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Wang L, Lu W, Song Y, Liu S, Fu YV. Using machine learning to identify environmental factors that collectively determine microbial community structure of activated sludge. ENVIRONMENTAL RESEARCH 2024; 260:119635. [PMID: 39025351 DOI: 10.1016/j.envres.2024.119635] [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: 05/14/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Activated sludge (AS) microbial communities are influenced by various environmental variables. However, a comprehensive analysis of how these variables jointly and nonlinearly shape the AS microbial community remains challenging. In this study, we employed advanced machine learning techniques to elucidate the collective effects of environmental variables on the structure and function of AS microbial communities. Applying Dirichlet multinomial mixtures analysis to 311 global AS samples, we identified four distinct microbial community types (AS-types), each characterized by unique microbial compositions and metabolic profiles. We used 14 classical linear and nonlinear machine learning methods to select a baseline model. The extremely randomized trees demonstrated optimal performance in learning the relationship between environmental factors and AS types (with an accuracy of 71.43%). Feature selection identified critical environmental factors and their importance rankings, including latitude (Lat), longitude (Long), precipitation during sampling (Precip), solids retention time (SRT), effluent total nitrogen (Effluent TN), average temperature during sampling month (Avg Temp), mixed liquor temperature (Mixed Temp), influent biochemical oxygen demand (Influent BOD), and annual precipitation (Annual Precip). Significantly, Lat, Long, Precip, Avg Temp, and Annual Precip, influenced metabolic variations among AS types. These findings emphasize the pivotal role of environmental variables in shaping microbial community structures and enhancing metabolic pathways within activated sludge. Our study encourages the application of machine learning techniques to design artificial activated sludge microbial communities for specific environmental purposes.
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Affiliation(s)
- Lu Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weilai Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Fei F, Su Z, Liu R, Gao R, Sun C. Efficient biodegradation of poly(butylene adipate-co-terephthalate) in mild temperature by cutinases derived from a marine fungus. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136008. [PMID: 39368353 DOI: 10.1016/j.jhazmat.2024.136008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/12/2024] [Accepted: 09/28/2024] [Indexed: 10/07/2024]
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT) waste gradually accumulates in the environment, posing ecological risks. Enzymatic hydrolysis holds great potential in the end-of-life management of PBAT, but reported enzymes require high reaction temperatures, limiting their practical industrial applications. In this study, we discovered that the marine fungus Alternaria alternata FB1 can efficiently degrade PBAT at 28 °C. Two cutinases designated as AaCut4 and AaCut10, were identified and verified as key enzymes responsible for this degradation process. Notably, the recombinant AaCut10 was able to depolymerize 82.14 % PBAT within 24 h and fully decompose it within 48 h at 37 °C. Through protein engineering, the yield of terephthalic acid monomer was increased to 96.01 %, highlighting its potential for facilitating PBAT upcycling. Furthermore, based on the investigation of the distribution patterns of PBAT hydrolases, novel degradative agents have been identified within unique ecological niches, leading to the establishment of a comprehensive screening repository of PBAT hydrolases. Overall, our study provides new candidates for enzymatic PBAT recycling with low energy consumption and offers insights into the PBAT degradation manner in ecosystems.
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Affiliation(s)
- Fan Fei
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhenjie Su
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | | | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266404, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China; College of Earth Science, University of Chinese Academy of Sciences, Beijing 101408, China.
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Shi K, Xu JM, Cui HL, Cheng HY, Liang B, Wang AJ. Microbiome regulation for sustainable wastewater treatment. Biotechnol Adv 2024; 77:108458. [PMID: 39343082 DOI: 10.1016/j.biotechadv.2024.108458] [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: 05/26/2024] [Revised: 08/30/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
Sustainable wastewater treatment is essential for attaining clean water and sanitation, aligning with UN Sustainable Development Goals. Wastewater treatment plants (WWTPs) have utilized environmental microbiomes in biological treatment processes in this effort for over a century. However, the inherent complexity and redundancy of microbial communities, and emerging chemical and biological contaminants, challenge the biotechnology applications. Over the past decades, understanding and utilization of microbial energy metabolism and interaction relationships have revolutionized the biological system. In this review, we discuss how microbiome regulation strategies are being used to generate actionable performance for low-carbon pollutant removal and resource recovery in WWTPs. The engineering application cases also highlight the real feasibility and promising prospects of the microbiome regulation approaches. In conclusion, we recommend identifying environmental risks associated with chemical and biological contaminants transformation as a prerequisite. We propose the integration of gene editing and enzyme design to precisely regulate microbiomes for the synergistic control of both chemical and biological risks. Additionally, the development of integrated technologies and engineering equipment is crucial in addressing the ongoing water crisis. This review advocates for the innovation of conventional wastewater treatment biotechnology to ensure sustainable wastewater treatment.
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Affiliation(s)
- Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Jia-Min Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Han-Lin Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Hao-Yi Cheng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China.
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Wang J, Jiao D, Yuan S, Chen H, Dai J, Wang X, Guo Y, Qiu D. Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135370. [PMID: 39088956 DOI: 10.1016/j.jhazmat.2024.135370] [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: 02/04/2024] [Revised: 07/17/2024] [Accepted: 07/27/2024] [Indexed: 08/03/2024]
Abstract
Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Han Chen
- Jingchu University of Technology, Jingmen 448000, China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Guo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Blair M, Garner E, Ji P, Pruden A. What is the Difference between Conventional Drinking Water, Potable Reuse Water, and Nonpotable Reuse Water? A Microbiome Perspective. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58. [PMID: 39258328 PMCID: PMC11428167 DOI: 10.1021/acs.est.4c04679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024]
Abstract
As water reuse applications expand, there is a need for more comprehensive means to assess water quality. Microbiome analysis could provide the ability to supplement fecal indicators and pathogen profiling toward defining a "healthy" drinking water microbiota while also providing insight into the impact of treatment and distribution. Here, we utilized 16S rRNA gene amplicon sequencing to identify signature features in the composition of microbiota across a wide spectrum of water types (potable conventional, potable reuse, and nonpotable reuse). A clear distinction was found in the composition of microbiota as a function of intended water use (e.g., potable vs nonpotable) across a very broad range of U.S. water systems at both the point of compliance (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.71) and point of use (Betadisper p > 0.01; ANOSIM p < 0.01, r-stat = 0.41). Core and discriminatory analysis further served in identifying distinct differences between potable and nonpotable water microbiomes. Taxa were identified at both the phylum (Desulfobacterota, Patescibacteria, and Myxococcota) and genus (Aeromonas and NS11.12_marine_group) levels that effectively discriminated between potable and nonpotable waters, with the most discriminatory taxa being core/abundant in nonpotable waters (with few exceptions, such as Ralstonia being abundant in potable conventional waters). The approach and findings open the door to the possibility of microbial community signature profiling as a water quality monitoring approach for assessing efficacy of treatments and suitability of water for intended use/reuse application.
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Affiliation(s)
- Matthew
F. Blair
- Via
Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Emily Garner
- Wadsworth
Department of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Pan Ji
- Via
Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Via
Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Wasmund K, Singleton C, Dahl Dueholm MK, Wagner M, Nielsen PH. The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches. mSystems 2024:e0030124. [PMID: 39254351 DOI: 10.1128/msystems.00301-24] [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: 02/27/2024] [Accepted: 08/08/2024] [Indexed: 09/11/2024] Open
Abstract
In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.
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Affiliation(s)
- Kenneth Wasmund
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Lu Y, Xu J, Feng Y, Jiang J, Wu C, Chen Y. How can the microbial community in watershed sediment maintain its resistance in the presence of shifting antibiotic residuals? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122242. [PMID: 39163669 DOI: 10.1016/j.jenvman.2024.122242] [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: 06/28/2024] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024]
Abstract
The widespread presence of antibiotics in global watershed environments poses a serious threat to public health and ecosystems. It is essential to examine the resistance of microbial communities in watershed environments in response to shifting antibiotic residues. Sediment samples were collected from seven sites across a watershed, encompassing surface sediment (0-10 cm) and bottom sediment (30-40 cm) depths. The aim was to replicate exposure scenarios to different antibiotics (oxytetracycline (OTC) and sulfadiazine (SD)) at varying concentrations (0, 10, and 100 μg/L) in sediment overlying water, within controlled laboratory settings. The study findings revealed significant variations in the microbial community structure of sediments between different treatments, with distinct differences observed in the upper stream and top sediment layers compared to the sediments located downstream and in the bottom layers. After the introduction of antibiotics, a significant decrease in microbial nodes was observed in the genus-level co-occurrence network analysis of the bottom sediment layer, particularly in the OTC treatment groups. In contrast, the downstream region displayed more robust correlations among the top 20 genera than the upstream area. There was no significant variance observed in the expression of Antibiotic resistance genes (ARGs), consisting of tetracycline resistance genes (tetC, tetG, tetM, tetW, and tetX) and sulfonamide resistance genes (sul1, sul2, and sul3), between sediments in the top and bottom layers. Nevertheless, downstream samples exhibited significantly higher levels of ARGs when compared to upstream samples. Network correlation analysis indicated notably lower correlations between ARGs and bacterial genera in sediments from upstream or surface layers compared to those in downstream or deeper layers. Moreover, correlations in the sediments from surface layers and upstream regions showed a decreasing trend with increasing SD exposure concentrations, while those in deeper layers and downstream areas remained relatively stable. The presence of antibiotics notably enhanced the correlation between sediment properties and ARGs, particularly emphasizing associations with total carbon, nitrogen, and sulfur content. However, the introduction of SD and OTC resulted in a decrease in the influence of these sediment factors on microbial community functions related to sulfur and nitrogen metabolism, as indicated by KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation. The research provided empirical evidence on how microbial resistance responds to changes in antibiotics in sediment samples taken from various depths and locations within a watershed. It emphasized the urgent need for heightened awareness of the movement and alteration of antibiotic resistance patterns in watershed ecosystems.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541000, China
| | - Jinghua Xu
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China
| | - Ying Feng
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China
| | - Jinping Jiang
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541000, China
| | - Chunfa Wu
- School of Ecology and Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yongshan Chen
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China.
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Nieto EE, Jurburg SD, Steinbach N, Festa S, Morelli IS, Coppotelli BM, Chatzinotas A. DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories. MICROBIOME 2024; 12:146. [PMID: 39113100 PMCID: PMC11305082 DOI: 10.1186/s40168-024-01865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/26/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation. RESULTS Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. CONCLUSION Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.
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Affiliation(s)
- Esteban E Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Stephanie D Jurburg
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nicole Steinbach
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas de La Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Xu G, Zhao S, He J. Underexplored Organohalide-Respiring Bacteria in Sewage Sludge Debrominating Polybrominated Diphenyl Ethers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39031078 DOI: 10.1021/acs.est.4c00906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants prevalent in the environment. Organohalide-respiring bacteria (OHRB) can attenuate PBDEs via reductive debromination, but often producing toxic end-products. Debromination of PBDEs to diphenyl ether remains a rare phenomenon and is so far specifically associated with Dehalococcoides isolated from e-waste polluted sites. The occurrence of PBDE debromination in other ecosystems and underpinning OHRB are underexplored. Here we found that debromination of PBDEs is a common trait of sewage sludge microbiota, and diphenyl ether was produced as the end-product at varying quantities (0.6-52.9% mol of the parent PBDEs) in 76 of 84 cultures established with bioreactor sludge. Diverse debromination pathways converting PBDEs to diphenyl ether, including several new routes, were identified. Although Dehalococcoides contributed to PBDE debromination, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia likely played more important roles than previously recognized. Multiple reductive dehalogenase genes (including bdeA, pcbA4, pteA, and tceA) were also prevalent and coexisted in bioreactor sludge. Collectively, these findings contribute to enhancing our comprehension of the environmental fate of PBDEs, expanding the diversity of microorganisms catalyzing PBDE debromination, and developing consortia for bioremediation application.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
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Yu H, Pu Z, Wang S, Chen Y, Wang C, Wan Y, Dong Y, Wang J, Wan S, Wang D, Xie Z. Mitigating microplastic stress on peanuts: The role of biochar-based synthetic community in the preservation of soil physicochemical properties and microbial diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172927. [PMID: 38719057 DOI: 10.1016/j.scitotenv.2024.172927] [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: 03/08/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Tire-derived rubber crumbs (RC), as a new type of microplastics (MPs), harms both the environment and human health. Excessive use of plastic, the decomposition of which generates microplastic particles, in current agricultural practices poses a significant threat to the sustainability of agricultural ecosystems, worldwide food security and human health. In this study, the application of biochar, a carbon-rich material, to soil was explored, especially in the evaluation of synthetic biochar-based community (SynCom) to alleviate RC-MP-induced stress on plant growth and soil physicochemical properties and soil microbial communities in peanuts. The results revealed that RC-MPs significantly reduced peanut shoot dry weight, root vigor, nodule quantity, plant enzyme activity, soil urease and dehydrogenase activity, as well as soil available potassium, and bacterial abundance. Moreover, the study led to the identification highly effective plant growth-promoting rhizobacteria (PGPR) from the peanut rhizosphere, which were then integrated into a SynCom and immobilized within biochar. Application of biochar-based SynCom in RC-MPs contaminated soil significantly increased peanut biomass, root vigor, nodule number, and antioxidant enzyme activity, alongside enhancing soil enzyme activity and rhizosphere bacterial abundance. Interestingly, under high-dose RC-MPs treatment, the relative abundance of rhizosphere bacteria decreased significantly, but their diversity increased significantly and exhibited distinct clustering phenomenon. In summary, the investigated biochar-based SynCom proved to be a potential soil amendment to mitigate the deleterious effects of RC-MPs on peanuts and preserve soil microbial functionality. This presents a promising solution to the challenges posed by contaminated soil, offering new avenues for remediation.
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Affiliation(s)
- Hong Yu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China
| | - Zitian Pu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China
| | - Shuaibing Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Chao Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China
| | - Yongshan Wan
- College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Yuanjie Dong
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China
| | - Jianguo Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shubo Wan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China.
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian 271018, China.
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11
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Brown CL, Maile-Moskowitz A, Lopatkin AJ, Xia K, Logan LK, Davis BC, Zhang L, Vikesland PJ, Pruden A. Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment. Nat Commun 2024; 15:5412. [PMID: 38926391 PMCID: PMC11208604 DOI: 10.1038/s41467-024-49742-8] [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: 11/03/2023] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.
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Affiliation(s)
- Connor L Brown
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA
| | | | | | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | | | - Benjamin C Davis
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, USA
| | - Liqing Zhang
- Dept. of Computer Science, Virginia Tech, Blacksburg, USA
| | - Peter J Vikesland
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
| | - Amy Pruden
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
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12
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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [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: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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13
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Radford EJ, Whitworth DE. The genetic basis of predation by myxobacteria. Adv Microb Physiol 2024; 85:1-55. [PMID: 39059819 DOI: 10.1016/bs.ampbs.2024.04.001] [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: 07/28/2024]
Abstract
Myxobacteria (phylum Myxococcota) are abundant and virtually ubiquitous microbial predators. Facultatively multicellular organisms, they are able to form multicellular fruiting bodies and swarm across surfaces, cooperatively hunting for prey. Myxobacterial communities are able to kill a wide range of prey microbes, assimilating their biomass to fuel population growth. Their mechanism of predation is exobiotic - hydrolytic enzymes and toxic metabolites are secreted into the extracellular environment, killing and digesting prey cells from without. However, recent observations of single-cell predation and contact-dependent prey killing challenge the dogma of myxobacterial predation being obligately cooperative. Regardless of their predatory mechanisms, myxobacteria have a broad prey range, which includes Gram-negative bacteria, Gram-positive bacteria and fungi. Pangenome analyses have shown that their extremely large genomes are mainly composed of accessory genes, which are not shared by all members of their species. It seems that the diversity of accessory genes in different strains provides the breadth of activity required to prey upon such a smorgasbord of microbes, and also explains the considerable strain-to-strain variation in predatory efficiency against specific prey. After providing a short introduction to general features of myxobacterial biology which are relevant to predation, this review brings together a rapidly growing body of work into the molecular mechanisms and genetic basis of predation, presenting a summary of current knowledge, highlighting trends in research and suggesting strategies by which we can potentially exploit myxobacterial predation in the future.
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Affiliation(s)
- Emily J Radford
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - David E Whitworth
- Department of Life Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
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14
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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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15
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Fang GY, Liu XQ, Jiang YJ, Mu XJ, Huang BW. Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168908. [PMID: 38013098 DOI: 10.1016/j.scitotenv.2023.168908] [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: 09/04/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
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16
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Li X, Yi S, Chen L, Hafeez M, Zhang Z, Zhang J, Zhou S, Dong W, Huang J, Lu Y. The application of entomopathogenic nematode modified microbial communities within nesting mounds of the red imported fire ants, Solenopsis invicta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168748. [PMID: 38008315 DOI: 10.1016/j.scitotenv.2023.168748] [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: 06/20/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Entomopathogenic microorganisms (e.g., fungi, bacteria, nematodes) have been widely used in biological control of soil-dwelling pests, including the red imported fire ant (RIFA), Solenopsis invicta, a notorious invasive pest worldwide. The application of large amounts of entomopathogenic microorganisms to soil may affect the indigenous soil microbial communities. However, reports about the effect of entomopathogenic nematodes (EPN) on soil microbial communities are very few. In this study, the effects of EPN on RIFA populations and microbial communities in mounds were investigated. Our results showed that the application of the EPN Steinernema carpocapsae. All strain on mounds efficaciously suppressed RIFA worker populations, without forming significantly more satellite mounds compared with the control treatment. The application of EPN did not impact the bacterial and fungal diversity in soils derived from the RIFA mounds. However, it slightly altered the taxonomic make-up of the bacterial communities, but significantly altered the taxonomic composition of fungal communities at the phylum, family, and genus levels. The abundances of some beneficial bacteria and fungi, such as Streptomyces, decreased, while those of plant and animal pathogenic bacteria and fungi, dramatically increased, after EPN treatment. On the other hand, the abundances of some entomopathogenic fungi, such as Fusicolla, Clonostachys, and Mortierella, increased. Redundancy analysis or canonical correspondence analysis revealed a positive correlation between the efficacious EPN control and the presence of the insect-resistant bacteria, Sinomonas, as well as entomopathogenic fungi Fusicolla and Mortierella. This suggests that the interactions between EPN and entomopathogenic fungi may play a role in the biological control of RIFA. Our discoveries shed light on the interactions among EPN, RIFA, and soil microbial communities, and emphasize a possible mutualistic relationship between EPN and entomopathogenic fungi in the biological control of RIFA.
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Affiliation(s)
- Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Songwang Yi
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Limin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jinming Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shuxing Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanying Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Institute of Bio-Interaction, Xianghu Laboratory, Hangzhou 311258, China.
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17
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Li N, Wang Y, Zhou L, Fu D, Chen T, Chen X, Wang Q, Zhu W. The joint action of biochar and plant roots on U-stressed soil remediation: Insights from bacteriomics and metabolomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132635. [PMID: 37793252 DOI: 10.1016/j.jhazmat.2023.132635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
Although biological remediation of U-stressed soil has been studied for a long time, the combined effects of biochar and plant roots are rarely discussed and its influence on rhizosphere microecology are still unknown. Based on pot experiments, we explored the combined efforts of biochar addition and plant roots on U-stressed rhizosphere soil in several ways, including soil physicochemical properties, soil enzyme activities, uranium chemical speciation, bacterial community structure and metabolic pathways. Our results indicates that the content of DTPA-extractable U decreased by 49.31% after biochar and plant roots application, whereas plant roots only treatment just decreased by 25.46%. Further research has found that the pH, CEC, enzyme activities and nutritional level of rhizosphere soil were more significantly improved after biochar and plant roots application. Meanwhile, the abundance and diversity of bacterial community was also upregulated, which was also suggested by the stronger metabolisms of lipids, carbohydrate, nucleotides as well as amino acids. Correlation analyses also certified the positive associations between soil properties, bacterial communities and metabolism. We speculated that the uranium immobilization was mainly attributed to the direct fixation of biochar for its alkalinity, CEC, DOC, etc. and the joint action of biochar and plant roots for their stimulating effects on bacteria. Our findings suggested that combination of biochar and plant roots could limit bioaccessibility of U in a larger extend than plant roots only, which may be a better strategy for rapid remediation of U-streesed soil.
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Affiliation(s)
- Nan Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Yilin Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Li Zhou
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Dengjiang Fu
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Tao Chen
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Xiaoming Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Qing Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
| | - Wenkun Zhu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
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18
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Zhou Y, Chen H, Jiang H, Yao Q, Zhu H. Characteristics of a lipase ArEstA with lytic activity against drug-resistant pathogen from a novel myxobacterium, Archangium lipolyticum sp. nov. Front Microbiol 2024; 14:1320827. [PMID: 38239728 PMCID: PMC10794672 DOI: 10.3389/fmicb.2023.1320827] [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: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
Bacteriolytic myxobacteria are versatile micropredators and are proposed as potential biocontrol agents against diverse bacterial and fungal pathogens. Isolation of new myxobacteria species and exploration of effective predatory products are necessary for successful biocontrol of pathogens. In this study, a myxobacterium strain CY-1 was isolated from a soil sample of a pig farm using the Escherichia coli baiting method. Based on the morphological observation, physiological test, 16S rRNA gene sequence, and genomic data, strain CY-1 was identified as a novel species of the myxobacterial genus Archangium, for which the name Archangium lipolyticum sp. nov. was proposed. Subsequent predation tests indicated that the strain efficiently lysed drug-resistant pathogens, with a higher predatory activity against E. coli 64 than Staphylococcus aureus GDMCC 1.771 (MRSA). The lysis of extracellular proteins against ester-bond-containing substrates (tributyrin, tween 80, egg-yolk, and autoclaved drug-resistant pathogens) inspired the mining of secreted predatory products with lipolytic activity. Furthermore, a lipase ArEstA was identified from the genome of CY-1, and the heterologously expressed and purified enzyme showed bacteriolytic activity against Gram-negative bacteria E. coli 64 but not against Gram-positive MRSA, possibly due to different accessibility of enzyme to lipid substrates in different preys. Our research not only provided a novel myxobacterium species and a candidate enzyme for the development of new biocontrol agents but also reported an experimental basis for further study on different mechanisms of secreted predatory products in myxobacterial killing and degrading of Gram-negative and Gram-positive preys.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haixin Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, South China Agricultural University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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19
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Liu L, Xu F, Lei J, Wang P, Zhang L, Wang J, Zhao J, Mao D, Ye X, Huang Y, Hu G, Cui Z, Li Z. Genome analysis of a plasmid-bearing myxobacterim Myxococcus sp. strain MxC21 with salt-tolerant property. Front Microbiol 2023; 14:1250602. [PMID: 37789850 PMCID: PMC10544341 DOI: 10.3389/fmicb.2023.1250602] [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: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Myxobacteria are widely distributed in various habitats of soil and oceanic sediment. However, it is unclear whether soil-dwelling myxobacteria tolerate a saline environment. In this study, a salt-tolerant myxobacterium Myxococcus sp. strain MxC21 was isolated from forest soil with NaCl tolerance >2% concentration. Under 1% salt-contained condition, strain MxC21 could kill and consume bacteria prey and exhibited complex social behaviors such as S-motility, biofilm, and fruiting body formation but adopted an asocial living pattern with the presence of 1.5% NaCl. To investigate the genomic basis of stress tolerance, the complete genome of MxC21 was sequenced and analyzed. Strain MxC21 consists of a circular chromosome with a total length of 9.13 Mbp and a circular plasmid of 64.3 kb. Comparative genomic analysis revealed that the genomes of strain MxC21 and M. xanthus DK1622 share high genome synteny, while no endogenous plasmid was found in DK1622. Further analysis showed that approximately 21% of its coding genes from the genome of strain MxC21 are predominantly associated with signal transduction, transcriptional regulation, and protein folding involved in diverse niche adaptation such as salt tolerance, which enables social behavior such as gliding motility, sporulation, and predation. Meantime, a high number of genes are also found to be involved in defense against oxidative stress and production of antimicrobial compounds. All of these functional genes may be responsible for the potential salt-toleration. Otherwise, strain MxC21 is the second reported myxobacteria containing indigenous plasmid, while only a small proportion of genes was specific to the circular plasmid of strain MxC21, and most of them were annotated as hypothetical proteins, which may have a direct relationship with the habitat adaptation of strain MxC21 under saline environment. This study provides an inspiration of the adaptive evolution of salt-tolerant myxobacterium and facilitates a potential application in the improvement of saline soil in future.
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Affiliation(s)
- Lin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fengjuan Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jinhui Lei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Peiwen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jihong Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jingya Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dongmei Mao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gang Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Kuroda K, Tomita S, Kurashita H, Hatamoto M, Yamaguchi T, Hori T, Aoyagi T, Sato Y, Inaba T, Habe H, Tamaki H, Hagihara Y, Tamura T, Narihiro T. Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems. WATER RESEARCH X 2023; 20:100196. [PMID: 37662426 PMCID: PMC10469934 DOI: 10.1016/j.wroa.2023.100196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/12/2023] [Indexed: 09/05/2023]
Abstract
Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Shun Tomita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Hazuki Kurashita
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Masashi Hatamoto
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka-Machi, Nagaoka, Niigata 940-2188 Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16–1, Onogawa, Tsukuba, Ibaraki 305–8569, Japan
| | - Hideyuki Tamaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshihisa Hagihara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2‐17‐2‐1 Tsukisamu‐Higashi, Toyohira‐Ku, Sapporo, Hokkaido 062‐8517 Japan
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [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: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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