrient limitation and rhizosphere imbalance often constrain the productivity and quality of leafy vegetables in intensively managed greenhouse soils. This study evaluated the effects of conventional fertilization (CK), micronutrient supplementation (Mi), and micronutrient supplementation combined with a compound microbial inoculant (MM) on bur clover (Medicago polymorpha L.) yield, quality, rhizosphere chemical properties, and soil microbial communities. Compared with CK, Mi increased yield by 26.53%, whereas MM increased yield by 40.77%. MM also significantly increased SPAD, soluble protein, and soluble sugar, while reducing plant nitrate content by 22.86%; Mi had no significant effect on nitrate reduction. MM decreased soil pH from 8.62 to 8.34 and increased EC, available P and K, water-soluble Ca, Mg, and K, and available Zn and B, indicating improved rhizosphere chemical conditions. Mantel analysis showed that yield and plant nitrate were significantly associated with several soil variables. MM also markedly reshaped rhizosphere microbial communities, with clear treatment separation for both bacteria and fungi. The bacterial community was significantly explained by selected soil variables, whereas the fungal model was not significant. Overall, micronutrient supplementation mainly promoted yield, while its combination with microbial inoculation further improved rhizosphere conditions, crop quality, and nitrate control. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health: Second Edition)
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15 pages, 1720 KB  
Article
DNA-Based Bacterial Community Profiles in Air-Dried Historical Soil Archives Are More Representative than Those from Rewetted Soils
by Peng Lu, Bingjie Ji, Yuan Yan, Shulan Zhang and Xueyun Yang
Microorganisms 2026, 14(3), 595; https://doi.org/10.3390/microorganisms14030595 - 6 Mar 2026
Cited by 1 | Viewed by 503
Abstract
Recording and tracking the long-term dynamic changes in microbial populations is as essential as monitoring other soil properties for evaluating soil quality and health; however, this area has significantly lagged due to technical constraints and challenges in storing fresh soil samples. Historically archived [...] Read more.
Recording and tracking the long-term dynamic changes in microbial populations is as essential as monitoring other soil properties for evaluating soil quality and health; however, this area has significantly lagged due to technical constraints and challenges in storing fresh soil samples. Historically archived soil samples offer a unique opportunity to characterize the temporal dynamics of microorganisms over several decades. To determine whether archived air-dried soils can be utilized for this purpose, we compared the structure and composition of bacterial communities across fresh soils, air-dried soil archives stored for varying durations, and their corresponding rewetted counterparts, all sourced from a long-term fertilization experiment on calcareous loess soil. Soil microbial features were characterized using the MiSeq sequencing platform. The results indicated that the similarity of DNA-based bacterial community composition between fresh soil and both archived and rewetted soils followed a downward quadratic curve as archiving time increased. Specifically, the DNA-based community structure of soils air-dried and preserved for one year, as well as those rewetted after eight years of archiving, remained highly similar to that of fresh soil. Regarding taxonomic shifts, the relative abundance of Actinobacteria in both air-dried and rewetted soils increased with storage time. Conversely, the relative abundances of Acidobacteria and Gemmatimonadetes significantly increased in air-dried soils but decreased upon rewetting over time. The relative abundances of Chloroflexi and Firmicutes remained stable in air-dried soils; however, after rewetting, the former decreased while the latter increased dramatically. Furthermore, Proteobacteria, Rokubacteria, Planctomycetes, Bacteroidetes, and Latescibacteria exhibited a decreasing trend in both air-dried and rewetted soils. These findings suggest that air-dried soils preserve DNA-based community profiles more effectively than rewetted soils, particularly for samples stored for less than eight years. This study provides a valuable reference for utilizing archived historical soil samples from long-term experiments to investigate microbial community evolution. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health: Second Edition)
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32 pages, 3540 KB  
Article
Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China
by Man Guo, Dong Liu, Zhilan Xia, Tao Xie, Luofeng Su, Jesus Pérez-Moreno and Fuqiang Yu
Microorganisms 2025, 13(11), 2431; https://doi.org/10.3390/microorganisms13112431 - 23 Oct 2025
Viewed by 2206
Abstract
Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. [...] Read more.
Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5–V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R2 = 0.46, p < 0.001) was a stronger structuring force than tissue type (R2 = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health: Second Edition)
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24 pages, 3029 KB  
Article
Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding
by Maria Tokamani, Panagiotis Liakopoulos, Konstantinos Tegopoulos, Aristea-Marina Zigkou, George Triantaphyllidis, Nikolaos Kamidis, Maria E. Grigoriou, Raphael Sandaltzopoulos and Petros Kolovos
Microorganisms 2025, 13(10), 2373; https://doi.org/10.3390/microorganisms13102373 - 15 Oct 2025
Viewed by 1328
Abstract
The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing [...] Read more.
The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea. Full article
(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health: Second Edition)
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