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Wang Y, Zhou Z, Zhang W, Guo J, Li N, Zhang Y, Gong D, Lyu Y. Metabolic mechanism of Cr(VI) pollution remediation by Alicycliphilus denitrificans Ylb10. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169135. [PMID: 38070572 DOI: 10.1016/j.scitotenv.2023.169135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Cr(VI) is a well-known toxic pollutant and its remediation has attracted great attention. It is important to continuously discover and explore new high-efficiency Cr(VI) reducing bacteria to further improve the efficiency of Cr(VI) pollution remediation. In this paper, metabolic mechanism of Cr(VI) reduction in a new highly efficient Cr(VI) reducing bacterium, Alicycliphilus denitrificans Ylb10, was investigated. The results showed that Ylb10 could tolerate and completely reduce 450 mg/L Cr(VI). Cr(VI) can be reduced in the intracellular compartment, membrane and the extracellular compartment, with the plasma membrane being the main active site for Cr(VI) reduction. With the addition of NADH, the reduction efficiency of cell membrane components for Cr(VI) increased 2.3-fold. The omics data analysis showed that sulfite reductase CysJ, thiosulfate dehydrogenase TsdA, nitrite reductase NrfA, nitric oxide reductase NorB, and quinone oxidoreductase ChrR play important roles in the reduction of Cr(VI), in the intracellular, and the extracellular compartment, and the membrane of Ylb10, and therefore Cr(VI) was reduced by the combined action of several reductases at these three locations.
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Affiliation(s)
- Yue Wang
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Zhiyi Zhou
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Wen Zhang
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China; Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang 443002, China; Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang 443002, China
| | - Jinling Guo
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China; Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang 443002, China; Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang 443002, China
| | - Ning Li
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang 443002, China
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, USA
| | - Dachun Gong
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China; Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang 443002, China; Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang 443002, China
| | - Yucai Lyu
- College of Biological & Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China; Hubei Engineering Research Center for Biological Jiaosu, China Three Gorges University, Yichang 443002, China; Key Laboratory of Functional Yeast, China National Light Industry, China Three Gorges University, Yichang 443002, China.
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2
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Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Won M, Heo J, Lee D, Han BH, Hong SB, Kwon SW. Melaminivora suipulveris sp. nov., isolated from pigpen dust. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748604 DOI: 10.1099/ijsem.0.005701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A bacterial strain designated SC2-9T was isolated from the dust collector of a pigpen located in Wanju-gun, Jeollabuk-do, Republic of Korea. Cells were strictly aerobic, Gram-stain-negative, flagellated and rod-shaped. The strain was catalase- and oxidase-positive, and grew optimally 28-30 °C, pH 8.0 and 0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed 99.1 and 98.3 % similarities to Melaminivora jejuensis KBB12T and Melaminivora alkalimesophila CY1T, and revealing less than 97 % similarity to other validly named species. The genomic DNA G+C content of strain SC2-9T was 68.2 %. The orthologous average nucleotide identity and dDDH values of strain SC2-9T with the closest species Melaminivora jejuensis KCTC 32230T were 85.6 and 29.3 %, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids and one unidentified lipid. The major fatty acids (>10 %) were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω6c and/ or C18 : 1 ω7c). The predominant isoprenoid quinone was ubiquinone-8. Based on phenotypic, chemotaxonomic and phylogenetic data, strain SC2-9T should be assigned as a novel species of the genus Melaminivora, for which the name Melaminivora suipulveris sp. nov. is proposed. The type strain is SC2-9T (=KACC 19310T=NBRC 113103T).
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Affiliation(s)
- Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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Korth B, Pous N, Hönig R, Haus P, Corrêa FB, Nunes da Rocha U, Puig S, Harnisch F. Electrochemical and Microbial Dissection of Electrified Biotrickling Filters. Front Microbiol 2022; 13:869474. [PMID: 35711746 PMCID: PMC9197458 DOI: 10.3389/fmicb.2022.869474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Electrified biotrickling filters represent sustainable microbial electrochemical technology for treating organic carbon-deficient ammonium-contaminated waters. However, information on the microbiome of the conductive granule bed cathode remains inexistent. For uncovering this black box and for identifying key process parameters, minimally invasive sampling units were introduced, allowing for the extraction of granules from different reactor layers during reactor operation. Sampled granules were analyzed using cyclic voltammetry and molecular biological tools. Two main redox sites [-288 ± 18 mV and -206 ± 21 mV vs. standard hydrogen electrode (SHE)] related to bioelectrochemical denitrification were identified, exhibiting high activity in a broad pH range (pH 6-10). A genome-centric analysis revealed a complex nitrogen food web and the presence of typical denitrifiers like Pseudomonas nitroreducens and Paracoccus versutus with none of these species being identified as electroactive microorganism so far. These are the first results to provide insights into microbial structure-function relationships within electrified biotrickling filters and underline the robustness and application potential of bioelectrochemical denitrification for environmental remediation.
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Affiliation(s)
- Benjamin Korth
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Narcís Pous
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Girona, Spain
| | - Richard Hönig
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Philip Haus
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Felipe Borim Corrêa
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Sebastià Puig
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Girona, Spain
| | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
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5
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Yu Q, Zhou R, Wang Y, Su W, Yang J, Feng T, Dou Y, Li H. Carcass decay deteriorates water quality and modifies the nirS denitrifying communities in different degradation stages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147185. [PMID: 33933763 DOI: 10.1016/j.scitotenv.2021.147185] [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: 02/09/2021] [Revised: 03/19/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Corpse degradation may release amounts of hazardous materials (e.g., cadaverine, putrescine and ammonia) into surrounding areas, which deteriorate environments and result in nitrogen contamination. Nitrate or nitrite can be reduced to nitrogen gas by denitrifying bacteria, thus alleviating nitrogen contamination and purifying aquatic environments. However, the reaction of nirS-encoding denitrifiers to carcass degradation is less studied. Therefore, water physiochemical analysis and high-throughput sequencing were applied to explore the successional pattern of nirS denitrifying communities in the Yellow River water and tap water during three stages of animal cadaver decay (submerged fresh, advanced floating decay as well as sunken remains) and relevant control group. Nitrate nitrogen (NO3-N) and ammonia nitrogen (NH4+-N) concentration in corpse groups were highly elevated compared with control groups. The dominant phylum for nirS denitrifying communities was Proteobacteria. Abundant denitrifying genera Paracoccus, Alicycliphilus and Diaphorobacter were detected, and these genera have been reported to participate in the degradation of organic pollutants. Particularly, nirS-type community structures were remarkably influenced by corpse decay and became similar with succession. Water total dissolved solids (TDS), salinity, conductivity (CON) and phosphate were primary impacting factors driving the community structures, but the effect of water type was almost negligible. Notably, denitrifying community assembly was dominated by deterministic processes rather than stochastic processes, and the relative importance of deterministic processes among most corpse groups was higher than that in control groups, indicating that environmental filtering regulates the denitrifying communities. Our results provide new insight into environmental purification for hazardous materials produced by corpse degradation, thereby providing valuable advice to environmental administration.
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Affiliation(s)
- Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yaqi Dou
- Hubei Aquaculture Technology Extension Center (Hubei Aquatic Breeds Introduction and Breeding Center), Wuhan 430070, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China..
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6
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Shlimon A, Mansurbeg H, Othman R, Head I, Kjeldsen KU, Finster K. Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI). Biodegradation 2021; 32:251-271. [PMID: 33782778 DOI: 10.1007/s10532-021-09931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8-C17 alkanes and up to 28% degradation of C18-C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.
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Affiliation(s)
- Adris Shlimon
- Department of Biology, Soran University, Soran, Iraq. .,Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark.
| | - Howri Mansurbeg
- Department of Petroleum Geoscience, Soran University, Soran, Iraq.,Department of Earth and Environmental Sciences, University of Windsor, Windsor, ON, Canada
| | - Rushdy Othman
- Department of Petroleum Geoscience, Soran University, Soran, Iraq
| | - Ian Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Kasper U Kjeldsen
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Kai Finster
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
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7
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Development of nitrate stimulated hydrocarbon degrading microbial consortia from refinery sludge as potent bioaugmenting agent for enhanced bioremediation of petroleum contaminated waste. World J Microbiol Biotechnol 2020; 36:156. [DOI: 10.1007/s11274-020-02925-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022]
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Zheng D, Gu W, Zhou Q, Zhang L, Wei C, Yang Q, Li D. Ammonia oxidation and denitrification in a bio-anode single-chambered microbial electrolysis cell. BIORESOURCE TECHNOLOGY 2020; 310:123466. [PMID: 32388207 DOI: 10.1016/j.biortech.2020.123466] [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: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
In this study, anodic ammonia oxidation and denitrification were performed in single-chamber bioelectrochemical systems at a wide range of anodic potentials (-400 to +400 mV) versus Ag/AgCl. The low coulombic efficiencies (~30.84%) in reactors were mainly due to electrons being transferred to atmospheric oxygen through the electrode and reversal of the electrode. The removal efficiencies of acetate, ammonia, and total nitrogen were 100%, 100%, and 40.44% at +200 mV and 100%, 100%, and 50.24% at -200 mV, respectively. The nitrogen-removal mechanisms were nitrogen respiration/nitrate reduction at +200 mV and denitrification at -200 mV, and ammonia oxidation occurred by coupling with sulfate-reducing at -300 and -400 mV. Thauera, Comamonas, Alicycliphilus, Nitrosomonas, Desulforhabdus, Dethiosulfatibacter, and Desulfomicrobium were the dominant genera at the anode which participated in the nitrification/denitrification or sulfate-reducing processes. In summary, ammonia oxidation and denitrification could be coupled with carbon-removal or sulfur-reduction using a bio-anode with a suitable anodic potential.
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Affiliation(s)
- Decong Zheng
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzhi Gu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinmao Zhou
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Zhang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuicui Wei
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingzhuoma Yang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daping Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Boada E, Santos-Clotas E, Bertran S, Cabrera-Codony A, Martín MJ, Bañeras L, Gich F. Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading. CHEMOSPHERE 2020; 240:124908. [PMID: 31726596 DOI: 10.1016/j.chemosphere.2019.124908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.
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Affiliation(s)
- Ellana Boada
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Eric Santos-Clotas
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Salvador Bertran
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Alba Cabrera-Codony
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Maria J Martín
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Lluís Bañeras
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Frederic Gich
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain.
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10
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Xu W, Brand VR, Suresh S, Jensen MA, Davis RW, Criddle CS, St Onge RP, Hyman RW. Community members in activated sludge as determined by molecular probe technology. WATER RESEARCH 2020; 168:115104. [PMID: 31639592 PMCID: PMC6873225 DOI: 10.1016/j.watres.2019.115104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/13/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
The use of molecular probe technology is demonstrated for routine identification and tracking of cultured and uncultured microorganisms in an activated sludge bioreactor treating domestic wastewater. A key advantage of molecular probe technology is that it can interrogate hundreds of microbial species of interest in a single measurement. In environmental niches where a single genus (such as Competibacteraceae) dominates, it can be difficult and expensive to identify microorganisms that are present at low relative abundance. With molecular probe technology, it is straightforward. Members of the Competibacteraceae family, none of which have been grown in pure culture, are abundant in an activated sludge system in the San Francisco Bay Area, California, USA. Molecular probe ensembles with and without Competibacteraceae probes were constructed. Whereas the probe ensemble with Competibacteraceae probes identified a total of ten bacteria, the molecular probe ensemble without Competibacteraceae probes identified 29 bacteria, including many at low relative abundance and including some species of public health significance.
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Affiliation(s)
- Weihong Xu
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Veronica R Brand
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA
| | | | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA; Department of Genetics, Stanford University Medical College, Stanford, CA, 94305, USA
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA
| | - Richard W Hyman
- Stanford Genome Technology Center, Palo Alto, CA, 94304, USA; Department of Biochemistry, Stanford University Medical College, Stanford, CA, 94305, USA.
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Li K, Wu H, Wei J, Qiu G, Wei C, Cheng D, Zhong L. Simultaneous decarburization, nitrification and denitrification (SDCND) in coking wastewater treatment using an integrated fluidized-bed reactor. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 252:109661. [PMID: 31634728 DOI: 10.1016/j.jenvman.2019.109661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/14/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
There are two problems in biological treatment of coking wastewater (CWW): incapability of pre-anaerobic treatment to eliminate the toxicity in wastewater, and the lack of carbon source for subsequent denitrification in pre-aerobic treatment. To achieve simultaneous decarburization, nitrification and denitrification (SDCND) in CWW treatment, biological carrier materials was used to build an integrated fluidized-bed reactor (Reactor B, RB). A conventional fluidized-bed reactor (Reactor A, RA) was used as a control reactor under the same condition. The results showed that RB was more advantageous since its removal efficiencies of COD and TN were 90% and 87%, respectively, which were significantly higher than these in RA (82% and 45%), at a hydraulic retention time (HRT) of 60 h. Microelectrode measurement indicated that oxygen transfer was limited inside the carrier where the formation of a dissolved oxygen (DO) concentration gradient was observed. Microbial community analysis showed that the aerobic and anoxic microenvironments in RB promoted the co-existence of a wider variety of bacteria, thus achieving SDCND. These results indicated the integrated fluidized-bed reactor exhibited promising feasibility for simultaneous carbon and nitrogen removal in CWW treatment under the same aeration driven conditions. The SDCND process realized by fluidized-bed reactor provided a reference for the treatment of toxic industrial wastewater with high carbon to nitrogen ratio.
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Affiliation(s)
- Kui Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China.
| | - Jingyue Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Dangyu Cheng
- Huaxin Environmental Technology Company, Shaoguan, 512122, PR China
| | - Lianwen Zhong
- Huaxin Environmental Technology Company, Shaoguan, 512122, PR China
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Draft Genome Sequence of Acidovorax sp. Strain NB1, Isolated from a Nitrite-Oxidizing Enrichment Culture. Microbiol Resour Announc 2019; 8:8/33/e00547-19. [PMID: 31416864 PMCID: PMC6696639 DOI: 10.1128/mra.00547-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Acidovorax sp. strain NB1, isolated from an enrichment culture of nitrite-oxidizing bacteria (NOB). Genes involved in denitrification were found in the draft genome of NB1. The closest strain to NB1 based on genomic relatedness is Acidovorax sp. strain GW101-3H11, with 91.5% average nucleotide identity. Here, we report the draft genome sequence of Acidovorax sp. strain NB1, isolated from an enrichment culture of nitrite-oxidizing bacteria (NOB). Genes involved in denitrification were found in the draft genome of NB1. The closest strain to NB1 based on genomic relatedness is Acidovorax sp. strain GW101-3H11, with 91.5% average nucleotide identity.
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Heo J, Cho HY, Heo I, Hong SB, Kim JS, Kwon SW, Kim SJ. Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector. Int J Syst Evol Microbiol 2019; 69:1864-1869. [DOI: 10.1099/ijsem.0.003082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Ha-Young Cho
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Inbeom Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Seung-Bum Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
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14
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Solís-González CJ, Loza-Tavera H. Alicycliphilus: current knowledge and potential for bioremediation of xenobiotics. J Appl Microbiol 2019; 126:1643-1656. [PMID: 30661281 DOI: 10.1111/jam.14207] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/28/2018] [Accepted: 01/15/2019] [Indexed: 01/31/2023]
Abstract
Alicycliphilus is a promising candidate for participating in the development of novel xenobiotics bioremediation processes. Members of the Alicycliphilus genus are environmental bacteria mostly found in polluted sites such as landfills and contaminated watercourses, and in sewage sludges from wastewater treatment plants. They exhibit a versatile metabolism and the ability to use oxygen, nitrate and chlorate as terminal electron acceptors, which allow them to biodegrade xenobiotics under oxic or anoxic conditions. Pure cultures of Alicycliphilus strains are able to biodegrade some pollutants such as industrial solvents (acetone, cyclohexanol and N-methylpyrrolidone), aromatic hydrocarbons (benzene, toluene and anthracene), as well as polyurethane varnishes and foams, and they can even transform Cr(VI) to Cr(III). In addition, Alicycliphilus has also been identified in bacterial communities involved in wastewater treatment plants for denitrification, and the degradation of emerging pollutants such as triclosan, nonylphenol, N-heterocyclic aromatic compounds (indole and quinoline), and antibiotics (tetracycline and oxytetracycline). This work summarizes the current knowledge on the Alicycliphilus genus, describing its different metabolic characteristics, focusing on its xenobiotic biodegradation abilities and examining the distinct pathways and molecular bases that sustain them. We also discuss the progress made in genetic manipulation and 'omics' analyses, as well as Alicycliphilus participation in novel bioremediation strategies.
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Affiliation(s)
- C J Solís-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - H Loza-Tavera
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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15
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Shi X, Ngo HH, Sang L, Jin P, Wang XC, Wang G. Functional evaluation of pollutant transformation in sediment from combined sewer system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:85-93. [PMID: 29547865 DOI: 10.1016/j.envpol.2018.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/04/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
In this study, a pilot combined sewer system was constructed to characterize the pollutant transformation in sewer sediment. The results showed that particulate contaminants deposited from sewage could be transformed into dissolved matter by distinct pollutant transformation pathways. Although the oxidation-reduction potential (ORP) was varied from -80 mV to -340 mV in different region of the sediment, the fermentation was the dominant process in all regions of the sediment, which induced hydrolysis and decomposition of particulate contaminants. As a result, the accumulation of dissolved organic matter and the variation of ORP values along the sediment depth led to the depth-dependent reproduction characteristics of methanogens and sulfate-reducing bacteria, which were existed in the middle and deep layer of the sediment respectively. However, the diversity of nitrifying and polyphosphate-accumulating bacteria was low in sewer sediment and those microbial communities showed a non-significant correlation with nitrogen and phosphorus contaminants, which indicated that the enrichment of nitrogen and phosphorus contaminants was mainly caused by physical deposition process. Thus, this study proposed a promising pathway to evaluate pollutant transformation and can help provide theoretical foundation for urban sewer improvement.
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Affiliation(s)
- Xuan Shi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW, 2007, Australia
| | - Langtao Sang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Pengkang Jin
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China.
| | - Xiaochang C Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, Shaanxi Province, 710055, China
| | - Guanghua Wang
- Guangzhou Municipal Engineering Design & Research Institute, Guangzhou, Guangdong Province, 510060, China
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16
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Spatial Pattern of Bacterial Community Diversity Formed in Different Groundwater Field Corresponding to Electron Donors and Acceptors Distributions at a Petroleum-Contaminated Site. WATER 2018. [DOI: 10.3390/w10070842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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17
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Sposob M, Cydzik-Kwiatkowska A, Bakke R, Dinamarca C. Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Comprehensive evaluation of autohydrogenotrophic membrane biofilm reactor treating OTC-enriched water medium. Bioprocess Biosyst Eng 2018; 41:1261-1269. [DOI: 10.1007/s00449-018-1954-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
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19
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Xu Z, Song L, Dai X, Chai X. PHBV polymer supported denitrification system efficiently treated high nitrate concentration wastewater: Denitrification performance, microbial community structure evolution and key denitrifying bacteria. CHEMOSPHERE 2018; 197:96-104. [PMID: 29334654 DOI: 10.1016/j.chemosphere.2018.01.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/21/2017] [Accepted: 01/06/2018] [Indexed: 06/07/2023]
Abstract
Biodegradable polymer supported denitrification (BPD) system shows good denitrification performance for the wastewater with low nitrate concentrations. In this study, a BPD system using Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) polymer as carbon source was developed to treat the wastewater with high nitrate concentrations. The denitrification performance, utilization ratio of PHBV polymers, and microbial community structure evolution and key denitrifying bacteria were comprehensively studied. Results indicated that an average nitrate removal efficiency of 99% could be achieved with an influent NO3--N concentration of 100 mg L-1 and a hydraulic retention time (HRT) of 7.25 h. Mass balance model predicted that 80% of the PHBV polymers were consumed by denitrifying bacteria, close to 72% consumption in real condition, suggesting the model might be useful for PHBV polymers management in BPD system. Further, the bacterial community structures varied along the bioreactor profile, which closely linked to the concentration profiles of nitrate and ammonia. Metatranscriptomic analysis identified the key denitrifying bacteria as Comamonas, Acidovorax and Dechloromonas. The PHBV supported denitrification system developed in this study shows potential for removal of high concentration of nitrate from wastewater.
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Affiliation(s)
- Zhongshuo Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Liyan Song
- Environmental Microbiology and Ecology Research Center, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science (CAS), Chongqing, 400714, China
| | - Xiaohu Dai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaoli Chai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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20
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Influence of Carbon Source on the Efficiency of Nitrogen Removal and Denitrifying Bacteria in Biofilm from Bioelectrochemical SBBRs. WATER 2018. [DOI: 10.3390/w10040393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Mekuto L, Ntwampe SKO, Mudumbi JBN. Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions. 3 Biotech 2018; 8:93. [PMID: 29430355 PMCID: PMC5796949 DOI: 10.1007/s13205-018-1124-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/16/2018] [Indexed: 11/26/2022] Open
Abstract
This study focused on the identification of free cyanide (CDO) and thiocyanate (TDO) degrading microbial communities using a culture-dependent and independent approach. Culturable microbial species were isolated from the CDOs (n = 13) and TDOs (n = 18). The CDOs were largely dominated by Bacillus sp. while the TDOs were dominated by Bacillus sp., Klebsiella oxytoca, Providencia sp. and Pseudomonas sp. However, 16S rRNA amplicon gene-sequencing revealed the complexity and diversity of the microbial communities in contrast to the organisms that were detected using culture-dependent technique. Overall, the organisms were mainly dominated by Myroides odoratimimus and Proteus sp. at 37.82 and 30.5% for CDOs, and 35.26 and 17.58% for TDOs, respectively. The co-culturing of the CDOs and TDOs resulted in biochemical changes of key metabolic enzymes, and this resulted in the complete degradation of CN- and SCN- simultaneously; a phenomenon which has not been witnessed, especially under alkaline conditions. Current ongoing studies are focused on the application of these organisms for the biodegradation of CN- and SCN- in a continuous system, under changing operational parameters, to assess their effectiveness in the biodegradation of CN- and SCN-.
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Affiliation(s)
- Lukhanyo Mekuto
- Department of Biotechnology, Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, PO Box 652, Cape Town, 8000 South Africa
| | - Seteno Karabo Obed Ntwampe
- Department of Biotechnology, Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, PO Box 652, Cape Town, 8000 South Africa
| | - John Baptist N. Mudumbi
- Department of Biotechnology, Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, PO Box 652, Cape Town, 8000 South Africa
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22
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Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1. Appl Environ Microbiol 2017; 84:AEM.02136-17. [PMID: 29030443 DOI: 10.1128/aem.02136-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
The molecular mechanisms underlying the biodegradation of N-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown. Alicycliphilus sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode an N-methylhydantoin amidohydrolase that transforms NMP to γ-N-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the nmp gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the nmpABCD genes. Similarly, Escherichia coli MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover, E. coli GABA-AT deletion mutants complemented with nmpABCD genes retained the ability to grow in NMP, supporting the possibility that γ-N-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.IMPORTANCEN-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for Alicycliphilus sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.
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23
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Vaz-Moreira I, Narciso-da-Rocha C, Lopes AR, Carvalho G, Lobo-da-Cunha A, Whitman WB, Snauwaert C, Vandamme P, Manaia CM, Nunes OC. Oryzisolibacter propanilivorax gen. nov., sp. nov., a propanil-degrading bacterium. Int J Syst Evol Microbiol 2017; 67:3752-3758. [PMID: 28895512 DOI: 10.1099/ijsem.0.002184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain EPL6T, a Gram-negative, motile, short rod was isolated from a propanil and 3,4-dichloroaniline enrichment culture produced from rice paddy soil. Based on the analyses of the 16S rRNA gene sequence, strain EPL6T was observed to be a member of the family Comamonadaceae, sharing the highest pairwise identity with type strains of the species Alicycliphilus denitrificans K601T (96.8 %) and Melaminivora alkalimesophila CY1T (96.8 %). Strain EPL6T was able to grow in a temperature range of 15-37 °C, pH 6-9 and in the presence of up to 4 % (w/v) NaCl and tested positive for catalase and oxidase reactions. The major respiratory quinone was Q8. The genomic DNA had a G+C content of 69.4±0.9 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, and the major fatty acid methyl esters comprised C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). Comparison of the genome sequence of strain EPL6T and of its closest neighbours, Melaminivora alkalimesophila CY1T and Alicycliphilus denitrificans K601T, yielded values of ANI ≤84.1 % and of AAI ≤80.3 %. Therefore, the genetic, phylogenetic, phenotypic and chemotaxonomic characteristics support the classification of this organism into a new taxon. Considering the genetic divergence of strain EPL6T from the type strains of the closest species, which belong to distinct genera, we propose a new genus within the family Comamonadaceae, named Oryzisolibacter propanilivorax gen. nov., sp. nov., represented by the isolate EPL6T as the type strain of the species (=LMG 28427T=CECT 8927T).
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Affiliation(s)
- Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.,LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carlos Narciso-da-Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Ana Rita Lopes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Gilda Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Alexandre Lobo-da-Cunha
- Laboratory of Cell Biology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-003 Porto, Portugal
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, USA
| | - Cindy Snauwaert
- Laboratorium voor Microbiologie and BCCM/LMG Bacteria Collection, Vakgroep Biochemie en Microbiologie, Universiteit Gent, Gent, Belgium
| | - Peter Vandamme
- Laboratorium voor Microbiologie and BCCM/LMG Bacteria Collection, Vakgroep Biochemie en Microbiologie, Universiteit Gent, Gent, Belgium
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Lin W, Sun S, Wu C, Xu P, Ye Z, Zhuang S. Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:14-21. [PMID: 28384499 DOI: 10.1016/j.ecoenv.2017.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/18/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Bio-treatment of flotation wastewater has been proven to be both effective and economical, as a treatment method. Despite this, little is known regarding the effects of toxic organic floatation reagents such as Dianilinodithiophosphoric acid (DDA), on the microbial community performance or dynamics, which are critical to the effective performance of the bio-treatment reactor. A submerged membrane bioreactor (sMBR) was constructed to continuously treat simulated wastewater contaminated with DDA, an organic flotation reagent that is now considered a significant pollutant. The performance of the sMBR system was investigated at different DDA loading concentrations, with assessment of the effects of DDA on the microbial communities within the sMBR, in particular the biodiversity and succession within the microbial community. Results showed that, with increased DDA loadings, the performance of the sMBR was initially negatively affected, but the system adapted efficiently and consistently reached a COD removal rate of up to 80%. Increased DDA loading concentrations had an adverse effect on the activity of both the activated sludge and microbial communities, resulting in a large alteration in microbial dynamics, especially during the start-up stage and the high DDA loading stage. Strains capable of adapting to the presence of DDA, capable of degrading DDA or utilizing its byproducts, were enriched within the sMBR community, such as Zoogloea, Clostridium, Sideroxydans lithotrophicus, Thiobacillus, Thauera amino aromatica and Alicycliphilus denitrificans.
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Affiliation(s)
- Weixiong Lin
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China; School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Shuiyu Sun
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China.
| | - Chun Wu
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China
| | - Pingting Xu
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China
| | - Ziwei Ye
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Shengwei Zhuang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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25
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Khan IU, Hussain F, Tian Y, Habib N, Xian WD, Jiang Z, Amin A, Yuan CG, Zhou EM, Zhi XY, Li WJ. Tibeticola sediminis gen. nov., sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:1133-1139. [PMID: 28068215 DOI: 10.1099/ijsem.0.001777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two closely related thermophilic bacterial strains, designated YIM 73013T and YIM 73008, were isolated from a sediment sample collected from a hot spring in Tibet, western Tibet province, China. The taxonomic positions of the two isolates were investigated using a polyphasic approach. The novel isolates were Gram-stain-negative, aerobic, short-rod-shaped and motile by means of a polar flagellum. They were oxidase- and catalase-positive and were able to grow at 30-55 °C (optimum, 37-45 °C), at pH 6.0-8.0 (optimum, pH 7.0) and with NaCl tolerance up to 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 73013T and YIM 73008 formed a distinct lineage with respect to closely related genera in the family Comamonadaceae and shared highest 16S rRNA gene sequences similarities with Acidovorax caeni R-24608T (96.3 and 96.4 %, respectively). The respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids observed were C17 : 1ω6c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C contents of strains YIM 73013T and YIM 73008 were 68.7 and 68.3 mol%, respectively. Based on the morphological, phylogenetic and chemotaxonomic results, the two isolates represent a novel species in a new genus, for which the name Tibeticola sediminis gen. nov., sp. nov. is proposed. The type strain of Tibeticola sediminis is YIM 73013T (=DSM 101684T=KCTC 42873T).
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Affiliation(s)
- Inam Ullah Khan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Firasat Hussain
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Ye Tian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Neeli Habib
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Arshia Amin
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan.,Department of Microbiology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Chang-Guo Yuan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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26
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Arnaud-Haond S, Aires T, Candeias R, Teixeira SJL, Duarte CM, Valero M, Serrão EA. Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia. Mol Ecol 2017; 26:2379-2391. [PMID: 28133884 DOI: 10.1111/mec.14030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and β diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.
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Affiliation(s)
- S Arnaud-Haond
- IFREMER, Station de Sète, UMR MARBEC, Avenue Jean Monnet, CS 30171, 34203, Sète Cedex, France.,OREME - Station Marine, Université Montpellier, 2 rue des Chantiers - CC 99009, 34200, Sète, France.,CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - T Aires
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - R Candeias
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - S J L Teixeira
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - C M Duarte
- RSRC (Red Sea Research Center), King Abdullah University of Science and Technology (KAUST), Building 2, Level 3, Room 3219, Thuwal, 23955-6900, Saudi Arabia
| | - M Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, UPMC, PUCCh, UACH, Station Biologique de Roscoff, Sorbonne Universités, CS 90074, Place Georges Teissier, 29688, Roscoff Cedex, France
| | - E A Serrão
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
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27
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Twing KI, Brazelton WJ, Kubo MDY, Hyer AJ, Cardace D, Hoehler TM, McCollom TM, Schrenk MO. Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH. Front Microbiol 2017; 8:308. [PMID: 28298908 PMCID: PMC5331062 DOI: 10.3389/fmicb.2017.00308] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022] Open
Abstract
Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.
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Affiliation(s)
- Katrina I Twing
- Department of Microbiology and Molecular Genetics, Michigan State University, East LansingMI, USA; Department of Biology, University of Utah, Salt Lake CityUT, USA
| | | | | | - Alex J Hyer
- Department of Biology, University of Utah, Salt Lake City UT, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston RI, USA
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field CA, USA
| | - Tom M McCollom
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder CO, USA
| | - Matthew O Schrenk
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI, USA
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28
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Bai N, Abuduaini R, Wang S, Zhang M, Zhu X, Zhao Y. Nonylphenol biodegradation characterizations and bacterial composition analysis of an effective consortium NP-M2. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:95-104. [PMID: 27638455 DOI: 10.1016/j.envpol.2016.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/08/2016] [Accepted: 09/11/2016] [Indexed: 06/06/2023]
Abstract
Nonylphenol (NP), ubiquitously detected as the degradation product of nonionic surfactants nonylphenol polyethoxylates, has been reported as an endocrine disrupter. However, most pure microorganisms can degrade only limited species of NP with low degradation efficiencies. To establish a microbial consortium that can effectively degrade different forms of NP, in this study, we isolated a facultative microbial consortium NP-M2 and characterized the biodegradation of NP by it. NP-M2 could degrade 75.61% and 89.75% of 1000 mg/L NP within 48 h and 8 days, respectively; an efficiency higher than that of any other consortium or pure microorganism reported so far. The addition of yeast extract promoted the biodegradation more significantly than that of glucose. Moreover, surface-active compounds secreted into the extracellular environment were hypothesized to promote high-efficiency metabolism of NP. The detoxification of NP by this consortium was determined. The degradation pathway was hypothesized to be initiated by oxidization of the benzene ring, followed by step-wise side-chain biodegradation. The bacterial composition of NP-M2 was determined using 16S rDNA library, and the consortium was found to mainly comprise members of the Sphingomonas, Pseudomonas, Alicycliphilus, and Acidovorax genera, with the former two accounting for 86.86% of the consortium. The high degradation efficiency of NP-M2 indicated that it could be a promising candidate for NP bioremediation in situ.
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Affiliation(s)
- Naling Bai
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Rexiding Abuduaini
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Sheng Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Meinan Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xufen Zhu
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuhua Zhao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China.
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29
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An X, Baker P, Li H, Su J, Yu C, Cai C. The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:21766-21779. [PMID: 27522211 DOI: 10.1007/s11356-016-7381-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO42- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe-environment interactions and provide a strong foundation for qualitative exploration of the bacterial diversity in rare earth tailings groundwater that might ultimately be incorporated into the remediation of environmental contamination.
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Affiliation(s)
- Xinli An
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Paul Baker
- Bangor University, Bangor, Gwynedd, LL572DG, UK
| | - Hu Li
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqiang Su
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Changping Yu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chao Cai
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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30
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Rodriguez-Sanchez A, Munoz-Palazon B, Maza-Marquez P, Gonzalez-Lopez J, Vahala R, Gonzalez-Martinez A. Process performance and bacterial community dynamics of partial-nitritation biofilters subjected to different concentrations of cysteine amino acid. Biotechnol Prog 2016; 32:1254-1263. [PMID: 27453498 DOI: 10.1002/btpr.2331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/07/2016] [Indexed: 11/06/2022]
Abstract
Partial-nitritation processes are used for the biological treatment of high nitrogen-low organic carbon effluents, such as anaerobic digestion reject water. The release of certain products generated during the anaerobic digestion process, such as amino acids, could potentially reduce the performance of these partial-nitritation bioprocesses. To investigate this, four partial-nitritation biofilters were subjected to continuous addition of 0, 150, 300, and 500 mg L-1 cysteine amino acid in their influents. The addition of the amino acid had an impact over the performance of the partial-nitritation process and the bacterial community dynamics of the systems analyzed. Ammonium oxidation efficiency decreased with the addition of the amino acid, and a net nitrogen elimination occurred in presence of cysteine through the operation period. Bacterial community dynamics showed a decrease of Nitrosomonas species and a proliferation of putative heterotrophs with nitrification capacity, such as Pseudomonas, or denitrification capacity, such as Denitrobacter or Alicycliphilus. The addition of cysteine irreversible affected the bioreactors, which could not achieve the performance obtained before the addition of the amino acid. A mathematical predictive equation of the process performance depending on cysteine concentration added and operational time under such concentration was developed. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1254-1263, 2016.
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Affiliation(s)
| | - Barbara Munoz-Palazon
- Inst. of Water Research, University of Granada C/Ramon Y Cajal 4, Granada, 18071, Spain
| | - Paula Maza-Marquez
- Inst. of Water Research, University of Granada C/Ramon Y Cajal 4, Granada, 18071, Spain
| | - Jesus Gonzalez-Lopez
- Inst. of Water Research, University of Granada C/Ramon Y Cajal 4, Granada, 18071, Spain
| | - Riku Vahala
- Dept. of Built Environment, School of Engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland
| | - Alejandro Gonzalez-Martinez
- Dept. of Built Environment, School of Engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076, Espoo, Finland. alejandro.gonzalezmartinez@aalto
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31
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Identification of Quorum-Sensing Signal Molecules and a Biosynthetic Gene in Alicycliphilus sp. Isolated from Activated Sludge. SENSORS 2016; 16:s16081218. [PMID: 27490553 PMCID: PMC5017383 DOI: 10.3390/s16081218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/19/2016] [Accepted: 07/29/2016] [Indexed: 01/09/2023]
Abstract
Activated sludge is a complicated mixture of various microorganisms that is used to treat sewage and industrial wastewater. Many bacteria produce N-acylhomoserine lactone (AHL) as a quorum-sensing signal molecule to regulate the expression of the exoenzymes used for wastewater treatment. Here, we isolated an AHL-producing bacteria from an activated sludge sample collected from an electronic component factory, which we named Alicycliphilus sp. B1. Clone library analysis revealed that Alicycliphilus was a subdominant genus in this sample. When we screened the activated sludge sample for AHL-producing strains, 12 of 14 the AHL-producing isolates were assigned to the genus Alicycliphilus. A putative AHL-synthase gene, ALISP_0667, was cloned from the genome of B1 and transformed into Escherichia coli DH5α. The AHLs were extracted from the culture supernatants of the B1 strain and E. coli DH5α cells harboring the ALISP_0667 gene and were identified by liquid chromatography-mass spectrometry as N-(3-hydroxydecanoyl)-l-homoserine lactone and N-(3-hydroxydodecanoyl)-l-homoserine lactone. The results of comparative genomic analysis suggested that the quorum-sensing genes in the B1 strain might have been acquired by horizontal gene transfer within activated sludge.
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32
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Grijalbo L, Garbisu C, Martín I, Etxebarria J, Gutierrez-Mañero FJ, Lucas Garcia JA. Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater. JOURNAL OF WATER AND HEALTH 2015; 13:1006-1019. [PMID: 26608762 DOI: 10.2166/wh.2015.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate.
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Affiliation(s)
- Lucía Grijalbo
- Department of Pharmaceutical and Health Sciences, Facultad Farmacia, Universidad San Pablo CEU., Urb. Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain E-mail:
| | - Carlos Garbisu
- Department of Ecology and Natural Resources, Soil Microbial Ecology Group, NEIKER-Tecnalia, c/Berreaga 1, E-48160 Derio, Spain
| | - Iker Martín
- Department of Ecology and Natural Resources, Soil Microbial Ecology Group, NEIKER-Tecnalia, c/Berreaga 1, E-48160 Derio, Spain
| | - Javier Etxebarria
- GAIKER Tecnological Centre, IK4 Research Alliance, E-48170 Zamudio, Spain
| | - F Javier Gutierrez-Mañero
- Department of Pharmaceutical and Health Sciences, Facultad Farmacia, Universidad San Pablo CEU., Urb. Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain E-mail:
| | - Jose Antonio Lucas Garcia
- Department of Pharmaceutical and Health Sciences, Facultad Farmacia, Universidad San Pablo CEU., Urb. Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain
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33
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Hyun DW, Oh SJ, Kim MS, Whon TW, Jung MJ, Shin NR, Kim PS, Kim HS, Lee JY, Kang W, Bae JW. Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 2015; 65:4689-4694. [DOI: 10.1099/ijsem.0.000635] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).
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Affiliation(s)
- Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Sei Joon Oh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327). GENOME ANNOUNCEMENTS 2015; 3:3/6/e01378-15. [PMID: 26586902 PMCID: PMC4653804 DOI: 10.1128/genomea.01378-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to Acidovorax caeni strain R-24608 is Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.
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35
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Aires T, Moalic Y, Serrao EA, Arnaud-Haond S. Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa). FEMS Microbiol Ecol 2015; 91:fiv067. [PMID: 26099965 DOI: 10.1093/femsec/fiv067] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/14/2022] Open
Abstract
The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts (< 1% of the total community), (2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, which might represent environmentally acquired bacteria and (3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.
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Affiliation(s)
- Tania Aires
- CCMAR, Centre of Marine Sciences, University of Algarve, Gambelas, 8005-139 Faro, Portugal
| | - Yann Moalic
- IFREMER- Technopole de Brest-Iroise, BP 70, 29280 Plouzané, France UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale (UBO) Institut Universitaire Européen de la Mer (IUEM), CNRS, Plouzané, France
| | - Ester A Serrao
- CCMAR, Centre of Marine Sciences, University of Algarve, Gambelas, 8005-139 Faro, Portugal
| | - Sophie Arnaud-Haond
- CCMAR, Centre of Marine Sciences, University of Algarve, Gambelas, 8005-139 Faro, Portugal UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) Bd Jean Monnet, BP 171, 34203 Sète Cedex - France
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36
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Wei XL, Han MS, Xia CC, Ding SL, Xu L, Lin YB, Wang L, Wei GH. Diaphorobacter ruginosibacter sp. nov., isolated from soybean root nodule, and emended description of the genus Diaphorobacter. Arch Microbiol 2015; 197:683-92. [PMID: 25763990 DOI: 10.1007/s00203-015-1102-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/01/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
Abstract
A gram-negative bacterium designated BN30(T), which is motile with a polar flagellum, non-endospores forming, oxidase- and catalase-positive, was isolated from soybean root nodule. The organism is facultative anaerobic and surface-wrinkled rod. It can grow at 10-40 °C, pH 6-8 and 6 % (w/v) NaCl. BLASTn search based on 16S rRNA gene sequence revealed that the strain is closely related to Diaphorobacter aerolatus 8604S-37(T), Alicycliphilus denitrificans K601(T), Simplicispira limi EMB325(T), Diaphorobacter nitroreducens NA10B(T) and Diaphorobacter oryzae RF3(T), which all belonged to the family Comamonadaceae in class Betaproteobacteria. Phylogenetic analysis showed that the strain formed a firm clade with three Diaphorobacter species, being closest to Diaphorobacter aerolatus 8604S-37(T) with similarity of 98.64 %. DNA-DNA relatedness values between strain BN30(T) and five reference strains ranged from 11.5 to 35.9 %. All the results of phylogenetic analysis, chemotaxonomical data (predominant fatty acids are C16:0, sum feature 3, sum feature 8 and C17:0 cyclo; major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol; major quinone is Q-8; G+C of total DNA is 65.2 %), physiological and phenotypic results supported that BN30(T) represented a novel species within the genus Diaphorobacter. The name Diaphorobacter ruginosibacter was proposed, and the type strain is BN30(T) (=ACCC06116(T) = DSM 27467(T)).
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Affiliation(s)
- Xiu Li Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
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Draft Genome Sequence of Alicycliphilus sp. B1, an N-Acylhomoserine Lactone-Producing Bacterium, Isolated from Activated Sludge. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00424-15. [PMID: 25977425 PMCID: PMC4432331 DOI: 10.1128/genomea.00424-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the draft genome sequence of Alicycliphilus sp. B1, isolated from activated sludge in a wastewater treatment plant of an electronic component factory as an N-acylhomoserine lactone-producing strain. The draft genome is 7,465,959 bp in length, with 59 large contigs. About 7,391 protein-coding genes, 82 tRNAs, and 13 rRNAs are predicted from this assembly.
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Li C, Cao J, Ren H, Li Y, Tang S. Comparison on kinetics and microbial community among denitrification process fed by different kinds of volatile fatty acids. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Al Ashhab A, Gillor O, Herzberg M. Biofouling of reverse-osmosis membranes under different shear rates during tertiary wastewater desalination: microbial community composition. WATER RESEARCH 2014; 67:86-95. [PMID: 25262553 DOI: 10.1016/j.watres.2014.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 06/03/2023]
Abstract
We investigated the influence of feed-water shear rate during reverse-osmosis (RO) desalination on biofouling with respect to microbial community composition developed on the membrane surface. The RO membrane biofilm's microbial community profile was elucidated during desalination of tertiary wastewater effluent in a flat-sheet lab-scale system operated under high (555.6 s(-1)), medium (370.4 s(-1)), or low (185.2 s(-1)) shear rates, corresponding to average velocities of 27.8, 18.5, and 9.3 cm s(-1), respectively. Bacterial diversity was highest when medium shear was applied (Shannon-Weaver diversity index H' = 4.30 ± 0.04) compared to RO-membrane biofilm developed under lower and higher shear rates (H' = 3.80 ± 0.26 and H' = 3.42 ± 0.38, respectively). At the medium shear rate, RO-membrane biofilms were dominated by Betaproteobacteria, whereas under lower and higher shear rates, the biofilms were dominated by Alpha- and Gamma- Proteobacteria, and the latter biofilms also contained Deltaproteobacteria. Bacterial abundance on the RO membrane was higher at low and medium shear rates compared to the high shear rate: 8.97 × 10(8) ± 1.03 × 10(3), 4.70 × 10(8) ± 1.70 × 10(3) and 5.72 × 10(6) ± 2.09 × 10(3) copy number per cm(2), respectively. Interestingly, at the high shear rate, the RO-membrane biofilm's bacterial community consisted mainly of populations known to excrete high amounts of extracellular polymeric substances. Our results suggest that the RO-membrane biofilm's community composition, structure and abundance differ in accordance with applied shear rate. These results shed new light on the biofouling phenomenon and are important for further development of antibiofouling strategies for RO membranes.
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Affiliation(s)
- Ashraf Al Ashhab
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel.
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel.
| | - Moshe Herzberg
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel.
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Abstract
A bacterial strain, designated GAU11T, was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11T showed high similarity to those of
Comamonas zonglianii
BF-3T (98.8 %),
Pseudacidovorax intermedius
CC21T (96.4 %),
Acidovorax caeni
R-24608T (96.2 %),
Alicycliphilus denitrificans
K601T (96.2 %),
Pseudorhodoferax soli
TBEA3T (95.9 %) and
Comamonas terrigena
LMG 1253T (95.9 %). Strain GAU11T contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11T was 68.2 mol%. The DNA–DNA relatedness between strain GAU11T and
C. zonglianii
DSM 22523T was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11T represents a member of the genus
Comamonas
, but at the same time distinguished it from
C. zonglianii
DSM 22523T. From polyphasic characterization, this strain should be classified as representing a novel species of the genus
Comamonas
, for which the name Comamonas humi sp. nov. (type strain GAU11T = JCM 19903T = DSM 28451T) is proposed.
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Affiliation(s)
- Kouta Hatayama
- Sagami Chemical Research Institute, Ayase, Kanagawa 252-1193, Japan
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41
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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Wang H, Li J, Hu A, Qin D, Xu H, Yu CP. Melaminivora alkalimesophila gen. nov., sp. nov., a melamine-degrading betaproteobacterium isolated from a melamine-producing factory. Int J Syst Evol Microbiol 2014; 64:1938-1944. [DOI: 10.1099/ijs.0.055103-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain CY1T, which is a novel bacterium isolated from wastewater sludge of a melamine-producing factory in Sanming city, Fujian, China. Strain CY1T was shown to rapidly and completely degrade melamine to NH3 and CO2 under aerobic conditions. The isolate was Gram-stain-negative, short-rod-shaped and motile by one unipolar flagellum. Growth was observed at salinities from 0 to 7 % NaCl (optimum, 0.1 %), at temperatures from 15 to 50 °C (optimum, 40–45 °C) and at pH 7–9.5 (optimum pH 9.5). Quinone-8 was detected as the major respiratory quinone. 16S rRNA gene sequence comparisons showed that strain CY1T was affiliated to the family
Comamonadaceae
in the class
Betaproteobacteria
. It was most closely related to members of the genera
Alicycliphilus
(95.5 %),
Diaphorobacter
(94.6–95.1 %),
Acidovorax
(92.9–95.4 %),
Delftia
(93.0–93.6 %) and
Comamonas
(92.6–93.9 %). The average nucleotide identity (ANI) values between strain CY1T and those representing related genera ranged from 84.0 to 86.1 % using Mummer, and from 74.9 to 81.1 % using blast. The dominant fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0, C10 : 0 3-OH and C18 : 1ω7c and/or C18 : 1ω6c, and the major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and one unidentified aminophospholipid. The G+C content of the chromosomal DNA was 69.5 mol%. On the basis of the phenotypic and phylogenetic data, strain CY1T represents a novel species of a new genus, for which the name Melaminivora alkalimesophila gen. nov., sp. nov. is proposed. The type strain of Melaminivora alkalimesophila is CY1T ( = CCTCC AB 2012024T = DSM 26006T).
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Affiliation(s)
- Han Wang
- College of Ecology and Resources Engineering, Wuyi University, Wuyishan City 354300, PR China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Jiangwei Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Anyi Hu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Dan Qin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Heli Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Chang-Ping Yu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
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Resch V, Jin J, Chen BS, Hanefeld U. Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase? AMB Express 2014; 4:30. [PMID: 24949265 PMCID: PMC4052635 DOI: 10.1186/s13568-014-0030-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
The Michael hydratase – alcohol dehydrogenase (MhyADH) from Alicycliphilus denitrificans was previously identified as a bi-functional enzyme performing a hydration of α,β-unsaturated ketones and subsequent oxidation of the formed alcohols. The investigations of the bi-functionality were based on a spectrophotometric assay and an activity staining in a native gel of the dehydrogenase. New insights in the recently discovered organocatalytic Michael addition of water led to the conclusion that the previously performed experiments to identify MhyADH as a bi-functional enzyme and their results need to be reconsidered and the reliability of the methodology used needs to be critically evaluated.
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Al Ashhab A, Herzberg M, Gillor O. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition. WATER RESEARCH 2014; 50:341-349. [PMID: 24231030 DOI: 10.1016/j.watres.2013.10.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 06/02/2023]
Abstract
Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community.
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Affiliation(s)
- Ashraf Al Ashhab
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
| | - Moshe Herzberg
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede-Boqer Campus, 84990, Israel.
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45
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Azo dye remediation in periodic discontinuous batch mode operation: Evaluation of metabolic shifts of the biocatalyst under aerobic, anaerobic and anoxic conditions. Sep Purif Technol 2013. [DOI: 10.1016/j.seppur.2013.06.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Flowers JJ, He S, Malfatti S, del Rio TG, Tringe SG, Hugenholtz P, McMahon KD. Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME JOURNAL 2013; 7:2301-14. [PMID: 23887171 DOI: 10.1038/ismej.2013.117] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/14/2013] [Accepted: 06/11/2013] [Indexed: 11/09/2022]
Abstract
Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80-90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.
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Affiliation(s)
- Jason J Flowers
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
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Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SAB, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AAM, Gerritse J, van Berkel WJH, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJM. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.). PLoS One 2013; 8:e66971. [PMID: 23825601 PMCID: PMC3692508 DOI: 10.1371/journal.pone.0066971] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/14/2013] [Indexed: 12/04/2022] Open
Abstract
The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.
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Affiliation(s)
| | - Teun Veuskens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Hajnalka E. Daligault
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - David C. Bruce
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Roxanne Tapia
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Cliff S. Han
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Miriam L. Land
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Loren J. Hauser
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | | | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholz Centre for Infection Research, Braunschweig, Germany
| | - Howard Junca
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Bogotá, Colombia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Gosse Schraa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- * E-mail:
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48
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Identification of triclosan-degrading bacteria in a triclosan enrichment culture using stable isotope probing. Biodegradation 2013; 25:55-65. [DOI: 10.1007/s10532-013-9640-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 04/08/2013] [Indexed: 10/26/2022]
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49
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Shen Z, Zhou Y, Hu J, Wang J. Denitrification performance and microbial diversity in a packed-bed bioreactor using biodegradable polymer as carbon source and biofilm support. JOURNAL OF HAZARDOUS MATERIALS 2013; 250-251:431-438. [PMID: 23500423 DOI: 10.1016/j.jhazmat.2013.02.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/10/2013] [Accepted: 02/13/2013] [Indexed: 06/01/2023]
Abstract
A novel kind of biodegradable polymer, i.e., starch/polycaprolactone (SPCL) was prepared and used as carbon source and biofilm support for biological denitrification in a packed-bed bioreactor. The denitrification performances and microbial diversity of biofilm under different operating conditions were investigated. The results showed that the average denitrification rate was 0.64 ± 0.06 kg N/(m(3)d), and NH3-N formation (below 1mg/L) was observed during denitrification. The nitrate removal efficiency at 15°C was only 55.06% of that at 25°C. An initial excess release of DOC could be caused by rapid biodegradation of starch in the surfaces of SPCL granules, then it decreased to 10.08 mg/L. The vast majority of species on SPCL biofilm sample (99.71%) belonged to six major phyla: Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Spirochaetes and Actinobacteria. Proteobacteria were the most abundant phylum (85.50%) and mainly consisted of β-proteobacteria (82.39%). Diaphorobacter and Acidovorax constituted 52.75% of the identified genera which were denitrifying bacteria.
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Affiliation(s)
- Zhiqiang Shen
- Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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50
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Shen Z, Zhou Y, Wang J. Comparison of denitrification performance and microbial diversity using starch/polylactic acid blends and ethanol as electron donor for nitrate removal. BIORESOURCE TECHNOLOGY 2013; 131:33-39. [PMID: 23321665 DOI: 10.1016/j.biortech.2012.12.169] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 06/01/2023]
Abstract
Starch/polylactic acid (SPLA9) was prepared and used as electron donor for biological nitrate removal. The denitrification performance and microbial diversity were investigated and compared with that of ethanol supported denitrification system. The results showed that the SPLA9 system had richer microbial diversity by analyzing Shannon's diversity index, but the ethanol system showed higher denitrification rate. The formation of NH3-N was observed during denitrification for both systems, but its concentration in the SPLA9 system was lower than that in the ethanol system. The quick release and accumulation of dissolved organic carbon (DOC) were observed in SPLA9 system during the start-up period. Fortunately it decreased to about 5mg/L. Proteobacteria was the major phylum and Alicycliphilus and Thauera were the most abundant genera for both systems. Organisms from the genus Desulfovibrio were identified in both systems, which probably contributed to the dissimilatory nitrate reduction to ammonia (DNRA) reaction.
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Affiliation(s)
- Zhiqiang Shen
- Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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