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 6756

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 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
  • 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 (8 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

16 pages, 4152 KB  
Article
Microbial Community Succession During Bioremediation of Petroleum-Contaminated Soils Using Rhodococcus sp. OS62-1 and Pseudomonas sp. P35
by Xiaodong Liu, Yuxi Ma, Yingying Jiang, Yidan Guo, Zhenshan Deng and Xiaolong He
Microorganisms 2026, 14(1), 7; https://doi.org/10.3390/microorganisms14010007 - 19 Dec 2025
Abstract
Oil pollution poses a persistent threat to soil ecosystems globally, and bioremediation using bacterial consortia has emerged as a cost-effective remediation strategy. However, the role of weak petroleum-degrading bacteria in enhancing the efficiency of specialized petroleum-degrading bacteria remains unclear. This study explores the [...] Read more.
Oil pollution poses a persistent threat to soil ecosystems globally, and bioremediation using bacterial consortia has emerged as a cost-effective remediation strategy. However, the role of weak petroleum-degrading bacteria in enhancing the efficiency of specialized petroleum-degrading bacteria remains unclear. This study explores the synergy and remediation potential of a two-bacterial consortium: the petroleum-degrading bacterium Rhodococcus sp. OS62-1 and the weak petroleum-degrading bacterium Pseudomonas sp. P35. A 25-day microcosm experiment was conducted with petroleum-contaminated soil, and four treatments were set: (1) uninoculated control, (2) inoculation with Rhodococcus sp. OS62-1 alone, (3) inoculation with Pseudomonas sp. P35 alone, and (4) inoculation with the consortium. Soil samples were collected periodically to analyze petroleum degradation efficiency, soil enzyme activities (dehydrogenase, catalase, polyphenol oxidase, and lipase), and microbial community composition (16S rRNA gene sequencing). Inoculating the soils with this consortium produced a higher petroleum degradation rate, microbial activity, and soil enzyme activity than inoculation with strain OS62-1 or P35 alone. Inoculation with strain P35 also contributed to the maintenance of strain OS62-1 during bioremediation. The study of microbial community structure found that the relative abundance of phylum Acidobacteriota (57.6 ± 5.3% to 75.6 ± 8.1%) and the Nocardioides genus (36.4 ± 4.5% to 53.0 ± 9.2%) increased dramatically during the bioremediation process. Pearson’s correlation analysis revealed that inoculation with strain OS62-1 and/or strain P35 increases the soil enzyme activity, boosts native oil-degrading bacteria, and accelerates the degradation of petroleum contaminants. Molecular ecological networks analysis revealed that inoculation with strain OS62-1 and/or strain P35 increased the complexity and robustness of the microbial network. These findings confirm that weak petroleum-degrading bacteria can synergistically enhance the bioremediation efficiency of specialized petroleum-degrading bacteria, providing a practical strategy for optimizing the design of bacterial consortia in the bioremediation of oil-polluted soils. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

18 pages, 5332 KB  
Article
Influence of Pseudomonas sp. NEEL19 Expelled Volatile Compounds on Growth and Development of Crop Seedlings
by Poovarasan Neelakandan, Fo-Ting Shen, Shih-Yao Lin, Shih-Han Lin and Chiu-Chung Young
Microorganisms 2025, 13(12), 2754; https://doi.org/10.3390/microorganisms13122754 - 4 Dec 2025
Viewed by 178
Abstract
This research intended to investigate the airborne chemical communication that occurs via volatile substances released by phyllosphere-associated bacteria, and it has been investigated whether it is beneficial to plants. The composition of halotolerant Pseudomonas sp. NEEL19 volatiles and impact on mung bean and [...] Read more.
This research intended to investigate the airborne chemical communication that occurs via volatile substances released by phyllosphere-associated bacteria, and it has been investigated whether it is beneficial to plants. The composition of halotolerant Pseudomonas sp. NEEL19 volatiles and impact on mung bean and fenugreek growth and metabolism were examined through co-culture in PPD. NEEL19 volatile mixtures (NEEL19 V+) enhanced the shoot and root length and chlorophyll content of mung bean under different saline conditions on short-term exposure. In particular, total chlorophyll a + b showed percentage increases of 58.15%, 67.00%, and 29.5% at 0, 50, and 100 mM NaCl, respectively. Furthermore, fenugreek seedlings’ biomass, shoot length, and chlorophyll content significantly increased while exposed to NEEL19 V+. In order to identify the range of volatile organic compounds (VOCs) that NEEL19 released, SPME-GCMS was utilized. The predominant VOC was dimethyl disulfide, while volatile inorganic compounds (VICs), including CO2 and NH3, were examined using the volatile trapping method. Saline stress of 100 mM NaCl influences the quantity and composition of both VOCs and VICs production in NEEL19. The consequences of aqueous NH4OH (1–5 μL) exposure seed PPD assay disclosed that NH3 is one of the responsible volatile substances that trigger substantial alterations in shoot length, root length, total chlorophyll, and stomatal structure in mung bean seedlings. Whereas, fenugreek seedlings exhibited a high chlorophyll content overall. This study indicates that the release of volatile mixtures from NEEL19 promotes the growth and development of mung bean and fenugreek seedlings. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
►▼ Show Figures

Figure 1

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 812
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 696
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 459
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 2 | Viewed by 1530
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 975
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
Cited by 2 | Viewed by 1508
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 1-8
Back to TopTop