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Fei S, Li X, Han Z, Sun F, Xiao X, Dong F, Shen C, Su X. Enhanced dechlorination and degradation of Aroclor 1260 by resuscitation-promoting factor under alternating anaerobic-aerobic conditions: Superior performance and associated microbial populations. ENVIRONMENTAL RESEARCH 2025; 276:121531. [PMID: 40185272 DOI: 10.1016/j.envres.2025.121531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 03/31/2025] [Accepted: 04/01/2025] [Indexed: 04/07/2025]
Abstract
The combined processes of dechlorination and degradation are essential for the effective bioremediation of environments contaminated with complex polychlorinated biphenyl (PCB) mixtures. Although resuscitation-promoting factor (Rpf) has been reported to enhance anaerobic dechlorination and aerobic degradation of PCBs by microorganisms, its impact on microbial populations during alternating anaerobic-aerobic treatments remains unexplored. This study investigated the dechlorination and degradation of Aroclor 1260 under anaerobic (AN), aerobic (AE), and alternating anaerobic-aerobic (AA) conditions, both with and without Rpf supplementation. The results demonstrated that Rpf significantly promoted Aroclor 1260 dechlorination under AN conditions, enhanced degradation under AE conditions, and markedly improved both processes under AA conditions, achieving nearly twice the degradation efficiency compared to AE alone. Furthermore, Rpf supplementation significantly increased the abundance of dechlorination-associated microbial taxa, including members of Firmicutes, Chloroflexi, Bacteroidota, and Desulfobacterota under AN conditions, as well as degradation-associated genera such as Pseudomonas and Sphingomonas under AE and AA conditions. Rpf also strengthened microbial interactions by enhancing positive correlations among functional populations and increasing network complexity. These findings establish Rpf as a powerful enhancer of PCB dechlorination and degradation, which provide valuable insights into its superior efficiency in PCB removal under AA conditions.
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Affiliation(s)
- Sijia Fei
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Xiaonan Li
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Zhen Han
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Xiao Xiao
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Feng Dong
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China.
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Han Z, Fei S, Sun F, Dong F, Xiao X, Shen C, Su X. Enhanced microbial dechlorination of PCBs by anaerobic digested sludge and enrichment of low-abundance PCB dechlorinators. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136376. [PMID: 39500182 DOI: 10.1016/j.jhazmat.2024.136376] [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: 07/24/2024] [Revised: 10/15/2024] [Accepted: 10/30/2024] [Indexed: 12/01/2024]
Abstract
The slow rate of anaerobic microbial dechlorination in natural environments limits the application of polychlorinated biphenyl (PCB) bioremediation. Anaerobic digested sludge (ADS), abundant in nutrients and microorganisms, could be an effective additive to improve microbial dechlorination. This research investigates the influence of ADS on Aroclor 1260 dechlorination performance, microbial community composition, and the abundance of functional genes. Moreover, further enrichment of organohalide-respiring bacteria (OHRB) was examined using tetrachloroethene (PCE) as the electron acceptor, followed by the serial dilution-to-extinction method in conjunction with resuscitation promoting factor (Rpf) supplementation. The results demonstrated that the addition of 5 g/L ADS achieved more extensive and efficient dechlorination of PCBs. ADS enhanced the removal of meta- and para-chlorine without significantly changing the dechlorination pathways. The abundances of dechlorinators, including Dehalobium and Dehalobacter within the Chloroflexi and Firmicutes phyla, as well as non-dechlorinators from the Desulfobacterota, Euryarchaeota, and Bacteroidetes phyla, were significantly increased with ADS amendment. Similarly, an increased abundance of bacteria, OHRB, reductive dehalogenase (RDase) genes, and archaeal 16S rRNA genes was observed. Additionally, obligate OHRB, such as Dehalobacter and Dehalobium, were further enriched. These findings indicate that ADS effectively enhances microbial reductive dechlorination and highlight the potential for enriching and isolating OHRB with Rpf.
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Affiliation(s)
- Zhen Han
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Sijia Fei
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Feng Dong
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Xiao Xiao
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
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3
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Li X, Song C, Kang X, Chen F, Li A, Wang Y, Zou J, Yin J, Li Y, Sun Z, Ma X, Liu J. Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122503. [PMID: 39299104 DOI: 10.1016/j.jenvman.2024.122503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 08/30/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.
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Affiliation(s)
- Xia Li
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, Shandong, China
| | - Chuansheng Song
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, Shandong, China
| | - Xiaofei Kang
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, Shandong, China
| | - Fengzhen Chen
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, Shandong, China
| | - Ao Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuancheng Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Junzhu Zou
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jiahui Yin
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; College of Horticulture, Jilin Agricultural University, Changchun, 130000, Jilin, China
| | - Yingying Li
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, Shandong, China
| | - Zhenyuan Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaodong Ma
- Department of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan, 250100, Shandong, China.
| | - Junxiang Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Duan X, Li J, Li Y, Xu Y, Chai H, Chao S. Removal, accumulation, and micro-ecosystem impacts of typical POPs in bioretention systems with different media: A runoff infiltration study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174278. [PMID: 38925397 DOI: 10.1016/j.scitotenv.2024.174278] [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: 03/27/2024] [Revised: 05/31/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Bioretention systems prove effective in purifying common persistent organic pollutants (POPs) found in urban rainfall runoff. However, the response process of the microecosystem in the media becomes unclear when POPs accumulate in bioretention systems. In this study, we constructed bioretention systems and conducted simulated rainfall tests to elucidate the evolution of micro-ecosystems within the media under typical POPs pollution. The results showed all POPs in runoff were effectively removed by surface adsorption in different media, with load reduction rates of >85 % for PCBs and OCPs and > 80 % for PAHs. Bioretention soil media (BSM) + water treatment residuals (WTR) media exhibited greater stability in response to POPs contamination compared to BSM and pure soil (PS) media. POPs contamination significantly impacted the microecology of the media, reducing the number of microbial species by >52.6 % and reducing diversity by >27.6 % at the peak of their accumulation. Enzyme activities were significantly inhibited, with reductions ranging from 44.42 % to 60.33 %. Meanwhile, in terms of ecological functions, the metabolism of exogenous carbon sources significantly increased (p < 0.05), while nitrogen and sulfur cycling processes were suppressed. Microbial diversity and enzyme activities showed some recovery during the dissipation of POPs but did not reach the level observed before the experiment. Dominant bacterial species and abundance changed significantly during the experiment. Proteobacteria were suppressed, but remained the dominant phylum (all relative abundances >41 %). Bacteroidota, Firmicutes, and Actinobacteria adapted well to the contamination. Pseudomonas, a typical POPs-degrading bacterium, displayed a positive correlation between its relative abundance and POPs levels (mean > 10 %). Additionally, POPs and media properties, including TN and pH, are crucial factors that collectively shape the microbial community. This study provides new insights into the impacts of POPs contamination on the microbial community of the media, which can improve media design and operation efficiency.
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Affiliation(s)
- Xiaolong Duan
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Jiake Li
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China.
| | - Yajiao Li
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Yefeng Xu
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Senhao Chao
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
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Blázquez-Pallí N, Torrentó C, Marco-Urrea E, Garriga D, González M, Bosch M. Pilot tests for the optimization of the bioremediation strategy of a multi-layered aquifer at a multi-focus site impacted with chlorinated ethenes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173093. [PMID: 38768723 DOI: 10.1016/j.scitotenv.2024.173093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
A multi-layered aquifer in an industrial area in the north of the Iberian Peninsula is severely contaminated with the chlorinated ethenes (CEs) tetrachloroethylene, trichloroethylene, cis-1,2-dichloroethylene, and vinyl chloride. Both shallow and deep aquifers are polluted, with two differentiated north and south CEs plumes. Hydrogeochemical and isotopic data (δ13C of CEs) evidenced natural attenuation of CEs. To select the optimal remediation strategy to clean-up the contamination plumes, laboratory treatability studies were performed, which confirmed the intrinsic biodegradation potential of the north and south shallow aquifers to fully dechlorinate CEs to ethene after injection of lactate, but also the combination of lactate and sulfidized mZVI as an alternative treatment for the north deep aquifer. In the lactate-amended microcosms, full dechlorination of CEs was accompanied by an increase in 16S rRNA gene copies of Dehalococcoides and Dehalogenimonas, and the tceA, vcrA and bvcA reductive dehalogenases. Three in situ pilot tests were implemented, which consisted in injections of lactate in the north and south shallow aquifers, and injections of lactate and sulfidized mZVI in the north deep aquifer. The hydrogeochemical, isotopic and molecular analyses used to monitor the pilot tests evidenced that results obtained mimicked the laboratory observations, albeit at different dechlorination rates. It is likely that the efficiency of the injections was affected by the amendment distribution. In addition, monitoring of the pilot tests in the shallow aquifers showed the release of CEs due to back diffusion from secondary sources, which limited the use of isotopic data for assessing treatment efficiency. In the pilot test that combined the injection of lactate and sulfidized mZVI, both biotic and abiotic pathways contributed to the production of ethene. This study demonstrates the usefulness of integrating different chemical, isotopic and biomolecular approaches for a more robust selection and implementation of optimal remediation strategies in CEs polluted sites.
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Affiliation(s)
- Natàlia Blázquez-Pallí
- LITOCLEAN, S.L., Environmental site assessment and remediation, c/ Numància 36, 08029 Barcelona, Spain.
| | - Clara Torrentó
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Hidrogeologia (MAGH), Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Martí Franquès s/n, 08028 Barcelona, Spain; Serra Húnter Fellowship, Generalitat de Catalunya, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), c/ de les Sitges s/n, 08193 Cerdanyola del Vallès, Spain
| | - David Garriga
- LITOCLEAN, S.L., Environmental site assessment and remediation, c/ Numància 36, 08029 Barcelona, Spain
| | - Marta González
- LITOCLEAN, S.L., Environmental site assessment and remediation, c/ Numància 36, 08029 Barcelona, Spain
| | - Marçal Bosch
- LITOCLEAN, S.L., Environmental site assessment and remediation, c/ Numància 36, 08029 Barcelona, Spain
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Abstract
In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.
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Affiliation(s)
- André Freches
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Joana Costa Fradinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
- Department of Chemistry, UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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7
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Hu S, Jiang L, Jiang L, Tang L, Wickrama Arachchige AUK, Yu H, Deng Z, Li L, Wang C, Zhang D, Chen C, Lin S, Chen X, Zhang C. Spatial distribution characteristics of carbazole and polyhalogenated carbazoles in water column and sediments in the open Western Pacific Ocean. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133956. [PMID: 38460258 DOI: 10.1016/j.jhazmat.2024.133956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
Polyhalogenated carbazoles (PHCZs), an emerging persistent halogenated organic pollutant, have been detected in the environment. However, our understanding of PHCZs in the ocean remains limited. In this study, 47 seawater samples (covering 50 - 4000 m) and sediment samples (49 surface and 3 cores) were collected to investigate the occurrence and spatial distribution patterns of carbazole and its halogenated derivants (CZDs) in the Western Pacific Ocean. In seawater, the detection frequencies of CZ (97.87%) and 3-CCZ (57.45%) were relatively high. In addition, the average concentration of ΣPHCZs in the upper water (< 150 m, 0.23 ± 0.21 ng/L) was significantly lower than that in the deep ocean (1000 - 4000 m, 0.65 ± 0.56 ng/L, P < 0.05), which may indicate the vertical transport of PHCZs in the marine environment. The concentration of ΣCZDs in surface sediment ranges from 0.46 to 6.48 ng/g (mean 1.54 ng/g), among which CZ and 36-CCZ were the predominant components. Results from sediment cores demonstrate a noteworthy negative correlation between the concentration of CZDs and depth, indicating the ongoing natural degradation process occurring in sediment cores over a long period. This study offers distinctive insights into the occurrence, composition, and vertical features of CZDs in oceanic environments.
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Affiliation(s)
- Songtao Hu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Lijia Jiang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Lingbo Jiang
- Zhoushan Institute for Food and Drug Control, Zhoushan 316021, Zhejiang, China
| | - Leiming Tang
- Zhoushan Institute for Food and Drug Control, Zhoushan 316021, Zhejiang, China
| | | | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Ocean Research Center of Zhoushan, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Longyu Li
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Dongsheng Zhang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Chunlei Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Shiquan Lin
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Xiang Chen
- Zhoushan Institute for Food and Drug Control, Zhoushan 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China.
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Yan PF, Dong S, Woodcock MJ, Manz KE, Garza-Rubalcava U, Abriola LM, Pennell KD, Cápiro NL. Biotransformation of 6:2 fluorotelomer sulfonate and microbial community dynamics in water-saturated one-dimensional flow-through columns. WATER RESEARCH 2024; 252:121146. [PMID: 38306753 DOI: 10.1016/j.watres.2024.121146] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Nearly all per- and polyfluoroalkyl substances (PFAS) biotransformation studies reported to date have been limited to laboratory-scale batch reactors. The fate and transport of PFAS in systems that more closely represent field conditions, i.e., in saturated porous media under flowing conditions, remain largely unexplored. This study investigated the biotransformation of 6:2 fluorotelomer sulfonate (6:2 FTS), a representative PFAS of widespread environmental occurrence, in one-dimensional water-saturated flow-through columns packed with soil obtained from a PFAS-contaminated site. The 305-day column experiments demonstrated that 6:2 FTS biotransformation was rate-limited, where a decrease in pore-water velocity from 3.7 to 2.4 cm/day, resulted in a 21.7-26.1 % decrease in effluent concentrations of 6:2 FTS and higher yields (1.0-1.4 mol% vs. 0.3 mol%) of late-stage biotransformation products (C4C7 perfluoroalkyl carboxylates). Flow interruptions (2 and 7 days) were found to enhance 6:2 FTS biotransformation during the 6-7 pore volumes following flow resumption. Model-fitted 6:2 FTS column biotransformation rates (0.039-0.041 cmw3/gs/d) were ∼3.5 times smaller than those observed in microcosms (0.137 cmw3/gs/d). Additionally, during column experiments, planktonic microbial communities remained relatively stable, whereas the composition of the attached microbial communities shifted along the flow path, which may have been attributed to oxygen availability and the toxicity of 6:2 FTS and associated biotransformation products. Genus Pseudomonas dominated in planktonic microbial communities, while in the attached microbial communities, Rhodococcus decreased and Pelotomaculum increased along the flow path, suggesting their potential involvement in early- and late-stage 6:2 FTS biotransformation, respectively. Overall, this study highlights the importance of incorporating realistic environmental conditions into experimental systems to obtain a more representative assessment of in-situ PFAS biotransformation.
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Affiliation(s)
- Peng-Fei Yan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States.
| | - Sheng Dong
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | | | - Katherine E Manz
- School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | | | - Linda M Abriola
- School of Engineering, Brown University, Providence, RI, United States
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, United States
| | - Natalie L Cápiro
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States.
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9
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Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
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10
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Romantschuk M, Lahti-Leikas K, Kontro M, Galitskaya P, Talvenmäki H, Simpanen S, Allen JA, Sinkkonen A. Bioremediation of contaminated soil and groundwater by in situ biostimulation. Front Microbiol 2023; 14:1258148. [PMID: 38029190 PMCID: PMC10658714 DOI: 10.3389/fmicb.2023.1258148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.
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Affiliation(s)
- Martin Romantschuk
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Katariina Lahti-Leikas
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Merja Kontro
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | | | - Harri Talvenmäki
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Suvi Simpanen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - John A. Allen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Aki Sinkkonen
- Natural Resources Institute Finland (Luke), Horticulture Technologies, Turku, Finland
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11
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Xu L, Tang Y, Liu S, Chen X, Wang Y, Liu Z, Qin Q, Fu D, Xu Y. Short-chain fatty acids facilitated long-term dechlorination of PCBs in Taihu Lake sediment microcosms: Evidence from PCB congener and microbial community analyses. CHEMOSPHERE 2023; 340:139935. [PMID: 37619750 DOI: 10.1016/j.chemosphere.2023.139935] [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: 03/30/2023] [Revised: 07/12/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Microbial reductive dechlorination hosts great promise as an in situ bioremediation strategy for polychlorinated biphenyls (PCBs) contamination. However, the slow dechlorination in sediments limits natural attenuation. Short-chain fatty acids, as preferred carbon sources and electron donors for dechlorinating microorganisms, might stimulate PCB dechlorination. Herein, two sets of short-chain fatty acids, sole acetate and a fatty acid mixture (acetate, propionate, and butyrate), were amended periodically into Taihu Lake (China) sediment microcosms containing nine PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170) after 24 weeks of incubation. Short-chain fatty acids facilitated the long-term PCB dechlorination and the promoting effect of the fatty acid mixture compared favorably with that of sole acetate. By the end of 108 weeks, the total PCB mass concentrations in acetate amended and fatty acid mixture amended microcosms significantly declined by 7.6% and 10.3% compared with non-amended microcosms (P < 0.05), respectively. Short-chain fatty acids selectively favored the removal of flanked meta and single-flanked para chlorines. Notably, a rare ortho dechlorination pathway, PCB25 (24-3-CB) to PCB13 (3-4-CB), was enhanced. Supplementary fatty acids significantly increased reductive dehalogenases (RDase) gene pcbA5 instead of improving the growth of Dehalococcoides. These findings highlight the merits of low cost short-chain fatty acids on in situ biostimulation in treating PCBs contamination.
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Affiliation(s)
- Lei Xu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yanqiang Tang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Sha Liu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Xi Chen
- Water Affairs Bureau of Nanjing Pukou District, Nanjing, 211899, China
| | - Ying Wang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Zheming Liu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Qingdong Qin
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Dafang Fu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yan Xu
- School of Civil Engineering, Southeast University, Nanjing, 210096, China.
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12
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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13
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Wiegand S, Sobol M, Schnepp-Pesch LK, Yan G, Iqbal S, Vollmers J, Müller JA, Kaster AK. Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes. Microorganisms 2023; 11:2612. [PMID: 37894270 PMCID: PMC10608941 DOI: 10.3390/microorganisms11102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; (S.W.); (M.S.); (L.K.S.-P.); (G.Y.); (S.I.); (J.V.); (J.A.M.)
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14
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Yin Y, Wang X, Hu Y, Li F, Cheng H. Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132043. [PMID: 37453349 DOI: 10.1016/j.jhazmat.2023.132043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.
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Affiliation(s)
- Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiaojie Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuanan Hu
- MOE Laboratory of Groundwater Circulation and Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fadong Li
- State Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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15
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Marques MVA, Lopes BC, Silvério THR, von Sperling M, Neves TDA. Persistence of pathogens and bacterial community dynamics in tropical soil after application of raw sewage. Sci Rep 2023; 13:13435. [PMID: 37596413 PMCID: PMC10439161 DOI: 10.1038/s41598-023-40718-0] [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: 04/04/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
The objective of this work was to evaluate the persistence of faecal indicators and pathogenic organisms (Salmonella spp., Escherichia coli and viable helminth eggs) and the structure/diversity of bacterial communities in soil receiving raw sewage (RS) for an extended period of application (3 uninterrupted years). In the experimental design, three treatments were defined: (1) Control soil, characterized by the analysis of a composite sample collected in an area of similar soil, but not a recipient of RS (TSC); (2) Soil receiving conventional mineral fertilization, and furrow irrigation with supply water (TW); and (3) Fertirrigated soil with RS applied by furrows (TF). The results of persistence of pathogenic organisms and indicators in TF indicated a sanitary quality similar to the control soil (TSC), thus potentially bringing low risks of contamination with pathogens present in the soil. The presence of viable helminth eggs was not identified in any treatment studied, because of its low concentration in the raw sewage of the studied system. The TW, TF and TSC treatments had 34.8% of bacterial diversity in common. The bacterial composition of the soil showed a predominance of the Proteobacteria phylum in all treatments studied; however, TF was the one with the highest relative abundance of this phylum (44.8%).
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Affiliation(s)
- Marcus Vinícius Araújo Marques
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil.
| | - Bruna Coelho Lopes
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil
| | - Thiago Henrique Ribeiro Silvério
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil
| | - Marcos von Sperling
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Alencar Neves
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (Universidade Federal de Minas Gerais), Belo Horizonte, Minas Gerais, Brazil
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16
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Gao S, Du Z, Ju F, Yan P, Niu B, Yao Y. Effect of rhizosphere microorganisms on aflatoxin contamination of maize. Heliyon 2023; 9:e15949. [PMID: 37215779 PMCID: PMC10192528 DOI: 10.1016/j.heliyon.2023.e15949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
The continued large consumption of maize makes it one of the most important food crops worldwide. However, the yield and quality of maize are greatly affected by global warming, and mycotoxin pollution keeps increasing. The effect of environmental factors, especially rhizosphere microorganisms, on mycotoxin pollution of maize is not completely clear, so we carried out relevant studies. In this study, we found that microbial communities inhabiting the maize rhizosphere, which consists of soil particles firmly attached to roots, as well as the soil, have a significant influence on the aflatoxin pollution of maize. The ecoregion and soil properties also had considerable effects on the microbial structure and diversity. The bacterial communities from the rhizosphere soil were profiled using a high-throughput next-generation sequencing method. The ecoregion and soil properties had considerable effects on the microbial structure and diversity. A comparison of the aflatoxin high concentration group with the low concentration group found that bacteria of the phylum Gemmatimonadetes and order Burkholderiales were significantly more abundant in the high concentration samples. Furthermore, these bacteria were significantly correlated with aflatoxin contamination and could aggravate its contamination of maize. The results of these analyses showed that seeding location could cause significant shifts in the root microbiota of maize, and the bacteria enriched in high aflatoxin contamination area soils should attract special concern. These findings will support strategies for improving maize yield and aflatoxin contamination control.
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Affiliation(s)
- Suyan Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Zhaolin Du
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Feng Ju
- Westlake University, Hangzhou 310024, China
| | - Peisheng Yan
- Harbin Institute of Technology, Weihai 264200, China
| | - Ben Niu
- Northeast Forestry University, Haerbin 150000, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
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17
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Zhang X, Geng K, Wu N, Hu G, Fan B, He J, Qiao W. Sustained anaerobic degradation of 4-chloro-2-methylphenoxyacetic acid by acclimated sludge in a continuous-flow reactor. CHEMOSPHERE 2023; 330:138749. [PMID: 37086982 DOI: 10.1016/j.chemosphere.2023.138749] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
4-Chloro-2-methylphenoxyacetic acid (MCPA) is a widely used herbicide across the world. MCPA is persistent and easily transports into anoxic environment, such as groundwater, sediments and deep soils. However, little research on anaerobic microbial degradation of MCPA was carried out. The functional microorganisms as well as the catabolic pathway are still unknown. In this research, an anaerobic MCPA-degrading bacterial consortium was enriched from the river sediment near a pesticide-manufacturing plant. After about 6 months' acclimation, the MCPA transformation rate of the consortium reached 4.32 μmol g-1 day-1, 25 times faster than that of the original sludge. 96% of added MCPA (2.5 mM) was degraded within 9 d of incubation. Three metabolites including 4-chloro-2-methylphenol (MCP), 2-methylphenol (2-MP) and phenol were identified during the anaerobic degradation of MCPA. An anaerobic catabolic pathway was firstly proposed: firstly, MCPA was transformed to MCP via the cleavage of the aryl ether, then MCP was reductively dechlorinated to 2-MP which was further demethylated to phenol. The 16S rRNA gene amplicon sequencing revealed a substantial shift in the bacterial community composition after the acclimation. SBR1031, Acidaminococcaceae, Aminicenantales, Syntrophorhabdus, Acidaminobacter, Bacteroidetes_vadinHA17, Methanosaeta, Bathyarchaeia, KD4-96, Anaeromyxobacter, and Dehalobacter were significantly increased in the enriched consortium after acclimation, and positively correlated with the anaerobic degradation of MCPA as suggested by heat map correlation analysis. This study provides a basis for further elucidation of the anaerobic catabolism of MCPA, and contributes to developing efficient and low-cost anaerobic treatment technologies for MCPA pollution.
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Affiliation(s)
- Xuan Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Keke Geng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Ningning Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Gang Hu
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Ben Fan
- College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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Mohamed HF, Abd‐Elgawad A, Cai R, Luo Z, Xu C. The bacterial signature offers vision into the machinery of coral fitness across high-latitude coral reef in the South China Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:13-30. [PMID: 36054576 PMCID: PMC10103774 DOI: 10.1111/1758-2229.13119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/15/2022] [Indexed: 05/20/2023]
Abstract
Coral-bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High-throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site-wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self-sustaining tool in coral restoration.
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Affiliation(s)
- Hala F. Mohamed
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
- Al‐Azhar University (Girls Branch)Faculty of Science, Botany & Microbiology DepartmentCairoEgypt
| | - Amro Abd‐Elgawad
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
- Tourism Developing AuthorityCentral Adminstration for Environmental AffairsCairoEgypt
| | - Rongshuo Cai
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
| | - Zhaohe Luo
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
| | - Changan Xu
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
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19
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Resuscitation-Promoting Factor Accelerates Enrichment of Highly Active Tetrachloroethene/Polychlorinated Biphenyl-Dechlorinating Cultures. Appl Environ Microbiol 2023; 89:e0195122. [PMID: 36629425 PMCID: PMC9888273 DOI: 10.1128/aem.01951-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The anaerobic bioremediation of polychlorinated biphenyls (PCBs) is largely impeded by difficulties in massively enriching PCB dechlorinators in short periods of time. Tetrachloroethene (PCE) is often utilized as an alternative electron acceptor to preenrich PCB-dechlorinating bacteria. In this study, resuscitation promoting factor (Rpf) was used as an additive to enhance the enrichment of the microbial communities involved in PCE/PCBs dechlorination. The results indicated that Rpf accelerates PCE dechlorination 3.8 to 5.4 times faster than control cultures. In Aroclor 1260-fed cultures, the amendment of Rpf enables significantly more rapid and extensive dechlorination of PCBs. The residual high-chlorinated PCB congeners (≥5 Cl atoms) accounted for 36.7% and 59.8% in the Rpf-amended cultures and in the corresponding controls, respectively. This improvement was mainly attributed to the enhanced activity of the removal of meta-chlorines (47.7 mol % versus 14.7 mol %), which did not appear to affect dechlorination pathways. The dechlorinators, including Dehalococcoides in Chloroflexi and Desulfitobacterium in Firmicutes, were greatly enriched via Rpf amendment. The abundance of nondechlorinating populations, including Methanosarcina, Desulfovibrio, and Bacteroides, was also greatly enhanced via Rpf amendment. These results suggest that Rpf serves as an effective additive for the rapid enrichment of active dechlorinating cultures so as to provide a new approach by which to massively cultivate bioinoculants for accelerated in situ anaerobic bioremediation. IMPORTANCE The resuscitation promoting factor (Rpf) of Micrococcus luteus has been reported to resuscitate and stimulate the growth of functional microorganisms that are involved in the aerobic degradation of polychlorinated biphenyls (PCBs). However, few studies have been conducted to investigate the role of Rpf on anaerobic microbial populations. In this study, the enhancement of Rpf on the anaerobic microbial dechlorination of PCE/PCBs was discovered. Additionally, the Rpf-responsive populations underlying the enhanced dechlorination were uncovered. This report reveals the rapid enrichment of active dechlorinating cultures via Rpf amendment, and this sheds light on massively enriching PCB dechlorinators in short periods of time. The enhanced in situ anaerobic bioremediation of PCBs could be expected by supplementing Rpf.
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20
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Tong W, Li J, Cong W, Zhang C, Xu Z, Chen X, Yang M, Liu J, Yu L, Deng X. Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita. THE PLANT PATHOLOGY JOURNAL 2022; 38:583-592. [PMID: 36503187 PMCID: PMC9742794 DOI: 10.5423/ppj.oa.08.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 06/17/2023]
Abstract
Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.
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Affiliation(s)
- Wenjie Tong
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Wenfeng Cong
- National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193,
China
| | - Cuiping Zhang
- Yuxi Branch of Yunnan Provincial Tobacco Company, Yuxi 653100, Yunnan,
China
| | - Zhaoli Xu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
| | - Xiaolong Chen
- Tobacco Leaf Purchase Center, China Tobacco Henan Industrial Co., Ltd., Zhengzhou 450000,
China
| | - Min Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming 650214, Yunnan,
China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan,
China
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21
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Dutta N, Usman M, Ashraf MA, Luo G, Zhang S. A critical review of recent advances in the bio-remediation of chlorinated substances by microbial dechlorinators. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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22
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Zhu R, Liu C, Xu YD, He W, Liu J, Chen J, An Y, Shi S. Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks. Front Microbiol 2022; 13:968551. [PMID: 36160210 PMCID: PMC9493311 DOI: 10.3389/fmicb.2022.968551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.
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Affiliation(s)
- Ruifen Zhu
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chang Liu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yuan Dong Xu
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Wei He
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Jielin Liu
- Pratacultural Institute Science, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jishan Chen
- Pratacultural Institute, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Yajun An
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou, China
| | - Shangli Shi
- Pratacultural College, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shangli Shi
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23
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Zhang Y, Yang Z, Ni J, Ma Y, Xiong H, Jian W. Toxicity and modulation of silver nanoparticles synthesized using abalone viscera hydrolysates on bacterial community in aquatic environment. Front Microbiol 2022; 13:968650. [PMID: 36110292 PMCID: PMC9468672 DOI: 10.3389/fmicb.2022.968650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Polysaccharide decorated silver nanoparticles (AgNPs) are a new type of antibacterial agent in aquaculture, but their effects on the bacterial community structure in aquaculture water are still unknown. In this study, the primary hydrolysate from abalone (Haliotis discus hannai) viscera (AVH) was used to biosynthesize AVH-AgNPs by in situ reduction, and the crystallinity nature, size, morphology, and chemical composition were analyzed by high-resolution characterization techniques such as Ultraviolet–visible spectroscopy (UV–vis), X-rays diffraction (XRD), Transmission Electron Microscope (TEM), Dynamic light scattering (DLS), Zeta potential, inductively coupled plasma-optical emission spectrometry (ICP-OES) and Turbiscan stability index (TSI) values. Furthermore, the acute toxicity of AVH-AgNPs to zebrafish (Danio rerio) and their effects on bacterial community structure in fish culture water at low concentrations were studied. The results showed that the spherical AVH-AgNPs with an average diameter of 54.57 ± 12.96 nm had good stability, low toxicity, and good in vitro antibacterial activity. Within the experimental concentration range, all AVH-AgNPs treatments had decreased the bacterial diversity in zebrafish culture water to varying degrees. The bacteria with significantly decreased abundances were pathogenic or potential pathogenic, such as Aeromonas veronii, Flavobacterium columnare, and genera Flectobacillus and Bosea. The abundance of Haliscomenobacter sp. JS224, which might cause sludge swelling, also decreased significantly. On the other hand, the relative abundance of some bacterial taxa could remove xenobiotics (e.g., Runella defluvii and Phenylobacterium), control water eutrophication (Sediminibacterium), and reduce toxic algae proliferation (Candidatus Intestinusbacter nucleariae and Candidatus Finniella), increased significantly. Thus, the application of AVH-AgNPs in aquaculture water at low concentrations is relatively safe and has positive significance for improving the aquaculture environment. Also, AVH-AgNPs have good prospects in aquaculture.
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Affiliation(s)
- Yue Zhang
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, Xiamen, China
| | - Zhuan Yang
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, Xiamen, China
| | - Jing Ni
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, Xiamen, China
| | - Ying Ma
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fisheries College of Jimei University, Xiamen, China
- *Correspondence: Ying Ma,
| | - Hejian Xiong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Hejian Xiong,
| | - Wenjie Jian
- Institute of Respiratory Diseases, Xiamen Medical College, Xiamen, China
- Wenjie Jian,
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24
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Ewald JM, Schnoor JL, Mattes TE. Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants. FEMS Microbiol Ecol 2022; 98:6602352. [PMID: 35665806 DOI: 10.1093/femsec/fiac067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.
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Affiliation(s)
- Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Jerald L Schnoor
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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25
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Sun L, Mo Y, Zhang L. A mini review on bio-electrochemical systems for the treatment of azo dye wastewater: State-of-the-art and future prospects. CHEMOSPHERE 2022; 294:133801. [PMID: 35104551 DOI: 10.1016/j.chemosphere.2022.133801] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Azo dyes are typical toxic and refractory organic pollutants widely used in the textile industry. Bio-electrochemical systems (BESs) have great potential for the treatment of azo dyes with the help of microorganisms as biocatalysts and have advanced significantly in recent years. However, the latest and significant advancement and achievements of BESs treating azo dyes have not been reviewed since 8 years ago. This review thus focuses on the recent investigations of BESs treating azo dyes from the year of 2013-2020 in order to broaden the knowledge and deepen the understanding in this field. In this review, azo dyes degradation mechanisms of BESs are first elaborated, followed by the introduction of BES configurations with the emphasis on the novelties. The azo dye degradation performance of BESs is then presented to demonstrate their effectiveness in azo dye removal. Effects of various operating parameters on the overall performance of BESs are comprehensively elucidated, including electrode materials, external resistances and applied potentials, initial concentrations of azo dyes, and co-substrates. Predominant microorganisms responsible for degradation of azo dyes in BESs are highlighted in details. Furthermore, the combination of BESs with other processes to further improve the azo dye removal are discussed. Finally, an outlook on the future research directions and challenges is provided from the viewpoint of realistic applications of the technology.
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Affiliation(s)
- Liping Sun
- State Key Laboratory of Separation Membranes and Membrane Processes, National Center for International Joint Research on Membrane Science and Technology, Tiangong University, Tianjin, 300387, China; School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Yinghui Mo
- State Key Laboratory of Separation Membranes and Membrane Processes, National Center for International Joint Research on Membrane Science and Technology, Tiangong University, Tianjin, 300387, China; School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, China.
| | - Lu Zhang
- State Key Laboratory of Separation Membranes and Membrane Processes, National Center for International Joint Research on Membrane Science and Technology, Tiangong University, Tianjin, 300387, China; School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, China
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26
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Puigserver D, Herrero J, Nogueras X, Cortés A, Parker BL, Playà E, Carmona JM. Biotic and abiotic reductive dechlorination of chloroethenes in aquitards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151532. [PMID: 34752872 DOI: 10.1016/j.scitotenv.2021.151532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated solvents occur as dense nonaqueous phase liquid (DNAPL) or as solutes when dissolved in water. They are present in many pollution sites in urban and industrial areas. They are toxic, carcinogenic, and highly recalcitrant in aquifers and aquitards. In the latter case, they migrate by molecular diffusion into the matrix. When aquitards are fractured, chlorinated solvents also penetrate as a free phase through the fractures. The main objective of this study was to analyze the biogeochemical processes occurring inside the matrix surrounding fractures and in the joint-points zones. The broader implications of this objective derive from the fact that, incomplete natural degradation of contaminants in aquitards generates accumulation of daughter products. This causes steep concentration gradients and back-diffusion fluxes between aquitards and high hydraulic conductivity layers. This offers opportunities to develop remediation strategies based, for example, on the coupling of biotic and reactive abiotic processes. The main results showed: 1) Degradation occurred especially in the matrix adjacent to the orthogonal network of fractures and textural heterogeneities, where texture contrasts favored microbial development because these zones constituted ecotones. 2) A dechlorinating bacterium not belonging to the Dehalococcoides genus, namely Propionibacterium acnes, survived under the high concentrations of dissolved perchloroethene (PCE) in contact with the PCE-DNAPL and was able to degrade it to trichloroethene (TCE). Dehalococcoides genus was able to conduct PCE reductive dechlorination at least up to cis-1,2-dichloroethene (cDCE), which shows again the potential of the medium to degrade chloroethenes in aquitards. 3) Degradation of PCE in the matrix resulted from the coupling of reactive abiotic and biotic processes-in the first case, promoted by Fe2+ sorbed to iron oxides, and in the latter case, related to dechlorinating microorganisms. The dechlorination resulting from these coupling processes is slow and limited by the need for an adequate supply of electron donors.
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Affiliation(s)
- Diana Puigserver
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB), Serra Húnter Tenure-elegible Lecturer, C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - Jofre Herrero
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - Xènia Nogueras
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain; Health Section of the City Council of Mataró (Barcelona), Specialized Support Technician, Carrer de la Riera, 48, 08301 Mataró, Barcelona, Spain.
| | - Amparo Cortés
- Department of Biology, Health and Environment, Faculty of Pharmacy, University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.
| | - Beth L Parker
- School of Engineering, University of Guelph, 50, Stone Road East, Guelph, N1G 2W1, Ontario, Canada.
| | - E Playà
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - José M Carmona
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
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27
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Zhao C, Yin X, Chen J, Cao F, Abou-Elwafa SF, Huang M. Effect of rapeseed straw-derived biochar on soil bacterial community structure at tillering stage of Oryza Sativa. Can J Microbiol 2022; 68:483-492. [PMID: 35344674 DOI: 10.1139/cjm-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Numerous studies have reported the dynamics of microbes when biochar was applied, whereas the information on the alterations of bacterial community after application of rapeseed straw-derived biochar is limited. A pot experiment with two rapeseed straw-derived biochar application treatments (with biochar application at the rate of 200 g/pot, C1) and (without biochar application, 0 g/pot, C0) was conducted. No significant differences were observed in the number of operational taxonomic units, observed species, Shannon index, Simpson index, Chao1, ACE, and phylogenetic diversity whole tree between the C1 and C0 treatments. Taxonomic analysis at the genus level showed that the abundances of Gracilibacter, Lentimicrobium, unidentified Rikenellaceae, Hydrogenophaga, and Bacillus were higher in the C1 compared to the C0 treatment, while Candidatus Solibacter, Candidatus Koribacter, and Lutispora abundances were found to be higher abundant in the C0 compared to the C1 treatment. Obvious clusters were observed between the C1 and C0 in both principal component analysis and non-metric multidimensional scaling. These results indicate that soil bacterial community was altered after rapeseed straw-derived biochar was applied.
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Affiliation(s)
- Chunrong Zhao
- Hunan Agricultural University, 12575, Changsha, China, 410128;
| | - Xiaohong Yin
- Hunan Agricultural University, 12575, Changsha, China;
| | - Jiana Chen
- Hunan Agricultural University, 12575, Changsha, China;
| | - Fangbo Cao
- Hunan Agricultural University, 12575, Changsha, China;
| | | | - Min Huang
- Hunan Agricultural University, 12575, Changsha, Hunan, China;
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28
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Jiang L, Yang Y, Jin H, Wang H, Swift CM, Xie Y, Schubert T, Löffler FE, Yan J. Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3430-3440. [PMID: 35239320 DOI: 10.1021/acs.est.1c05952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XRDCA and XRTCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XRTCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XRDCA and XRTCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XRTCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 × 107 and 1.18 ± 0.14 × 107 cells per μmol Cl- released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.
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Affiliation(s)
- Lisi Jiang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Huijuan Jin
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Torsten Schubert
- Research Group Anaerobic Microbiology, Friedrich Schiller University, Jena 07743, Germany
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
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29
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Feng X, Wang Q, Sun Y, Zhang S, Wang F. Microplastics change soil properties, heavy metal availability and bacterial community in a Pb-Zn-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127364. [PMID: 34879561 DOI: 10.1016/j.jhazmat.2021.127364] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/22/2021] [Accepted: 09/25/2021] [Indexed: 05/06/2023]
Abstract
Microplastics (MPs) co-occur widely with diverse contaminants in soils. However, few data are available on their impacts on soil chemical and microbial properties of heavy metal-contaminated soils. For the first time, we investigated the changes in chemical and microbial properties of a Pb-Zn-contaminated soil as induced by six different MPs, including polyethylene (PE), polystyrene (PS), polyamide (PA), polylactic acid (PLA), polybutylene succinate (PBS), and polyhydroxybutyrate (PHB), at two doses (0.2% and 2%, w/w). After 120 days of soil incubation, significant changes were observed in soil pH, dissolved organic carbon (DOC), NH4+-N, NO3--N, available P, the availability of Zn and Pb, and the activities of soil enzymes. Overall, MPs especially at the dose of 2% decreased the richness and diversity of bacterial communities and altered microbial community composition, causing special enrichments of specific taxa. MPs increased predicted functional genes involved in xenobiotics biodegradation and metabolism. Generally, impacts were dependent on MPs' type and dose. Changes in soil properties and heavy metal availability had significant correlations with bacterial community diversity and composition. Our findings imply that MPs co-occurring with heavy metals may change metal mobility, soil fertility, and microbial diversity and functions, thus causing a potential threat to soil ecosystem multifunctionality.
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Affiliation(s)
- Xueying Feng
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Quanlong Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Shuwu Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China
| | - Fayuan Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong Province, 266042, PR China.
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30
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6577122. [DOI: 10.1093/femsec/fiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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31
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Yi M, Zhang L, Qin C, Lu P, Bai H, Han X, Yuan S. Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene. CHEMOSPHERE 2022; 286:131709. [PMID: 34340117 DOI: 10.1016/j.chemosphere.2021.131709] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.
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Affiliation(s)
- Meiling Yi
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lilan Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Cunli Qin
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Peili Lu
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Hongcheng Bai
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Xinkuan Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shupei Yuan
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
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Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics. Microorganisms 2021; 10:microorganisms10010071. [PMID: 35056520 PMCID: PMC8777777 DOI: 10.3390/microorganisms10010071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.
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Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis. Appl Environ Microbiol 2021; 88:e0218121. [PMID: 34910572 DOI: 10.1128/aem.02181-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Influence of cosubstrate and hydraulic retention time on the removal of drugs and hygiene products in sanitary sewage in an anaerobic Expanded Granular Sludge Bed reactor. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113532. [PMID: 34614559 DOI: 10.1016/j.jenvman.2021.113532] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Diclofenac (DCF), ibuprofen (IBU), propranolol (PRO), triclosan (TCS) and linear alkylbenzene sulfonate (LAS) can be recalcitrant in Wastewater Treatment Plants (WWTP). The removal of these compounds was investigated in scale-up (69 L) Expanded Granular Sludge Bed (EGSB) reactor, fed with sanitary sewage from the São Carlos-SP (Brazil) WWTP and 200 mg L-1 of ethanol. The EGSB was operated in three phases: (I) hydraulic retention time (HRT) of 36±4 h; (II) HRT of 20±2 h and (III) HRT of 20±2 h with ethanol. Phases I and II showed no significant difference in the removal of LAS (63 ± 11-65 ± 12 %), DCF (37 ± 18-35 ± 11 %), IBU (43 ± 18-44 ± 16 %) and PRO (46 ± 25-51 ± 23 %) for 13±2-15 ± 2 mg L-1, 106 ± 32-462 ± 294 μg L-1, 166 ± 55-462 ± 213 μg L-1 and 201 ± 113-250 ± 141 μg L-1 influent, respectively. Higher TCS removal was obtained in phase I (72 ± 17 % for 127 ± 120 μg L-1 influent) when compared to phase II (51 ± 13 % for 135 ± 119 μg L-1 influent). This was due to its greater adsorption (40 %) in the initial phase. Phase III had higher removal of DCF (42 ± 10 % for 107 ± 26 μg L-1 influent), IBU (50 ± 15 % for 164 ± 47 μg L-1 influent) and TCS (85 ± 15 % for 185 ± 148 μg L-1 influent) and lower removal of LAS (35 ± 14 % for 12 ± 3 mg L-1 influent) and PRO (-142 ± 177 % for 188 ± 88 μg L-1 influent). Bacteria similar to Syntrophobacter, Smithella, Macellibacteroides, Syntrophus, Blvii28_wastewater-sludge_group and Bacteroides were identified in phase I with relative abundance of 3.1 %-4.7 %. Syntrophobacter was more abundant (15.4 %) in phase II, while in phase III, it was Smithella (12.7 %) and Caldisericum (15.1 %). Regarding the Archaea Domain, Methanosaeta was more abundant in phases I (84 %) and II (67 %), while in phase III it was Methanobacterium (86 %).
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington LuizHighway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
| | - Pedro S Fadini
- Federal University of São Carlos, Washington LuizHighway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, Zipcode 13566-590, São Carlos, SP, Brazil.
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Zhang X, Li R, Song J, Ren Y, Luo X, Li Y, Li X, Li T, Wang X, Zhou Q. Combined phyto-microbial-electrochemical system enhanced the removal of petroleum hydrocarbons from soil: A profundity remediation strategy. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126592. [PMID: 34265647 DOI: 10.1016/j.jhazmat.2021.126592] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
The soil contaminated by petroleum hydrocarbons has been a global environmental problem and its remediation is urgent. A combined phyto-microbial-electrochemical system (PMES) was constructed to repair the oil-contaminated soil in this study. During the 42-day operation time, a total petroleum hydrocarbons (TPHs) of 18.0 ± 3.0% were removed from PMES, which increased by 414% compared with the control group (CK1). The supervision of physicochemical properties of pore water in soil exhibited an enhanced microbial consumption of the total organic carbon (TOC) and N source under the applied potential with the generation of bio-current. The microbial succession indicated that the Dietzia, Georgenia and Malbranchea possibly participated in the degradation and current output in PMES. And a collaborative network of potential degrading microorganisms including unclassified norank_f__JG30-KF-CM45 (in Chloroflexi), Dietzia and Malbranchea was discovered in PMES. While the functional communities of microorganism were re-enriched with the reconstructed interactions in the system which was started with the sterilized soil (S+MEC). The superiority of TPHs degradation in S+MEC compared to P + CK2 (removing the electrochemical effect relative to CK1) revealed the key role of external potential in regulating the degradation microflora. The study provided a strategy of the potential regulated phyto-microbial interaction for the removal of TPHs.
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Affiliation(s)
- Xiaolin Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Ruixiang Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Jintong Song
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Yuanyuan Ren
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xi Luo
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Yi Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Qixing Zhou
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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Ujang FA, Roslan AM, Osman NA, Norman A, Idris J, Farid MAA, Halmi MIE, Gozan M, Hassan MA. Removal behaviour of residual pollutants from biologically treated palm oil mill effluent by Pennisetum purpureum in constructed wetland. Sci Rep 2021; 11:18257. [PMID: 34521938 PMCID: PMC8440592 DOI: 10.1038/s41598-021-97789-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/27/2021] [Indexed: 02/08/2023] Open
Abstract
The reason for such enormous efforts in palm oil mill effluent research would be what has been singled out as one of the major sources of pollution in Malaysia, and perhaps the most costly and complex waste to manage. Palm oil mill final discharge, which is the treated effluent, will usually be discharged to nearby land or river since it has been the least costly way to dispose of. Irrefutably, the quality level of the treated effluent does not always satisfy the surface water quality in conformity to physicochemical characteristics. To work on improving the treated effluent quality, a vertical surface-flow constructed wetland system was designed with Pennisetum purpureum (Napier grass) planted on the wetland floor. The system effectively reduced the level of chemical oxygen demand by 62.2 ± 14.3%, total suspended solid by 88.1 ± 13.3%, ammonia by 62.3 ± 24.8%, colour by 66.6 ± 13.19%, and tannin and lignin by 57.5 ± 22.3%. Heat map depicted bacterial diversity and relative abundance in life stages from the wetland soil, whereby bacterial community associated with the pollutant removal was found to be from the families Anaerolineaceae and Nitrosomonadaceae, and phyla Cyanobacteria and Acidobacteria.
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Affiliation(s)
- Farhana Aziz Ujang
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
| | - Ahmad Muhaimin Roslan
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia.
| | - Nurul Atiqah Osman
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
| | - Ashreen Norman
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
| | - Juferi Idris
- Faculty of Chemical Engineering, College of Engineering, Universiti Teknologi MARA (UiTM), Sarawak Branch, Samarahan Campus, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mohammed Abdillah Ahmad Farid
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Izuan Effendi Halmi
- Department of Soil Management, Faculty of Agriculture, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
| | - Misri Gozan
- Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Kampus Baru UI, Depok, Jawa Barat, 16424, Indonesia
| | - Mohd Ali Hassan
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, UPM Serdang, Selangor, Malaysia
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Degenhardt J, Merder J, Heyerhoff B, Simon H, Engelen B, Waska H. Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. Microorganisms 2021; 9:1720. [PMID: 34442799 PMCID: PMC8399146 DOI: 10.3390/microorganisms9081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.
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Affiliation(s)
- Julius Degenhardt
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Julian Merder
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Hannelore Waska
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Influence of metabolic cosubstrates on methanogenic potential and degradation of triclosan and propranolol in sanitary sewage. ENVIRONMENTAL RESEARCH 2021; 199:111220. [PMID: 33992637 DOI: 10.1016/j.envres.2021.111220] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/27/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Triclosan (TCS) and propranolol (PRO) are emerging micropollutants that are difficult to remove in wastewater treatment plants. In this study, methanogenic potential (P) of anaerobic sludge submitted to TCS (3.6 ± 0.1 to 15.5 ± 0.1 mg L-1) and PRO (6.1 ± 0.1 to 55.9 ± 1.2 mg L-1) in sanitary sewage, was investigated in batch reactors. The use of cosubstrates (200 mg L-1 of organic matter) ethanol, methanol:ethanol and fumarate was evaluated for micropollutant degradation. Without cosubstrates, P values for 5.0 ± 0.1 mgTCS L-1, 15.5 ± 0.1 mgTCS L-1 and 55.0 ± 1.3 mgPRO L-1 were 50.53%, 98.24% and 17.66% lower in relation to Control assay (855 ± 5 μmolCH4) with sanitary sewage, without micropollutants and cosubstrates, respectively. The use of fumarate, ethanol and methanol:ethanol favored greater methane production, with P values of 2144 ± 45 μmolCH4, 2960 ± 185 μmolCH4 and 2239 ± 171 μmolCH4 for 5.1 ± 0.1 mgTCS L-1, respectively; and of 10,827 ± 185 μmolCH4, 10,946 ± 108 μmolCH4 and 10,809 ± 210 μmolCH4 for 55.0 ± 1.3 mgPRO L-1, respectively. Greater degradation of TCS (77.1 ± 0.1% for 5.1 ± 0.1 mg L-1) and PRO (24.1 ± 0.1% for 55.9 ± 1.2 mg L-1) was obtained with ethanol. However, with 28.5 ± 0.5 mg PRO L-1, greater degradation (88.4 ± 0.9%) was obtained without cosubstrates. With TCS, via sequencing of rRNA 16S gene, for Bacteria Domain, greater abundance of phylum Chloroflexi and of the genera Longilinea, Arcobacter, Mesotoga and Sulfuricurvum were identified. With PRO, the genus VadinBC27 was the most abundant. Methanosaeta was dominant in TCS with ethanol, while in PRO without cosubstrates, Methanobacterium and Methanosaeta were the most abundant. The use of metabolic cosubstrates is a favorable strategy to obtain greater methanogenic potential and degradation of TCS and PRO.
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
| | - Pedro S Fadini
- Federal University of São Carlos, Washington Luiz Highway, Km 235, Zipcode 13565-905, São Carlos, SP, Brazil.
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo. Ave Trabalhador São-Carlense, no. 400, Zipcode, 13566-590, São Carlos, SP, Brazil.
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Shang H, Wang Q, Ok YS, Zhang S, Zhu X. Magnetic biochar production alters the molecular characteristics and biological response of pyrolysis volatile-derived water-soluble organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146142. [PMID: 33714822 DOI: 10.1016/j.scitotenv.2021.146142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The formed Fe oxides (minerals) in the magnetic biochar production process can facilitate its recovery and carbon retention rate. However, the influence of Fe oxides on pyrolysis volatile-derived water-soluble organic matter (PVWSOM, also called wood vinegar) has been largely overlooked. Results demonstrated that in-situ formed Fe oxides (α-Fe2O3 and Fe3O4) could obviously inhibit biomass cracking and accordingly reduce PVWSOM emissions, as indicated by decreased PVWSOM concentrations from 28.7 to 6.8 mg C/g biomass. FT-ICR MS results further indicated that Fe oxides suppressed the formation of large-molecular-weight PVWSOM compounds with high degree of unsaturation (DBE value > 5) and oxygen content (oxygen number > 5), leading to lower polarity and aromaticity. Therefore, the changes in PVWSOM molecular structures caused by Fe oxides relieved its toxicity on wheat seed growth, and reduced negative impact on soil microbial diversity and promoted soil bacterial Proteobacteria and Acidobacteria. These results indicate that molecular structures of PVWSOM from biomass pyrolysis also can be changed by Fe oxides to affect its application.
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Affiliation(s)
- Hua Shang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Qian Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Yong Sik Ok
- Korea Biochar Research Center, APRU Sustainable Waste Management Program & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, South Korea
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
| | - Xiangdong Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China.
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Rong L, Zhao L, Zhao L, Cheng Z, Yao Y, Yuan C, Wang L, Sun H. LDPE microplastics affect soil microbial communities and nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145640. [PMID: 33582358 DOI: 10.1016/j.scitotenv.2021.145640] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/05/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Microplastics (MPs) are a contaminant of increasing concern in the environment. However, the impacts of MPs on soil ecosystems and biogeochemical processes like nitrogen cycle have not been well elucidated. In this study, we designed an indoor microcosm experiment to investigate the effects of exposure to low density polyethylene (LDPE) MPs on soil bacterial community and nitrogen cycling function over a 90-day incubation. Next-generation sequencing of the 16S rRNA genes revealed that both 2% and 7% LDPE MPs exposure slightly affected the soil bacterial diversity. Further analysis at the genus level showed differential tolerance to LDPE MPs, the genera Pedomicrobium, Steroidobacter, Pseudonocardia, Nitrospira and Turicibacter were enriched in the soil with 2% (w/w) LDPE MPs amendment, while the genera Pedomicrobium, Mycobacterium and Hyphomicrobium were significantly enriched in the soil with 7% (w/w) LDPE MPs amendment on days 15 and 30. Co-occurrence network analysis further suggested that LDPE MPs changed bacterial network complexity and modularity and Acidobacteria formed intimate associations with each other in responding to LDPE MPs exposure. Additionally, LDPE MPs in soil increased the abundance of nifH, AOBamoA and nirK genes involved in nitrogen cycling in different incubation phases compared to the control. The abundance of AOAamoA genes decreased on day 15 and then increased. Conversely, the abundance of nirS genes increased during the first 15 days and then decreased. These results suggested that both 2% and 7% LDPE MPs impact soil bacterial network structure and alters functional groups involved in soil nitrogen cycling processing.
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Affiliation(s)
- Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Longfei Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Leicheng Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Zhipeng Cheng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chaolei Yuan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol 2021; 12:632731. [PMID: 34017316 PMCID: PMC8129789 DOI: 10.3389/fmicb.2021.632731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/02/2021] [Indexed: 01/21/2023] Open
Abstract
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Devon Payne
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jian-Yu Jiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Rebecca Lau
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katherine B Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alicia Clum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alex Spunde
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Manoj Pillay
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Krishnaveni Palaniappan
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Mikhailova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - I-Min Chen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Dimitrios Stamatis
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - T B K Reddy
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronan O'Malley
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris Daum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicole Shapiro
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos C Kyrpides
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Emiley Eloe-Fadrosh
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Zhang W, Han J, Wu H, Zhong Q, Liu W, He S, Zhang L. Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China. PeerJ 2021; 9:e11231. [PMID: 33959419 PMCID: PMC8053383 DOI: 10.7717/peerj.11231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. METHODS In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. RESULTS The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potassium (K) significantly affected fungal community composition in park soils in Shanghai. Soil available Zn was also the most important factor affecting the bacterial community composition in this study. CONCLUSION There were significant differences in the soil molecular biomass, fungal abundance, and the community composition and co-occurrence relations of both soil bacterial and fungal communities between urban and suburban park soils. Soil available Zn played an important part in shaping the structures of both the bacterial and fungal communities in park soils in Shanghai.
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Affiliation(s)
- Weiwei Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Jigang Han
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Haibing Wu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Qicheng Zhong
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Wen Liu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Shanwen He
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Lang Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
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Hao J, Chai YN, Lopes LD, Ordóñez RA, Wright EE, Archontoulis S, Schachtman DP. The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA. Appl Environ Microbiol 2021; 87:AEM.02673-20. [PMID: 33310710 PMCID: PMC7851703 DOI: 10.1128/aem.02673-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 02/03/2023] Open
Abstract
This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.
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Affiliation(s)
- Jingjie Hao
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Yen Ning Chai
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Lucas Dantas Lopes
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Raziel A Ordóñez
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, Iowa, USA
- Department of Plant Science and Industries Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily E Wright
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, Iowa, USA
| | | | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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Zerva I, Remmas N, Kagalou I, Melidis P, Ariantsi M, Sylaios G, Ntougias S. Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant. Life (Basel) 2021; 11:68. [PMID: 33477775 PMCID: PMC7832327 DOI: 10.3390/life11010068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 11/17/2022] Open
Abstract
The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.
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Affiliation(s)
- Ioanna Zerva
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
- Department of Civil Engineering, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Nikolaos Remmas
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Ifigeneia Kagalou
- Department of Civil Engineering, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Paraschos Melidis
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Marina Ariantsi
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Georgios Sylaios
- Department of Environmental Engineering, Laboratory of Ecological Engineering and Technology, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Spyridon Ntougias
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
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Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils. Appl Environ Microbiol 2021; 87:AEM.01643-20. [PMID: 33187999 DOI: 10.1128/aem.01643-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 11/20/2022] Open
Abstract
Recent work revealed an active biological chlorine cycle in coastal Arctic tundra of northern Alaska. This raised the question of whether chlorine cycling was restricted to coastal areas or if these processes extended to inland tundra. The anaerobic process of organohalide respiration, carried out by specialized bacteria like Dehalococcoides, consumes hydrogen gas and acetate using halogenated organic compounds as terminal electron acceptors, potentially competing with methanogens that produce the greenhouse gas methane. We measured microbial community composition and soil chemistry along an ∼262-km coastal-inland transect to test for the potential of organohalide respiration across the Arctic Coastal Plain and studied the microbial community associated with Dehalococcoides to explore the ecology of this group and its potential to impact C cycling in the Arctic. Concentrations of brominated organic compounds declined sharply with distance from the coast, but the decrease in organic chlorine pools was more subtle. The relative abundances of Dehalococcoides were similar across the transect, except for being lower at the most inland site. Dehalococcoides correlated with other strictly anaerobic genera, plus some facultative ones, that had the genetic potential to provide essential resources (hydrogen, acetate, corrinoids, or organic chlorine). This community included iron reducers, sulfate reducers, syntrophic bacteria, acetogens, and methanogens, some of which might also compete with Dehalococcoides for hydrogen and acetate. Throughout the Arctic Coastal Plain, Dehalococcoides is associated with the dominant anaerobes that control fluxes of hydrogen, acetate, methane, and carbon dioxide. Depending on seasonal electron acceptor availability, organohalide-respiring bacteria could impact carbon cycling in Arctic wet tundra soils.IMPORTANCE Once considered relevant only in contaminated sites, it is now recognized that biological chlorine cycling is widespread in natural environments. However, linkages between chlorine cycling and other ecosystem processes are not well established. Species in the genus Dehalococcoides are highly specialized, using hydrogen, acetate, vitamin B12-like compounds, and organic chlorine produced by the surrounding community. We studied which neighbors might produce these essential resources for Dehalococcoides species. We found that Dehalococcoides species are ubiquitous across the Arctic Coastal Plain and are closely associated with a network of microbes that produce or consume hydrogen or acetate, including the most abundant anaerobic bacteria and methanogenic archaea. We also found organic chlorine and microbes that can produce these compounds throughout the study area. Therefore, Dehalococcoides could control the balance between carbon dioxide and methane (a more potent greenhouse gas) when suitable organic chlorine compounds are available to drive hydrogen and acetate uptake.
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Yuan ZS, Liu F, Liu ZY, Huang QL, Zhang GF, Pan H. Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis). Sci Rep 2021; 11:1574. [PMID: 33452327 PMCID: PMC7810855 DOI: 10.1038/s41598-021-80971-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/31/2020] [Indexed: 01/29/2023] Open
Abstract
The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.
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Affiliation(s)
- Zong-Sheng Yuan
- grid.449133.80000 0004 1764 3555Institute of Oceanography, Minjiang University, Minhou County, Fuzhou, 350108 Fujian China
| | - Fang Liu
- grid.256111.00000 0004 1760 2876College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Zhen-Yu Liu
- grid.440622.60000 0000 9482 4676College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Qiu-Liang Huang
- grid.256111.00000 0004 1760 2876College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Guo-Fang Zhang
- grid.256111.00000 0004 1760 2876College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hui Pan
- grid.449133.80000 0004 1764 3555Institute of Oceanography, Minjiang University, Minhou County, Fuzhou, 350108 Fujian China
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The bacterial composition associated with Atriolum robustum, a common ascidian from Xisha coral reef, China. Symbiosis 2021. [DOI: 10.1007/s13199-020-00742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Izaki K, Haruta S. Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ 2020; 35. [PMID: 32418929 PMCID: PMC7308566 DOI: 10.1264/jsme2.me20015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light, although their production was strongly suppressed in the dark. The transcription levels of genes related to the synthesis of bacteriochlorophylls, photosystems, and chlorosomes: bchM, bchU, pufL, pufBA, and csmM, were markedly increased by illumination. These results suggest that C. aurantiacus continuously synthesizes ATP by photophosphorylation even in the presence of O2.
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Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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Granatto CF, Grosseli GM, Sakamoto IK, Fadini PS, Varesche MBA. Methanogenic potential of diclofenac and ibuprofen in sanitary sewage using metabolic cosubstrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140530. [PMID: 32629260 DOI: 10.1016/j.scitotenv.2020.140530] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Diclofenac (DCF) and ibuprofen (IBU) are widely used anti-inflammatory drugs and are frequently detected in wastewater from Wastewater Treatment Plants and in aquatic environments. In this study, the methanogenic potential (P) of anaerobic sludge subjected to DCF (7.11 ± 0.02 to 44.41 ± 0.05 mg L-1) and IBU (6.11 ± 0.01 to 42.61 ± 0.05 mg L-1), in sanitary sewage, was investigated in batch reactors. Cosubstrates (200 mg L-1 of organic matter) in the form of ethanol, methanol:ethanol and fumarate were tested separately for the removal of drugs. In the DCF assays, P was 6943 ± 121 μmolCH4, 9379 ± 259 μmolCH4, 9897 ± 212 μmolCH4 and 11,530 ± 368 μmolCH4 for control, fumarate, methanol:ethanol and ethanol conditions, respectively. In the IBU assays, under the same conditions, P was 6145 ± 101 μmolCH4, 6947 ± 66 μmolCH4, 8141 ± 191 μmolCH4and 10,583 ± 512 μmolCH4, respectively. Without cosubstrates, drug removal was below 18% for 43.10 ± 0.01 mgDCF L-1 and 43.12 ± 0.03 mgIBU L-1, respectively. Higher P and removal of DCF (28.24 ± 1.10%) and IBU (18.72 ± 1.60%) with ethanol was observed for 43.20 ± 0.01 mgDCF L-1 and 43.42 ± 0.03 mgIBU L-1, respectively. This aspect was better evidenced with DCF due to its molecular structure, a condition that resulted in a higher diversity of bacterial populations. Through the 16S rRNA sequencing, bacteria genera capable of performing aromatic ring cleavage, β-oxidation and oxidation of ethanol and fatty acids were identified. Higher relative abundance (>0.6%) was observed for Smithella, Sulfuricurvum and Synthophus for the Bacteria Domain and Methanosaeta (>79%) for the Archaea Domain. The use of ethanol favored greater mineralization of organic matter and greater methane production, which can directly assist in the metabolic pathways of microorganisms.
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Affiliation(s)
- Caroline F Granatto
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil..
| | - Guilherme M Grosseli
- Federal University of São Carlos, Washington Luiz Highway, Km 235, 13565-905 São Carlos, SP, Brazil
| | - Isabel K Sakamoto
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil
| | - Pedro S Fadini
- Federal University of São Carlos, Washington Luiz Highway, Km 235, 13565-905 São Carlos, SP, Brazil
| | - Maria Bernadete A Varesche
- Department of Hydraulics and Sanitation Engineering, São Carlos School of Engineering, University of São Paulo, Ave Trabalhador São-Carlense, No. 400, 13566-590 São Carlos, SP, Brazil..
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Chen L, Hao Z, Li K, Sha Y, Wang E, Sui X, Mi G, Tian C, Chen W. Effectsof growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China. Microb Biotechnol 2020; 14:535-550. [PMID: 33166080 PMCID: PMC7936301 DOI: 10.1111/1751-7915.13693] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/04/2022] Open
Abstract
Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth‐promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%–29%. Real‐time quantitative PCR and high‐throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4‐96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.
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Affiliation(s)
- La Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhanhong Hao
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Keke Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ye Sha
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Entao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico D.F., 11340, Mexico
| | - Xinhua Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Changfu Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenxin Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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