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Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024; 74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Hongyu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark.
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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Gutbier U, Korp J, Scheufler L, Ostermann K. Genetic modules for α-factor pheromone controlled growth regulation of Saccharomyces cerevisiae. Eng Life Sci 2024; 24:e2300235. [PMID: 39113811 PMCID: PMC11300815 DOI: 10.1002/elsc.202300235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 08/10/2024] Open
Abstract
Saccharomyces cerevisiae is a commonly used microorganism in the biotechnological industry. For the industrial heterologous production of compounds, it is of great advantage to work with growth-controllable yeast strains. In our work, we utilized the natural pheromone system of S. cerevisiae and generated a set of different strains possessing an α-pheromone controllable growth behavior. Naturally, the α-factor pheromone is involved in communication between haploid S. cerevisiae cells. Perception of the pheromone initiates several cellular changes, enabling the cells to prepare for an upcoming mating event. We exploited this natural pheromone response system and developed two different plasmid-based modules, in which the target genes, MET15 and FAR1, are under control of the α-factor sensitive FIG1 promoter for a controlled expression in S. cerevisiae. Whereas expression of MET15 led to a growth induction, FAR1 expression inhibited growth. The utilization of low copy number or high copy number plasmids for target gene expression and different concentrations of α-factor allow a finely adjustable control of yeast growth rate.
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Affiliation(s)
- Uta Gutbier
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
- Else Kröner Fresenius Center for Digital HealthFaculty of Medicine Carl Gustav CarusTUD Dresden University of TechnologyDresdenGermany
| | - Juliane Korp
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Lennart Scheufler
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Kai Ostermann
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
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3
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Guo L, Xi B, Lu L. Strategies to enhance production of metabolites in microbial co-culture systems. BIORESOURCE TECHNOLOGY 2024; 406:131049. [PMID: 38942211 DOI: 10.1016/j.biortech.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.
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Affiliation(s)
- Lichun Guo
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bingwen Xi
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China
| | - Liushen Lu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China.
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Sun Y, Xia W, Tang L, Xiu Z, Jin W, Wang X, Tao J, Liu H, An H, Li Y, Tong Y. Effects of thermophilic and acidophilic microbial consortia on maize wet-milling steeping. BIORESOUR BIOPROCESS 2024; 11:68. [PMID: 39012554 PMCID: PMC11252109 DOI: 10.1186/s40643-024-00783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
To understand the ecology of species and promote biotechnology through beneficial strain selection for improving starch yield in maize wet-milling steeping, bacterial diversity and community structure during the counter-current steeping process in a commercial steeping system were characterized and investigated. The microbial diversity in the steeping liquor, which consisted of 16 phyla, 131 families, and 290 genera, was more abundant compared to those present on the surface of unsteeped maize. As the counter-current steeping progressed, exposing newer maize to the older steepwater, Lactobacillus dominated, replacing Rahnella, Pseudomonas, Pantoea, and Serratia. The thermophilic and acidophilic microbial consortia were enriched through adaptive evolution engineering and employed to improve starch yield. Several steeping strategies were evaluated, including water alone, SO2 alone, mono-culture of B. coagulans, microbial consortia, and a combination of consortium and SO2. Combining the microbial consortium with SO2 significantly increased the starch yield to, about 66.4 ± 0.5%, a 22% and 46% increase over SO2 alone and the consortium alone, respectively. Scanning electron microscope (SEM) of steeped maize structure indicated that the combination of consortium and SO2 disrupted the protein matrix and widened gaps between starch granules in maize endosperm. This released proteins into the steepwater and left starch granules in the aleurone layer. The steeping strategy of using thermophilic and acidophilic microbial consortium as additives shows potential application as an environmentally friendly alternative to conventional maize steeping procedures.
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Affiliation(s)
- Yaqin Sun
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, P.R. China.
| | - Wenjing Xia
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, P.R. China
| | - Langjun Tang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, P.R. China
| | - Zhilong Xiu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, Liaoning Province, 116024, P.R. China
| | - Weiwu Jin
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Xiaoyan Wang
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Jin Tao
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Haijun Liu
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Hongyan An
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Yi Li
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China
| | - Yi Tong
- Jilin COFCO Biochemistry Co., Ltd. (National Engineering Research Center of Corn Deep Processing), 1717 Xiantai Street, Nanguan District, Changchun City, Jilin Province, 130033, P.R. China.
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Rezaei Z, Moghimi H. Fungal-bacterial consortia: A promising strategy for the removal of petroleum hydrocarbons. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116543. [PMID: 38833981 DOI: 10.1016/j.ecoenv.2024.116543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/06/2024]
Abstract
Nowadays, petroleum hydrocarbon pollution is one of the most widespread types of contamination that poses a serious threat to both public health and the environment. Among various physicochemical methods, bioremediation is an eco-friendly and cost-effective way to eliminate petroleum hydrocarbon pollutants. The successful degradation of all hydrocarbon components and the achievement of optimal efficiency are necessary for the success of this process. Using potential microbial consortia with rich metabolic networks is a promising strategy for addressing these challenges. Mixed microbial communities, comprising both fungi and bacteria, exhibit diverse synergistic mechanisms to degrade complex hydrocarbon contaminants, including the dissemination of bacteria by fungal hyphae, enhancement of enzyme and secondary metabolites production, and co-metabolism of pollutants. Compared to pure cultures or consortia of either fungi or bacteria, different studies have shown increased bioremediation of particular contaminants when combined fungal-bacterial treatments are applied. However, antagonistic interactions, like microbial competition, and the production of inhibitors or toxins can observed between members. Furthermore, optimizing environmental factors (pH, temperature, moisture, and initial contaminant concentration) is essential for consortium performance. With the advancements in synthetic biology and gene editing tools, it is now feasible to design stable and robust artificial microbial consortia systems. This review presents an overview of using microbial communities for the removal of petroleum pollutants by focusing on microbial degradation pathways, and their interactions. It also highlights the new strategies for constructing optimal microbial consortia, as well as the challenges currently faced and future perspectives of applying fungal-bacterial communities for bioremediation.
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Affiliation(s)
- Zeinab Rezaei
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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Holt JR, Cavichiolli de Oliveira N, Medina RF, Malacrinò A, Lindsey ARI. Insect-microbe interactions and their influence on organisms and ecosystems. Ecol Evol 2024; 14:e11699. [PMID: 39041011 PMCID: PMC11260886 DOI: 10.1002/ece3.11699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Microorganisms are important associates of insect and arthropod species. Insect-associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect-associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect-microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect-microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities.
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Affiliation(s)
| | | | - Raul F. Medina
- Department of EntomologyTexas A&M University, Minnie Bell Heep CenterCollege StationTexasUSA
| | - Antonino Malacrinò
- Department of AgricultureUniversità Degli Studi Mediterranea di Reggio CalabriaReggio CalabriaItaly
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Alam M, Pandit B, Moin A, Iqbal UN. Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture. Indian J Microbiol 2024; 64:343-366. [PMID: 39011025 PMCID: PMC11246410 DOI: 10.1007/s12088-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/07/2024] [Indexed: 07/17/2024] Open
Abstract
Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.
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Affiliation(s)
- Masrure Alam
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Baishali Pandit
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
- Department of Botany, Surendranath College, 24/2 MG Road, Kolkata, West Bengal 700009 India
| | - Abdul Moin
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
| | - Umaimah Nuzhat Iqbal
- Microbial Ecology and Physiology Lab, Department of Biological Sciences, Aliah University, IIA/27 New Town, Kolkata, West Bengal 700160 India
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Atoki AV, Aja PM, Shinkafi TS, Ondari EN, Awuchi CG. Naringenin: its chemistry and roles in neuroprotection. Nutr Neurosci 2024; 27:637-666. [PMID: 37585716 DOI: 10.1080/1028415x.2023.2243089] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
According to epidemiological research, as the population ages, neurological illnesses are becoming a bigger issue. Despite improvements in the treatment of these diseases, there are still widespread worries about how to find a long-lasting remedy. Several neurological diseases can be successfully treated with natural substances. As a result, current research has been concentrated on finding effective neuroprotective drugs with improved efficacy and fewer side effects. Naringenin is one potential treatment for neurodegenerative diseases. Many citrus fruits, tomatoes, bergamots, and other fruits are rich in naringenin, a flavonoid. This phytochemical is linked to a variety of biological functions. Naringenin has attracted a lot of interest for its ability to exhibit neuroprotection through several mechanisms. In the current article, we present evidence from the literature that naringenin reduces neurotoxicity and oxidative stress in brain tissues. Also, the literatures that are currently accessible shows that naringenin reduces neuroinflammation and other neurological anomalies. Additionally, we found several studies that touted naringenin as a promising anti-amyloidogenic, antidepressant, and neurotrophic treatment option. This review's major goal is to reflect on advancements in knowledge of the molecular processes that underlie naringenin's possible neuroprotective effects. Furthermore, this article also provides highlights of Naringenin with respect to its chemistry and pharmacokinetics.
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Affiliation(s)
| | - Patrick Maduabuchi Aja
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Erick Nyakundi Ondari
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- School of Pure and Applied Sciences, Department of Biological Sciences, Kisii University, Kisii, Kenya
| | - Chinaza Godswill Awuchi
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- School of Natural and Applied Sciences, Kampala International University, Kampala, Uganda
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Visca A, Di Gregorio L, Clagnan E, Bevivino A. Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality. ENVIRONMENTAL RESEARCH 2024; 248:118395. [PMID: 38307185 DOI: 10.1016/j.envres.2024.118395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.
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Affiliation(s)
- Andrea Visca
- Department for Sustainability, Biotechnologies and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123, Rome, Italy.
| | - Luciana Di Gregorio
- Department for Sustainability, Biotechnologies and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123, Rome, Italy
| | - Elisa Clagnan
- Department for Sustainability, Biotechnologies and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123, Rome, Italy
| | - Annamaria Bevivino
- Department for Sustainability, Biotechnologies and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123, Rome, Italy
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Liu Y, Xue B, Liu H, Wang S, Su H. Rational construction of synthetic consortia: Key considerations and model-based methods for guiding the development of a novel biosynthesis platform. Biotechnol Adv 2024; 72:108348. [PMID: 38531490 DOI: 10.1016/j.biotechadv.2024.108348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The rapid development of synthetic biology has significantly improved the capabilities of mono-culture systems in converting different substrates into various value-added bio-chemicals through metabolic engineering. However, overexpression of biosynthetic pathways in recombinant strains can impose a heavy metabolic burden on the host, resulting in imbalanced energy distribution and negatively affecting both cell growth and biosynthesis capacity. Synthetic consortia, consisting of two or more microbial species or strains with complementary functions, have emerged as a promising and efficient platform to alleviate the metabolic burden and increase product yield. However, research on synthetic consortia is still in its infancy, with numerous challenges regarding the design and construction of stable synthetic consortia. This review provides a comprehensive comparison of the advantages and disadvantages of mono-culture systems and synthetic consortia. Key considerations for engineering synthetic consortia based on recent advances are summarized, and simulation and computational tools for guiding the advancement of synthetic consortia are discussed. Moreover, further development of more efficient and cost-effective synthetic consortia with emerging technologies such as artificial intelligence and machine learning is highlighted.
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Affiliation(s)
- Yu Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Boyuan Xue
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Hao Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
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Liao J, Pan H, Huang G, Gong H, Chen Z, Yin T, Zhang B, Chen T, Zheng M, Cai L. T cell cascade regulation initiates systemic antitumor immunity through living drug factory of anti-PD-1/IL-12 engineered probiotics. Cell Rep 2024; 43:114086. [PMID: 38598335 DOI: 10.1016/j.celrep.2024.114086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Immune checkpoint blockade (ICB) has revolutionized cancer therapy but only works in a subset of patients due to the insufficient infiltration, persistent exhaustion, and inactivation of T cells within a tumor. Herein, we develop an engineered probiotic (interleukin [IL]-12 nanoparticle Escherichia coli Nissle 1917 [INP-EcN]) acting as a living drug factory to biosynthesize anti-PD-1 and release IL-12 for initiating systemic antitumor immunity through T cell cascade regulation. Mechanistically, INP-EcN not only continuously biosynthesizes anti-PD-1 for relieving immunosuppression but also effectively cascade promote T cell activation, proliferation, and infiltration via responsive release of IL-12, thus reaching a sufficient activation threshold to ICB. Tumor targeting and colonization of INP-EcNs dramatically increase local drug accumulations, significantly inhibiting tumor growth and metastasis compared to commercial inhibitors. Furthermore, immune profiling reveals that anti-PD-1/IL-12 efficiently cascade promote antitumor effects in a CD8+ T cell-dependent manner, clarifying the immune interaction of ICB and cytokine activation. Ultimately, such engineered probiotics achieve a potential paradigm shift from T cell exhaustion to activation and show considerable promise for antitumor bio-immunotherapy.
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Affiliation(s)
- Jianhong Liao
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Hong Pan
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China.
| | - Guojun Huang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Han Gong
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Ze Chen
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Ting Yin
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Baozhen Zhang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Tingtao Chen
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang 330031, China.
| | - Mingbin Zheng
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China; National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518112, China.
| | - Lintao Cai
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen 518055, China; Sino-Euro Center of Biomedicine and Health, Luohu Shenzhen 518024, China.
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12
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Li X, Li G, Wang J, Li X, Yang Y, Song D. Elucidating polyethylene microplastic degradation mechanisms and metabolic pathways via iron-enhanced microbiota dynamics in marine sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133655. [PMID: 38310843 DOI: 10.1016/j.jhazmat.2024.133655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/06/2024]
Abstract
The extensive use of plastics has given rise to microplastics, a novel environmental contaminant that has sparked considerable ecological and environmental concerns. Biodegradation offers a more environmentally friendly approach to eliminating microplastics, but their degradation by marine microbial communities has received little attention. In this study, we used iron-enhanced marine sediment to augment the natural bacterial community and facilitate the decomposition of polyethylene (PE) microplastics. The introduction of iron-enhanced sediment engendered an augmented bacterial biofilm formation on the surface of polyethylene (PE), thereby leading to a more pronounced degradation effect. This novel observation has been ascribed to the oxidative stress-induced generation of a variety of oxygenated functional groups, including hydroxyl (-OH), carbonyl (-CO), and ether (-C-O) moieties, within the microplastic substrate. The analysis of succession in the community structure of sediment bacteria during the degradation phase disclosed that Acinetobacter and Pseudomonas emerged as the principal bacterial players in PE degradation. These taxa were directly implicated in oxidative metabolic pathways facilitated by diverse oxidase enzymes under iron-facilitated conditions. The present study highlights bacterial community succession as a new pivotal factor influencing the complex biodegradation dynamics of polyethylene (PE) microplastics. This investigation also reveals, for the first time, a unique degradation pathway for PE microplastics orchestrated by the multifaceted marine sediment microbiota. These novel insights shed light on the unique functional capabilities and internal biochemical mechanisms employed by the marine sediment microbiota in effectively degrading polyethylene microplastics.
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Affiliation(s)
- Xionge Li
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guangbi Li
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jiaxin Wang
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xinyi Li
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuru Yang
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Donghui Song
- College of Marine and Environmental, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin 300457, China.
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13
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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14
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Zhou T, Wu J, Tang H, Liu D, Jeon BH, Jin W, Wang Y, Zheng Y, Khan A, Han H, Li X. Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer. NPJ Biofilms Microbiomes 2024; 10:6. [PMID: 38245564 PMCID: PMC10799920 DOI: 10.1038/s41522-024-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jingyuan Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Haibo Tang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Korea
| | - Weilin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yiqing Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | | | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huawen Han
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China.
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China.
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15
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Gao Y, Li F, Luo Z, Deng Z, Zhang Y, Yuan Z, Liu C, Rao Y. Modular assembly of an artificially concise biocatalytic cascade for the manufacture of phenethylisoquinoline alkaloids. Nat Commun 2024; 15:30. [PMID: 38167860 PMCID: PMC10761944 DOI: 10.1038/s41467-023-44420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Plant-derived alkaloids are an important class of pharmaceuticals. However, they still rely on phytoextraction to meet their diverse market demands. Since multistep biocatalytic cascades have begun to revolutionize the manufacture of natural or unnatural products, to address the synthetic challenges of alkaloids, herein we establish an artificially concise four-enzyme biocatalytic cascade with avoiding plant-derived P450 modification for synthesizing phenethylisoquinoline alkaloids (PEIAs) after enzyme discovery and enzyme engineering. Efficient biosynthesis of diverse natural and unnatural PEIAs is realized from readily available substrates. Most importantly, the scale-up preparation of the colchicine precursor (S)-autumnaline with a high titer is achieved after replacing the rate-limiting O-methylation by the plug-and-play strategy. This study not only streamlines future engineering endeavors for colchicine biosynthesis, but also provides a paradigm for constructing more artificial biocatalytic cascades for the manufacture of diverse alkaloids through synthetic biology.
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Affiliation(s)
- Yue Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Fei Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zhengshan Luo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zhiwei Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Yan Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Changmei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China.
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16
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Li L, Li N, Fu J, Liu J, Ping Wen X, Cao H, Xu H, Zhang Y, Cao R. Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar. Food Res Int 2024; 175:113742. [PMID: 38129049 DOI: 10.1016/j.foodres.2023.113742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/09/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Traditional bran vinegar brewing unfolds through natural fermentation, a process driven by spontaneous microbial activity. The unique metabolic activities of various microorganisms lead to distinct flavors and qualities in each batch of vinegar, making it challenging to consistently achieve the desired characteristic flavor compounds. Therefore, identifying the critical microbial species responsible for flavor production and designing starter cultures with improved fermentation efficiency and characteristic flavors are effective methods to address this discrepancy. In this study, 11 core functional microbial species affecting the fermentation flavor of Sichuan shai vinegar (Cupei were placed outside solarization and night-dew for more than one year, and vinegar was the liquid leached from Cupei) (SSV), were revealed by combining PacBio full-length diversity sequencing based on previous metagenomics. The effects of environmental factors and microbial interactions on the growth of 11 microorganisms during fermentation were verified using fermentation experiments. Ultimately, the microbial community was strategically synthesized using a 'top-down' approach, successfully replicating the distinctive flavor profile of Sichuan shai vinegar (SSV). The results showed that the interaction between microorganisms and environmental factors affected microorganism growth. Compared with traditional fermentation, the synthetic microbial community's vinegar-fermented grains (Cupei) can reproduce the key flavor of SSV and is conducive to the production of amino acids. In this study, the key flavor of SSV was reproduced through rational design of the synthetic microbial community. This achievement holds profound significance for the broader application of microbiome assembly strategies in the realm of fermented foods.
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Affiliation(s)
- Li Li
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Yibin 644000, China.
| | - Na Li
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Yibin 644000, China
| | - Junjie Fu
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Yibin 644000, China
| | - Jun Liu
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Yibin 644000, China
| | - Xue Ping Wen
- College of Biotechnology Engineering, Sichuan University of Science and Engineering, Yibin 644000, China
| | - Hong Cao
- Sichuan Taiyuanjing vinegar Co., Ltd, Zigong 643000, China
| | - Hongwei Xu
- Sichuan Taiyuanjing vinegar Co., Ltd, Zigong 643000, China
| | - Ying Zhang
- Sichuan Taiyuanjing vinegar Co., Ltd, Zigong 643000, China
| | - Rong Cao
- Sichuan Taiyuanjing vinegar Co., Ltd, Zigong 643000, China
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17
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Effendi SSW, Ng IS. Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production. Biotechnol Adv 2023; 69:108270. [PMID: 37852421 DOI: 10.1016/j.biotechadv.2023.108270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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18
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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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19
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Qi J, Zhou Q, Huang D, Yu Z, Meng F. Construction of synthetic anti-fouling consortia: fouling control effects and polysaccharide degradation mechanisms. Microb Cell Fact 2023; 22:230. [PMID: 37936187 PMCID: PMC10631183 DOI: 10.1186/s12934-023-02235-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
The physical states and chemical components of bulk sludge determine the occurrence and development of membrane fouling in membrane bioreactors. Thus, regulation of sludge suspensions can provide new strategies for fouling control. In this study, we used "top-down" enrichment to construct a synthetic anti-fouling consortium (SAC) from bio-cake and evaluate its roles in preventing membrane fouling. The SAC was identified as Massilia-dominated and could almost wholly degrade the alginate solution (1,000 mg/L) within 72 h. Two-dimensional Fourier transformation infrared correlation spectroscopy (2D-FTIR-CoS) analysis demonstrated that the SAC induced the breakage of glycosidic bond in alginates. The co-cultivation of sludge with a low dosage of SAC (ranging from 0 to 1%) led to significant fouling mitigation, increased sludge floc size, and decreased unified membrane fouling index value (0.55 ± 0.06 and 0.11 ± 0.05). FTIR spectra and X-ray spectroscopy analyses demonstrated that the addition of SAC decreased the abundance of the O-acetylation of polysaccharides in extracellular polymeric substances. Secondary derivatives analysis of amide I spectra suggested a strong reduction in the α-helix/(β-sheet + random coil) ratio in the presence of SAC, which was expected to enhance cell aggregation. Additionally, the extracellular secretions of SAC could both inhibit biofilm formation and strongly disperse the existing biofilm strongly during the biofilm incubation tests. In summary, this study illustrates the feasibility and benefits of using SAC for fouling control and provides a new strategy for fouling control.
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Affiliation(s)
- Ji Qi
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qicheng Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Danlei Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China.
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20
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Llamas M, Greses S, Magdalena JA, González-Fernández C, Tomás-Pejó E. Microbial co-cultures for biochemicals production from lignocellulosic biomass: A review. BIORESOURCE TECHNOLOGY 2023; 386:129499. [PMID: 37460020 DOI: 10.1016/j.biortech.2023.129499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Global reliance on fossil oil should shift to cleaner alternatives to get a decarbonized society. One option to achieve this ambitious goal is the use of biochemicals produced from lignocellulosic biomass (LCB). The inherent low biodegradability of LCB and the inhibitory compounds that might be released during pretreatment are two main challenges for LCB valorization. At microbiological level, constraints are mostly linked to the need for axenic cultures and the preference for certain carbon sources (i.e., glucose). To cope with these issues, this review focuses on efficient LCB conversion via the sugar platform as well as an innovative carboxylate platform taking advantage of the co-cultivation of microorganisms. This review discusses novel trends in the use of microbial communities and co-cultures aiming at different bioproducts co-generation in single reactors as well as in sequential bioprocess combination. The outlook and further perspectives of these alternatives have been outlined for future successful development.
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Affiliation(s)
- Mercedes Llamas
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Silvia Greses
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain
| | - Jose Antonio Magdalena
- LBE, Univ Montpellier, INRAE, 102 avenue des Étangs, F-11100 Narbonne, France; Vicerrectorado de Investigación y Transferencia de la Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Cristina González-Fernández
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, Valladolid 47011, Spain; Institute of Sustainable Processes, Dr. Mergelina, s/n, Valladolid 47011, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy, Madrid, Spain.
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21
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Shan X, Guo H, Ma F, Shan Z. Enhanced treatment of synthetic wastewater by bioaugmentation with a constructed consortium. CHEMOSPHERE 2023; 338:139520. [PMID: 37454986 DOI: 10.1016/j.chemosphere.2023.139520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Bioaugmentation by adding well-functioning mixed microorganism consortia represents a potentially useful approach to improve contaminant removal in wastewater treatment plants (WWTPs). However, unfavorable environmental conditions (i.e., low temperatures) can severely inhibit microbial activity, drawing our attention to constructing cold-tolerant microorganism preparations and investigating their availability in practical applications. Here we screened four in situ functional isolates from the activated sludge of secondary sedimentation tanks in WWTPs to construct a psychrophilic microbial consortium, which was used to perform bioaugmentation for enhanced removal of nitrogen and phosphorus under low temperatures. The consortium was established by cocultivation of four isolates, characterized by 16 S rRNA as the COD-degrading bacterium Aeromonas sp. Z3, aerobic denitrifying bacterium Acinetobacter sp. HF9, nitrifying bacterium Klebsiella sp. X8, and polyphosphate-accumulating bacterium Pseudomonas sp. PC5 respectively. The microorganism preparation was composed of Z3, HF9, X8, and PC5 under the ratio of 1: 1: 3: 1, which can exert optimal pollutant removal under the conditions of 12 °C, 6.0-9.0 pH, 120-200 r‧min-1, and a dosage of 5% (V/V). A 30-day continuous operation of the bioaugmented and control sequencing batch reactors (SBRs) was investigated, and the bioaugmented SBR showed a shorter start-up stage and a more stable operating situation. Compared to the control SBR, the COD, NH4+-N, TN, and TP removal efficiency of the bioaugmented SBR increased by an average of 7.95%, 9.05%, 9.54%, and 7.45% respectively. The analysis of the microbial community revealed that the introduced isolates were dominant in the activated sludge and that functional taxa such as Proteobacteria, Bacteroidota, and Actinobacteria were further enriched after a period of bioaugmentation. The study provides some basis and guidance for the practical application of how to strengthen the stable operation of WWTPs under low temperatures.
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Affiliation(s)
- Xiaoqing Shan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Haijuan Guo
- School of Environment, Liaoning University, Shenyang, 110036, PR China.
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; School of Environment, Liaoning University, Shenyang, 110036, PR China.
| | - Zelin Shan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
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22
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Ma Y, Wu S, Xu Y, Zhou X, Ruan A. Degradation characteristics of polyethylene film by microorganisms from lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122115. [PMID: 37385361 DOI: 10.1016/j.envpol.2023.122115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
Polyethylene (PE) exists widely in many habitats as a persistent organic pollution and poses a major threat to the ecological environment. In this study, bacterial communities in freshwater lake sediments were exposed to culture media using PE films as the sole carbon source in aerobic and anaerobic microculture environments, and they were able to adhere and adapt to the PE films for a longer period of time. The results demonstrated that the pH value of the medium in the two cultural conditions was distinct, as were the rates of films weight loss and surface functional group alterations. We also concluded the certain bacterial genera from freshwater lake sediments who may be able to degrade PE films under either aerobic or anaerobic conditions. Simultaneously, the dominating bacterial communities between the medium and the film differed significantly under two cultural settings, as did the community composition, while metabolism was the primary function.
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Affiliation(s)
- Yunmei Ma
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Yaofei Xu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Xiaotian Zhou
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; College of Hydrology and Water Resources, Hohai University, Nanjing, 210098, China.
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23
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Li C, Zheng H, Li H, Liu L, Wang J, Ni J. Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis. Chembiochem 2023; 24:e202300122. [PMID: 37401840 DOI: 10.1002/cbic.202300122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.
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Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
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24
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Liu Z, Xu Y, Wang Z, Zhu L, Li Z, Jiang Y, Zhan X, Gao M. Promoting substrates uptake and curdlan synthesis of Agrobacterium sp. by attenuating the exopolysaccharide encapsulation. Carbohydr Polym 2023; 315:120941. [PMID: 37230642 DOI: 10.1016/j.carbpol.2023.120941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023]
Abstract
During curdlan production by Agrobacterium sp., the secreted exopolysaccharide (EPS) gradually encapsulated Agrobacterium sp., accompanied by cell aggregation, resulted in inhibited substrate uptake and curdlan synthesis. To relieve the EPS encapsulation effect, the shake-flask culture medium was quantitatively supplemented with 2 % to 10 % endo-β-1,3-glucanase (BGN), while obtaining curdlan with a decreased weight-average molecular weight ranging from 18.99 × 104 Da to 3.20 × 104 Da. In a 7-L bioreactor, the 4 % BGN supplement substantially attenuated the EPS encapsulation, resulting in increased glucose consumption and curdlan yield to 66.41 g/L and 34.53 g/L after fermentation of 108 h, which improved 43 % and 67 %, respectively compared with the control. The disruption of EPS encapsulation with BGN treatment accelerated the regeneration of ATP and UTP, resulting in sufficient uridine diphosphate glucose for curdlan synthesis. The upregulation of related genes at the transcription level reveals that the respiratory metabolic intensity, the energy regeneration efficiency, and the curdlan synthetase activity were enhanced. This study presents a simple and novel strategy of relieving the effects of EPS encapsulation on the metabolism of Agrobacterium sp. for the high-yield and value-added production of curdlan, which could be potentially applied in producing other EPSs.
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Affiliation(s)
- Zhilei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Ying Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Zichao Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Li Zhu
- L & F Biotech. Ltd., 7144 Collister Dr., Burnaby, BC V5A3P6, Canada
| | - Zhitao Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Yun Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Xiaobei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Minjie Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China.
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25
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Jin H, Nie Z, Niu H, Tan J, Huang S, Yan B, Cheng B, Yang H. Detoxification of typical nitrogenous heterocyclic compound from pharmaceutical wastewater by mixed microbial consortia. CHEMOSPHERE 2023:139000. [PMID: 37217008 DOI: 10.1016/j.chemosphere.2023.139000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/10/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
Microbial consortia HY3 and JY3 with high degradation efficiency of 2-Diethylamino-4-hydroxy-6-methylpyrimidine (DHMP) were isolated from aerobic and parthenogenic ponds of DHMP-containing pharmaceutical wastewater, respectively. Both consortia were enriched and reached stable degradation performance with a DHMP concentration of 1500 mg L-1. The DHMP degradation efficiencies of HY3 and JY3 were 95.66% ± 0.24% and 92.16% ± 2.34% under the condition of shaking at 180 r·min-1 and the temperature of 30 °C for 72 h. And the removal efficiencies of chemical oxygen demand were 89.14% ± 4.78% and 80.30% ± 11.74%, respectively. High-throughput sequencing results indicated that three bacterial phyla of Proteobacteria, Bacteroidetes, and Actinobacteria were dominant in both HY3 and JY3, but their dominances varied. At the genus level, the richness of Unclassified Comamonadaceae (34.23%), Paracoccus (14.75%), and Brevundimonas (13.94%) ranked top three in HY3 whereas Unclassified Comamonadaceae (40.80%), Unclassified Burkholderiales (13.81%) and Delftia (13.11%) were dominant in JY3. The metabolites of DHMP degradation by HY3 and JY3 were analyzed in detail. Two pathways for cleavage of the nitrogenous heterocyclic ring were speculated, one of which was identified for the first time in this study.
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Affiliation(s)
- Hongyu Jin
- College of Resources and Environment, Hunan Agricultural University, 410128, Changsha, China; Yueyang Agricultural and Rural Development Group Co., Ltd., 414022, Yueyang, China
| | - Zimeng Nie
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hongyu Niu
- College of Resources and Environment, Hunan Agricultural University, 410128, Changsha, China
| | - Ju Tan
- Changsha Environmental Monitoring Center Station, 410001, Changsha, China
| | - Shuie Huang
- Changsha Xinkaipu Water Purification Factory, 410002, Changsha, China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, 410128, Changsha, China
| | - Bozhi Cheng
- Changsha Ecological Environment Bureau, 410128, Changsha, China
| | - Haijun Yang
- College of Resources and Environment, Hunan Agricultural University, 410128, Changsha, China.
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26
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Han JC, Ahmad M, Yousaf M, Rahman SU, Sharif HMA, Zhou Y, Yang B, Huang Y. Strategic analysis on development of simultaneous adsorption and catalytic biodegradation over advanced bio-carriers for zero-liquid discharge of industrial wastewater. CHEMOSPHERE 2023; 332:138871. [PMID: 37172628 DOI: 10.1016/j.chemosphere.2023.138871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/15/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
With rapid industrial development, millions of tons of industrial wastewater are produced that contain highly toxic, carcinogenic, mutagenic compounds. These compounds may consist of high concentration of refractory organics with plentiful carbon and nitrogen. To date, a substantial proportion of industrial wastewater is discharged directly to precious water bodies due to the high operational costs associated with selective treatment methods. For example, many existing treatment processes rely on activated sludge-based treatments that only target readily available carbon using conventional microbes, with limited capacity for nitrogen and other nutrient removal. Therefore, an additional set-up is often required in the treatment chain to address residual nitrogen, but even after treatment, refractory organics persist in the effluents due to their low biodegradability. With the advancements in nanotechnology and biotechnology, novel processes such as adsorption and biodegradation have been developed, and one promising approach is integration of adsorption and biodegradation over porous substrates (bio-carriers). Regardless of recent focus in a few applied researches, the process assessment and critical analysis of this approach is still missing, and it highlights the urgency and importance of this review. This review paper discussed the development of the simultaneous adsorption and catalytic biodegradation (SACB) over a bio-carrier for the sustainable treatment of refractory organics. It provides insights into the physico-chemical characteristics of the bio-carrier, the development mechanism of SACB, stabilization techniques, and process optimization strategies. Furthermore, the most efficient treatment chain is proposed, and its technical aspects are critically analysed based on updated research. It is anticipated that this review will contribute to the knowledge of academia and industrialist for sustainable upgradation of existing industrial wastewater treatment plants.
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Affiliation(s)
- Jing-Cheng Han
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Muhammad Ahmad
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Maryam Yousaf
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Shafeeq Ur Rahman
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Hafiz Muhammad Adeel Sharif
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China; School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Film and Integrated Devices, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Yang Zhou
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Bo Yang
- Water Science and Environmental Engineering Research Center, College of Chemical and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yuefei Huang
- State Key Laboratory of Hydroscience and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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27
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Qiu Y, Lei P, Wang R, Sun L, Luo Z, Li S, Xu H. Kluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications. Biotechnol Adv 2023; 64:108125. [PMID: 36870581 DOI: 10.1016/j.biotechadv.2023.108125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.
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Affiliation(s)
- Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Zhengshan Luo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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28
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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29
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Zhang C, Mu Y, Li T, Jin FJ, Jin CZ, Oh HM, Lee HG, Jin L. Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the "Plastisphere". Front Microbiol 2023; 14:1181967. [PMID: 37138608 PMCID: PMC10150012 DOI: 10.3389/fmicb.2023.1181967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment.
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Affiliation(s)
- Chengxiao Zhang
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yulin Mu
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Taihua Li
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
- Hyung-Gwan Lee,
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Long Jin,
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30
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Ningthoujam R, Satiraphan M, Sompongchaiyakul P, Bureekul S, Luadnakrob P, Pinyakong O. Bacterial community shifts in a di-(2-ethylhexyl) phthalate-degrading enriched consortium and the isolation and characterization of degraders predicted through network analyses. CHEMOSPHERE 2023; 310:136730. [PMID: 36209845 DOI: 10.1016/j.chemosphere.2022.136730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used and toxic phthalate plasticizer that is widely reported in marine environments. Degradation of DEHP by bacteria from several environments have been studied, but little is known about marine sediment bacteria that can degrade DEHP and other phthalate plasticizers. Therefore, in this study, we enriched a bacterial consortium C10 that can degrade four phthalate plasticizers of varying alkyl chain lengths (DEHP, dibutyl phthalate, diethyl phthalate, and dimethyl phthalate) from marine sediment. The major bacterial genera in C10 during degradation of the phthalate plasticizers were Glutamicibacter, Ochrobactrum, Pseudomonas, Bacillus, Stenotrophomonas, and Methylophaga. Growth of C10 on DEHP intermediates (mono-ethylhexyl phthalate, 2-ethylhexanol, phthalic acid, and protocatechuic acid) was studied and these intermediates enhanced the Brevibacterium, Ochrobactrum, Achromobacter, Bacillus, Sporosarcina, and Microbacterium populations. Using a network-based approach, we predicted that Bacillus, Stenotrophomonas, and Microbacterium interacted cooperatively and were the main degraders of phthalate plasticizers. Through selective isolation techniques, we obtained twenty isolates belonging to Bacillus, Microbacterium, Sporosarcina, Micrococcus, Ochrobactrum, Stenotrophomonas, Alcaligenes, and Cytobacillus. The best DEHP-degraders were Stenotrophomonas acidaminiphila OR13, Microbacterium esteraromaticum OR16, Sporosarcina sp. OR19, and Cytobacillus firmus OR20 (83.68%, 59.1%, 43.4%, and 40.6% degradation of 100 mg/L DEHP in 8 d), which agrees with the prediction of key degraders. This is the first report of DEHP degradation by all four bacteria and, thus, our findings reveal as yet unknown PAE-degradation capabilities of marine sediment bacteria. This study provides insights into how bacterial communities adapt to degrade or resist the toxicities of different PAEs and demonstrates a simple approach for the prediction and isolation of potential pollutant degraders from complex and dynamic bacterial communities.
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Affiliation(s)
- Ritu Ningthoujam
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand
| | - Meyawee Satiraphan
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Penjai Sompongchaiyakul
- Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sujaree Bureekul
- Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pontipa Luadnakrob
- Southeast Asian Fisheries Development Center/Training Department, Samut Prakan, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand.
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31
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Cao Z, Yan W, Ding M, Yuan Y. Construction of microbial consortia for microbial degradation of complex compounds. Front Bioeng Biotechnol 2022; 10:1051233. [PMID: 36561050 PMCID: PMC9763274 DOI: 10.3389/fbioe.2022.1051233] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Increasingly complex synthetic environmental pollutants are prompting further research into bioremediation, which is one of the most economical and safest means of environmental restoration. From the current research, using microbial consortia to degrade complex compounds is more advantageous compared to using isolated bacteria, as the former is more adaptable and stable within the growth environment and can provide a suitable catalytic environment for each enzyme required by the biodegradation pathway. With the development of synthetic biology and gene-editing tools, artificial microbial consortia systems can be designed to be more efficient, stable, and robust, and they can be used to produce high-value-added products with their strong degradation ability. Furthermore, microbial consortia systems are shown to be promising in the degradation of complex compounds. In this review, the strategies for constructing stable and robust microbial consortia are discussed. The current advances in the degradation of complex compounds by microbial consortia are also classified and detailed, including plastics, petroleum, antibiotics, azo dyes, and some pollutants present in sewage. Thus, this paper aims to support some helps to those who focus on the degradation of complex compounds by microbial consortia.
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Affiliation(s)
- Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China,*Correspondence: Mingzhu Ding,
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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Huang J, Weng L, Zhang X, Long K, An X, Bao J, Wu H, Zhou X, Zhang S. Trypoxylus dichotomus Gut Bacteria Provides an Effective System for Bamboo Lignocellulose Degradation. Microbiol Spectr 2022; 10:e0214722. [PMID: 35993784 PMCID: PMC9602259 DOI: 10.1128/spectrum.02147-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/02/2022] [Indexed: 12/31/2022] Open
Abstract
Fast-growing bamboo may be a source of high-quality cellulose with the potential to contribute to energy sustainability, if an efficient and low-cost solution to bamboo cellulose decomposition can be developed. This study compared the gut microbiomes of rhinoceros beetle (Trypoxylus dichotomus) feeding on bamboo and wood fiber. The results revealed that diet has a distinctive effect on microbial composition in the midgut, including its most abundant microorganisms that in the fermentation and chemoheterotroph pathways. After identifying the 13 efficient bacterial isolates, we constructed a natural bacterial system based on the microbial relative abundance and an artificial bacterial system with equal proportions of each isolate to catabolize bamboo lignocellulose. The isolate Enterobacter sp. AZA_4_5 and the natural system showed higher degradation efficiency than other single strains or the artificial system. The results can thus serve as important reference for further research and development of a synthetic bacterial consortium to maximize lignocellulolytic ability. IMPORTANCE Bamboo produces a great yield of lignocellulosic biomass due to its high efficiency in carbon fixing. The gut microbiome of Trypoxylus dichotomus differed between bamboo and wood fiber diets. The lignocellulosic pathways were enriched in the gut bacteria of the bamboo diet. The highly efficient bacterial isolates were identified from midgut, whereas the natural bacterial system as well as one isolate showed the higher degradation efficiency of bamboo lignocellulose. The results indicate that the gut bacteria could provide an effective system to utilize the bamboo lignocellulosic biomass.
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Affiliation(s)
- Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Linyao Weng
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Xinqi Zhang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Kui Long
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Xiaojiao An
- College of Chemistry and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou, China
| | - Jinliang Bao
- Shanzhizhou Ecological Agriculture Company Limited, Pan’an, China
| | - Hong Wu
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Xudong Zhou
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Shouke Zhang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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Zhu J, Liu J, Li W, Ru Y, Sun D, Liu C, Li Z, Liu W. Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose. BIORESOUR BIOPROCESS 2022; 9:110. [PMID: 38647799 PMCID: PMC10991580 DOI: 10.1186/s40643-022-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.
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Affiliation(s)
- Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Weilin Li
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunrui Ru
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
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Guo C, Zhang LQ, Jiang W. Biodegrading plastics with a synthetic non-biodegradable enzyme. Chem 2022. [DOI: 10.1016/j.chempr.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Liu J, Zhou X, Wang T, Fan L, Liu S, Wu N, Xu A, Qian X, Li Z, Jiang M, Zhou J, Dong W. Construction and comparison of synthetic microbial consortium system (SMCs) by non-living or living materials immobilization and application in acetochlor degradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129460. [PMID: 35803189 DOI: 10.1016/j.jhazmat.2022.129460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The microbial degradation of pesticides by pure or mixed microbial cultures has been thoroughly explored, however, they are still difficult to apply in real environmental remediation. Here, we constructed a synthetic microbial consortium system (SMCs) through the immobilization technology by non-living or living materials to improve the acetochlor degradation efficiency. Rhodococcus sp. T3-1, Delftia sp. T3-6 and Sphingobium sp. MEA3-1 were isolated for the SMCs construction. The free-floating consortium with the composition ratio of 1:2:2 (Rhodococcus sp. T3-1, Delftia sp. T3-6 and Sphingobium sp. MEA3-1) demonstrated 94.8% degradation of acetochlor, and the accumulation of intermediate metabolite 2-methyl-6-ethylaniline was decreased by 3 times. The immobilized consortium using composite materials showed synergistic effects on the acetochlor degradation with maximum degradation efficiency of 97.81%. In addition, a novel immobilization method with the biofilm of Myxococcus xanthus DK1622 as living materials was proposed. The maximum 96.62% degradation was obtained in non-trophic media. Furthermore, the immobilized SMCs showed significantly enhanced environmental robustness, reusability and stability. The results indicate the promising application of the immobilization methods using composite and living materials in pollutant-contaminated environments.
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Affiliation(s)
- Jingyuan Liu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xiaoli Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Tong Wang
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Lingling Fan
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Shixun Liu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Nan Wu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Anming Xu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xiujuan Qian
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Zhoukun Li
- Key Laboratory of Agriculture Environmental Microbiology, College of Life Science, Nanjing Agriculture University, Nanjing 210095, PR China
| | - Min Jiang
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jie Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
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Pradhan S, Tyagi R, Sharma S. Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges. J Appl Microbiol 2022; 133:2742-2759. [PMID: 36039728 DOI: 10.1111/jam.15799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022]
Abstract
Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.
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Affiliation(s)
- Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
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Lin H, Qin K, Dong Y, Li B. A newly-constructed bifunctional bacterial consortium for removing butyl xanthate and cadmium simultaneously from mineral processing wastewater: Experimental evaluation, degradation and biomineralization. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115304. [PMID: 35588671 DOI: 10.1016/j.jenvman.2022.115304] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Due to the technological limitations associated with beneficiation technology, large amounts of flotation reagents and heavy metals remain in mineral processing wastewater. Unfortunately, however, no treatment methods are available to mitigate the resulting pollution by them. In this study, a bacterial consortium SDMC (simultaneously degrade butyl xanthate and biomineralize cadmium) was constructed in an effort to simultaneously degrade butyl xanthate (BX) and biomineralize cadmium (Cd) by screening and domesticating two different bacterial species including Hypomicrobium and Sporosarcina. SDMC is efficient in removing the combined pollution due to BX and Cd with a 100% degradation rate for BX and 99% biomineralization rate for Cd within 4 h. Besides, SDMC can tolerate high concentrations of Fe(III) (0-40 mg/L). It has an excellent ability to utilize Fe(III) for enhanced removal of the combined pollutants. SDMC can effectively remove pollutants with a pH range of 6-9. Further, we discussed pathways for potential degradation and biomineralization: Cd(BX)2-Cd2+, BX-; BX--CS2, butyl perxanthate (BPX); Cd2+-(Ca0.67,Cd0.33)CO3. The removal of the combined pollutants primarily entails decomposition, degradation, and biomineralization, C-O bond cleavage, and microbially induced carbonate precipitation (MICP). SDMC is a simple, efficient, and eco-friendly bifunctional bacterial consortium for effective treatment of BX-Cd combined pollution in mineral processing wastewater.
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Affiliation(s)
- Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Kangjia Qin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
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38
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Ma Q, Tan H, Song J, Li M, Wang Z, Parales RE, Li L, Ruan Z. Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119477. [PMID: 35598816 DOI: 10.1016/j.envpol.2022.119477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.
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Affiliation(s)
- Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Hao Tan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jinlong Song
- Chinese Academy of Fishery Sciences, Beijing, 100141, PR China
| | - Miaomiao Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, PR China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, PR China; College of Life Sciences, Yantai University, Yantai, 264005, PR China.
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Rapid biodegradation of high molecular weight semi-crystalline polylactic acid at ambient temperature via enzymatic and alkaline hydrolysis by a defined bacterial consortium. Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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40
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Wei F, Xu R, Xu Y, Cheng T, Ma Y. Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 57:723-735. [PMID: 35903918 DOI: 10.1080/10934529.2022.2105631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
To promote the exploitation of unconventional oil resources by indigenous microorganisms, the bacterial community profiles of oil shale and sandstone in Ordos Basin were investigated using Illumina Miseq sequencing combined with the culture-based method, which was performed and reported in this literature for the first time. A total of 601 operational taxonomic units (OTUs) were obtained from collected samples, the predominant phylum present in all samples was Proteobacteria (76.96%-93.07%). Discriminatory bacterial community profiles existed in those samples by culture-dependent and culture-independent methods, with variations not only in diversity indices but also in the abundance of bacteria at different genus levels. The dominant genera in cultured sandstone sample (SCB), uncultured sandstone sample (SUB), cultured shale sample (YCB), uncultured shale sample (YUB) were Enhydrobacter (71.62%), Acidovorax (42.44%), Pseudomonas (40.13%), Variovorax (70.02%), respectively. Both sample sources and culturing methods were the principal factors affecting the variation, while the communities' structures were favored primarily by culture-dependent or culture-independent approaches. The high abundance of hydrocarbon degradation-related genes was exhibited in YCB, which reveals a great potential for utilization of the culture-dependent method in shale oil exploitation. This study provided guidance for the exploitation of shale oil and sandstone oil by artificial utilization of indigenous bacteria.
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Affiliation(s)
- Fengdan Wei
- College of Life Science, Northwest University, Xi'an, China
| | - Rui Xu
- College of Life Science, Northwest University, Xi'an, China
| | - Yuanyuan Xu
- College of Life Science, Northwest University, Xi'an, China
| | - Tao Cheng
- College of Life Science, Northwest University, Xi'an, China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi, China
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Menezes O, Owens C, Rios-Valenciana EE, Sierra-Alvarez R, Field JA, Spain JC. Designing bacterial consortia for the complete biodegradation of insensitive munitions compounds in waste streams. Biotechnol Bioeng 2022; 119:2437-2446. [PMID: 35706349 DOI: 10.1002/bit.28160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/24/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022]
Abstract
Insensitive munitions compounds (IMCs), such as 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO), are replacing conventional explosives in munitions formulations. Manufacture and use of IMCs generate waste streams in manufacturing plants and load/assemble/pack facilities. There is a lack of practical experience in executing biodegradation strategies to treat IMCs waste streams. This study establishes a proof-of-concept that bacterial consortia can be designed to mineralize IMCs and co-occurring nitroaromatics in waste streams. First, DNAN, 4-nitroanisole (4-NA), and 4-chloronitrobenzene (4-CNB) in a synthetic DNAN-manufacturing waste stream were biodegraded using an aerobic fluidized-bed reactor (FBR) inoculated with Nocardioides sp. JS 1661 (DNAN degrader), Rhodococcus sp. JS 3073 (4-NA degrader), and Comamonadaceae sp. LW1 (4-CNB degrader). No biodegradation was detected when the FBR was operated under anoxic conditions. Second, DNAN and NTO were biodegraded in a synthetic load/assemble/pack waste stream during a sequential treatment comprising: (i) aerobic DNAN biodegradation in the FBR; (ii) anaerobic NTO biotransformation to 3-amino-1,2,4-triazol-5-one (ATO) by an NTO-respiring enrichment; and (iii) aerobic ATO mineralization by an ATO-oxidizing enrichment. Complete biodegradation relied on switching redox conditions. The results provide the basis for designing consortia to treat mixtures of IMCs and related waste products by incorporating microbes with the required catabolic capabilities.
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Affiliation(s)
- Osmar Menezes
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Cameron Owens
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida, USA
| | - Erika E Rios-Valenciana
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Jim C Spain
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida, USA.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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Rafieenia R, Atkinson E, Ledesma-Amaro R. Division of labor for substrate utilization in natural and synthetic microbial communities. Curr Opin Biotechnol 2022; 75:102706. [DOI: 10.1016/j.copbio.2022.102706] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 01/30/2023]
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Climate-Resilient Microbial Biotechnology: A Perspective on Sustainable Agriculture. SUSTAINABILITY 2022. [DOI: 10.3390/su14095574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We designed this review to describe a compilation of studies to enlighten the concepts of plant–microbe interactions, adopted protocols in smart crop farming, and biodiversity to reaffirm sustainable agriculture. The ever-increasing use of agrochemicals to boost crop production has created health hazards to humans and the environment. Microbes can bring up the hidden strength of plants, augmenting disease resistance and yield, hereafter, crops could be grown without chemicals by harnessing microbes that live in/on plants and soil. This review summarizes an understanding of the functions and importance of indigenous microbial communities; host–microbial and microbial–microbial interactions; simplified experimentally controlled synthetic flora used to perform targeted operations; maintaining the molecular mechanisms; and microbial agent application technology. It also analyzes existing problems and forecasts prospects. The real advancement of microbiome engineering requires a large number of cycles to obtain the necessary ecological principles, precise manipulation of the microbiome, and predictable results. To advance this approach, interdisciplinary collaboration in the areas of experimentation, computation, automation, and applications is required. The road to microbiome engineering seems to be long; however, research and biotechnology provide a promising approach for proceeding with microbial engineering and address persistent social and environmental issues.
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Gao H, Manishimwe C, Yang L, Wang H, Jiang Y, Jiang W, Zhang W, Xin F, Jiang M. Applications of synthetic light-driven microbial consortia for biochemicals production. BIORESOURCE TECHNOLOGY 2022; 351:126954. [PMID: 35288267 DOI: 10.1016/j.biortech.2022.126954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Synthetic microbial consortia provide a versatile and efficient platform for biochemicals production through the labor division. Especially, microbial communities composed of phototrophs and heterotrophs offer a promising alternative, as they can directly convert carbon dioxide (CO2) into chemicals. Within this system, photoautotrophic microbes can convert CO2 into organic carbon for microbial growth and metabolites synthesis by the heterotrophic partners. In return, heterotrophs can provide additional CO2 to support the growth of photoautotrophic microbes. However, the unmatched growing conditions, low stability and production efficiency of synthetic microbial consortia hinder their further applications. Thus, design and construction of mutualistic and stable synthetic light-driven microbial consortia are urgently needed. In this review, the progress of synthetic light-driven microbial consortia for chemicals production was comprehensively summarized. In addition, space-efficient synthetic light-driven microbial consortia in hydrogel system were reviewed. Perspectives on orderly distribution of light-driven microbial consortia associated with 3D printing technology in biomanufacturing were also addressed.
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Affiliation(s)
- Hao Gao
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Clarisse Manishimwe
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Lu Yang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Hanxiao Wang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Fengxue Xin
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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Song HM, Zhu LJ, Wang Y, Wang G, Zeng ZX. Fe-based Prussian blue cubes confined in graphene oxide nanosheets for the catalytic degradation of dyes in wastewater. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Abstract
Crude oil is a viscous dark liquid resource composed by a mix of hydrocarbons which, after refining, is used for the elaboration of distinct products. A major concern is that many petroleum components are highly toxic due to their teratogenic, hemotoxic, and carcinogenic effects, becoming an environmental concern on a global scale, which must be solved through innovative, efficient, and sustainable techniques. One of the most widely used procedures to totally degrade contaminants are biological methods such as bioremediation. Synthetic biology is a scientific field based on biology and engineering principles, with the purpose of redesigning and restructuring microorganisms to optimize or create new biological systems with enhanced features. The use of this discipline offers improvement of bioremediation processes. This article will review some of the techniques that use synthetic biology as a platform to be used in the area of hydrocarbon bioremediation.
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Massot F, Bernard N, Alvarez LMM, Martorell MM, Mac Cormack WP, Ruberto LAM. Microbial associations for bioremediation. What does "microbial consortia" mean? Appl Microbiol Biotechnol 2022; 106:2283-2297. [PMID: 35294589 DOI: 10.1007/s00253-022-11864-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/02/2022]
Abstract
Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.
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Affiliation(s)
- Francisco Massot
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Nathalie Bernard
- Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Lucas M Martinez Alvarez
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - María M Martorell
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Walter P Mac Cormack
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina
| | - Lucas A M Ruberto
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina. .,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. .,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina.
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48
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Lin Z, Pang S, Zhou Z, Wu X, Li J, Huang Y, Zhang W, Lei Q, Bhatt P, Mishra S, Chen S. Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:127841. [PMID: 34844804 DOI: 10.1016/j.jhazmat.2021.127841] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
The microbial degradation of acephate in pure cultures has been thoroughly explored, but synergistic metabolism at the community level has rarely been investigated. Here, we report a novel microbial consortium, ZQ01, capable of effectively degrading acephate and its toxic product methamidophos, which can use acephate as a source of carbon, phosphorus and nitrogen. The degradation conditions with consortium ZQ01 were optimized using response surface methodology at a temperature of 34.1 °C, a pH of 8.9, and an inoculum size of 2.4 × 108 CFU·mL-1, with 89.5% of 200 mg L-1 acephate degradation observed within 32 h. According to the main products methamidophos, acetamide and acetic acid, a novel degradation pathway for acephate was proposed to include hydrolysis and oxidation as the main pathways of acephate degradation. Moreover, the bioaugmentation of acephate-contaminated soils with consortium ZQ01 significantly enhanced the removal rate of acephate. The results of the present work demonstrate the potential of microbial consortium ZQ01 to degrade acephate in water and soil environments, with a different and complementary acephate degradation pathway.
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Affiliation(s)
- Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaozhen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Krujatz F, Dani S, Windisch J, Emmermacher J, Hahn F, Mosshammer M, Murthy S, Steingroewer J, Walther T, Kühl M, Gelinsky M, Lode A. Think outside the box: 3D bioprinting concepts for biotechnological applications – recent developments and future perspectives. Biotechnol Adv 2022; 58:107930. [DOI: 10.1016/j.biotechadv.2022.107930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022]
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50
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Yuan W, Ruan S, Qi G, Wang R, Zhao X. Plant growth-promoting and antibacterial activities of cultivable bacteria alive in tobacco field against Ralstonia solanacearum. Environ Microbiol 2022; 24:1411-1429. [PMID: 35112429 DOI: 10.1111/1462-2920.15868] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Bacterial wilt disease caused by Ralstonia solanacearum leads to decrease of crops yield. Investigation of cultivable bacteria diversity provides more microbial species for screening antagonistic bacteria. In the present study, a variety of cultivation methods were used to investigate the diversity of cultivable bacteria alive in tobacco field. A total of 441 bacterial strains were obtained that belonged to four phyla, 49 genera and 146 species. Actinobacteria and Proteobacteria were the dominant phyla. Agrobacterium, Arthrobacter, Bacillus, Klebsiella, Paenarthrobacter, Pseudomonas and Pseudarthrobacter were the dominant genera. Some rare genera were discovered including Bosea, Cedecea, Delftia and Dyella. Diversity, species and abundances of bacteria altered under different cultivation conditions. One hundred three bacterial strains showed plant growth-promoting attributes. Twenty Bacillus strains showed high antibacterial activity against R. solanacearum. In field experiments, individual strain and consortia of Bacillus subtilis, B. siamensis and B. vallismortis effectively inhibited bacterial wilt. The core genes that controlled synthesis of secondary metabolites were knocked out in B. vallismortis SSB-10. Difficidin, which was synthesized by dif operon and controlled by sfp gene, was the antibacterial substance produced by SSB-10. Difficidin destroyed cell wall and cell membrane of R. solanacearum and inhibited its motility, production of extracellular polysaccharides and cellulase activity.
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Affiliation(s)
- Wenfang Yuan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Song Ruan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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