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Ikarashi T, Bandaranayake US, Watari T, Yamaguchi T, Hatamoto M. Unique gel-like colony forming bacterium Novosphingobium pituita sp. nov., isolated from a membrane bioreactor (MBR) treating sewage. Heliyon 2024; 10:e38795. [PMID: 39717744 PMCID: PMC11665390 DOI: 10.1016/j.heliyon.2024.e38795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/17/2024] [Accepted: 09/30/2024] [Indexed: 12/25/2024] Open
Abstract
A novel, gelatinous, colony-forming, rod-shaped bacterial strain, designated IK01T was isolated from biofilms formed on the membrane surface of a sewage-treating membrane bioreactor (MBR). Strain IK01T produced gelatinous and almost transparent colonies at lower medium concentrations. Fourier transform infrared analysis of the gelatinous colony matrix showed that the matrix could be a biofilm substance. This suggests that strain IK01T is a fouling-causing bacteria in the MBR. Furthermore, 16S rRNA gene sequence analysis showed that strain IK01T was phylogenetically placed in the genus Novosphingobium. The average nucleotide identity values for IK01T and the other 50 species of the genus Novosphingobium ranged from 78.5 to 83.9 %. Correspondingly, the estimated digital DNA-DNA hybridization values ranged from 20.8 to 24.4 %. The genomic DNA G + C content was 66.0 %. The predominant fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and C14:0 2-OH. A polar lipid profile revealed phosphatidylethanolamine, two unidentified phospholipids, and three aminoglycophospholipids as major compounds. The major respiratory quinone was ubiquinone Q-10. Genotypic, chemotaxonomic, and phenotypic analyses characterized the newly identified strain IK01T, as a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium pituita sp. nov. The type strain is IK01T (NBRC 116408T = DSM 116658T).
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Affiliation(s)
- Tomoya Ikarashi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Uchini S. Bandaranayake
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Niigata, 940-2188, Japan
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Li D, Han S, Zhang K, Xu G, Zhang H, Chen F, Wang L, Liu Q, Guo Z, Zhang J, Li J. Genome Analysis and Safety Assessment of Achromobacter marplatensis Strain YKS2 Strain Isolated from the Rumen of Yaks in China. Probiotics Antimicrob Proteins 2024; 16:1638-1656. [PMID: 37491503 DOI: 10.1007/s12602-023-10124-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Achromobacter marplatensis strain YKS2 isolated from the yak rumen has the feature of producing cellulose. This study aims to analyze the genome and safety of strain YKS2 in vivo, considering its future research and application prospects. The genome of strain YKS2 was sequenced and used for genomic in silico studies. The administration of strain YKS2 in three doses was carried out on mice for 3 days of oral and 7 days of clinical observation tests. The BW, FI, organ indices, gut microbiota, and histological appearances of organs and intestines, along with hematological parameters and serum biochemistry, were measured in mice. The chromosome size of strain YKS2 was 6,588,568 bp, with a GC content of 65.27%. The 6058 coding sequences of strain YKS2 without plasmid were predicted and annotated and have multiple functions. The mice in all groups were alive, with good mental states and functional activities. Compared with the control group, there was no significant difference in the three dose groups on BW, FI, hematological parameters (WBC, LYM, etc.), and serum biochemistry (ALB, ALT, etc.). No abnormalities were observed in the main visceral organs, intestinal tissue, and V/C value in groups. However, the IEL number of duodenum and gut microbiota diversity (Shannon's index) in the high-dose group was significantly higher than in the control group (p < 0.05). Besides, the low dose of strain YKS2 also significantly affected the bacterial abundance of Firmicutes, Actinobacteria, and desulphurizing Bacteroidetes at the phylum level. There was no significant effect at genus levels in groups. In conclusion, the study revealed the genome and potential functional genes of strain YKS2, which is beneficial to understanding the features of the A. marplatensis strain and proved strain YKS2 to be without acute toxicity to mice. However, a long-term feeding toxicity experiment in vivo should be performed to further ensure its potential application value strain in the animal industry.
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Affiliation(s)
- Dapeng Li
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- College of Veterinary Medicine, Hebei Agricultural University, Hebei, 071000, China
| | - Songwei Han
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Kang Zhang
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Guowei Xu
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Hong Zhang
- Agricultural Products Quality and Safety Inspection and Testing Center of Gansu Province, Lanzhou, 730050, China
| | - Fubing Chen
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Lei Wang
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qin Liu
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Zhiting Guo
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jingyan Zhang
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Jianxi Li
- Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
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Tsiareshyna M, Wang TH, Lin YS, Piorkowski D, Huang SYT, Huang YL, Chao WT, Chang YJ, Liao CP, Wang PH, Tso IM. Bacteria inhabiting spider webs enhance host silk extensibility. Sci Rep 2024; 14:11011. [PMID: 38744937 PMCID: PMC11093983 DOI: 10.1038/s41598-024-61723-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Spider silk is a promising material with great potential in biomedical applications due to its incredible mechanical properties and resistance to degradation of commercially available bacterial strains. However, little is known about the bacterial communities that may inhabit spider webs and how these microorganisms interact with spider silk. In this study, we exposed two exopolysaccharide-secreting bacteria, isolated from webs of an orb spider, to major ampullate (MA) silk from host spiders. The naturally occurring lipid and glycoprotein surface layers of MA silk were experimentally removed to further probe the interaction between bacteria and silk. Extensibility of major ampullate silk produced by Triconephila clavata that was exposed to either Microbacterium sp. or Novosphigobium sp. was significantly higher than that of silk that was not exposed to bacteria (differed by 58.7%). This strain-enhancing effect was not observed when the lipid and glycoprotein surface layers of MA silks were removed. The presence of exopolysaccharides was detected through NMR from MA silks exposed to these two bacteria but not from those without exposure. Here we report for the first time that exopolysaccharide-secreting bacteria inhabiting spider webs can enhance extensibility of host MA silks and silk surface layers play a vital role in mediating such effects.
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Affiliation(s)
| | - Te-Hsin Wang
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Ying-Sheng Lin
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | | | - Sammi Yen-Ting Huang
- Department of Life Science, Tunghai University, Taichung, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yi-Lun Huang
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Wei-Ting Chao
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Yuan Jay Chang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Chen-Pan Liao
- Department of Life Science, Tunghai University, Taichung, Taiwan
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Pi-Han Wang
- Department of Life Science, Tunghai University, Taichung, Taiwan.
- Center for Ecology and Environment, Tunghai University, Taichung, Taiwan.
| | - I-Min Tso
- Department of Life Science, Tunghai University, Taichung, Taiwan.
- Center for Ecology and Environment, Tunghai University, Taichung, Taiwan.
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Goto S, Urase T, Nakakura K. Novel and Simple Method for Quantification of 2,4,6-Trichlorophenol with Microbial Conversion to 2,4,6-Trichloroanisole. Microorganisms 2023; 11:2133. [PMID: 37763977 PMCID: PMC10535749 DOI: 10.3390/microorganisms11092133] [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: 07/15/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Contamination with 2,4,6-trichloroanisole (TCA) often causes taste and odor (T&O) problems in drinking water due to its low odor threshold concentration. Microbial O-methylation of the precursor 2,4,6-trichlorophenol (TCP) would be the dominant mechanism for TCA formation. Simple and rapid measurement of TCP in the low concentration range is necessary to control the problems induced by TCA. In this study, the combination of microbial conversion and instrumental analysis was proposed as a method of TCP quantification. Fungi and bacteria were isolated from various water samples and examined for their ability to produce TCA from TCP. As a result, a strain exhibiting quantitative TCA production and a high growth rate was obtained and named Mycolicibacterium sp. CB14. The conversion rate of TCP to TCA by this strain was found to be high and stable (85.9 ± 5.3%), regardless of the applied TCP concentration, although within the range of 0.1-10 µg/L. The limits of detection and quantification for TCP by this proposed method were determined to be 5.2 ng/L and 17.3 ng/L, respectively. By improving the methods, Mycolicibacterium sp. CB14 could be used for the quantification of TCP at very low concentration levels, which is sufficient to manage the T&O problem caused by TCA.
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Affiliation(s)
| | - Taro Urase
- School of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo 192-0982, Japan; (S.G.)
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Belmok A, de Almeida FM, Rocha RT, Vizzotto CS, Tótola MR, Ramada MHS, Krüger RH, Kyaw CM, Pappas GJ. Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid. Braz J Microbiol 2023; 54:239-258. [PMID: 36701110 PMCID: PMC9944591 DOI: 10.1007/s42770-022-00900-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 10/02/2022] [Indexed: 01/27/2023] Open
Abstract
A novel bacterial strain, designated GeG2T, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2T revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285T showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2T cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2T presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2T showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2T and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2T (= CBMAI 2313T = CBAS 753 T).
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Affiliation(s)
- Aline Belmok
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Felipe Marques de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Rodrigo Theodoro Rocha
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Carla Simone Vizzotto
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Faculdade de Tecnologia, Universidade de Brasília, Brasilia, DF, Brazil
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasilia, DF, Brazil
| | - Ricardo Henrique Krüger
- Laboratório de Enzimologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Cynthia Maria Kyaw
- Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.
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Peltoniemi K, Velmala S, Fritze H, Jyske T, Rasi S, Pennanen T. Impacts of coniferous bark-derived organic soil amendments on microbial communities in arable soil - a microcosm study. FEMS Microbiol Ecol 2023; 99:7022313. [PMID: 36725205 PMCID: PMC10013654 DOI: 10.1093/femsec/fiad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
A decline in the carbon content of agricultural soils has been reported globally. Amendments of forest industry side-streams might counteract this. We tested the effects of industrial conifer bark and its cascade process materials on the soil microbiome under barley (Hordeum vulgare L.) in clay and silt soil microcosms for 10 months, simulating the seasonal temperature changes of the boreal region. Microbial gene copy numbers were higher in clay soils than in silt. All amendments except unextracted bark increased bacterial gene copies in both soils. In turn, all other amendments, but not unextracted bark from an anaerobic digestion process, increased fungal gene copy numbers in silt soil. In clay soil, fungal increase occurred only with unextracted bark and hot water extracted bark. Soil, amendment type and simulated season affected both the bacterial and fungal community composition. Amendments increased bacteria originating from the anaerobic digestion process, as well as dinitrogen fixers and decomposers of plant cells. In turn, unextracted and hot water extracted bark determined the fungal community composition in silt. As fungal abundance increase and community diversification are related to soil carbon acquisition, bark-based amendments to soils can thus contribute to sustainable agriculture.
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Affiliation(s)
- Krista Peltoniemi
- Corresponding author. Soil Ecosystems, Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland.E-mail:
| | - Sannakajsa Velmala
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
| | - Hannu Fritze
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
| | - Tuula Jyske
- Production Systems, Natural Resources Institute Finland (Luke), Viikinkaari 9, FI-00720 Helsinki, Finland
| | - Saija Rasi
- Production Systems, Natural Resources Institute Finland (Luke), Survontie 9, FI-40500 Jyväskylä, Finland
| | - Taina Pennanen
- Natural Resources, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00720 Helsinki, Finland
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Tombuloglu H, Yaman C, Boudellioua I, Cevik E, Anil I, Aga O, Yaman AB, Qureshi A, Gunday ST. Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation. 3 Biotech 2023; 13:40. [PMID: 36636577 PMCID: PMC9829945 DOI: 10.1007/s13205-023-03460-y] [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: 08/11/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03460-y.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441 Saudi Arabia
| | - Cevat Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Imane Boudellioua
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, P.O. Box 2205, Dhahran, 31261 Saudi Arabia
| | - Emre Cevik
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
| | - Ismail Anil
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Omer Aga
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Ayse B. Yaman
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Aleem Qureshi
- Environmental Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, Saudi Arabia
| | - Seyda Tugba Gunday
- Bioenergy Research Unit, Department of Biophysics, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, PO Box:1982, Dammam, 31441 Saudi Arabia
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Anan’ina LN, Plotnikova EG. Halophilic Bacteria as a Promising Basis of Biopreparations for Improving the Growth of Autochthonous Strains-Destructors in Salinization Conditions. BIO WEB OF CONFERENCES 2023. [DOI: 10.1051/bioconf/20235709003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In some cases, pollution of ecosystems with persistent toxic organic compounds, including polycyclic aromatic hydrocarbons (PAHs), is accompanied by salinization, which significantly inhibits the degradation of these compounds by autochthonous communities of microorganisms. Therefore, new methods of reclamation of such polluted territories are being sought and developed. One of the approaches can be the introduction of bacteria that stimulate the physiological activity of autochthonous destructors. In the course of the conducted study, the moderately halophilic strain Halomonas sp. SMB31 was identified as the most competitive for the intermediates of the destruction of naphthalene (model compound PAH), and its effect on the growth of the halotolerant destructor strain Rhodococcus sp. SMB38 has been evaluated during the degradation of naphthalene under conditions of high salinity (7% NaCl). It is shown that the joint cultivation of Rhodococcus sp. SMB38 and Halomonas sp. SMB31 led to a significant reduction in the duration of the period of adaptation to environmental conditions and an increase in the specific growth rate of the destructor strain. Thus, the obtained results showed the prospects of the studied moderately halophilic strain Halomonas sp. SMB31 for use as a biological preparation for the purpose of activating the physiological processes of autochthonous microorganisms-destructors under conditions of salinization of the environment.
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9
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Zharikova NV, Korobov VV, Zhurenko EI. Flavin-Dependent Monooxygenases Involved in Bacterial Degradation of Chlorophenols. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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10
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Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
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Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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Nazarova EA, Nazarov AV, Egorova DO, Anan'ina LN. Influence of destructive bacteria and red clover (trifolium pratense L.) on the pesticides degradation in the soil. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:399-408. [PMID: 33515377 DOI: 10.1007/s10653-021-00821-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 01/07/2021] [Indexed: 05/26/2023]
Abstract
Lindane and DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) are pesticides from the group of persistent organic pollutants. These compounds, due to lipophilic properties, accumulate in tissues of organisms, are transmitted through the food chain and ultimately threaten human health. The long-term use of pesticides led to soil and water pollution. Microbial degradation of organochlorine compounds is the most eco-friendly method of polluted soil recultivation. Effective degradation of lindane and DDT soil pollution under the influence of introduced destructive bacteria was shown in the laboratory conditions. The concentration of lindane in the soil decreased by 75% and of DDT-by 56% in 30 days. The red clover seedlings increased pesticides degradation in the soil by 20%. The destruction of pesticides in soil was more intense than in the mineral medium. The DGGE analysis of microorganism associations introduced in contaminated soil was possible to follow the survival of the introduced associations. The use of microorganisms-destructors of organochlorine compounds, and plants as well as the biodegradation potential of the soil is a promising direction in the recultivation of polluted soils.
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Affiliation(s)
- Elmira A Nazarova
- Institute of Ecology and Genetics of Microorganisms Ural Branch, Russian Academy of Sciences, 13 Golev str, Perm, Russia, 614081.
| | - Alexey V Nazarov
- Institute of Ecology and Genetics of Microorganisms Ural Branch, Russian Academy of Sciences, 13 Golev str, Perm, Russia, 614081
| | - Daria O Egorova
- Institute of Ecology and Genetics of Microorganisms Ural Branch, Russian Academy of Sciences, 13 Golev str, Perm, Russia, 614081
| | - Ludmila N Anan'ina
- Institute of Ecology and Genetics of Microorganisms Ural Branch, Russian Academy of Sciences, 13 Golev str, Perm, Russia, 614081
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12
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Wilmoth JL, Schaefer JK, Schlesinger DR, Roth SW, Hatcher PG, Shoemaker JK, Zhang X. The role of oxygen in stimulating methane production in wetlands. GLOBAL CHANGE BIOLOGY 2021; 27:5831-5847. [PMID: 34409684 PMCID: PMC9291790 DOI: 10.1111/gcb.15831] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Methane (CH4 ), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2 ). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O2 ) can stimulate CH4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O2 can increase CH4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O2 -dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H2 and CO2 . Higher CO2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O2 enhancement of CH4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH4 emissions; and guiding wetland C management strategies.
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Affiliation(s)
- Jared L. Wilmoth
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNJUSA
| | - Jeffra K. Schaefer
- Department of Environmental SciencesRutgers UniversityNew BrunswickNJUSA
| | | | - Spencer W. Roth
- Department of Environmental SciencesRutgers UniversityNew BrunswickNJUSA
| | | | - Julie K. Shoemaker
- Department of Chemistry and BiochemistryOld Dominion UniversityNorfolkVAUSA
| | - Xinning Zhang
- High Meadows Environmental InstitutePrinceton UniversityPrincetonNJUSA
- Department of GeosciencesPrinceton UniversityPrincetonNJUSA
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13
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Nazarova EA, Egorova DO, Anan’ina LN, Korsakova ES, Plotnikova EG. New Associations of Aerobic Bacteria that Actively Decompose Lindane. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821050112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Keller NS, Hornbruch G, Lüders K, Werban U, Vogt C, Kallies R, Dahmke A, Richnow HH. Monitoring of the effects of a temporally limited heat stress on microbial communities in a shallow aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146377. [PMID: 33794453 DOI: 10.1016/j.scitotenv.2021.146377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Aquifer thermal energy storage (ATES) is a key concept for the use of renewable energy resources. Interest in ATES performed at high temperature (HT-ATES; > 60 °C) is increasing due to higher energetic efficiencies. HT-ATES induces temperature fluctuations that exceed the natural variability in shallow aquifers, which could lead to adverse effects in subsurface ecosystems by altering the groundwater chemistry, biodiversity, and microbial metabolic activity, resulting in changes of the groundwater quality, biogeochemical processes, and ecosystem functions. The aim of this study was to emulate the initial operating phase of a HT-ATES system with a short-term infiltration of warm water into Pleistocene sandur sediment and, consequently, to monitor the thermal effects on the groundwater microbiome inhabiting an imitated affected space of an HT-ATES system. Therefore, local groundwater was withdrawn, heated up to 75 °C, and re-infiltrated into a shallow aquifer located near Wittstock/Dosse (Brandenburg, Germany) for around five days. Groundwater samples taken regularly before and after the infiltration were analyzed by 16S rRNA gene amplicon sequencing for microbial diversity analyses as well as total cell counting. During the infiltration, a thermal plume with groundwater temperatures increasing from 9 ± 2 to up to ~65 °C was recorded. The highest temperature at which groundwater samples were taken was 34.9 °C, a temperature typically arising in the affected space of an HT-ATES system. The microbial communities in the groundwater were mainly composed of Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, and Actinobacteria, and the total cell numbers ranged from 3.2 * 104 to 3.1 * 106 cells ml-1. Neither the compositions of the microbial communities nor the total number of cells in groundwater were significantly changed upon moderate temperature increase, indicating that the diverse groundwater microbiome was resilient to the temporally limited heat stress.
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Affiliation(s)
- Nina-Sophie Keller
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
| | - Götz Hornbruch
- University of Kiel, Institute for Geosciences, 24118 Kiel, Germany.
| | - Klas Lüders
- University of Kiel, Institute for Geosciences, 24118 Kiel, Germany.
| | - Ulrike Werban
- Helmholtz Centre for Environmental Research - UFZ, Department Monitoring & Exploration Technologies, 04318 Leipzig, Germany.
| | - Carsten Vogt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
| | - René Kallies
- Helmholtz Centre for Environmental Research - UFZ, Department Environmental Microbiology, 04318 Leipzig, Germany.
| | - Andreas Dahmke
- University of Kiel, Institute for Geosciences, 24118 Kiel, Germany.
| | - Hans Hermann Richnow
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
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15
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Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 2021; 4:604. [PMID: 34021239 PMCID: PMC8139981 DOI: 10.1038/s42003-021-02112-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/16/2021] [Indexed: 02/04/2023] Open
Abstract
The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.
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Affiliation(s)
- Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Pascal Hingamp
- Aix Marseille Univ., Université de Toulon, CNRS, Marseille, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Gipsi Lima-Mendez
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Jesús M Arrieta
- Spanish Institute of Oceanography (IEO), Oceanographic Center of The Canary Islands, Dársena Pesquera, Santa Cruz de Tenerife, Spain
| | - Intikhab S Alam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Allan Kamau
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
- VIB Center for Microbiology, Leuven, Belgium
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Matthew B Sullivan
- Department of Microbiology and Civil Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
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16
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Metze D, Popp D, Schwab L, Keller NS, da Rocha UN, Richnow HH, Vogt C. Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer. FEMS Microbiol Ecol 2021; 97:6055686. [PMID: 33378450 DOI: 10.1093/femsec/fiaa261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.
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Affiliation(s)
- Dennis Metze
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany.,Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Althanstraße 14, Austria
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Laura Schwab
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Nina-Sophie Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Permoserstraße 15, Germany
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17
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Influences of Dimethyl Phthalate on Bacterial Community and Enzyme Activity in Vertical Flow Constructed Wetland. WATER 2021. [DOI: 10.3390/w13060788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dimethyl phthalate (DMP), belonging to the family of Phthalate esters (PAEs), is a plasticizer and has been widely used in the world for many years. Nowadays, it has become a ubiquitous environmental pollutant and is listed as an environmental priority pollutant by China’s Environmental Monitoring Center. The purpose of this study is to estimate the responses of the bacterial community and enzyme activity to DMP contamination in three vertical flow constructed wetlands (VFCW), namely the constructed wetland A (planted with Pennisetum sinese Roxb), constructed wetland B (planted with Pennisetum purpureum Schum.), and constructed wetland C (unplanted), respectively. The results showed that the relative percentages of some genera associated with nitrogen metabolism and the function of degrading aromatic hydrocarbons were increased by DMP contamination, such as Dechloromonas agitata, Pleomorphomonas sp., Denitratisoma oestradiolicum, Plasticicumulans lactativorans, Novosphingobium sp., Alicycliphilus denitrificans, and Thauera sp. Meanwhile, principal coordinate analysis (PCA) analysis showed that the addition of DMP divided 12 samples into two groups as followed: one was the DMP group containing a-1, a-2, b-1, b-2, c-1 and c-2 while the other was no DMP group including A-1, A-2, B-1, B-2, C-1 and C-2. It indicated that DMP was the main reason for this change. In addition, by monitoring the activity of substrate enzymes, the activity of urease, phosphatase, catalase, and invertase in the wetlands before and after the experiment, these were significantly higher in the upper layer than in the lower layer and maintained high activity. Ultimately, the average influent concentration of DMP in three VFCWs was 8.12 mg/L and the average removal efficiency of the effluent was over 90%. Our results suggested that DMP was an important factor affecting the microbial community structure of wetland and the upper layer of the VFCW was the main site for the degradation of DMP. VFCW has great potential for the removal of the high concentration of DMP and it can be a good choice for the treatment of PAEs.
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18
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Sonthiphand P, Rattanaroongrot P, Mek-Yong K, Kusonmano K, Rangsiwutisak C, Uthaipaisanwong P, Chotpantarat S, Termsaithong T. Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes. PeerJ 2021; 9:e10653. [PMID: 33510973 PMCID: PMC7798605 DOI: 10.7717/peerj.10653] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/04/2020] [Indexed: 11/20/2022] Open
Abstract
The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3 --N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
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Affiliation(s)
- Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Kasarnchon Mek-Yong
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chalida Rangsiwutisak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Srilert Chotpantarat
- Department of Geology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand.,Research Unit of Green Mining (GMM), Chulalongkorn University, Bangkok, Thailand
| | - Teerasit Termsaithong
- Learning Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Theoretical and Computational Science Center (TaCS), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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19
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Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient. Viruses 2020; 12:v12101138. [PMID: 33049935 PMCID: PMC7600146 DOI: 10.3390/v12101138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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20
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Li Z, Yu E, Zhang K, Gong W, Xia Y, Tian J, Wang G, Xie J. Water Treatment Effect, Microbial Community Structure, and Metabolic Characteristics in a Field-Scale Aquaculture Wastewater Treatment System. Front Microbiol 2020; 11:930. [PMID: 32655501 PMCID: PMC7325950 DOI: 10.3389/fmicb.2020.00930] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/20/2020] [Indexed: 01/16/2023] Open
Abstract
Avoiding and mitigating the introduction of harmful effluent into the environment must be a key part of intensive industrial aquaculture development in order to minimize pollution impacts. We constructed a novel field-scale aquaculture wastewater treatment system (FAWTS) involving three-stage purification to efficiently remove nutrients from effluent wastewater. However, the mechanisms of nutrient attenuation in the FAWTS are still unclear. Since microbiota play an important role in the treatment of aquatic pollutants, we hypothesized that the different stages of FAWTS may have enriched various nutrient-metabolizing bacteria, with these promoting nutrient attenuation. We therefore tested microbial metabolic activity, microbial composition, and their metabolic potential using Biolog-GN2 microplate culture and high-throughput sequencing of prokaryotic 16S rRNA gene amplicons. Our results showed that the FAWTS displayed high removal efficiencies for chemical oxygen demand (COD, 74.4-91.2%), total nitrogen (TN, 66.9-86.8%), and total phosphorus (TP, 76.2-95.9%). Simultaneously, microbial metabolic activity for various carbon sources was significantly enhanced in FAWTS biofilms. Denitrifying and phosphorus-removing bacteria such as Rhodobacter were enriched in these biofilms, and genes participating in denitrification and the pathway from methylphosphonate to α-D-ribose-1,5-bisphosphate were increased in the biofilm communities. These results imply that the transformed multistep purification system effectively removed N, P, and COD from aquaculture wastewater by enhancing the bacterial communities involved in these processes. This suggests that contamination-free aquaculture is a feasible goal, and that microbial communities are central to pollutant removal.
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Affiliation(s)
- Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Ermeng Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Kai Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Yun Xia
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Jingjing Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
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21
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Lian S, Qu Y, Li S, Zhang Z, Zhang H, Dai C, Deng Y. Interaction of graphene-family nanomaterials with microbial communities in sequential batch reactors revealed by high-throughput sequencing. ENVIRONMENTAL RESEARCH 2020; 184:109392. [PMID: 32209499 DOI: 10.1016/j.envres.2020.109392] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
The accelerated development and application of graphene-family nanomaterials (GFNs) have increased their release to various environments and converged in wastewater treatment plants (WWTPs). However, little is known about the interactions between GFNs and microbes in WWTPs. In this study, the interaction of graphene oxide (GO) or graphene (G) at different concentrations with microbial communities in sequential batch reactors was investigated. Transmission electron microscopy and Raman spectroscopy analyses showed that the structures of GFNs were obviously changed, which suggested GFNs could be degraded by some microbes. Significantly higher DNA concentration and lower cell number in high-concentration GO group were detected by DNA leakage test and qPCR analysis, which confirmed the microbial toxicity of GO. The chemical oxygen demand and ammonia nitrogen removals were significantly affected by G and GO with high concentrations. Further, high-throughput sequencing confirmed the composition and dynamic changes of microbial communities under GFNs exposure. Saccharibacteria genera incertae sedis (12.55-28.05%) and Nakamurella (20.45-29.30%) were the predominant genera at two stages, respectively. FAPROTAX suggested 12 functional groups with obvious changes related to the biogeochemical cycle of C, N and S. Molecular ecological network analysis showed that the networks were more complex in the presence of GFNs, and the increased negative interactions reflected more competition relationships in microbial communities. This study is the first to report the effect of GFNs on network of microbial communities, which provides in-depth insights into the complex and highlights concerns regarding the risk of GFNs to WWTPs.
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Affiliation(s)
- Shengyang Lian
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Shuzhen Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Zhaojing Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Henglin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Chunxiao Dai
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
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22
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Chang YT, Chao WL, Chen HY, Li H, Boyd SA. Characterization of a Sequential UV Photolysis-Biodegradation Process for Treatment of Decabrominated Diphenyl Ethers in Sorbent/Water Systems. Microorganisms 2020; 8:E633. [PMID: 32349399 PMCID: PMC7284435 DOI: 10.3390/microorganisms8050633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 12/26/2022] Open
Abstract
Decabrominated diphenyl ether (BDE-209) is a primary component of the brominated flame retardants used in a variety of industrial and domestic applications. BDE-209 bioaccumulates in aquatic organisms and has been identified as an emerging contaminant that threatens human and ecosystem health. Sequential photolysis-microbial biodegradation processes were utilized here to treat BDE-209 in clay- or soil-water slurries. The removal efficiency of BDE-209 in the clay-water slurries was high; i.e., 96.5%, while that in the soil-water slurries was minimal. In the clay-water slurries the first order rate constants for the UV photolysis and biodegradation of BDE-209 were 0.017 1/day and 0.026 1/day, respectively. UV wavelength and intensity strongly influenced the BDE-209 photolysis and the subsequent biodegradation of photolytic products. Facultative chemotrophic bacteria, including Acidovorax spp., Pseudomonas spp., Novosphingobium spp. and Sphingomonas spp., were the dominant members of the bacterial community (about 71%) at the beginning of the biodegradation; many of these organisms have previously been shown to biodegrade BDE-209 and other polybrominated diphenyl ether (PBDE) congeners. The Achromobacter sp. that were isolated (NH-2; NH-4; NH-6) were especially effective during the BDE-209 degradation. These results indicated the effectiveness of the sequential UV photolysis and biodegradation for treating certain BDE-209-contaminated solids; e.g., clays; in bioreactors containing such solids as aqueous slurries. Achieving a similar treatment effectiveness for more heterogeneous solids containing natural organic matter, e.g., surface solids, appears to be significantly more difficult. Further investigations are needed in order to understand the great difference between the clay-water or soil-water slurries.
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Affiliation(s)
- Yi-Tang Chang
- Department of Microbiology, Soochow University, Shilin District, Taipei 11102, Taiwan; (W.-L.C.); (H.-Y.C.)
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Wei-Liang Chao
- Department of Microbiology, Soochow University, Shilin District, Taipei 11102, Taiwan; (W.-L.C.); (H.-Y.C.)
| | - Hsin-Yu Chen
- Department of Microbiology, Soochow University, Shilin District, Taipei 11102, Taiwan; (W.-L.C.); (H.-Y.C.)
| | - Hui Li
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA;
| | - Stephen A. Boyd
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA;
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23
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Asaf S, Numan M, Khan AL, Al-Harrasi A. Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Crit Rev Biotechnol 2020; 40:138-152. [PMID: 31906737 DOI: 10.1080/07388551.2019.1709793] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.
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Affiliation(s)
- Sajjad Asaf
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Muhammad Numan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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24
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Zhou X, Zhang K, Zhang T, Yang Y, Ye M, Pan R. Formation of odorant haloanisoles and variation of microorganisms during microbial O-methylation in annular reactors equipped with different coupon materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 679:1-11. [PMID: 31078770 DOI: 10.1016/j.scitotenv.2019.04.329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Taste and odor (T & O) issues in drinking water have become serious problems which cannot be ignored by customers. Several studies have confirmed that microbes in water can biotransform halophenols (HPs) to haloanisoles (HAs) with earthy and musty flavors via microbial O-methylation. In this paper, the formation of 2-chloroanisole (2-CA), 2,4-dichloroanisole (2,4-DCA), 2,4,6-trichloroanisole (2,4,6-TCA), 2,3,6-trichloroanisole (2,3,6-TCA) and 2,4,6-tribromoanisole (2,4,6-TBA), and the microbial variation during the microbial O-methylation were investigated in annular reactors (ARs) with three coupon materials. For precursors, 42.5% of 2-CP and 68.9% of 2,4-DCP decayed during the reaction. Among the five HAs, the formation rate constant followed an order of 2,4,6-TCA > 2-CA > 2,4,6-TBA > 2,4-DCA ~ 2,3,6-TCA, while [HA]max followed a totally opposite one. The simulated flow velocity had no significant effect (p > 0.05) on HA formation. Ductile iron (DI) AR could produce more HAs than stainless steel (SS) and polyvinyl chloride (PVC) ARs. The final HA molar concentration followed an order of 2,3,6-TCA > 2,4-DCA > 2,4,6-TBA ~ 2,4,6-TCA > 2-CA, which might be explained by multiple factors including HP's dissociation degree, halogen atom's steric hindrance and specificity of HP O-methyltransferases. During the reaction, the microbial biomass dramatically increased 6.8-9.0 times in bulk water but dropped significantly on coupon biofilms. The effect of HPs significantly changed the bacterial communities on coupon in terms of composition and diversity, and declined the relative abundance of HA-producing bacteria, while fungi and their HA-producing genus showed better resistance ability towards HPs. By using Pearson correlation analysis, a significant correlation (p = 0.0003) was found between [HA]max and initial coupon biofilm biomass. Finally, a linear relationship was established between initial total biomass and HA formation potential.
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Affiliation(s)
- Xinyan Zhou
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Kejia Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Tuqiao Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yulong Yang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Miaomiao Ye
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Renjie Pan
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, Zhejiang, China
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25
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Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone. WATER 2019. [DOI: 10.3390/w11061261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nutrients and organic pollutants transported by submarine groundwater discharge (SGD) play a significant role in controlling water quality, and can lead to the concerned deleterious effects on marine ecosystems. Subterranean estuaries are complicated habitats of diverse microbial communities that mediate different biogeochemical processes. However, there is less information on how microorganisms mediate biogeochemical cycles in the submarine groundwater system. In this study, we investigated the changes in bacterial and archaeal assemblages from two size fractions (0.2–0.45 μm and >0.45 μm) in the submarine groundwater of Qinzhou Bay, China. Phylogenetic analysis showed that Bathyarchaeota was dominant in archaeal communities in the >0.45 μm size fraction, but was seldom in the 0.2–0.45 μm fraction. The co-occurrence of sequences belonging to Bathyarchaeota and Methanosaeta was found in the >0.45 μm size fraction. Since a gene encoding acetate kinase of Bathyarchaeota is involved in acetate production, and acetate is also a necessary growth factor for Methanosaeta, the acetate produced by Bathyarchaeota can provide food or energy sources for Methanosaeta in this very >0.45 μm size fraction. The most abundant bacterial sequences in the >0.45 μm size fraction was closely related to biomineral iron-oxidizing Gallionella spp., whereas the dominant bacterial sequences in the 0.2–0.45 μm fraction were affiliated with Limnohabitans spp., which can utilize dissolved organic matter as an important source of growth substrates. Notably, approximately 10% of the bacterial sequences in both of the two size fractions belonged to Novosphingobium spp., which plays an important role in the degradation of pollutants, especially aromatic compounds. Furthermore, the predictive functional profiling also revealed that the pathways involved in the degradation of aromatic compounds by both bacteria and archaea were identified. The presence of nutrients or pollutants in our study site provides different substrates for the growth of the specific microbial groups; in turn, these microbes may help to deplete pollutants to the ocean through submarine groundwater. We suggest that these specific microbial groups could be potential candidates for effective in situ bioremediation of groundwater ecosystems.
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26
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Xian WD, Li MM, Salam N, Ding YP, Zhou EM, Yin YR, Liu L, Xiao M, Li WJ. Novosphingobium meiothermophilum sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2019; 69:1737-1743. [DOI: 10.1099/ijsem.0.003384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wen-Dong Xian
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Meng-Meng Li
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Nimaichand Salam
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yi-Ping Ding
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - En-Min Zhou
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
- 2School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming 650091, PR China
| | - Yi-Rui Yin
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Lan Liu
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Min Xiao
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- 1State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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27
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Özkaya B, Kaksonen AH, Sahinkaya E, Puhakka JA. Fluidized bed bioreactor for multiple environmental engineering solutions. WATER RESEARCH 2019; 150:452-465. [PMID: 30572277 DOI: 10.1016/j.watres.2018.11.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/10/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Fluidized bed bioreactors (FBR) are characterized by two-phase mixture of fluid and solid, in which the bed of solid particles is fluidized by means of downward or upward recirculation stream. FBRs are widely used for multiple environmental engineering solutions, such as wastewater treatment, as well as some industrial applications. FBR offers many benefits such as compact bioreactor size due to short hydraulic retention time, long biomass retention on the carrier, high conversion rates due to fully mixed conditions and consequently high mass transfer rates, no channelling of flow, dilution of influent concentrations due to recycle flow, suitability for enrichment of microbes with low Km values. The disadvantages of FBRs include bioreactor size limitations due to the height-to-diameter ratio, high-energy requirements due to high recycle ratios, and long start-up period for biofilm formation. This paper critically reviews some of the key studies on biomass enrichment via immobilisation of low growth yield microorganisms, high-rates via fully mixed conditions, technical developments in FBRs and ways of overcoming toxic effects via solution recycling. This technology has many potential new uses as well as hydrodynamic characteristics, which enable high-rate environmental engineering and industrial applications.
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Affiliation(s)
- Bestami Özkaya
- Tampere University, Faculty of Engineering and Natural Sciences, Laboratory of Chemistry and Bioengineering, P.O. Box 541, FI-33101, Tampere, Finland; Yıldız Technical University, Department of Environmental Engineering, Davutpasa, Istanbul, Turkey
| | - Anna H Kaksonen
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA, 6014, Australia
| | - Erkan Sahinkaya
- Istanbul Medeniyet University, Bioengineering Department, Goztepe, Istanbul, Turkey
| | - Jaakko A Puhakka
- Tampere University, Faculty of Engineering and Natural Sciences, Laboratory of Chemistry and Bioengineering, P.O. Box 541, FI-33101, Tampere, Finland.
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28
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Wang J, Wang C, Li J, Bai P, Li Q, Shen M, Li R, Li T, Zhao J. Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. Front Microbiol 2018; 9:2238. [PMID: 30319567 PMCID: PMC6167471 DOI: 10.3389/fmicb.2018.02238] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.
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Affiliation(s)
- Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jionghui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renhui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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29
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Mikkonen A, Yläranta K, Tiirola M, Dutra LAL, Salmi P, Romantschuk M, Copley S, Ikäheimo J, Sinkkonen A. Successful aerobic bioremediation of groundwater contaminated with higher chlorinated phenols by indigenous degrader bacteria. WATER RESEARCH 2018; 138:118-128. [PMID: 29574199 DOI: 10.1016/j.watres.2018.03.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
The xenobiotic priority pollutant pentachlorophenol has been used as a timber preservative in a polychlorophenol bulk synthesis product containing also tetrachlorophenol and trichlorophenol. Highly soluble chlorophenol salts have leaked into groundwater, causing severe contamination of large aquifers. Natural attenuation of higher-chlorinated phenols (HCPs: pentachlorophenol + tetrachlorophenol) at historically polluted sites has been inefficient, but a 4-year full scale in situ biostimulation of a chlorophenol-contaminated aquifer by circulation and re-infiltration of aerated groundwater was remarkably successful: pentachlorophenol decreased from 400 μg L-1 to <1 μg L-1 and tetrachlorophenols from 4000 μg L-1 to <10 μg L-1. The pcpB gene, the gene encoding pentachlorophenol hydroxylase - the first and rate-limiting enzyme in the only fully characterised aerobic HCP degradation pathway - was present in up to 10% of the indigenous bacteria already 4 months after the start of aeration. The novel quantitative PCR assay detected the pcpB gene in situ also in the chlorophenol plume of another historically polluted aquifer with no remediation history. Hotspot groundwater HCPs from this site were degraded efficiently during a 3-week microcosm incubation with one-time aeration but no other additives: from 5400 μg L-1 to 1200 μg L-1 and to 200 μg L-1 in lightly and fully aerated microcosms, respectively, coupled with up to 2400% enrichment of the pcpB gene. Accumulation of lower-chlorinated metabolites was observed in neither in situ remediation nor microcosms, supporting the assumption that HCP removal was due to the aerobic degradation pathway where the first step limits the mineralisation rate. Our results demonstrate that bacteria capable of aerobic mineralisation of xenobiotic pentachlorophenol and tetrachlorophenol can be present at long-term polluted groundwater sites, making bioremediation by simple aeration a viable and economically attractive alternative.
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Affiliation(s)
- Anu Mikkonen
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9 C, 40500 Jyväskylä, Finland.
| | - Kati Yläranta
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9 C, 40500 Jyväskylä, Finland
| | - Lara Ambrosio Leal Dutra
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9 C, 40500 Jyväskylä, Finland
| | - Pauliina Salmi
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9 C, 40500 Jyväskylä, Finland
| | - Martin Romantschuk
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland; Institute of Environmental Sciences, Kazan Federal University, 420008, Kremlevskaya 18, Kazan, Russia
| | - Shelley Copley
- Cooperative Institute for Research in Environmental Sciences and Molecular, Cellular and Developmental Biology, University of Colorado, CO 80309 Boulder, United States
| | | | - Aki Sinkkonen
- Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, 15140 Lahti, Finland
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30
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Kämpfer P, Busse HJ, Glaeser SP. Novosphingobium lubricantis sp. nov., isolated from a coolant lubricant emulsion. Int J Syst Evol Microbiol 2018; 68:1560-1564. [PMID: 29561253 DOI: 10.1099/ijsem.0.002702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain KSS165-70T) was isolated from a coolant lubricant emulsion. The 16S rRNA gene sequence analysis of strain KSS165-70T showed high sequence similarity to the type strains of Novosphingobium subterraneum (98.1 %), Novosphingobium lentum (97.9 %) and Novosphingobium taihuense (97.8 %). Sequence similarities to type strains of all other Novosphingobium species were below 97.5 %. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid C18 : 1ω7c and the typical 2-hydroxy fatty acid C14 : 0 2-OH were detected. The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid, phosphatidylcholine and two unidentified phospholipids. The polyamine pattern contained the major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain KSS165-70T represents a new species of the genus Novosphingobium. For this reason, we propose the name Novosphingobium lubricantis sp. nov. with the type strain KSS165-70T (=CIP 111490T=CCM 8814T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien, Austria
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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31
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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32
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Chen L, Krol ES, Sakharkar MK, Khan HA, Alhomida AS, Yang J. Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1. Sci Rep 2017; 7:18097. [PMID: 29273747 PMCID: PMC5741723 DOI: 10.1038/s41598-017-18475-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/12/2017] [Indexed: 02/08/2023] Open
Abstract
Maleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k cat /K m ) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.
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Affiliation(s)
- Lifeng Chen
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Agrisoma Biosciences Inc., 4410-110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Ed S Krol
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Meena K Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Haseeb A Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah S Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
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33
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Solyanikova IP, Suzina NE, Egozarjan NS, Polivtseva VN, Mulyukin AL, Egorova DO, El-Registan GI, Golovleva LA. Structural and functional rearrangements in the cells of actinobacteria Microbacterium foliorum BN52 during transition from vegetative growth to a dormant state and during germination of dormant forms. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717030171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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34
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Yang C, Wang Q, Simon PN, Liu J, Liu L, Dai X, Zhang X, Kuang J, Igarashi Y, Pan X, Luo F. Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake. Front Microbiol 2017; 8:1202. [PMID: 28713340 PMCID: PMC5492469 DOI: 10.3389/fmicb.2017.01202] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/13/2017] [Indexed: 12/23/2022] Open
Abstract
Particle-associated bacteria (PAB) and free-living bacteria (FLB) from aquatic environments during phytoplankton blooms differ in their physical distance from algae. Both the interactions within PAB and FLB community fractions and their relationship with the surrounding environmental properties are largely unknown. Here, by using high-throughput sequencing and network-based analyses, we compared the community and network characteristics of PAB and FLB from a plateau lake during a Microcystis aeruginosa bloom. Results showed that PAB and FLB differed significantly in diversity, structure and microbial connecting network. PAB communities were characterized by highly similar bacterial community structure in different sites, tighter network connections, important topological roles for the bloom-causing M. aeruginosa and Alphaproteobacteria, especially for the potentially nitrogen-fixing (Pleomorphomonas) and algicidal bacteria (Brevundimonas sp.). FLB communities were sensitive to the detected environmental factors and were characterized by significantly higher bacterial diversity, less connectivity, larger network size and marginal role of M. aeruginosa. In both networks, covariation among bacterial taxa was extensive (>88% positive connections), and bacteria potentially affiliated with biogeochemical cycling of nitrogen (i.e., denitrification, nitrogen-fixation and nitrite-oxidization) were important in occupying module hubs, such as Meganema, Pleomorphomonas, and Nitrospira. These findings highlight the importance of considering microbial network interactions for the understanding of blooms.
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Affiliation(s)
- Caiyun Yang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Qi Wang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Paulina N Simon
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jinyu Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Lincong Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xianzhu Dai
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xiaohui Zhang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and TechnologyKunming, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
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35
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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36
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Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice. Res Microbiol 2017; 168:113-121. [DOI: 10.1016/j.resmic.2016.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 01/29/2023]
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37
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Gu Q, Wu Q, Zhang J, Guo W, Wu H, Sun M. Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters. Front Microbiol 2016; 7:495. [PMID: 27148185 PMCID: PMC4828441 DOI: 10.3389/fmicb.2016.00495] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/27/2016] [Indexed: 11/13/2022] Open
Abstract
Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.
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Affiliation(s)
- Qihui Gu
- School of Bioscience and Bioengineering, South China University of TechnologyGuangzhou, China; Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied MicrobiologyGuangzhou, China
| | - Qingping Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology Guangzhou, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology Guangzhou, China
| | - Weipeng Guo
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology Guangzhou, China
| | - Huiqing Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology Guangzhou, China
| | - Ming Sun
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology Guangzhou, China
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38
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Lin Z, Zhen Z, Wu Z, Yang J, Zhong L, Hu H, Luo C, Bai J, Li Y, Zhang D. The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2016; 301:35-45. [PMID: 26342149 DOI: 10.1016/j.jhazmat.2015.08.034] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 06/05/2023]
Abstract
The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively.
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Affiliation(s)
- Zhong Lin
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, PR China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhen Zhen
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zhihao Wu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - Jiewen Yang
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Laiyuan Zhong
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Hanqiao Hu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Jing Bai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China.
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 2YW, UK.
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39
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Pereira LB, Vicentini R, Ottoboni LMM. Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine. Genet Mol Biol 2015; 38:484-9. [PMID: 26537607 PMCID: PMC4763313 DOI: 10.1590/s1415-475738420150025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/20/2015] [Indexed: 11/21/2022] Open
Abstract
The core microbiota of a neutral mine drainage and the surrounding high heavy metal content soil at a Brazilian copper mine were characterized by 16S rDNA pyrosequencing. The core microbiota of the drainage was dominated by the generalist genus Meiothermus. The soil samples contained a more heterogeneous bacterial community, with the presence of both generalist and specialist bacteria. Both environments supported mainly heterotrophic bacteria, including organisms resistant to heavy metals, although many of the bacterial groups identified remain poorly characterized. The results contribute to the understanding of bacterial communities in soils impacted by neutral mine drainage, for which information is scarce, and demonstrate that heavy metals can play an important role in shaping the microbial communities in mine environments.
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Affiliation(s)
- Letícia Bianca Pereira
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Laura M M Ottoboni
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
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40
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Kämpfer P, Martin K, McInroy JA, Glaeser SP. Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum. Int J Syst Evol Microbiol 2015; 65:2831-2837. [DOI: 10.1099/ijs.0.000339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Karin Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut., D-07745 Jena, Germany
| | - John A. McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama 36849, USA
| | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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41
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Singh H, Du J, Yang JE, Yin C, Kook M, Yi TH. Novosphingobium aquaticum sp. nov., isolated from lake water in Suwon, Republic of Korea. Antonie van Leeuwenhoek 2015. [PMID: 26205206 DOI: 10.1007/s10482-015-0539-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A novel Gram-stain negative, yellow coloured, strictly aerobic, rod-shaped, non-motile bacterium designated as THW-SA1(T), was isolated from lake water near Samsung apartment, Suwon, Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain THW-SA1(T) belongs to the genus Novosphingobium and is closely related to Novosphingobium taihuense (97.8 %) and Novosphingobium subterraneum (97.1 %). The DNA-DNA relatedness values between strain THW-SA1(T) and the most closely related type strains were found to be less than 30.0 %. The DNA G+C content was determined to be 67.5 mol%. The strain grows optimally at 25-28 °C, at pH 7.0, and in the presence of 0.5 % NaCl. The predominant isoprenoid quinone was identified as ubiquinone Q-10. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine, some unidentified phospholipids and some unidentified polar lipids. Fatty acids characteristic for this genus, such as C16:1, C14:0 2-OH, C16:1 ω6c and/or C16:1 ω7c (summed feature 3) and C18:1 ω6c and/or C18:1 ω7c (summed feature 8) were also detected. On the basis of the phenotypic and genotypic analysis, the strain THW-SA1(T) is considered to represent a novel species of the genus Novosphingobium, for which the name Novosphingobium aquaticum sp. nov. is proposed. The type strain is THW-SA1(T) (=KCTC 42608(T)=CCTCC AB 2015114(T)).
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Affiliation(s)
- Hina Singh
- Department of Oriental Medicine Biotechnology, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
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42
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Kämpfer P, Martin K, McInroy JA, Glaeser SP. Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere. Int J Syst Evol Microbiol 2015; 65:195-200. [DOI: 10.1099/ijs.0.070375-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1T) was isolated from the rhizosphere of a field-grown Zea mays plant in Auburn, AL, USA. 16S rRNA gene sequence analysis of strain JM-1T showed high sequence similarity to the type strains of
Novosphingobium capsulatum
(98.9 %),
Novosphingobium aromaticivorans
(97.4 %),
Novosphingobium subterraneum
(97.3 %) and
Novosphingobium taihuense
(97.1 %); sequence similarities to all other type strains of species of the genus
Novosphingobium
were below 97.0 %. DNA–DNA hybridizations of strain JM-1T and
N. capsulatum
DSM 30196T,
N. aromaticivorans
SMCC F199T and
N. subterraneum
SMCC B0478T showed low similarity values of 33 % (reciprocal: 21 %), 14 % (reciprocal 16 %) and 36 % (reciprocal 38 %), respectively. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid was C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid C14 : 0 2-OH (11.7 %) was detected. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain JM-1T represents a novel species of the genus
Novosphingobium
. For this species we propose the name Novosphingobium rhizosphaerae sp. nov. with the type strain JM-1T ( = LMG 28479T = CCM 8547T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Karin Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut., D-07745 Jena, Germany
| | - John A. McInroy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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43
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A comprehensive insight into tetracycline resistant bacteria and antibiotic resistance genes in activated sludge using next-generation sequencing. Int J Mol Sci 2014; 15:10083-100. [PMID: 24905407 PMCID: PMC4100141 DOI: 10.3390/ijms150610083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 11/17/2022] Open
Abstract
In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB) and antibiotic resistance genes (ARGs) in sludge cultured with different concentrations of tetracycline. Pyrosequencing of 16S rRNA gene revealed that tetracycline treatment greatly affected the bacterial community structure of the sludge. Nine genera consisting of Sulfuritalea, Armatimonas, Prosthecobacter, Hyphomicrobium, Azonexus, Longilinea, Paracoccus, Novosphingobium and Rhodobacter were identified as potential TRB in the sludge. Results of qPCR, molecular cloning and metagenomic analysis consistently indicated that tetracycline treatment could increase both the abundance and diversity of the tet genes, but decreased the occurrence and diversity of non-tetracycline ARG, especially sulfonamide resistance gene sul2. Cluster analysis showed that tetracycline treatment at subinhibitory concentrations (5 mg/L) was found to pose greater effects on the bacterial community composition, which may be responsible for the variations of the ARGs abundance. This study indicated that joint use of 454 pyrosequencing and Illumina high-throughput sequencing can be effectively used to explore ARB and ARGs in the environment, and future studies should include an in-depth investigation of the relationship between microbial community, ARGs and antibiotics in sewage treatment plant (STP) sludge.
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Shumkova ES, Egorova DO, Korsakova ES, Dorofeeva LV, Plotnikova EG. Molecular biological characterization of biphenyl-degrading bacteria and identification of the biphenyl 2,3-Dioxygenase α-subunit genes. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714010135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Chiao TH, Clancy TM, Pinto A, Xi C, Raskin L. Differential resistance of drinking water bacterial populations to monochloramine disinfection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:4038-47. [PMID: 24625288 DOI: 10.1021/es4055725] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The impact of monochloramine disinfection on the complex bacterial community structure in drinking water systems was investigated using culture-dependent and culture-independent methods. Changes in viable bacterial diversity were monitored using culture-independent methods that distinguish between live and dead cells based on membrane integrity, providing a highly conservative measure of viability. Samples were collected from lab-scale and full-scale drinking water filters exposed to monochloramine for a range of contact times. Culture-independent detection of live cells was based on propidium monoazide (PMA) treatment to selectively remove DNA from membrane-compromised cells. Quantitative PCR (qPCR) and pyrosequencing of 16S rRNA genes was used to quantify the DNA of live bacteria and characterize the bacterial communities, respectively. The inactivation rate determined by the culture-independent PMA-qPCR method (1.5-log removal at 664 mg·min/L) was lower than the inactivation rate measured by the culture-based methods (4-log removal at 66 mg·min/L). Moreover, drastic changes in the live bacterial community structure were detected during monochloramine disinfection using PMA-pyrosequencing, while the community structure appeared to remain stable when pyrosequencing was performed on samples that were not subject to PMA treatment. Genera that increased in relative abundance during monochloramine treatment include Legionella, Escherichia, and Geobacter in the lab-scale system and Mycobacterium, Sphingomonas, and Coxiella in the full-scale system. These results demonstrate that bacterial populations in drinking water exhibit differential resistance to monochloramine, and that the disinfection process selects for resistant bacterial populations.
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Affiliation(s)
- Tzu-Hsin Chiao
- Department of Civil and Environmental Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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Arora PK, Bae H. Bacterial degradation of chlorophenols and their derivatives. Microb Cell Fact 2014; 13:31. [PMID: 24589366 PMCID: PMC3975901 DOI: 10.1186/1475-2859-13-31] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 02/20/2014] [Indexed: 12/02/2022] Open
Abstract
Chlorophenols (CPs) and their derivatives are persistent environmental pollutants which are used in the manufacture of dyes, drugs, pesticides and other industrial products. CPs, which include monochlorophenols, polychlorophenols, chloronitrophenols, chloroaminophenols and chloromethylphenols, are highly toxic to living beings due to their carcinogenic, mutagenic and cytotoxic properties. Several physico-chemical and biological methods have been used for removal of CPs from the environment. Bacterial degradation has been considered a cost-effective and eco-friendly method of removing CPs from the environment. Several bacteria that use CPs as their sole carbon and energy sources have been isolated and characterized. Additionally, the metabolic pathways for degradation of CPs have been studied in bacteria and the genes and enzymes involved in the degradation of various CPs have been identified and characterized. This review describes the biochemical and genetic basis of the degradation of CPs and their derivatives.
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Affiliation(s)
- Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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47
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Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Huang HI, Young CC. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2014; 64:594-598. [DOI: 10.1099/ijs.0.054460-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped, DDT-resistant bacterium, designated strain CC-ALB-2T, was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-2T was able to grow at 25–37 °C, at pH 5.0–8.0, with 1.0 % (w/v) NaCl and tolerate up to 200 mg l−1 DDT. 16S rRNA gene sequence analysis of strain CC-ALB-2T showed highest sequence similarity to
Novosphingobium stygium
KCTC 2891T (97.1 %) and
Novosphingobium soli
DSM 22821T (96.8 %), and lower levels of similarity (<97.0 %) to other species of the genus
Novosphingobium
. The major fatty acid profile consisted of C14 : 0 2-OH (13.1 %), C16 : 0 (10.0 %), C15 : 0 iso 3-OH (5.8 %), C16 : 1ω7c/C16 : 1ω6c (summed feature 3, 24.7 %) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8, 42.4 %). The polar lipid profile constitutes sphingoglycolipid, glycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The polyamine pattern showed a predominance of spermidine as the major polyamine. The predominant quinone system was ubiquinone (Q-10). The DNA G+C content was 68.9±0.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-2T is proposed to represent a novel species of the genus
Novosphingobium
for which the name Novosphingobium arabidopsis sp. nov. is proposed. The type strain is CC-ALB-2T ( = BCRC 80571T = JCM 18896T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hsin-I Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
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Solyanikova IP, Plotnikova EG, Shumkova ES, Robota IV, Prisyazhnaya NV, Golovleva LA. Chloromuconolactone dehalogenase ClcF of actinobacteria. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2014; 49:422-431. [PMID: 24762180 DOI: 10.1080/03601234.2014.894778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This work investigated the distribution of the clcF gene in actinobacteria isolated from different ecotopes. The gene encodes chloromuconolactone dehalogenase (CMLD) ClcF, the enzyme found to date in only one representative of Gram-positive bacteria, Rhodococcus opacus 1CP, adapted to 2-chlorophenol (2CP). Using primers specific to the clcF gene, from the DNA matrix of rhodococcal strains closely related to species Rhodococcus wratislaviensis (P1, P12, P13, P20, G10, KT112, KT723, BO1) we obtained PCR products whose nucleotide sequences were 100% identical to that of the clcF gene from strain R. opacus 1CP. CMLDs isolated from the biomass of strains Rhodococcus spp. G10 and P1 grown on 2CP did not differ by their subunit molecular mass deduced from the known amino acid sequence of the clcF gene from the ClcF of strain R. opacus 1CP. Matrix-assisted laser dissociation/ionization time-of-flight mass spectrometry showed the presence of a peak with m/z 11,194-11,196 Da both in whole cells and in protein solutions with a ClcF activity. Thus, we have first time shown the distribution of ClcF among actinobacteria isolated from geographically distant habitats.
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Affiliation(s)
- Inna P Solyanikova
- a Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences , Pushchino , Moscow Region , Russia
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Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds. J CHEM-NY 2014. [DOI: 10.1155/2014/157974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This review was conducted to provide an overview of dehalogenases involved in aerobic biodegradation of chlorinated aromatic compounds. Additionally, biochemical and molecular characterization of hydrolytic, reductive, and oxygenolytic dehalogenases was reviewed. This review will increase our understanding of the process of dehalogenation of chlorinated aromatic compounds.
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Gan HM, Hudson AO, Rahman AYA, Chan KG, Savka MA. Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics 2013; 14:431. [PMID: 23809012 PMCID: PMC3704786 DOI: 10.1186/1471-2164-14-431] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/17/2013] [Indexed: 12/03/2022] Open
Abstract
Background Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures. Results The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme. Conclusions The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.
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Affiliation(s)
- Han Ming Gan
- Science Vision SB, Shah Alam, Selangor, Malaysia
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