1
|
Wang S, Tian R, Bi Y, Meng F, Zhang R, Wang C, Wang D, Liu L, Zhang B. A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems. CHEMOSPHERE 2024; 359:142264. [PMID: 38714248 DOI: 10.1016/j.chemosphere.2024.142264] [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: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/09/2024]
Abstract
Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.
Collapse
Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Ruimin Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Rui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Dong Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Bo Zhang
- Tianjin Eco-City Water Investment and Construction Co. Ltd, Hexu Road 276, Tianjin, 300467, China
| |
Collapse
|
2
|
Huang DQ, Fu JJ, Li ZY, Luan X, Huang Y, Fan NS, Jin RC. Removal of extracellular deoxyribonucleic acid increases the permeability and mass transfer of anammox granular sludge with different sizes. CHEMOSPHERE 2022; 302:134898. [PMID: 35561772 DOI: 10.1016/j.chemosphere.2022.134898] [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: 02/13/2022] [Revised: 04/21/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
As a key component of extracellular polymeric substances (EPS), extracellular deoxyribonucleic acid (eDNA) acts as a bridge in maintaining the structural stability of granular sludge. However, its ability of carrying antibiotic resistance genes (ARGs) promotes the gene horizontal transfer, raising a high risk for human health. In this study, a series of batch tests were performed to elucidate the response of anammox granular sludge (AnGS) with different sizes (S-AnGS with diameters lower than 0.9 mm and L-AnGS with diameters of 0.9-2 mm) to the removal of eDNA and corresponding mechanism. The results showed that the highest bioactivity of S-AnGS and L-AnGS was achieved by adding DNase I, and the absolute abundance of hzsA in the systems also increased. The dominant microorganism in each sludge was Candidatus Kuenenia, which maintained a higher relative abundance of 24% in S-AnGS. Settling experiments demonstrated that the permeability of AnGS was positively correlated with the addition of DNase I. The permeability index of granular sludge, Г, rose by 58.54% in S-AnGS and 11.79% in L-AnGS. The absence of eDNA is conducive to the increase in the permeability and porosity of AnGS. Similarity in the functional genes and microbial communities of intracellular and extracellular DNA implied the occurrence of gene transmembrane transfer. The findings enrich our knowledge of eDNA in anammox granules and provide a guidance for the specific control of gene transfer through reducing eDNA.
Collapse
Affiliation(s)
- Dong-Qi Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jin-Jin Fu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zi-Yue Li
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiao Luan
- Department of Irrigation and Drainage, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yong Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| |
Collapse
|
3
|
Jin Y, Xiong W, Zhou N, Xiao G, Wang S, Su H. Role of initial bacterial community in the aerobic sludge granulation and performance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 309:114706. [PMID: 35158114 DOI: 10.1016/j.jenvman.2022.114706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/22/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The structure of bacterial community was greatly varied from different seed sludge sources, which affected the sludge characteristics. To explore the role of different functional bacteria in AGS granulation and pollutant degradation, three different resources of seed sludge obtained from pharmaceutical wastewater (R1), livestock (R2), and municipal sludge (R3) were employed in this study. Results showed that the initial bacterial community had important significance for AGS formation and pollutants removal. Seed sludge taken from R3 granulated faster than those from R1 and R2. A large number of mature granules were formed after 20 days of operation in R3. In addition, the final mixed liquor suspended solids (MLSS) reached 6853 mg L-1, with 48 mL g-1 sludge volume index (SVI) in R3, indicating that it had better settling performance and granulation. In the stable stage of R3, the removal rates of COD, NH4+-N, and TN reached 99.2%, 98.5%, and 97.6%, respectively. The α-diversity analysis showed that the bacterial community of seed sludge greatly determined the microbial composition of AGS. Firmicutes, Gracilibacteria, and Spirochaetes were abundant in R3, which maintained the structures and functions of aerobic granules. This study might provide approaches and insights for AGS culture from different sludge sources.
Collapse
Affiliation(s)
- Yu Jin
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Wei Xiong
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Nan Zhou
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Gang Xiao
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shaojie Wang
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Haijia Su
- Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| |
Collapse
|
4
|
Chan SH, Ismail MH, Tan CH, Rice SA, McDougald D. Microbial predation accelerates granulation and modulates microbial community composition. BMC Microbiol 2021; 21:91. [PMID: 33773594 PMCID: PMC8004422 DOI: 10.1186/s12866-021-02156-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/08/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge. RESULTS Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of 'Candidatus Accumulibacter' was positively correlated with the formation of compact aggregates and granules. CONCLUSION Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of 'Candidatus Accumulibacter' was necessary for the formation of granules in the absence of protozoa.
Collapse
Affiliation(s)
- Siew Herng Chan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chuan Hao Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- The iThree Institute, University of Technology Sydney, Sydney, Australia.
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- The iThree Institute, University of Technology Sydney, Sydney, Australia.
| |
Collapse
|