Microbiota Dynamics in Environmental and Host Systems: From Ecology to Applications

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

Deadline for manuscript submissions: 31 July 2026 | Viewed by 1066

Special Issue Editors


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Guest Editor
Department of Environmental Engineering, University of Patras, Agrinio, Greece
Interests: microbial ecology; genomics; metagenomics; endosymbionts
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Environmental Engineering, Faculty of Engineering, Democritus University of Thrace, Vas. Sofias 12, Xanthi 67100, Greece
Interests: membrane bioreactors; activated sludge microbiota; biofouling; fouling prevention; environmental microbiology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Laboratory of Biotechnology and Valorisation of Bio-GeoRessources, University of Manouba, Ariana 2020, Tunisia
Interests: microbiome; drug resistance; cancer

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Guest Editor
Laboratoire de Biotechnologie et de Valorisation des Bio-Géo Ressources, Institut Supérieur de Biotechnologie, Université de la Manouba, Manouba, Tunisia
Interests: micobiolgy; molecular biology; genomics

Special Issue Information

Dear Colleagues,

This Special Issue will focus on the complex interactions between microorganisms and their environments, covering both natural ecosystems and host-associated microbiomes. We welcome original research articles, comprehensive reviews, and short communications that explore the following:

  • Environmental microbiome dynamics and community structure;
  • Host–microbe interactions across different organisms (plants, animals, humans);
  • Microbial ecology in extreme and changing environments;
  • Applications of microbiome research in biotechnology and medicine;
  • Novel methodological approaches in microbiome analysis;
  • Microbiome responses to environmental stressors and climate change.

This Special Issue aims to bridge the gap between fundamental microbial ecology research and practical applications, providing insights into how microbiota function across diverse systems.

Please proceed with creating the Special Issue website. We are ready to begin promoting it and inviting high-quality submissions.

Dr. George Tsiamis
Dr. Spyridon Ntougias
Dr. Soumaya Kouidhi
Dr. Mouna Mahjoubi
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 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

  • environment 
  • microbiome 
  • host–microbe interactions 
  • microbial ecology

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Published Papers (1 paper)

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Research

18 pages, 6303 KB  
Article
A Microbial Inoculum (PLC-8) Improves Composting of Spent Mushroom Substrate
by Jiamin Yin, Hairu Yu, Sen Qi, Yufu Hu, Di Chen, Hongyan Zhao and Zongjun Cui
Microorganisms 2025, 13(11), 2627; https://doi.org/10.3390/microorganisms13112627 - 19 Nov 2025
Cited by 5 | Viewed by 733
Abstract
Composting is a useful way to reduce and recycle agricultural and forestry waste; however, low-temperature environments can inhibit the microbial processes involved in composting. Spent mushroom substrate has a high lignocellulose content, making it particularly difficult to decompose. There is a need to [...] Read more.
Composting is a useful way to reduce and recycle agricultural and forestry waste; however, low-temperature environments can inhibit the microbial processes involved in composting. Spent mushroom substrate has a high lignocellulose content, making it particularly difficult to decompose. There is a need to explore methods for effectively promoting microbial activity and enhancing composting efficiency under low-temperature conditions. This study explored the use of C/N ratio adjustments and a microbial inoculum (PLC-8; comprising Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Basidiomycota, Ascomycota, and Cryptomonadales) to improve spent mushroom substrate composting in a low-temperature environment. The temperature, lignocellulose content, pH, and gas emissions were measured during composting, and the microbial community structure was determined to explore associations between biotic and abiotic factors. Compost piles with PLC-8 entered the high-temperature period in 25 days, which was 15 days earlier than the control pile. When the C/N ratio was adjusted to 30:1 and PLC-8 was applied, the cellulose and hemicellulose degradation rates after 60 days were 88.04% and 71.95%, whereas the control group only exhibited degradation rates of 25.39% and 35.64%. Moreover, PLC-8 significantly increased CH4 and CO2 emissions and reduced nitrous oxide emissions. Microbial community analysis showed that Proteobacteria and Ascomycota were the dominant phyla in the piles with PLC-8, and these phyla were responsible for lignocellulose decomposition and carbon metabolism. Full article
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