Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.7
4.2
Journals
Microorganisms
Special Issues
Interaction Between Microorganisms and Environment
share announcement

Interaction Between Microorganisms and Environment

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

Deadline for manuscript submissions: 31 March 2026 | Viewed by 4744

Special Issue Editors

Dr. Alexander Machado Cardoso

E-Mail Website
Guest Editor
Department of Biology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
Interests: environmental biotechnology; environmental sciences; microbial diversity and metagenome
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Li Zhu

E-Mail Website
Guest Editor Assistant
Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
Interests: isolation and identification of pathogenic microorganisms; microbial metabolism; bioinformatics; fermentation production; high-throughput screening; genetic engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms are ubiquitous, found in soil, water, the atmosphere, and within the bodies of animals and plants. They thrive and reproduce in diverse environments, influencing their surroundings through various metabolic activities. For instance, some microorganisms utilize environmental substances for fermentation, producing metabolites that impact the ecosystem. In natural ecological systems, microorganisms play a crucial role in material cycling and are significant forces regulating ecosystem functions. Investigating the interactions between microorganisms and their ecological environments—focusing on cells, metabolites, and genetics—can enhance our understanding of how these organisms contribute to environmental sustainability. This Special Issue aims to highlight the latest advancements in understanding the mechanisms of microbial interactions with soil, plants, oceans, and other ecological environments.

We sincerely invite submissions of the latest research reviews and original research papers in the field of microbial and environmental interactions related to oceans, soil, and plants. The primary research topics for this Special Issue include the isolation and identification of functional microorganisms, the screening and identification of natural active substances that can enhance the ecological environment, and the mechanisms by which microorganisms improve environmental conditions.

Dr. Alexander Machado Cardoso
Guest Editor

Prof. Dr. Li Zhu
Guest Editor Assistant

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

  • environmental
  • microbial
  • soil
  • plant
  • ocean
  • microbial fermentation
  • interaction mechanism

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

25 pages, 3767 KB  
Article
Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species
by Emma K. Stock, Ketlyn Rota, Brandi Dunn, Madelynn Vasquez, Daniela Hernandez-Velazquez, Alyssia Lespes, Solenn Bosmans, Jace C. Smith and John A. Kyndt
Microorganisms 2025, 13(10), 2369; https://doi.org/10.3390/microorganisms13102369 - 15 Oct 2025
Viewed by 509
Abstract
The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with [...] Read more.
The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

20 pages, 902 KB  
Article
Degradation of Dioxins and DBF in Urban Soil Microcosms from Lausanne (Switzerland): Functional Performance of Indigenous Bacterial Strains
by Rita Di Martino, Mylène Soudani, Patrik Castiglioni, Camille Rime, Yannick Gillioz, Loïc Sartori, Tatiana Proust, Flavio Neves Dos Santos, Fiorella Lucarini and Davide Staedler
Microorganisms 2025, 13(10), 2306; https://doi.org/10.3390/microorganisms13102306 - 5 Oct 2025
Viewed by 419
Abstract
Urban soils are often affected by long-term deposition of persistent organic pollutants, including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). This study evaluated the biodegradation potential of indigenous bacterial strains isolated from chronically contaminated soils in Lausanne, Switzerland. Using selective enrichment techniques, [...] Read more.
Urban soils are often affected by long-term deposition of persistent organic pollutants, including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). This study evaluated the biodegradation potential of indigenous bacterial strains isolated from chronically contaminated soils in Lausanne, Switzerland. Using selective enrichment techniques, five strains were isolated, with no biosafety concerns for human health and environmental applications. These isolates were screened for their ability to degrade dibenzofuran (DBF) and 2,7-dichlorodibenzo-p-dioxin (2,7-DD) under mineral medium conditions. A simplified two-strain consortium (Acinetobacter bohemicus and Bacillus velezensis) and a broader five-strain co-culture were then applied to real soil microcosms over a 24-week period. This work provides the first experimental evidence that A. bohemicus and B. velezensis can degrade DBF and 2,7-DD under controlled conditions. Dioxin concentrations were monitored at 4, 8, and 24 weeks using a Gas Chromatography Mass Spectrometry (GC-MS). In laboratory conditions, co-cultures showed enhanced degradation compared to individual strains, likely due to metabolic complementarity. In soil, the simplified two-strain consortium performed better at dioxin degradation, especially at earlier time points. Although no statistically significant reductions were observed due to high variability and limited sample size, consistent trends emerged, particularly at the most contaminated site. These findings support the relevance of testing bioremediation strategies under realistic environmental conditions. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

11 pages, 1822 KB  
Article
Comparative Analysis of Bacterial Diversity and Functional Potential in Two Athalassohaline Lagoons in the Monegros Desert (NE Spain)
by Mercedes Berlanga, Arnau Blasco, Ricardo Guerrero, Andrea Butturini and Jordi Urmeneta
Microorganisms 2025, 13(10), 2224; https://doi.org/10.3390/microorganisms13102224 - 23 Sep 2025
Viewed by 337
Abstract
This study compared bacterial diversity and putative functionality between two saline lagoons, La Muerte and Salineta, in the Monegros desert ecosystem. Amplicon sequencing analysis revealed distinct taxonomic and functional patterns between the lagoons. Pseudomonadota dominated both systems, averaging 31.0% in La Muerte and [...] Read more.
This study compared bacterial diversity and putative functionality between two saline lagoons, La Muerte and Salineta, in the Monegros desert ecosystem. Amplicon sequencing analysis revealed distinct taxonomic and functional patterns between the lagoons. Pseudomonadota dominated both systems, averaging 31.0% in La Muerte and 47.4% in Salineta, reflecting their well-documented osmotic stress tolerance. However, significant compositional differences were observed: Cyanobacteriota comprised 18.4% of La Muerte communities but remained below 1% in Salineta, while Bacteroidota showed higher abundance in La Muerte (16.6%) compared to Salineta (6.7%). Principal coordinate analysis demonstrated strong community differentiation between lagoons (Bray–Curtis dissimilarity p < 0.05). Functional profiling revealed contrasting metabolic capabilities: La Muerte communities showed enhanced autotrophic carbon fixation pathways (especially the Calvin–Benson cycle) and nitrogen cycling processes, while Salineta exhibited stronger denitrification signatures indicative of anoxic conditions. Carbohydrate indices suggested different organic matter quality and polymer composition between lagoons. La Muerte demonstrated significantly elevated stress response mechanisms compared to Salineta, which can be attributed to its ephemeral, shallow, and high evaporation rates that collectively generate more severe osmotic, thermal, and oxidative stress conditions for the sediment microbiota. These findings demonstrate that site-specific environmental factors, including hydroperiod variability and salinity dynamics, strongly influence microbial community structure and metabolic potential in saline wetland ecosystems. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

15 pages, 4647 KB  
Article
Adaptability and Sensitivity of Trichoderma spp. Isolates to Environmental Factors and Fungicides
by Allinny Luzia Alves Cavalcante, Andréia Mitsa Paiva Negreiros, Naama Jéssica de Assis Melo, Fernanda Jéssica Queiroz Santos, Carla Sonale Azevêdo Soares Silva, Pedro Sidarque Lima Pinto, Sabir Khan, Inês Maria Mendes Sales and Rui Sales Júnior
Microorganisms 2025, 13(7), 1689; https://doi.org/10.3390/microorganisms13071689 - 18 Jul 2025
Cited by 1 | Viewed by 1078
Abstract
Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations [...] Read more.
Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations and with synthetic fungicides with distinct modes of action. Three isolates were analyzed: URM-5911 and TRA-0048 (T. asperellum) and TRL-0102 (T. longibrachiatum). The results revealed substantial variability among the isolates, with the optimal mycelial growth temperatures ranging from 24.56 to 29.42 °C. All the isolates exhibited broad tolerance to the tested pH (5–9) and salinity levels (250–1000 mM), with TRL-0102 demonstrating the highest salt resistance. The fungicide treatments negatively affected mycelial growth across all the isolates, with Azoxystrobin + Difenoconazole and Boscalid causing growth reductions of up to 50%. Notably, Boscalid enhanced conidial production more compared to the control (126.0% for URM-5911, 13.7% for TRA-0048, and 148.5% for TRL-0102) and decreased the percentage of inactive conidia to less than 10% in all the isolates. These results provide strategic information for the application of Trichoderma spp. in agricultural systems, supporting the selection of more adapted and suitable isolates for integrated disease management programs. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

15 pages, 1465 KB  
Article
Propagule-Type Specificity in Arbuscular Mycorrhizal Fungal Communities in Early Growth of Allium tuberosum
by Irem Arslan, Kohei Takahashi, Naoki Harada and Kazuki Suzuki
Microorganisms 2025, 13(6), 1430; https://doi.org/10.3390/microorganisms13061430 - 19 Jun 2025
Viewed by 834
Abstract
Arbuscular mycorrhizal fungi (AMF) exhibit diverse strategies for colonization and survival, yet the extent to which different propagule types—roots, extraradical hyphae, and spores—contribute to these processes remains unclear. In a pot experiment using Allium tuberosum and soils from three field sites, we characterized [...] Read more.
Arbuscular mycorrhizal fungi (AMF) exhibit diverse strategies for colonization and survival, yet the extent to which different propagule types—roots, extraradical hyphae, and spores—contribute to these processes remains unclear. In a pot experiment using Allium tuberosum and soils from three field sites, we characterized AMF communities in root, hyphal, and spore fractions through 18S rRNA gene sequencing. A total of 427 OTUs were identified, with Glomus and Paraglomus dominating. Root fractions contained significantly more OTUs than hyphal fractions, suggesting strong specialization for intraradical colonization. Only a small subset of taxa occurred across all propagule types. Indicator species analysis revealed 21 OTUs with significant associations, mainly in root and hyphal fractions, while spore-specific taxa were rare. PERMANOVA revealed that both propagule type and soil type shaped the community structure, with propagule identity being the stronger factor. These results highlight propagule-type specialization as a key ecological trait in AMF and underscore the importance of examining multiple fungal compartments to fully capture AMF diversity and function. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

Review

Jump to: Research

16 pages, 864 KB  
Review
High-Value Bioactive Molecules Extracted from Microalgae
by Carla Arenas Colarte, Iván Balic, Óscar Díaz, Adrián A. Moreno, Maximiliano J. Amenabar, Tamara Bruna Larenas and Nelson Caro Fuentes
Microorganisms 2025, 13(9), 2018; https://doi.org/10.3390/microorganisms13092018 - 29 Aug 2025
Viewed by 1076
Abstract
Microalgae are unicellular photosynthetic organisms with considerable genetic diversity and remarkable metabolic capacity, positioning them as sustainable cellular biorefineries. They can be cultivated in open or closed systems, influenced by physical and chemical variables such as light, temperature, and nutrient availability. These conditions [...] Read more.
Microalgae are unicellular photosynthetic organisms with considerable genetic diversity and remarkable metabolic capacity, positioning them as sustainable cellular biorefineries. They can be cultivated in open or closed systems, influenced by physical and chemical variables such as light, temperature, and nutrient availability. These conditions modulate the synthesis of valuable biomolecules, including proteins, lipids, polysaccharides, and secondary metabolites. Microalgae are especially notable for their high protein content (up to 70% w/w in Spirulina sp.), polyunsaturated fatty acids (e.g., DHA and EPA), and β-glucans with bioactive properties. Choosing the correct extraction method (mechanical, enzymatic or combined) is very important to obtain and preserve the functionality of these compounds. Despite their biotechnological potential in functional foods, pharmaceuticals, and biofuels, industrial development faces challenges such as extraction efficiency, scalability, and regulatory approval. This review compiles current knowledge on the nutritional and bioactive potential of microalgae, highlights advances in extraction technologies and discusses their potential applications in health-oriented industrial innovation. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop