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Microorganisms
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Advances on Molecular Microbial Ecology
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Advances on Molecular Microbial Ecology

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 1319

Special Issue Editor

Prof. Dr. Nwadiuto Esiobu

E-Mail Website
Guest Editor
Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
Interests: molecular microbial ecology; biotechnology

Special Issue Information

Dear Colleagues,

This special issue of "Molecular Microbial Ecology" is dedicated to exploring the latest advancements in molecular approaches to understanding the intricate relationships between microbes and their biotic and abiotic environments, with a focus on human and plant microbiomes, environmental and public health, synthetic biology, and rapid detection methods. We invite original research and review articles that contribute to the following areas:

  1. Human Microbiome Dynamics: Studies investigating the composition, function, and dynamics of the human microbiome in health and disease, and its influence on host immunity, metabolism, and disease susceptibility.
  2. Plant Microbiome Interactions: Research on the plant microbiome, including root-associated, endophytic, and phyllosphere microbiomes, and their roles in plant growth, health, and response to environmental stressors.
  3. Environmental Microbiome and Public Health: Contributions examining the role of environmental microbiomes in public health, including microbial indicators of environmental quality, pathogen transmission, and the impact of environmental microbes on human health.
  4. Synthetic Biology in Microbial Ecology: Innovative applications of synthetic biology to engineer or enhance microbial ecosystems, including the design of synthetic microbial communities, genetic circuits, and bioproduction systems.
  5. Rapid Detection and Diagnostics: Development and evaluation of molecular tools and techniques for the rapid detection and diagnosis of microbial species, including metagenomics, CRISPR-based diagnostics, and biosensor technologies.
  6. Microbes and Environmental Sustainability: Research on how microbes contribute to environmental processes such as waste degradation, nutrient cycling, and soil health, and their potential in bioremediation and sustainable agriculture.
  7. Cultivation-Independent Methods: Studies employing cultivation-independent approaches to explore uncultured microbial diversity and function, including single-cell genomics and meta-omics techniques.
  8. Microbiome-Host Co-evolution: Insights into the co-evolutionary processes between microbes and their hosts, including the role of horizontal gene transfer and the impact on host adaptation and speciation.
  9. Microbiome Manipulation for Health and Disease: Strategies for manipulating the microbiome for therapeutic purposes, including probiotics, prebiotics, and fecal microbiota transplantation.
  10. Challenges and Opportunities in Microbiome Research: Discussions on the current challenges in microbiome research, such as reproducibility, standardization of methods, and ethical considerations, as well as future opportunities in the field.

Prof. Dr. Nwadiuto Esiobu
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

  • molecular microbial ecology
  • human microbiomes
  • plant microbiomes
  • environmental microbiome and public health
  • synthetic biology
  • rapid detection methods

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

19 pages, 4595 KiB  
Article
Rhizosphere Microbiomes of Citrus Plants in Historically Undisturbed 100-Year-Old Groves Appear to Mitigate Susceptibility to Citrus Greening Disease
by Nwadiuto Esiobu, Karim Dawkins, Yasmine Sanhaji, Melissa Voorn, Karina Murillo, Zachary Hill, Faiza Naeem, Joel Edouard and Donald McCorquodale
Microorganisms 2025, 13(4), 763; https://doi.org/10.3390/microorganisms13040763 - 27 Mar 2025
Viewed by 302
Abstract
Microbiome studies aimed at combating the citrus greening devastation caused by Liberibacter asiaticus abound. However, the role of farming practices, such as the massive use of herbicides, pesticides, and inorganic fertilizers on specific taxa and plant population immunity remains an important inquiry. To [...] Read more.
Microbiome studies aimed at combating the citrus greening devastation caused by Liberibacter asiaticus abound. However, the role of farming practices, such as the massive use of herbicides, pesticides, and inorganic fertilizers on specific taxa and plant population immunity remains an important inquiry. To test our hypothesis that agricultural practices in managed Citrus groves induce root microbiome dysbiosis, potentially rendering citrus readily susceptible to citrus greening disease (CGD), we compared the CGD and root microbiome status of citrus plants in a rare > 130-year-old grove (no anthropogenic influence) to those of managed Valencia groves (symptomatic and asymptomatic). Citrus greening disease was detected by qPCR using the HLBa/HLBs/HLBp primer/probe combination, while root microbiome community structure was determined using 16S rDNA amplicon sequencing. The prevalence of CGD among citrus growing in the undisturbed, healthy soils was zero (Ct values > 36), while symptomatic and asymptomatic Valencia from managed groves was 100% positive (Ct < 34). Known beneficial plant symbionts (Actinomycetales, Bradyrhizobium, Verrucomicrobia, etc.) from Phylum Actinobacteria and Proteobacteria were depleted in the rhizosphere of the managed sites. This dysbiotic shift was characterized by enrichment with Acidobacterium, Nitrospira, and Sphingomonas spp. In highly infected Valencia oranges, beneficial taxa of the Alphaproteobacteria declined significantly (from 20–25% to 10–15%), while Bacillus sp. (a Firmicutes) was enriched 13-fold. Simpson and Shannon diversity indices were similar for all plant microbiomes except the heavily infected Valencia, which exhibited low diversity (p < 0.05), indicating that diversity indices alone are not reliable measures of soil health or rhizobiome homeostasis. Large reservoirs of known and novel putative beneficial rhizosphere microbes in undisturbed sites supported zero CGD, despite proximity to the managed sites where diverse non-beneficial taxa coincided with high disease rates. Supplementing the use of agrochemicals with carefully designed microbial products for plant disease control and sustainable soil health deserves acute attention. Full article
(This article belongs to the Special Issue Advances on Molecular Microbial Ecology)
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13 pages, 4078 KiB  
Article
An Engineered Yeast Expressing an Artificial Heavy Metal-Binding Protein Enhances the Phytoremediation of Alum Mine Soils
by Wenming Wang, Liling Xie, Lin Zhao and Qilin Yu
Microorganisms 2025, 13(3), 612; https://doi.org/10.3390/microorganisms13030612 - 7 Mar 2025
Viewed by 572
Abstract
Alum mining leads to significant heavy metal and acid pollution within soils. Phytoremediation is a common strategy used to treat alum mine soils, but its efficiency is frequently compromised by the alum-mining-induced impairment of plant growth. To improve the strength of plants against [...] Read more.
Alum mining leads to significant heavy metal and acid pollution within soils. Phytoremediation is a common strategy used to treat alum mine soils, but its efficiency is frequently compromised by the alum-mining-induced impairment of plant growth. To improve the strength of plants against mine pollution, this study constructed the artificial yeast strain ScHB (heavy metal-binding protein-containing Saccharomyces cerevisiae) expressing the de novo designed protein HBGFP (heavy metal-binding green fluorescence protein) and investigated its effect on the phytoremediation of alum mine soils with soil physiochemical assays and heavy metal quantification. This protein was composed of an N-terminal signal peptide, an HB (heavy metal-binding) domain, and a GFP (green fluorescence protein) domain, as well as a C-terminal glycolphosphatidylinositol-anchoring fragment. The exposure of the HBGFP on the ScHB surface increased the growth rate of the yeast cells and enhanced cadmium capture from the cadmium-containing medium. After culturing Medicago sativa in the alum mine soils for 30 days, ScHB remarkably increased the plants’ average height from 17.5 cm to 27.9 cm and their biomass from 3.03 g/plant to 4.35 g/plant, as well as increasing the accumulation of antioxidant agents in the plants. Moreover, the ScHB cells strongly improved the soil quality, with an increase in the soil pH values from 5.47 to 6.21 to 6.9, and increased the levels of soil organic matter, total nitrogen, available phosphorus, and living bacteria. Furthermore, ScHB efficiently improved the plants’ abilities to remove soil heavy metals, decreasing the levels of cadmium, lead, chromium, and copper by 90%, 86%, 97%, and 88%, respectively. This study developed a genetic engineering method to improve the efficiency of phytoremediation against pollution from alum mining. Full article
(This article belongs to the Special Issue Advances on Molecular Microbial Ecology)
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