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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: 28 February 2025 | Viewed by 6362

Special Issue Editors

Dr. Moussa Diarra

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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
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 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

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

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Published Papers (6 papers)

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Research

22 pages, 5058 KiB  
Article
Characterization of the Blood Bacterial Microbiota in Lowland Tapirs (Tapirus terrestris), a Vulnerable Species in Brazil
by Anna Claudia Baumel Mongruel, Emília Patrícia Medici, Rosangela Zacarias Machado, Keith Clay and Marcos Rogério André
Microorganisms 2024, 12(11), 2270; https://doi.org/10.3390/microorganisms12112270 (registering DOI) - 8 Nov 2024
Viewed by 335
Abstract
Microbiome studies targeting hypervariable regions of the 16S rRNA gene are suitable for understanding interactions between animals and their associated bacteria. While many studies focus on the gut microbiome, assessments of blood microbiota remain scarce despite the prevalence of blood-borne pathogens in vertebrates. [...] Read more.
Microbiome studies targeting hypervariable regions of the 16S rRNA gene are suitable for understanding interactions between animals and their associated bacteria. While many studies focus on the gut microbiome, assessments of blood microbiota remain scarce despite the prevalence of blood-borne pathogens in vertebrates. This study aimed to investigate the bacterial community in blood samples from 79 living and 7 road-killed lowland tapirs (Tapirus terrestris), a vulnerable species, sampled in two biomes in midwestern Brazil: Pantanal and Cerrado. Animals were categorized by condition (living or road-killed), sex, age, and biome. V3–V4 16S rRNA fragments were obtained from 86 blood samples and 4 negative controls. After filtering contaminants, 13,742,198 sequences representing 2146 ASVs were analyzed. Alpha diversity significantly differed by condition, while beta diversity differed by condition, site, and age (adults vs. sub-adults). For living animals (79/86 samples), alpha diversity showed no significant differences, but beta diversity differed by age. Different vector-borne bacterial pathogens, including Anaplasmataceae, Bartonella, and Borrelia spp., were detected. Additionally, evidence of transient translocation of microbial communities from other body regions to the bloodstream was observed. Amplification of bacterial 16S rRNA from blood samples of wild T. terrestris provided novel information about the diversity of blood-borne microbiota of lowland tapirs, members of a poorly studied mammalian family. Next-generation sequencing proved to be a valuable tool for screening potential vector-borne pathogens in this host. 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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30 pages, 3542 KiB  
Article
Shifts in Fusarium Communities and Mycotoxins in Maize Residues, Soils, and Wheat Grains throughout the Wheat Cycle: Implications for Fusarium Head Blight Epidemiology
by Toan Bao Hung Nguyen, Amandine Henri-Sanvoisin, Monika Coton, Gaétan Le Floch and Adeline Picot
Microorganisms 2024, 12(9), 1783; https://doi.org/10.3390/microorganisms12091783 - 28 Aug 2024
Viewed by 652
Abstract
Fusarium Head Blight (FHB), predominantly caused by Fusarium species, is a devastating cereal disease worldwide. While considerable research has focused on Fusarium communities in grains, less attention has been given to residues and soil, the primary inoculum sources. Knowledge of Fusarium spp. diversity, [...] Read more.
Fusarium Head Blight (FHB), predominantly caused by Fusarium species, is a devastating cereal disease worldwide. While considerable research has focused on Fusarium communities in grains, less attention has been given to residues and soil, the primary inoculum sources. Knowledge of Fusarium spp. diversity, dynamics, and mycotoxin accumulation in these substrates is crucial for assessing their contribution to wheat head infection and the complex interactions among Fusarium communities throughout the wheat cycle. We monitored six minimum-tillage wheat fields, with maize as the preceding crop, over two years. Soils, maize residues, and wheat grains were sampled at four stages. Fusarium composition was analyzed using a culture-dependent method, species-specific qPCR, and EF1α region metabarcoding sequencing, enabling species-level resolution. The Fusarium communities were primarily influenced by substrate type, accounting for 35.8% of variance, followed by sampling location (8.1%) and sampling stage (3.2%). Among the 32 identified species, F. poae and F. graminearum dominated grains, with mean relative abundances of 47% and 29%, respectively. Conversely, residues were mainly contaminated by F. graminearum, with a low presence of F. poae, as confirmed by species-specific qPCR. Notably, during periods of high FHB pressure, such as in 2021, F. graminearum was the dominant species in grains. However, in the following year, F. poae outcompeted F. graminearum, resulting in reduced disease pressure, consistent with the lower pathogenicity of F. poae. Source Tracker analysis indicated that residues were a more significant source of Fusarium contamination on wheat in 2021 compared to 2022, suggesting that F. graminearum in 2021 primarily originated from residues, whereas F. poae’s sources of infection need further investigation. Additionally, multiple mycotoxins were detected and quantified in maize residues during the wheat cycle, raising the question of their ecological role and impact on the soil microbiota. 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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21 pages, 3203 KiB  
Article
Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation
by Yichao Shi, Alison Claire Gahagan, Malcolm J. Morrison, Edward Gregorich, David R. Lapen and Wen Chen
Microorganisms 2024, 12(8), 1635; https://doi.org/10.3390/microorganisms12081635 - 10 Aug 2024
Viewed by 1046
Abstract
Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil [...] Read more.
Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0–15 cm and 15–30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn–soybean–wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4–V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15–30 cm compared to CT, while no significant differences were found at 0–15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0–15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin–Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture. 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, 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 1325
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
Cited by 1 | Viewed by 752
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 1447
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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