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Zhu S, Tan Z, Guo Z, Zheng H, Zhang B, Qin Z, Xie J, Lin Y, Sheng B, Qiu G, Preis S, Wei C. Symbiotic virus-bacteria interactions in biological treatment of coking wastewater manipulating bacterial physiological activities. WATER RESEARCH 2024; 257:121741. [PMID: 38744061 DOI: 10.1016/j.watres.2024.121741] [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: 11/08/2023] [Revised: 04/11/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
Biological treatment is commonly used in coking wastewater (CWW) treatment. Prokaryotic microbial communities in CWW treatment have been comprehensively studied. However, viruses, as the critical microorganisms affecting microbial processes and thus engineering parameters, still remain poorly understood in CWW treatment context. Employing viromics sequencing, the composition and function of the viral community in CWW treatment were discovered, revealing novel viral communities and key auxiliary metabolic functions. Caudovirales appeared to be the predominant viral order in the oxic-hydrolytic-oxic (OHO) CWW treatment combination, showing relative abundances of 62.47 %, 56.64 % and 92.20 % in bioreactors O1, H and O2, respectively. At the family level, Myoviridae, Podoviridae and Siphoviridae mainly prevailed in bioreactors O1 and H while Phycodnaviridae dominated in O2. A total of 56.23-92.24% of novel viral contigs defied family-level characterization in this distinct CWW habitat. The virus-host prediction results revealed most viruses infecting the specific functional taxa Pseudomonas, Acidovorax and Thauera in the entire OHO combination, demonstrating the viruses affecting bacterial physiology and pollutants removal from CWW. Viral auxiliary metabolic genes (AMGs) were screened, revealing their involvement in the metabolism of contaminants and toxicity tolerance. In the bioreactor O1, AMGs were enriched in detoxification and phosphorus ingestion, where glutathione S-transferase (GSTs) and beta-ketoadipyl CoA thiolase (fadA) participated in biodegradation of polycyclic aromatic hydrocarbons and phenols, respectively. In the bioreactors H and O2, the AMGs focused on cell division and epicyte formation of the hosts, where GDPmannose 4,6-dehydratase (gmd) related to lipopolysaccharides biosynthesis was considered to play an important role in the growth of nitrifiers. The diversities of viruses and AMGs decreased along the CWW treatment process, pointing to a reinforced virus-host adaptive strategy in stressful operation environments. In this study, the symbiotic virus-bacteria interaction patterns were proposed with a theoretical basis for promoting CWW biological treatment efficiency. The findings filled the gaps in the virus-bacteria interactions at the full-scale CWW treatment and provided great value for understanding the mechanism of biological toxicity and sludge activity in industrial wastewater treatment.
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Affiliation(s)
- Shuang Zhu
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
| | - Zhijie Tan
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ziyu Guo
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Huijian Zheng
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Baoshan Zhang
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Zhi Qin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Junting Xie
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yuexia Lin
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Binbin Sheng
- School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Sergei Preis
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn 19086, Estonia
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China.
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2
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Hong W, Mei H, Shi X, Lin X, Wang S, Ni R, Wang Y, Song L. Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant. ENVIRONMENTAL RESEARCH 2024; 247:118156. [PMID: 38199475 DOI: 10.1016/j.envres.2024.118156] [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: 09/21/2023] [Revised: 12/02/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Viruses manipulate bacterial community composition and impact wastewater treatment efficiency. Some viruses pose threats to the environment and human populations through infection. Improving the efficiency of wastewater treatment and ensuring the health of the effluent and receptor pools requires an understanding of how viral communities assemble and interact with hosts in wastewater treatment plants (WWTPs). We used metagenomic analysis to study the distribution, assembly mechanism, and sensitive hosts for the viral communities in raw water, anaerobic tanks, and returned activated sludge units of a large-scale industrial park WWTP. Uroviricota (53.42% ± 0.14%) and Nucleocytoviricota (26.1% ± 0.19%) were dominant in all units. Viral community composition significantly differed between units, as measured by β diversity (P = 0.005). Compared to raw water, the relative viral abundance decreased by 29.8% in the anaerobic tank but increased by 9.9% in the activated sludge. Viral community assembly in raw water and anaerobic tanks was predominantly driven by deterministic processes (MST <0.5) versus stochastic processes (MST >0.5) in the activated sludge, indicating that differences in diffusion limits may fundamentally alter the assembly mechanisms of viral communities between the solid and liquid-phase environments. Acidobacteria was identified as the sensitive host contributing to viral abundance, exhibiting strong interactions and a mutual dependence (degree = 59). These results demonstrate the occurrence and prevalence of viruses in WWTPs, their different assembly mechanism, and sensitive hosts. These observations require further study of the mechanisms of viral community succession, ecological function, and roles in the successive wastewater treatment units.
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Affiliation(s)
- Wenqing Hong
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Hong Mei
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Xianyang Shi
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Yan Wang
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
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Luo R, Guan A, Ma B, Gao Y, Peng Y, He Y, Xu Q, Li K, Zhong Y, Luo R, Cao R, Jin H, Lin Y, Shang P. Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups. Viruses 2024; 16:606. [PMID: 38675947 PMCID: PMC11054254 DOI: 10.3390/v16040606] [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: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.
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Affiliation(s)
- Runbo Luo
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (R.L.); (K.L.); (Y.Z.)
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Aohan Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Bin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Yuan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Yuna Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Yanling He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Qianshuai Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Kexin Li
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (R.L.); (K.L.); (Y.Z.)
| | - Yanan Zhong
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (R.L.); (K.L.); (Y.Z.)
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Ruibing Cao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China; (A.G.); (B.M.); (Y.G.); (Y.P.); (Y.H.); (Q.X.); (R.L.); (H.J.)
- College of Animal Medicine, Huazhong Agricultural University, Wuhan 430000, China
| | - Yan Lin
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Shang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (R.L.); (K.L.); (Y.Z.)
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Li Y, Yu H, Xiong L, Wei Y, Li H, Ji X. Viral AMGs-driven pentose phosphate pathway in natural wetland. J Basic Microbiol 2024; 64:e2300569. [PMID: 38078780 DOI: 10.1002/jobm.202300569] [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: 09/28/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 02/13/2024]
Abstract
Viruses exist anywhere on earth where there is life, and among them, virus-encoded auxiliary metabolic genes (AMGs) can maintain ecosystem balance and play a major role in the global ecosystem. Although the function of AMGs has been widely reported, the genetic diversity of AMGs in natural ecosystems is still poorly understood. Exploring the genetic diversity of viral community-wide AMGs is essential to gain insight into the complex interactions between viruses and hosts. In this article, we studied the phylogenetic tree, principal co-ordinates analysis (PCoA), α diversity, and metabolic pathways of viral auxiliary metabolism genes involved in the pentose phosphate pathway (PPP) through metagenomics, and the changes of metabolites and genes of host bacteria were further studied by using Pseudomonas mandelii SW-3 and its lytic phage based on metabolic flow and AMGs expression. We found that the viral AMGs in the Napahai plateau wetland were created by a combination of various external forces, which contributed to the rich genetic diversity, uniqueness, and differences of the virus, which promoted the reproduction of offspring and better adaptation to the environment. Overall, this study systematically describes the genetic diversity of AMGs associated with the PPP in plateau wetland ecosystems and further expands the understanding of phage-host unique interactions.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Xiuling Ji
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Medical School, Kunming University of Science and Technology, Kunming, China
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5
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Li Y, Yu H, Xiong L, Zeng K, Wei Y, Li H, Ji X. Diversity and function of viral AMGs associated with DNA biosynthesis in the Napahai plateau wetland. ENVIRONMENTAL TECHNOLOGY 2023:1-15. [PMID: 38126212 DOI: 10.1080/09593330.2023.2296531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Viruses play an important role in microbial community structure and biodiversity by lysing host cells, and can also affect host metabolic pathways by expressing auxiliary metabolic genes (AMGs). As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai has high research value. However, studies on the genetic diversity of AMGs and viruses associated with DNA biosynthesis have not been reported. Based on metagenomics, with the phylogenetic tree, PCoA, and α diversity analysis, we found that three DNA biosynthesis-related viral AMGs (cobS, mazG, and purM) in the Napahai plateau wetland were rich in genetic diversity, uniqueness, and differences compared with other habitats and host sources. Through the KEGG metabolic pathway and metabolic flow analysis of Pseudomonas mandelii (SW-3) and phage (VSW-3), the AMGs (cobS, mazG, and purM) genes of the three related viruses involved in DNA biosynthesis were upregulated and their expression increased significantly. In general, we systematically described the genetic diversity of AMGs associated with DNA biosynthesis in plateau wetland ecosystems and clarified the contribution of viral AMGs in the Napahai plateau wetland to DNA biosynthesis, as well as the changes of metabolites and genes. It further expands the understanding of phage-host interactions, which is of great significance for further revealing the role of viral AMGs in the biological evolution and biogeochemical cycle of wetland ecosystems.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
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Huang W, Li Y, Wang F, Feng L, Wang D, Ma Y, Wu Y, Luo J. Disinfectant sodium dichloroisocyanurate synergistically strengthened sludge acidogenic process and pathogens inactivation: Targeted upregulation of functional microorganisms and metabolic traits via self-adaptation. WATER RESEARCH 2023; 247:120787. [PMID: 37918196 DOI: 10.1016/j.watres.2023.120787] [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: 09/25/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
Harmless and resourceful treatment of waste activated sludge (WAS) have been the crucial goal for building environmental-friendly and sustainable society, while the synergistic realization approach is currently limited. This work skillfully utilized the disinfectant sodium dichloroisocyanurate (NaDCC) to simultaneously achieve the pathogenic potential inactivation (decreased by 60.1 %) and efficient volatile fatty acids (VFAs) recovery (increased by 221.9 %) during WAS anaerobic fermentation in rather cost-effective way (Chemicals costs:0.4 USD/kg VFAs versus products benefits: 2.68 USD/kg chemical). Mechanistic analysis revealed that the C=O and NCl bonds in NaDCC could spontaneously absorb sludge (binding energy -4.9 kJ/mol), and then caused the sludge disintegration and organic substrates release for microbial utilization due to the oxidizability of NaDCC. The disruption of sludge structure along with the increase of bioavailable fermentation substrates contributed to the selectively regulation of microbial community via enriching VFAs-forming microorganisms (e.g., Pseudomonas and Streptomyces) and reducing VFAs-consuming microorganisms, especially aceticlastic methanogens (e.g., Methanothrix and Methanospirillum). Correspondingly, the metabolic functions of membrane transport, substrate metabolism, pyruvate metabolism, and fatty acid biosynthesis locating in the central pathway of VFAs production were all upregulated while the methanogenic step was inhibited (especially acetate-type methanogenic pathway). Further exploration unveiled that for those enriched functional anaerobes were capable to activate the self-adaptive systems of DNA replication, SOS response, oxidative stress defense, efflux pump, and energy metabolism to counteract the unfavorable NaDCC stress and maintain high microbial activities for efficient VFAs yields. This study would provide a novel strategy for synergistic realization of harmless and resourceful treatment of WAS, and identify the interrelations between microbial metabolic regulations and adaptive responses.
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Affiliation(s)
- Wenxuan Huang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Feng Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Yingqun Ma
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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Tan Y, Yu P, Huang D, Yuan MM, Yu Z, Lu H, Alvarez PJJ, Zhu L. Enhanced Bacterium-Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17324-17337. [PMID: 37930060 DOI: 10.1021/acs.est.3c05452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Phages are increasingly recognized for their importance in microbial aggregates, including their influence on microbial ecosystem services and biotechnology applications. However, the adaptive strategies and ecological functions of phages in different aggregates remain largely unexplored. Herein, we used membrane bioreactors to investigate bacterium-phage interactions and related microbial functions within suspended and attached microbial aggregates (SMA vs AMA). SMA and AMA represent distinct microbial habitats where bacterial communities display distinct patterns in terms of dominant species, keystone species, and bacterial networks. However, bacteria and phages in both aggregates exhibited high lysogenicity, with 60% lysogenic phages in the virome and 70% lysogenic metagenome-assembled genomes of bacteria. Moreover, substantial phages exhibited broad host ranges (34% in SMA and 42% in AMA) and closely interacted with habitat generalist species (43% in SMA and 49% in AMA) as adaptive strategies in stressful operation environments. Following a mutualistic pattern, phage-carried auxiliary metabolic genes (pAMGs; 238 types in total) presumably contributed to the bacterial survival and aggregate stability. The SMA-pAMGs were mainly associated with energy metabolism, while the AMA-pAMGs were mainly associated with antioxidant biosynthesis and the synthesis of extracellular polymeric substances, representing habitat-dependent patterns. Overall, this study advanced our understanding of phage adaptive strategies in microbial aggregate habitats and emphasized the importance of bacterium-phage symbiosis in the stability of microbial aggregates.
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Affiliation(s)
- Yixiao Tan
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan 314100, China
| | - Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, United States
| | - Zhuodong Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Civil and Environmental Engineering Department, Rice University, Houston, Texas 77005, United States
| | - Liang Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan 314100, China
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Ashbolt NJ. Conceptual model to inform Legionella-amoebae control, including the roles of extracellular vesicles in engineered water system infections. Front Cell Infect Microbiol 2023; 13:1200478. [PMID: 37274310 PMCID: PMC10232903 DOI: 10.3389/fcimb.2023.1200478] [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: 04/05/2023] [Accepted: 05/08/2023] [Indexed: 06/06/2023] Open
Abstract
Extracellular vesicles (EVs or exosomes) are well described for bacterial pathogens associated with our gastrointestinal system, and more recently as a novel mechanism for environmental persistence, dissemination and infection for human enteric viruses. However, the roles played by EVs in the ancient arms race that continues between amoebae and one of their prey, Legionella pneumophila, is poorly understood. At best we know of intracellular vesicles of amoebae containing a mix of bacterial prey species, which also provides an enhanced niche for bacteriophage infection/spread. Free-living amoeba-associated pathogens have recently been recognized to have enhanced resistance to disinfection and environmental stressors, adding to previously understood (but for relatively few species of) bacteria sequestered within amoebal cysts. However, the focus of the current work is to review the likely impacts of large numbers of respiratory-sized EVs containing numerous L. pneumophila cells studied in pure and biofilm systems with mixed prey species. These encapsulated pathogens are orders of magnitude more resistant to disinfection than free cells, and our engineered systems with residual disinfectants could promote evolution of resistance (including AMR), enhanced virulence and EV release. All these are key features for evolution within a dead-end human pathogen post lung infection. Traditional single-hit pathogen infection models used to estimate the probability of infection/disease and critical environmental concentrations via quantitative microbial risk assessments may also need to change. In short, recognizing that EV-packaged cells are highly virulent units for transmission of legionellae, which may also modulate/avoid human host immune responses. Key data gaps are raised and a previous conceptual model expanded upon to clarify where biofilm EVs could play a role promoting risk as well as inform a more wholistic management program to proactively control legionellosis.
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