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Microorganisms
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Microbiota and Microbiomes in Plants, Animals and Environment: A One...
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Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective

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

Deadline for manuscript submissions: 31 August 2024 | Viewed by 2307

Special Issue Editors

Dr. Moussa Diarra

E-Mail Website
Guest Editor
Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
Interests: foods; antioxidative and cytoprotective efficacy; antimicrobial
Prof. Dr. Hermine Mkrtchyan

E-Mail Website
Guest Editor
School of Biomedical Sciences, University of West London, London W5 5RF, UK
Interests: clinical, livestock, environmental microbiology; pathogen ecology; detection and surveillance; antimicrobial resistance; microbiomes; climate change
Special Issues, Collections and Topics in MDPI journals
Dr. Wen Chen

E-Mail Website
Guest Editor
1. Ottawa Research and Development Centre, AAFC, Ottawa, ON K1A 0C6, Canada
2. Department of Biology, University of Ottawa, Ottawa, ON, Canada
Interests: microbial ecology; bioinformatics; biovigilance; phytomicrobiome; sustainable agriculture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Productivity and health are linked to inputs and environmental conditions, which are key factors to shape the compositional structure and function of host microbiota while influencing their environment. Accordingly, agricultural farming, food processing and clinical practices are accompanied by the emission of and exposure to environmental pollutants. Pathogens living in changing environmental conditions (e.g., temperature, precipitation, humidity, CO2, ammonium concentrations, greenhouse gasses, etc.) must adapt and evolve; their virulence potential may spread through horizontal gene transfer, a major mechanism of the antimicrobial resistance (AMR) gene acquisition, which increases with temperature. Therefore, health, climate change and AMR are interlinked and should be addressed to protect humans, livestock and plants. A “One Health approach,” using “omics” in the control and surveillance under public health policies, is needed to understand and mitigate the impacts of climate change on the environment, the evolution of microbiomes, and their relationships with health and productivity.

Thus, this Special Issue entitled “Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective”. Original research or review articles and short communications dealing with microbiomes in humans, environment, plants, farm animals and food productions are welcome.

We look forward to receiving your manuscript for review. 

Dr. Moussa Diarra
Prof. Dr. Hermine Mkrtchyan
Dr. Wen Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net 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

  • microbiota/microbiome
  • antimicrobial
  • disease and health
  • environment
  • climate

Published Papers (3 papers)

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Research

17 pages, 2146 KiB  
Article
Effect of Bacterial Extracellular Polymeric Substances from Enterobacter spp. on Rice Growth under Abiotic Stress and Transcriptomic Analysis
by Yosra Aoudi, Shin-ichiro Agake, Safiullah Habibi, Gary Stacey, Michiko Yasuda and Naoko Ohkama-Ohtsu
Microorganisms 2024, 12(6), 1212; https://doi.org/10.3390/microorganisms12061212 - 16 Jun 2024
Viewed by 572
Abstract
Plant biostimulants have received attention as sustainable alternatives to chemical fertilizers. Extracellular polymeric substances (EPSs), among the compounds secreted by plant growth-promoting rhizobacteria (PGPRs), are assumed to alleviate abiotic stress. This study aims to investigate the effect of purified EPSs on rice under [...] Read more.
Plant biostimulants have received attention as sustainable alternatives to chemical fertilizers. Extracellular polymeric substances (EPSs), among the compounds secreted by plant growth-promoting rhizobacteria (PGPRs), are assumed to alleviate abiotic stress. This study aims to investigate the effect of purified EPSs on rice under abiotic stress and analyze their mechanisms. A pot experiment was conducted to elucidate the effects of inoculating EPSs purified from PGPRs that increase biofilm production in the presence of sugar on rice growth in heat-stress conditions. Since all EPSs showed improvement in SPAD after the stress, Enterobacter ludwigii, which was not characterized as showing higher PGP bioactivities such as phytohormone production, nitrogen fixation, and phosphorus solubilization, was selected for further analysis. RNA extracted from the embryos of germinating seeds at 24 h post-treatment with EPSs or water was used for transcriptome analysis. The RNA-seq analysis revealed 215 differentially expressed genes (DEGs) identified in rice seeds, including 139 up-regulated and 76 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the ROS scavenging processes, detoxification pathways, and response to oxidative stress. For example, the expression of the gene encoding OsAAO5, which is known to function in detoxifying oxidative stress, was two times increased by EPS treatment. Moreover, EPS application improved SPAD and dry weights of shoot and root by 90%, 14%, and 27%, respectively, under drought stress and increased SPAD by 59% under salt stress. It indicates that bacterial EPSs improved plant growth under abiotic stresses. Based on our results, we consider that EPSs purified from Enterobacter ludwigii can be used to develop biostimulants for rice. Full article
(This article belongs to the Special Issue Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective)
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17 pages, 2499 KiB  
Article
Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific
by Joicye Hernández-Zulueta, Sharix Rubio-Bueno, María del Pilar Zamora-Tavares, Ofelia Vargas-Ponce, Alma Paola Rodríguez-Troncoso and Fabián A. Rodríguez-Zaragoza
Microorganisms 2024, 12(6), 1195; https://doi.org/10.3390/microorganisms12061195 - 13 Jun 2024
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Abstract
The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species’ physiology and ecology. We [...] Read more.
The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species’ physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus’ holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition. Full article
(This article belongs to the Special Issue Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective)
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17 pages, 3346 KiB  
Article
Baseline Skin Microbiota of the Leatherback Sea Turtle
by Samantha G. Kuschke, Jeanette Wyneken and Debra Miller
Microorganisms 2024, 12(5), 925; https://doi.org/10.3390/microorganisms12050925 - 1 May 2024
Viewed by 1055
Abstract
The integumentary system of the leatherback sea turtle (Dermochelys coriacea) is the most visible and defining difference of the species, with its smooth and waxy carapace and finely scaled skin, distinguishing it from the other six sea turtle species. The skin [...] Read more.
The integumentary system of the leatherback sea turtle (Dermochelys coriacea) is the most visible and defining difference of the species, with its smooth and waxy carapace and finely scaled skin, distinguishing it from the other six sea turtle species. The skin is the body’s largest organ and serves as a primary defense against the outside world and is thus essential to health. To date, we have begun to understand that the microorganisms located on the skin aid in these functions. However, many host–microbial interactions are not yet fully defined or understood. Prior to uncovering these crucial host–microbial interactions, we must first understand the communities of microorganisms present and how they differ through life-stage classes and across the body. Here, we present a comprehensive bacterial microbial profile on the skin of leatherbacks. Using next-generation sequencing (NGS), we identified the major groups of bacteria on the skin of neonates at emergence, neonates at 3–4 weeks of age (i.e., post-hatchlings), and nesting females. These data show that the predominant bacteria on the skin of the leatherback are different at each life-stage class sampled. This suggests that there is a shift in the microbial communities of the skin associated with life-stage class or even possibly age. We also found that different sample locations on the nesting female (i.e., carapace and front appendages = flipper) have significantly different communities of bacteria present. This is likely due to differences in the microhabitats of these anatomic locations and future studies should explore if this variation also holds true for neonates. These data define baseline skin microbiota on the leatherback and can serve as a foundation for additional work to broaden our understanding of the leatherbacks’ host–microbial interactions, the impacts of environmental changes or stressors over time, and even the pathogenicity of disease processes. Full article
(This article belongs to the Special Issue Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective)
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