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Microorganisms in the Environment
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Microorganisms in the Environment

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 30 May 2025 | Viewed by 15924

Special Issue Editors

Dr. Diby Paul

E-Mail Website
Guest Editor
Pilgram Marpeck School of STEM, Truett McConnell University, 100 Alumni Dr., Cleveland, GA 30528, USA
Interests: microbial biofilm; quorum sensing and quorum quenching; rhizobacteria; microbial indicators
Special Issues, Collections and Topics in MDPI journals
Dr. Udai B. Singh

E-Mail Website
Guest Editor
Plant-Microbe Interaction & Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Mau Nath Bhanjan-275103, Uttar Pradesh, India
Interests: plant–microbe interaction; rhizosphere biology; biological control; bioremediation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Microorganisms play an important role in ecosystem functioning. Beyond being involved in the carbon, nitrogen, and sulfur cycles, they also participate in other biogeochemical cycles. Microbial metabolic activities lie at the heart of numerous interactions between the environment, plants, and microorganisms that recruit and shape the dynamics of particular ecosystems. Simultaneously, climate change plays a vital role in the perceived temporal and spatial variations in microbial communities of particular ecosystem. Microbes are also involved in bioremediation, decomposition of organic matters, degradation of pollutants, degradation and removal of contaminants, restoration of degraded land, etc.

Plants recruit and interact with soil microorganisms that can alleviate biotic and abiotic stress in host plants. A better understanding of microbial functions will support the development of strategies for plant protection against pathogens and improve the use of beneficial microbes for specific purposes such as plant growth stimulation and increased tolerance to environmental stress. Microbial components interacting with plant signalling and the resulting cross-talk are of interest.

Bacterial quorum sensing (QS) is mediated by certain chemical signal compounds that accumulate according to population density, triggering bacterial community responses that directly contribute to pathogenesis through the synchronized production of virulence factors such as toxins, enzymes, and biofilm formation.  It has important implications in human and veterinary medicine, agriculture, as well as food safety and quality. Studies aiming at elucidating the mechanisms of bacterial virulence and cell-to-cell communication have revealed promising strategies in the development of drugs.

This Special Issue thus aims to provide a state-of-the-art overview of the role of microorganisms in ecosystems functioning under various environmental conditions. We welcome the following article types: original articles, critical reviews, mini-reviews, opinions, research notes, and short communications. Descriptions of cutting-edge methods are also accepted. In this issue, we aim to provide a snapshot of microbial biodiversity, biogeochemical cycles, bioremediation processes, decomposition of organic matters, degradation of pollutants, degradation and removal of contaminants, restoration of degraded land, environmental health sciences, and public health. We also welcome research and review articles on plant growth-promoting Rhizobacteria and quorum sensing by environmental and pathogenic bacteria.

Important Note: All contributions to this Special Issue must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. The journal reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of the peer review. Spontaneous submissions will be considered only if preceded by an abstract describing the focus of the planned contribution.

Dr. Diby Paul
Dr. Udai B. Singh
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 microbiology
  • Bioremediation
  • Microbial biofilm
  • Plant–Microbe Interaction

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Published Papers (4 papers)

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Research

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18 pages, 7479 KiB  
Article
Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes
by Yiran Hou, Rui Jia, Wei Sun, Bing Li and Jian Zhu
Int. J. Mol. Sci. 2024, 25(7), 3786; https://doi.org/10.3390/ijms25073786 - 28 Mar 2024
Cited by 1 | Viewed by 1203
Abstract
Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we [...] Read more.
Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils. Full article
(This article belongs to the Special Issue Microorganisms in the Environment)
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15 pages, 550 KiB  
Article
Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil
by Marta Roszak, Joanna Jabłońska, Xymena Stachurska, Kamila Dubrowska, Justyna Kajdanowicz, Marta Gołębiewska, Anna Kiepas-Kokot, Beata Osińska, Adrian Augustyniak and Jolanta Karakulska
Int. J. Mol. Sci. 2021, 22(24), 13469; https://doi.org/10.3390/ijms222413469 - 15 Dec 2021
Cited by 14 | Viewed by 3734
Abstract
The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were [...] Read more.
The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process. Full article
(This article belongs to the Special Issue Microorganisms in the Environment)
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Review

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26 pages, 2243 KiB  
Review
Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies
by Martha Inés Vélez-Mercado, Alicia Guadalupe Talavera-Caro, Karla María Escobedo-Uribe, Salvador Sánchez-Muñoz, Miriam Paulina Luévanos-Escareño, Fernando Hernández-Terán, Alejandra Alvarado and Nagamani Balagurusamy
Int. J. Mol. Sci. 2021, 22(22), 12249; https://doi.org/10.3390/ijms222212249 - 12 Nov 2021
Cited by 15 | Viewed by 4045
Abstract
Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms [...] Read more.
Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate. Full article
(This article belongs to the Special Issue Microorganisms in the Environment)
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23 pages, 569 KiB  
Review
Selection of Endophytic Strains for Enhanced Bacteria-Assisted Phytoremediation of Organic Pollutants Posing a Public Health Hazard
by Magdalena Anna Karaś, Sylwia Wdowiak-Wróbel and Wojciech Sokołowski
Int. J. Mol. Sci. 2021, 22(17), 9557; https://doi.org/10.3390/ijms22179557 - 3 Sep 2021
Cited by 14 | Viewed by 3492
Abstract
Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and [...] Read more.
Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and derivatives of common organic compounds are currently not included in these regulations. Classical methods of removal of organic pollutants involve economically challenging processes. In this regard, remediation with biological agents can be an alternative. For in situ decontamination, the plant-based approach called phytoremediation can be used. However, the main disadvantages of this method are the limited accumulation capacity of plants, sensitivity to the action of high concentrations of hazardous pollutants, and no possibility of using pollutants for growth. To overcome these drawbacks and additionally increase the efficiency of the process, an integrated technology of bacteria-assisted phytoremediation is being used recently. For the system to work, it is necessary to properly select partners, especially endophytes for specific plants, based on the knowledge of their metabolic abilities and plant colonization capacity. The best approach that allows broad recognition of all relationships occurring in a complex community of endophytic bacteria and its variability under the influence of various factors can be obtained using culture-independent techniques. However, for practical application, culture-based techniques have priority. Full article
(This article belongs to the Special Issue Microorganisms in the Environment)
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