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Zhang L, Guo L, Cui Z, Ju F. Exploiting predatory bacteria as biocontrol agents across ecosystems. Trends Microbiol 2024; 32:398-409. [PMID: 37951768 DOI: 10.1016/j.tim.2023.10.005] [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: 06/30/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Predatory bacteria have been increasingly known for their ubiquity in environments and great functional potentials in controlling unwanted microorganisms. Fundamental understanding of the predation mechanisms, population dynamics, and interaction patterns underlying bacterial predation is required for wise exploitation of predatory bacteria for enhancing ecoenvironmental, animal, and human health. Here, we review the recent achievements on applying predatory bacteria in different systems as biocontrol agents and living antibiotics as well as new findings in their phylogenetic diversity and predation mechanisms. We finally propose critical issues that deserve priority research and highlight the necessity to combine classic culture-based and advanced culture-independent approaches to push research frontiers of bacterial predation across ecosystems for promising biocontrol and therapy strategies towards a sustainable ecoenvironment and health.
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Affiliation(s)
- Lu Zhang
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lingyun Guo
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
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Krohn C, Khudur L, Dias DA, van den Akker B, Rees CA, Crosbie ND, Surapaneni A, O'Carroll DM, Stuetz RM, Batstone DJ, Ball AS. The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge. Front Microbiol 2022; 13:1079136. [PMID: 36590430 PMCID: PMC9801413 DOI: 10.3389/fmicb.2022.1079136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.
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Affiliation(s)
- Christian Krohn
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia,*Correspondence: Christian Krohn,
| | - Leadin Khudur
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
| | - Daniel Anthony Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, STEM College, RMIT University, Bundoora, VIC, Australia
| | | | | | | | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
| | - Denis M. O'Carroll
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Richard M. Stuetz
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Damien J. Batstone
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia,Australian Centre for Water and Environmental Biotechnology, Gehrmann Building, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew S. Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora, VIC, Australia
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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Wu P, Yin X, Liu Q, Wu W, Chen C. Recombinant T7 Phage with FMDV AKT-III Strain VP1 Protein is a Potential FMDV Vaccine. Biotechnol Lett 2020; 43:35-41. [PMID: 32989662 DOI: 10.1007/s10529-020-03012-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022]
Abstract
OBJECTIVES The capsid protein (VP1) of the foot-and-mouth (FMD) AKT-III strain was expressed on the surface of the T7 phage capsid (AKT-T7 strain) and the potential of AKT-T7 strain as an FMD vaccine was evaluated. RESULTS The AKT-T7 strain was successfully constructed and was not cytotoxic to BHK-21, MDBK, or sheep kidney cells. The AKT-T7 strain was well phagocytosed by mouse macrophages. Immunization of BALB/c mice revealed that animals were quickly induced and produced high levels of FMDV antibodies. Monitoring data indicated that FMDV antibody levels could be maintained at higher levels for longer periods of time. The AKT-T7 strain induced high levels of IFN-γ levels in mice with little effect on IL-4. CONCLUSIONS The AKT-T7 induced the mice to produce FMDV antibodies, which has the advantage of phage and FMDV, and is a potential candidate for an FMD vaccine.
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Affiliation(s)
- Peng Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Xinyue Yin
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Qingqing Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Wenxing Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China.
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Fan NS, Qi R, Huang BC, Jin RC, Yang M. Factors influencing Candidatus Microthrix parvicella growth and specific filamentous bulking control: A review. CHEMOSPHERE 2020; 244:125371. [PMID: 31835053 DOI: 10.1016/j.chemosphere.2019.125371] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/19/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Candidatus Microthrix parvicella has been frequently detected as the dominant filamentous bacteria in bulking sludge and thus seriously affects the stable operation of activated sludge processes. The extremely low growth rate of Ca. M. parvicella and its sensitivity to environmental variations greatly limit the development of effective techniques to control filamentous bulking. Based on previous investigations, a variety of restrictive substrates, operating and culture conditions, environmental factors and other potential inhibitors have varying degrees of impact on the growth of this microorganism. This review systematically summarizes the key factors affecting Ca. M. parvicella growth with a focus on the influencing mechanism. Recent filamentous bulking control strategies are also critically reviewed and discussed. Additionally, research needs for the next few years are proposed with the aim of establishing effective and specific control strategies for filamentous sludge bulking.
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Affiliation(s)
- Nian-Si Fan
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Rong Qi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bao-Cheng Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Min Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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