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Microorganisms
Special Issues
Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion
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Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 2812

Special Issue Editors

Dr. Xin Zhao

E-Mail Website
Guest Editor
Department of Environmental Engineering, School of Resources and Civil Engineering, Northeastern University, Shenyang 110819, China
Interests: wastes anaerobic fermentation; bioenergy recovery, biological processes; wastes conversion and biological treatment; wastewater treatment
Special Issues, Collections and Topics in MDPI journals
Dr. Lei Zhang

E-Mail Website
Guest Editor
School of Civil and Environmental Engineering, Queensland University of Technology, Brisbane, QLD, Australia
Interests: anaerobic digestion; value added products production; circular economy; resource recovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, the escalating challenges posed by waste management have necessitated innovative approaches to enhance sustainability. This Special Issue focuses on the cutting-edge bio3 technological methods employed in the treatment and conversion of various waste materials.

Key Topics:

Biodegradation:

  • Mechanisms and pathways through which microorganisms break down organic waste;
  • Roles of enzymes and microbial consortia in enhancing biodegradation processes;
  • Case studies showcasing the successful biodegradation of plastics, agricultural residues, and municipal solid waste.

Biotransformation:

  • Transformation of organic compounds into less harmful or more useful forms through microbial activity;
  • Applications of biotransformation in detoxifying hazardous wastes and recovering valuable resources;
  • Innovative strategies to optimize biotransformation processes using advanced biotechnology.

Bioconversion:

  • Processes that convert biomass and organics in wastewater into biofuels, bioplastics, and other bio-based products;
  • The integration of bioconversion technologies with circular economy principles;
  • Exploration of anaerobic digestion, fermentation, and enzyme-assisted processes for efficient waste-to-energy transformations.

This Special Issue will gather current research articles, communications, and reviews that discuss advancements in sustainable waste and wastewater management through biotechnological innovations. We encourage contributions that highlight interdisciplinary approaches, novel methodologies, and real-world applications that could lead to the enhanced recovery of resources from waste while minimizing environmental impact.

We invite researchers, practitioners, and educators to submit their work to contribute to this vital field and identify sustainable solutions to global waste challenges.

Dr. Xin Zhao
Dr. Lei Zhang
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. 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

  • waste biotechnologies
  • waste management
  • biodegradation
  • biotransformation
  • bioconversion

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

Published Papers (4 papers)

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Research

19 pages, 3549 KiB  
Article
Bacillus amyloliquefaciens SQ-2 and Biochar: A Promising Combination for Enhancing Rice Growth in Pb/Al-Contaminated Acidic Soils
by Guohui Gao, Xue Li, Jiajun Ma, Yumeng Cui, Ming Ying, Lei Huang and Meitong Li
Microorganisms 2025, 13(7), 1556; https://doi.org/10.3390/microorganisms13071556 - 2 Jul 2025
Viewed by 136
Abstract
In this study, Bacillus amyloliquefaciens SQ-2, previously isolated from a commercial watercress paste, was investigated for its potential in promoting rice growth in Pb/Al-contaminated acidic soil, especially when used in conjunction with corn straw biochar. Firstly, the physiological properties of rice were enhanced, [...] Read more.
In this study, Bacillus amyloliquefaciens SQ-2, previously isolated from a commercial watercress paste, was investigated for its potential in promoting rice growth in Pb/Al-contaminated acidic soil, especially when used in conjunction with corn straw biochar. Firstly, the physiological properties of rice were enhanced, with the activities of catalase and superoxide dismutase increasing by 162.5% and 162.9%, respectively. Additionally, the total phenolic and chlorophyll contents of rice increased by 17.6% and 83.7%, respectively. Secondly, the nutrient content of the rice rhizosphere soil was improved. In particular, nitrate nitrogen, available potassium, and sucrase were enhanced by 9.4%, 45.9%, and 466.8%, respectively. Moreover, SQ-2–biochar was demonstrated to have a notable capacity for removing Pb2+ and Al3+. The mineralization of Pb2+ and Al3+ was achieved through the use of SQ-2–biochar, as revealed by SEM-EDS, XRD, XPS, and FT-IR analyses, with the main precipitates being Pb3(PO4)2 and AlPO4. Functional groups such as C-O-C, C=O, N-H, P-O, and -O-H on the microbial surface were found to be involved in the biosorption process of Pb2+ and Al3+. In summary, SQ-2–biochar can effectively mineralize Pb2+ and Al3+, enhance the physiological properties of rice, and improve soil nutrients, thereby augmenting the antioxidant capacity, photosynthesis, and stress resistance of rice and ultimately promoting rice growth. Full article
(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)
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15 pages, 2977 KiB  
Article
Tolerance and Metabolization of High-Concentration Heavy Crude Oil High-Concentration Heavy Crude Oil by Bacillus subtilis
by César Antonio Sáez-Navarrete and Jessica Zerimar Cáceres-Zambrano
Microorganisms 2025, 13(7), 1520; https://doi.org/10.3390/microorganisms13071520 - 29 Jun 2025
Viewed by 274
Abstract
In this comprehensive study, we investigated the degradation capacity and tolerance of the bacterial strain Bacillus subtilis in culture media with high concentrations of heavy crude oil (HCO) as the sole carbon source. Using a meticulously designed experimental approach conducted at room temperature [...] Read more.
In this comprehensive study, we investigated the degradation capacity and tolerance of the bacterial strain Bacillus subtilis in culture media with high concentrations of heavy crude oil (HCO) as the sole carbon source. Using a meticulously designed experimental approach conducted at room temperature (25 °C), we systematically examined various culture media with HCO concentrations of 20%, 35%, and 50% v/v over a 10-week period. The results revealed the microorganism’s remarkable resistance to these HCO concentrations. Biotransformation capacity was confirmed by quantifying CO2 production via gas chromatography, showing substantial bioconversion with a 42% increase in CO2 production. Additionally, changes in surface tension were monitored using the Du Noüy ring method, showing a reduction in the aqueous phase tension from 72.3 to 47.43 mN/m. At the end of the bioconversion period, all treated samples exhibited visible emulsification, indicative of biosurfactant production. This phenomenon was consistent with the observed decrease in surface tension, providing further evidence of biosurfactant-mediated mechanisms. These findings highlight the immense biotechnological potential of B. subtilis to address HCO-related challenges, offering promising prospects for crude oil bioremediation and bioupgrading. Full article
(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)
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11 pages, 3408 KiB  
Article
Study on the Mechanism by Which Fe3+ Promotes Toluene Degradation by Rhodococcus sp. TG-1
by Yue Qiao, Jiajun Ma, Lei Huang, Guohui Gao, Yihe Zhao, Agostinho Antunes and Meitong Li
Microorganisms 2025, 13(2), 468; https://doi.org/10.3390/microorganisms13020468 - 19 Feb 2025
Cited by 2 | Viewed by 713
Abstract
Volatile organic compound pollution caused by toluene has become a global issue. In order to solve this problem, biodegradation of toluene has been applied all over the world. This study investigated the effects of Fe3+ on toluene degradation by the Rhodococcus sp. [...] Read more.
Volatile organic compound pollution caused by toluene has become a global issue. In order to solve this problem, biodegradation of toluene has been applied all over the world. This study investigated the effects of Fe3+ on toluene degradation by the Rhodococcus sp. TG-1. The results show that 1 mg L−1 Fe3+ increased the degradation rate of 600 mg L−1 toluene from 61.9% to 87.2% at 16 h. The acceleration mechanism of Fe3+ was explicated using transmission electron microscope (TEM) and energy-dispersive X-ray spectroscopy (EDX) analyses, coupled plasma optical emission spectroscopy, an enzyme activity assay, and transcriptome analysis. Four genes were detected to be significantly up-regulated under Fe3+ induction, suggesting that Fe3+ might be implicated in toluene degradation. Meanwhile, Fe3+ was a component of the active center of catechol 1,2-dioxygenase (C12O) and significantly improved the enzyme activity of C12O. The mechanism by which Fe3+ accelerates toluene degradation was proposed based on the transcription levels of degradation genes and the enzyme activity of C12O. This study provided an improved method for enhancing the degradation effect of toluene and furthered our comprehension of the mechanism of toluene degradation. Full article
(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)
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15 pages, 3085 KiB  
Article
Biodegradation of Crude Oil and Aniline by Heavy Metal-Tolerant Strain Rhodococcus sp. DH-2
by Zetian Luo, Jiajun Ma, Lei Huang, Dahui Li, Guohui Gao, Yihe Zhao, Agostinho Antunes and Meitong Li
Microorganisms 2024, 12(11), 2293; https://doi.org/10.3390/microorganisms12112293 - 12 Nov 2024
Viewed by 1181
Abstract
Aniline and crude oil are common environmental pollutants that present a significant risk to both the ecological and human health environments. The implementation of efficacious bioremediation strategies is imperative for the elimination of these contaminants. In this study, a bacterial strain designated DH-2 [...] Read more.
Aniline and crude oil are common environmental pollutants that present a significant risk to both the ecological and human health environments. The implementation of efficacious bioremediation strategies is imperative for the elimination of these contaminants. In this study, a bacterial strain designated DH-2 was isolated from soil contaminated with aniline. The strain was identified as belonging to the genus Rhodococcus. The optimal conditions for the growth and aniline degradation by strain DH-2 were determined to be pH 8.0 and 35 °C, respectively. Under these conditions, the degradation rate of aniline at a concentration of 1000 mg/L exceeded 90% within 36 h. Even in the presence of 4% NaCl, the degradation rate remained above 60%. HPLC–MS analysis revealed that the aniline degradation pathway of strain DH-2 follows the catechol pathway. Additionally, strain DH-2 is capable of utilizing crude oil as the sole carbon source, achieving a degradation rate of 91.0% for 2% crude oil concentration within 4 days. In soil modeling experiments, strain DH-2 was observed to degrade aniline and crude oil under triple stress conditions, including 1000 mg/L aniline, 2% crude oil, and 20 mg/L Fe(II) or Pb(II). Complete degradation of aniline and crude oil was achieved after 3 days and 12 days, respectively. The addition of Fe(II) or Pb(II) ions was found to enhance the degradation ability of DH-2. These results demonstrate that strain DH-2 is an extremely effective biodegradable strain, with potential applications in the remediation of environments contaminated with aniline and crude oil, even in the presence of heavy metals. Full article
(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)
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