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Liu X, Ge W, Zhang X, Chai C, Wu J, Xiang D, Chen X. Biodegradation of aged polycyclic aromatic hydrocarbons in agricultural soil by Paracoccus sp. LXC combined with humic acid and spent mushroom substrate. J Hazard Mater 2019; 379:120820. [PMID: 31271936 DOI: 10.1016/j.jhazmat.2019.120820] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 06/09/2023]
Abstract
Paracoccus sp. LXC combined with humic acid (HA) and spent mushroom substrate (SMS) obtained from Auricularia auricular and Sarcomyxa edulis was tested for the remediation of agricultural soil contaminated with aged polycyclic aromatic hydrocarbons (PAHs). The biomass and diversity of bacteria and fungi and the soil enzyme activity were analyzed. PAH removal and dissipation kinetics were examined. The highest degradation rate of PAHs was 56.5% when soil was amended with Paracoccus sp. LXC combined with HA and unsterilized SMS from A. auricular. The half-life of PAHs decreased from 2323.3 days in natural attenuation to 66.6-277.2 days in amended treatments. Soil treated with Paracoccus sp. LXC combined with HA and SMS from A. auricular acquired high contents of organic matter and nutrients. HA and SMS aided the growth of PAH-degrading bacteria and promoted the diversity of bacteria but not of fungi. The degradation rate of PAHs was mainly correlated positively with soil laccase activity. Low- and middle-molecular-weight PAHs were significantly removed by Paracoccus sp. LXC, HA and SMS. High-molecular-weight PAHs were removed by SMS but not by Paracoccus sp. LXC. Biodegradation by Paracoccus sp. LXC combined with HA and SMS is a promising choice for remediating aged PAH-contaminated agricultural soils.
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Affiliation(s)
- Xiuchu Liu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Ge
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaomei Zhang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Chai
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Juan Wu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dan Xiang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoyu Chen
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
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Kwon JH, Park HJ, Lee YY, Cho KS. Evaluation of denitrification performance and bacterial community of a sequencing batch reactor under intermittent aeration. J Environ Sci Health A Tox Hazard Subst Environ Eng 2019; 55:179-192. [PMID: 31656118 DOI: 10.1080/10934529.2019.1681220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Effects of operational parameters (initial nitrite concentration, initial nitrate concentration, carbon source, and COD/N ratio) on denitrification performance was evaluated using a sequencing batch reactor (SBR) under intermittent aeration. Complete denitrification was observed without N2O accumulation when the initial nitrite concentration was 100-500 mg-N·L-1. When the initial nitrate concentration was 75-300 mg-N·L-1, 95-96% of NO3--N was completely reduced to N2 gas. Acetate was the most effective sole carbon source for the complete denitrification of the SBR under intermittent aeration, and 99% of NO3--N was reduced to N2 gas. The optimum COD/N ratio was 8-12 for the complete denitrification, while NO2- accumulation was observed at low COD/N ratios of 1 and 2. In this study, N2O accumulation was not observed during the denitrification process regardless of operational condition. Paracoccus (15-68%), a representative aerobic denitrifying bacterium, was dominant in the SBR during the denitrification process, and the intermittent aeration condition could affect the abundance of Paracoccus in this study.
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Affiliation(s)
- Ji Hyeon Kwon
- Department of Environmental Science and Engineering, Ewha Woman's University, Seoul, Republic of Korea
| | - Hyung-Joo Park
- Department of Environmental Science and Engineering, Ewha Woman's University, Seoul, Republic of Korea
| | - Yun-Yeong Lee
- Department of Environmental Science and Engineering, Ewha Woman's University, Seoul, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Woman's University, Seoul, Republic of Korea
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Mikrobiologiia EN, Doronina NV, Mustakhimov II, Agafonova NV, Trotsenko YA. [Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow Oblast]. Mikrobiologiia 2017; 86:107-113. [PMID: 30207149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
During the summer period (15–25°C), 34 strains of methylotrophic bacteria associated with different species of herbs, shrub, and trees in Pushchino (Moscow oblast, Russia) were isolated on the medium with methanol. Predominance of pink-colored Methylobacterium strains in the phyllosphere of many plants was confirmed by microscopy, enumeration of the colonies from grass leaves, and sequencing of the 16S rRNA genes. Colorless and yellow-pigmented methylotrophs belonged to the genera Methylophilus, Methylobacillus, Hansschlegelia, Methylopila, Xanthobacter, and Paracoccus. All isolates were able to synthesize plant hormones auxins from L-tryptophan (5−50 μg/mL) and are probably plant symbionts.
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Andjouh S, Blache Y. Screening of bromotyramine analogues as antifouling compounds against marine bacteria. Biofouling 2016; 32:871-881. [PMID: 27450150 DOI: 10.1080/08927014.2016.1200562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
Rapid and efficient synthesis of 23 analogues inspired by bromotyramine derivatives, marine natural products, by means of CuSO4-catalysed [3+2] alkyne-azide cycloaddition is described. The final target was then assayed for anti-biofilm activity against three Gram-negative marine bacteria, Pseudoalteromonas ulvae (TC14), Pseudoalteromonas lipolytica (TC8) and Paracoccus sp. (4M6). Most of the synthesised bromotyramine/triazole derivatives are more active than the parent natural products Moloka'iamine (A) and 3,5-dibromo-4-methoxy-β-phenethylamine (B) against biofilm formation by the three bacterial strains. Some of these compounds were shown to act as non-toxic inhibitors of biofilm development with EC50 < 200 μM without any effect on bacterial growth even at high concentrations (200 μM).
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Affiliation(s)
| | - Yves Blache
- a MAPIEM , Université de Toulon , La Garde , France
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Kor-Bicakci G, Pala-Ozkok I, Rehman A, Jonas D, Ubay-Cokgor E, Orhon D. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture. Bioresour Technol 2014; 166:219-228. [PMID: 24908607 DOI: 10.1016/j.biortech.2014.05.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response.
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Affiliation(s)
- G Kor-Bicakci
- Istanbul Technical University, Civil Engineering Faculty, Department of Environmental Engineering, 34469 Maslak, Istanbul, Turkey.
| | - I Pala-Ozkok
- Istanbul Technical University, Civil Engineering Faculty, Department of Environmental Engineering, 34469 Maslak, Istanbul, Turkey
| | - A Rehman
- Department of Environmental Health Sciences, University Medical Center Freiburg, Breisacher Strasse 115B, D-79106 Freiburg i.Br, Germany
| | - D Jonas
- Department of Environmental Health Sciences, University Medical Center Freiburg, Breisacher Strasse 115B, D-79106 Freiburg i.Br, Germany
| | - E Ubay-Cokgor
- Istanbul Technical University, Civil Engineering Faculty, Department of Environmental Engineering, 34469 Maslak, Istanbul, Turkey
| | - D Orhon
- Istanbul Technical University, Civil Engineering Faculty, Department of Environmental Engineering, 34469 Maslak, Istanbul, Turkey; ENVIS Energy and Environmental Systems Ltd., ITU Arı Teknokent, Arı 1 Binası, 16, 34469 Maslak, Istanbul, Turkey
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Liu Y, Li S, Chen Z, Megharaj M, Naidu R. Influence of zero-valent iron nanoparticles on nitrate removal by Paracoccus sp. Chemosphere 2014; 108:426-32. [PMID: 24630453 DOI: 10.1016/j.chemosphere.2014.02.045] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 05/24/2023]
Abstract
Nitrate contamination in drinking water is a major threat to public health. This study investigated the efficiency of denitrification of aqueous solutions in the co-presence of synthesized nanoscale zero-valent iron (nZVI; diameter: 20-80 nm) and a previously isolated Paracoccus sp. strain YF1. Various influencing factors were studied, such as oxygen, pH, temperature, and anaerobic corrosion products (Fe(2+), Fe(3+) and Fe3O4). With slight toxicity to the strain, nZVI promoted denitrification efficiency by providing additional electron sources under aerobic conditions. For example, 50 mg L(-1) nZVI increased the nitrate removal efficiency from 66.9% to 85.2%. However, a high concentration of nZVI could lead to increased production of Fe(2+), a toxic ion which could compromise the removal efficiency. Kinetic studies suggest that denitrification by both free cells, and nZVI-amended cells fitted well to the zero-order model. Temperature and pH are the major factors affecting nitrate removal and cell growth, with or without the presence of nZVI. In this study, nitrate removal and cell growth increased in the pH range of 6.5-8.0, and temperature range of 25-35 °C. These conditions favor the growth of the strain, which dominated denitrification in all scenarios involved. As for anaerobic corrosion products, compared with Fe(2+) and Fe(3+), Fe3O4 promoted denitrification by serving as an electron donor. Finally, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and X-ray diffraction (XRD) confirmed attachments of nZVI on the surface of the cell, and the formation of iron oxides. This study indicated that, as an electron donor source with minimal cellular toxicity, nZVI could be used to promote denitrification efficiency under biotic conditions.
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Affiliation(s)
- Yan Liu
- School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, Fujian Province, China; Fuzhou Research Academy of Environmental Sciences, Fuzhou 350011, Fujian Province, China
| | - Shibin Li
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX 79409-1163, USA
| | - Zuliang Chen
- School of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, Fujian Province, China; Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Mallavarapu Megharaj
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Ravi Naidu
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia
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Jiang C, Liu Y, Chen Z, Megharaj M, Naidu R. Impact of iron-based nanoparticles on microbial denitrification by Paracoccus sp. strain YF1. Aquat Toxicol 2013; 142-143:329-35. [PMID: 24090609 DOI: 10.1016/j.aquatox.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/02/2013] [Accepted: 09/05/2013] [Indexed: 05/20/2023]
Abstract
This study investigates the effects of Fe and Fe/Ni nanoparticles on biological denitrification when using Paracoccus sp. strain YF1. Results show that adding Fe and Fe/Ni nanoparticles to the cells decreased their growth and denitrification rate. Compared to that of free cells (control 89.47%), a decrease (64.33%) in the presence of 1000 mg/L Fe/Ni nanoparticles was observed, while a small decline in the denitrification rate (76.36%) was obtained when the concentration of Fe nanoparticles was 1000 mg/L. These were further confirmed by adding Fe(2+), Fe(3+), Fe3O4, Fe(2+)/Ni(2+) and Fe(3+)/Ni(2+) individually to the free cell system. Furthermore, Fe and Fe/Ni nanoparticles influenced the nitrate removal and bacterial growth under different pH and temperature conditions. SEM, XRD and EDS demonstrated that iron oxides formed as a result of nanoparticles corrosion in biological medium. Finally the presence of nanoparticles around some bacteria was observed.
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Affiliation(s)
- Chenghong Jiang
- School of Life Science, Fujian Normal University, Fuzhou 350108, China
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Qiao L, Zhao H, Wang JL. [Bioaugmented removal of pyridine and the microbial community dynamic analysis]. Huan Jing Ke Xue 2012; 33:2052-2060. [PMID: 22946195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The bioaugmented removal of pyridine was investigated through introducing immobilized Paracoccus sp. strain KT-5 capable of degrading pyridine into the lab-scale sequencing batch reactor (SBR) inoculated with activated sludge. The terminal restriction fragment length polymorphisms (T-RFLP) was used to analyzed the microbial community dynamics of two reactors during the whole operation process. The experimental results indicated that the introduction of immobilized strain KT-5 into the SBR could speed up the start-up of reactor, compared to the non-bioaugmented SBR. When the initial concentration of pyridine varied from 195.6 mg x L(-1) to 586.8 mg x L(-1), the bioaugmented effect was not significant; however, when the initial concentration of pyridine was 782.4-2934 mg x L(-1), the bioaugmentation role in pyridine degradation was obvious. The analysis of T-RFLP indicated that the introduced immobilized strain KT-5, as a dominant strain, always existed in both free and immobilized biomass of the bioaugmented SBR.
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Affiliation(s)
- Lin Qiao
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
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Qiao L, Wang JL. Microbial degradation of pyridine by Paracoccus sp. isolated from contaminated soil. J Hazard Mater 2010; 176:220-225. [PMID: 19945787 DOI: 10.1016/j.jhazmat.2009.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 11/03/2009] [Accepted: 11/03/2009] [Indexed: 05/28/2023]
Abstract
A pyridine-degrading strain was isolated from the contaminated soil near the pesticide plant, identified as Paracoccus sp., and designated as strain KT-5, on the basis of its partial 16S rRNA gene sequence analysis. The effect of different co-substrates including glucose, ammonium chloride and trace elements on biodegradation of pyridine by Paracoccus sp. KT-5 was investigated. The results showed that when the initial concentration of pyridine was about 900 mg L(-1), 100 mg L(-1) of glucose increased the growth of strain KT-5 and the removal of pyridine, but did not affect the release of nitrogen in the pyridine ring as ammonia. In addition, strain KT-5 was able to utilize 100 mg L(-1) of glucose and 900 mg L(-1) of pyridine simultaneously as the carbon source. 100 mg L(-1) of ammonium chloride inhibited the growth of strain KT-5 in 900 mg L(-1) of pyridine, and also slightly decreased the removal of pyridine, but did not affect the release of nitrogen in the pyridine ring as ammonia. However, lacking of trace elements not only inhibited the growth of strain KT-5 in 900 mg L(-1) of pyridine, but also decreased the removal of pyridine, while it did not affect the release of nitrogen in the pyridine ring as ammonia.
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Affiliation(s)
- Lin Qiao
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084, PR China
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Wang CC, Lee CM. Isolation of the epsilon-caprolactam denitrifying bacteria from a wastewater treatment system manufactured with acrylonitrile-butadiene-styrene resin. J Hazard Mater 2007; 145:136-41. [PMID: 17161908 DOI: 10.1016/j.jhazmat.2006.10.092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 10/28/2006] [Accepted: 10/31/2006] [Indexed: 05/12/2023]
Abstract
epsilon-Caprolactam has high COD and toxicity, so its discharge to natural water and soil systems may lead to an adverse environmental effect on water quality, endangering public health and welfare. This investigation attempts to isolate epsilon-caprolactam denitrifying bacteria from a wastewater treatment system manufactured with acrylonitrile-butadiene-styrene (ABS) resin. The goal is to elucidate the effectiveness of isolated pure strain and ABS mixed strains in treating epsilon-caprolactam from synthetic wastewater. The results reveal that Paracoccus versutus MDC-3 was isolated from the wastewater treatment system manufactured with ABS resin. The ABS mixed strains and P. versutus MDC-3 can consume up to 1539mg/l epsilon-caprolactam to denitrify from synthetic wastewater. Complete epsilon-caprolactam removal depended on the supply of sufficient electron acceptors (nitrate). Strain P. versutus MDC-3, Hyphomicrobium sp. HM, Methylosinus pucelana and Magnetospirillum sp. CC-26 are related closely, according to the phylogenetic analyses of 16S rDNA sequences.
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Affiliation(s)
- Chun-Chin Wang
- Department of Environmental Engineering, Hungkuang University, Shalu, Taichung 433, Taiwan.
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Gusmão VR, Chinalia FA, Sakamoto IK, Varesche MBA. Performance of a reactor containing denitrifying immobilized biomass in removing ethanol and aromatic hydrocarbons (BTEX) in a short operating period. J Hazard Mater 2007; 139:301-9. [PMID: 16872740 DOI: 10.1016/j.jhazmat.2006.06.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 06/11/2006] [Accepted: 06/12/2006] [Indexed: 05/11/2023]
Abstract
A horizontal-flow anaerobic immobilized biomass reactor (HAIB) containing denitrifying biomass was evaluated with respect to its ability to remove, separately and in a short operating period (30 days), organic matter, nitrate, and the hydrocarbons benzene (41.4 mg L-1), toluene (27.8 mg L-1), ethylbenzene (31.1 mg L-1), o-xylene (28.5 mg L-1), m-xylene (28.4 mg L-1) and p-xylene (32.1 mg L-1). The purified culture, which was grown in the presence of the specific hydrocarbon, was used as the source of cells to be immobilized in the polyurethane foam. After 30 days of operation, the foam was removed and a new immobilized biomass was grown in the presence of another hydrocarbon. The average hydrocarbon removal efficiency attained was 97%. The organic matter, especially ethanol, was removed with an average efficiency of 83% at a mean influent concentration of 1185.0 mg L-1. A concomitant removal of 97% of nitrate was observed for a mean influent concentration of 423.4 mg L-1. The independent removal of each hydrocarbon demonstrated that these contaminants can be biodegraded separately, without the need for a compound to be the primary substrate for the degradation of another. This study proposes the application of the system for treatment of areas contaminated with these compounds, with substitution and formation of a biofilm in a 30-day period.
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Affiliation(s)
- Valquiria Ribeiro Gusmão
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo (USP), Av. Trabalhador São-carlense 400, São Carlos 13566-590, SP, Brazil.
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Abstract
Sulfamate is an analogue of thiosulfate, and the sodium and potassium salts of sulfamic acid inhibited the chemolithoautotrophic growth on thiosulfate of Acidithiobacillus ferrooxidans and Halothiobacillus neapolitanus. The chemo-organotrophic growth of Paracoccus versutus on sucrose was similarly inhibited by sulfamate. Thiosulfate oxidation by suspensions of H. neapolitanus was, however, unaffected by sulfamate, showing that sulfamate did not directly affect thiosulfate uptake, activation or oxidation. Inhibition of P. versutus was not relieved by cysteine and methionine, indicating that sulfate uptake and sulfur amino acid biosynthesis were not directly affected by sulfamate. Sulfamate was not degraded by any of the bacteria, and so could not serve as an alternative to thiosulfate as an energy-yielding substrate. Sulfamate is also an analogue of ammonia and might act like hydrazine by inhibiting ammonium uptake or an essential enzyme activity.
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Affiliation(s)
- James R Lusty
- University of Wales, Newport, Caerleon Campus, Newport, South Wales, UK
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Abstract
A bacterium strain, which is capable of degrading monocrotophos, was isolated from sludge collected from the bottom of a wastewater treatment system of a chemical factory, and named M-1. On the basis of the results of the cellular morphology, physiological and chemotaxonomic characteristics and phylogenetic similarity of 16S rDNA gene sequences, the strain was identified as a Paracoccus sp. The ability of the strain to mineralize monocrotophos was investigated under different culture conditions. Other organophosphorus insecticides and amide herbicides were also degraded by M-1. The key enzyme (s) involved in the initial biodegradation of monocrotophos in M-1 was shown to be a constitutively expressed cytosolic protein. The addition of M-1 (10(6) CFU g(-1)) to fluvo-aquic soil and a high-sand soil containing monocrotophos (50 mg kg(-1)) resulted in a higher degradation rate than that obtained from noninoculated soil. This microbial culture has great potential utility for the bioremediation of wastewater or soil contaminated with organophosphorus pesticides and amide herbicides.
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Affiliation(s)
- Kai-zhi Jia
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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Weinitschke S, Denger K, Smits THM, Hollemeyer K, Cook AM. The sulfonated osmolyte N-methyltaurine is dissimilated by Alcaligenes faecalis and by Paracoccus versutus with release of methylamine. Microbiology (Reading) 2006; 152:1179-1186. [PMID: 16549680 DOI: 10.1099/mic.0.28622-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Selective enrichments yielded bacterial cultures able to utilize the osmolyte N-methyltaurine as sole source of carbon and energy or as sole source of fixed nitrogen for aerobic growth. Strain MT1, which degraded N-methyltaurine as a sole source of carbon concomitantly with growth, was identified as a strain of Alcaligenes faecalis. Stoichiometric amounts of methylamine, whose identity was confirmed by matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry, and of sulfate were released during growth. Inducible N-methyltaurine dehydrogenase, sulfoacetaldehyde acetyltransferase (Xsc) and a sulfite dehydrogenase could be detected. Taurine dehydrogenase was also present and it was hypothesized that taurine dehydrogenase has a substrate range that includes N-methyltaurine. Partial sequences of a tauY-like gene (encoding the putative large component of taurine dehydrogenase) and an xsc gene were obtained by PCR with degenerate primers. Strain N-MT utilized N-methyltaurine as a sole source of fixed nitrogen for growth and could also utilize the compound as sole source of carbon. This bacterium was identified as a strain of Paracoccus versutus. This organism also expressed inducible (N-methyl)taurine dehydrogenase, Xsc and a sulfite dehydrogenase. The presence of a gene cluster with high identity to a larger cluster from Paracoccus pantotrophus NKNCYSA, which is now known to dissimilate N-methyltaurine via Xsc, allowed most of the overall pathway, including transport and excretion, to be defined. N-Methyltaurine is thus another compound whose catabolism is channelled directly through sulfoacetaldehyde.
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Affiliation(s)
- Sonja Weinitschke
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Karin Denger
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Theo H M Smits
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Klaus Hollemeyer
- Institute of Biochemical Engineering, Saarland University, Box 50 11 50, D-66041 Saarbrücken, Germany
| | - Alasdair M Cook
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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La HJ, Im WT, Ten LN, Kang MS, Shin DY, Lee ST. Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 2005; 55:1657-1660. [PMID: 16014497 DOI: 10.1099/ijs.0.63494-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, short rod- to coccus-shaped, non-spore-forming bacterium (Ch05(T)) was isolated from granules in an upflow anaerobic sludge blanket (UASB) reactor. On the basis of 16S rRNA gene sequence similarity, strain Ch05(T) was shown to belong to the subclass alpha-Proteobacteria, being related to Paracoccus solventivorans (97.5%), Paracoccus alkenifer (96.9%) and Paracoccus kocurii (96.4%). The phylogenetic distance from Paracoccus species with validly published names was always less than 96%. Physiological and chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C(18:1) and C(18:0)) supported the affiliation of strain Ch05(T) to the genus Paracoccus. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Ch05(T) from the 17 Paracoccus species with validly published names. Ch05(T) therefore represents a novel species, for which the name Paracoccus koreensis sp. nov. is proposed. The type strain is Ch05(T) (=KCTC 12238(T)=IAM 15216(T)).
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Affiliation(s)
- Hyun-Jun La
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Leonid N Ten
- National University of Uzbekistan, VUZ-gorodok, Tashkent 700-174, Uzbekistan
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Myung Suk Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Do-Yun Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
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16
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Koutny M, Zaoralkova L. Miniaturized kinetic growth inhibition assay with denitrifying bacteria Paracoccus denitrificans. Chemosphere 2005; 60:49-54. [PMID: 15910901 DOI: 10.1016/j.chemosphere.2005.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 01/03/2005] [Accepted: 01/13/2005] [Indexed: 05/02/2023]
Abstract
A method to cultivate anaerobic bacteria on standard 96-well microplates with automatic recording of growth curves is presented. The method was used as a kinetic growth inhibition assay with denitrifying bacteria Paracoccus denitrificans, and applied to various heavy metal ions and selected agrochemicals. Incorporated in a battery of other biotest the assay could take into account effects of toxicants on denitrifying organisms. The results (EC50) revealed that the assay was relatively sensitive. Performed in vials, the assay was also applied to toxicity testing of volatile compounds and represented a convenient method for assessing samples containing volatile constituents.
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Affiliation(s)
- Marek Koutny
- Department of Environment Protection Engineering, Faculty of Technology, Thomas Bata University, T.G.M. sq. 275, 76272 Zlin, Czech Republic.
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17
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Dolowy P, Mondzelewski J, Zawadzka R, Baj J, Bartosik D. Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1. Plasmid 2005; 53:239-50. [PMID: 15848227 DOI: 10.1016/j.plasmid.2004.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Revised: 11/10/2004] [Accepted: 11/21/2004] [Indexed: 11/30/2022]
Abstract
Using cointegrate formation, we constructed a basic replicon of the megaplasmid/mini-chromosome pTAV3 of Paracoccus versutus UW1. It is composed of two adjacent modules, responsible for plasmid replication (rep) and partitioning (par). Functional analysis of the par region identified a determinant of incompatibility (inc2), whose presence is crucial for proper partitioning (the partitioning site). Database searches revealed that the only known replicon with significant homology to that of pTAV3 is encoded by the chromosome cII of Rhodobacter sphaeroides 2.4.1. Incompatibility studies showed that closely related basic replicons are also encoded by megaplasmids (above 400 kb) harbored by four strains of P. pantotrophus. Basic replicons of the pTAV3-type are able to maintain large bacterial genomes, therefore they appear to be good candidates for the construction of vectors specific for Alphaproteobacteria.
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Affiliation(s)
- Patrycja Dolowy
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland
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18
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Nazarov NM, Doronina NV, Trotsenko IA, Malykh EI, Bitsadze NA. [Biotransformation of organic substances by an immobilized associative bacterial culture]. Aviakosm Ekolog Med 2004; 38:42-6. [PMID: 15605736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Bacterial strains were screened to transform to end-products (carbon monoxide and water) elevated concentrations of acetone, acidic acid, and ethanol in a biocatalyst with an immobilized bacterial association cultivated on solid foam polyvinyl acetate (FPVA). The innocuous association amalgamated Paracoccus denitrificans VKM V-1324, Pseudomonas esterophilus VKM V-1736D and Achromobacter parvulus VKM V-1541D. The biocatalyst was tested with the help of classic methods and equipment for microbes cultivation. Microbial growth was assessed in the optical density units. Comparative evaluation of the biocatalytic activity was performed on gas-chromatographer Pue Unicam-104. Based on test results, specific rates of oxidation of acidic acid, ethanol and acetone per one g of FPVA were 0.75, 0.72, and 0.67 mg/hr, respectively.
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19
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Abstract
Three novel insertion sequences (ISs) (ISPso1, ISPso2, and ISPso3) of the soil bacterium Paracoccus solventivorans DSM 11592 were identified by transposition into entrapment vector pMEC1. ISPso1 (1,400 bp) carries one large open reading frame (ORF) encoding a putative basic protein (with a DDE motif conserved among transposases [Tnps] of elements belonging to the IS256 family) with the highest levels of similarity with the hypothetical Tnps of Rhodospirillum rubrum and Sphingopyxis macrogoltabida. ISPso2 (832 bp) appeared to be closely related to ISPpa2 of Paracoccus pantotrophus DSM 11072 and IS1248 of Paracoccus denitrificans PdX22, both of which belong to the IS427 group (IS5 family). These elements contain two overlapping ORFs and a putative frameshift motif (AAAAG) responsible for production of a putative transframe Tnp. ISPso3 (1,286 bp) contains a single ORF, whose putative product showed homology with Tnps of ISs classified as members of a distinct subgroup of the IS5 group of the IS5 family. The highest levels of similarity were observed with ISSsp126 of Sphingomonas sp. and IS1169 of Bacteroides fragilis. Analysis of the distribution of ISs of P. solventivorans revealed that ISPso2-like elements are the most widely spread of the elements in nine species of the genus PARACOCCUS: ISPso1 and ISPso3 are present in only a few paracoccal strains, which suggests that they were acquired by lateral transfer. Phylogenetic analysis of Tnps of the novel ISs and their closest relatives showed their evolutionary relationships and possible directions of lateral transfer between various bacterial hosts.
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Affiliation(s)
- Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, 02-096 Warsaw, Poland.
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20
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Lee CM, Wang CC. Denitrification with epsilon-caprolactam by acclimated mixed culture and by pure culture of bacteria isolated from polyacrylonitrile fibre manufactured wastewater treatment system. Water Sci Technol 2004; 49:341-348. [PMID: 15137443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aim of this study is to isolate denitrifying bacteria utilizing epsilon-caprolactam as the substrate, from a polyacrylonitrile fibre manufactured wastewater treatment system. The aim is also to compare the performance of PAN (polyacrylonitrile) mixed bacteria cultures acclimated to epsilon-caprolactam and isolated pure strain for treating different initial epsilon-caprolactam concentrations from synthetic wastewater under anoxic conditions. The result showed that the PAN mixed bacteria cultures acclimated to epsilon-caprolactam could utilize 1538.5 mg/l of epsilon-caprolactam as a substrate for denitrification. Sufficient time and about 2200 mg/l of nitrate were necessary for the complete epsilon-caprolactam removal. Paracoccus thiophilus was isolated from the polyacrylonitrile fibre manufactured wastewater treatment system and it could utilize 1722.5 mg/l of epsilon-caprolactam as a substrate for denitrification. About 3500 mg/l of nitrate was necessary for the complete removal of epsilon-caprolactam. When the initial epsilon-caprolactam concentration was below 784.3 mg/l, the removal efficiency of epsilon-caprolactam by Paracoccus thiophilus was better than that for the PAN mixed bacteria cultures. The growth of Paracoccus thiophilus was better. However, when the initial epsilon-caprolactam concentration was as high as 1445.8 mg/l, both the epsilon-caprolactam removal efficiency by Paracoccus thiophilus and Paracoccus thiophilus specific growth rate were similar to the PAN mixed bacteria cultures.
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Affiliation(s)
- C M Lee
- Department of Environmental Engineering, National Chung Hsing University, Taichung 402, Chinese Taiwan.
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21
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Kim SG, Bae HS, Oh HM, Lee ST. Isolation and characterization of novel halotolerant and/or halophilic denitrifying bacteria with versatile metabolic pathways for the degradation of trimethylamine. FEMS Microbiol Lett 2003; 225:263-9. [PMID: 12951251 DOI: 10.1016/s0378-1097(03)00530-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Four denitrifying bacteria capable of degrading trimethylamine under both aerobic and denitrifying conditions were newly isolated from coastal sediments and wastewater contaminated by marine water. All strains were in alpha-Proteobacteria. Strain GP43 was classified as a member of genus Paracoccus, and strain PH32, PH34 and GRP21 were novel organisms with remote phylogenetic position from other genus alpha-Proteobacteria. Among these four strains were the halophilic strains PH32, PH34 and GRP21, which did not grow in the absence of sodium chloride in culture medium. Cells grown under denitrifying conditions possessed trimethylamine dehydrogenase while cells grown aerobically possessed two different enzymes for oxidation of trimethylamine, trimethylamine dehydrogenase and trimethylamine monooxygenase. The newly isolated strain PH32, PH34 and GRP21 may be the first halophilic bacteria to degrade trimethylamine under denitrifying conditions.
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Affiliation(s)
- Song-Gun Kim
- Environmental Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Gusong-Dong, Yusung-Gu, Daejeon 305-701, South Korea
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22
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Abstract
We studied diversity and distribution of transposable elements residing in different strains (DSM 11072, DSM 11073, DSM 65, and LMD 82.5) of a soil bacterium Paracoccus pantotrophus (alpha-Proteobacteria). With application of a shuttle entrapment vector pMEC1, several novel insertion sequences (ISs) and transposons (Tns) have been identified. They were sequenced and subjected to detailed comparative analysis, which allowed their characterization (i.e., identification of transposase genes, terminal inverted repeats, as well as target sequences) and classification into the appropriate IS or Tn families. The frequency of transposition of these elements varied and ranged from 10(-6) to 10(-3) depending on the strain. The copy number, localization (plasmid or chromosome), and distribution of these elements in the Paracoccus species P. pantotrophus, P. denitrificans, P. methylutens, P. solventivorans, and P. versutus were analyzed. This allowed us to distinguish elements that are common in paracocci (ISPpa2, ISPpa3--both of the IS5 family--and ISPpa5 of IS66 family) as well as strain-specific ones (ISPpa1 of the IS256 family, ISPpa4 of the IS5 family, and Tn3434 and Tn5393 of the Tn3 family), acquired by lateral transfer events. These elements will be of a great value in the design of new genetic tools for paracocci, since only one element (IS1248 of P. denitrificans) has been described so far in this genus.
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Affiliation(s)
- Dariusz Bartosik
- Warsaw University, Institute of Microbiology, Department of Bacterial Genetics, 02-096 Warsaw, Poland.
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Ellington MJK, Sawers G, Sears HJ, Spiro S, Richardson DJ, Ferguson SJ. Characterization of the expression and activity of the periplasmic nitrate reductase of Paracoccus pantotrophus in chemostat cultures. Microbiology (Reading) 2003; 149:1533-1540. [PMID: 12777493 DOI: 10.1099/mic.0.26277-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The periplasmic nitrate reductase (Nap) from Paracoccus pantotrophus has a role in cellular redox balancing. Previously, transcription from the nap promoter in P. pantotrophus was shown to be responsive to the oxidation state of the carbon substrate. During batch culture, expression was higher during growth on reduced substrates such as butyrate compared to more oxidized substrates such as succinate. In the present study the effect of growth rate on nap expression in succinate-, acetate- and butyrate-limited chemostat cultures was investigated. In all three cases transcription from the nap promoter and Nap enzyme activity showed a strong correlation. At the fastest growth rates tested for the three substrates nap expression and Nap activity were highest when growth occurred on the most reduced substrate (butyrate > acetate > succinate). However, in all three cases a bell-shaped pattern of expression was observed as a function of growth rate, with the highest levels of nap expression and Nap activity being observed at intermediate growth rates. This effect was most pronounced on succinate, where an approximately fivefold variation was observed, and at intermediate dilution rates nap expression and Nap activity were comparable on all three carbon substrates. Analysis of mRNA prepared from the succinate-grown cultures revealed that different transcription initiation start sites for the nap operon were utilized as the growth rate changed. This study establishes a new regulatory feature of nap expression in P. pantotrophus that occurs at the level of transcription in response to growth rate in carbon-limited cultures.
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Affiliation(s)
- M J K Ellington
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - G Sawers
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - H J Sears
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - S Spiro
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - D J Richardson
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - S J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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24
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Gates AJ, Hughes RO, Sharp SR, Millington PD, Nilavongse A, Cole JA, Leach ER, Jepson B, Richardson DJ, Butler CS. Properties of the periplasmic nitrate reductases from Paracoccus pantotrophus and Escherichia coli after growth in tungsten-supplemented media. FEMS Microbiol Lett 2003; 220:261-9. [PMID: 12670690 DOI: 10.1016/s0378-1097(03)00122-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Paracoccus pantotrophus grown anaerobically under denitrifying conditions expressed similar levels of the periplasmic nitrate reductase (NAP) when cultured in molybdate- or tungstate-containing media. A native PAGE gel stained for nitrate reductase activity revealed that only NapA from molybdate-grown cells displayed readily detectable nitrate reductase activity. Further kinetic analysis showed that the periplasmic fraction from cells grown on molybdate (3 microM) reduced nitrate at a rate of V(max)=3.41+/-0.16 micromol [NO(3)(-)] min(-1) mg(-1) with an affinity for nitrate of K(m)=0.24+/-0.05 mM and was heat-stable up to 50 degrees C. In contrast, the periplasmic fraction obtained from cells cultured in media supplemented with tungstate (100 microM) reduced nitrate at a much slower rate, with much lower affinity (V(max)=0.05+/-0.002 micromol [NO(3)(-)] min(-1) mg(-1) and K(m)=3.91+/-0.45 mM) and was labile during prolonged incubation at >20 degrees C. Nitrate-dependent growth of Escherichia coli strains expressing only nitrate reductase A was inhibited by sub-mM concentrations of tungstate in the medium. In contrast, a strain expressing only NAP was only partially inhibited by 10 mM tungstate. However, none of the above experimental approaches revealed evidence that tungsten could replace molybdenum at the active site of E. coli NapA. The combined data show that tungsten can function at the active site of some, but not all, molybdoenzymes from mesophilic bacteria.
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Affiliation(s)
- Andrew J Gates
- School of Cell and Molecular Biosciences, The Medical School, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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25
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Ellington MJK, Bhakoo KK, Sawers G, Richardson DJ, Ferguson SJ. Hierarchy of carbon source selection in Paracoccus pantotrophus: strict correlation between reduction state of the carbon substrate and aerobic expression of the nap operon. J Bacteriol 2002; 184:4767-74. [PMID: 12169601 PMCID: PMC135276 DOI: 10.1128/jb.184.17.4767-4774.2002] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2002] [Accepted: 05/28/2002] [Indexed: 11/20/2022] Open
Abstract
Paracoccus pantotrophus can express a periplasmic nitrate reductase (Nap) during aerobic growth. A proposed role for this enzyme is the dissipation of excess redox energy during oxidative metabolism of reduced carbon substrates. To investigate the regulation of nap expression, a transcriptional fusion between the nap promoter region of P. pantotrophus and the lacZ gene was constructed. When this fusion was used, analyses showed that transcription from the nap promoter increases as the average reduction state of the carbon atoms increases. Thus, beta-galactosidase activities increase as the carbon source changes in the order succinate-acetate-butyrate. This result was obtained regardless of which of the three carbon sources was used for culture of the inoculum. If two carbon sources were presented together, the beta-galactosidase activity was always the same as it was when the least-reduced carbon source was added alone. This suggests that the regulation is dependent upon metabolism of the more-reduced carbon sources rather than just their presence in the medium. Analysis of culture medium by (1)H nuclear magnetic resonance showed that for aerobic growth P. pantotrophus strictly selected its carbon source in the order succinate-acetate-butyrate. This was reflected by diauxic growth kinetics on medium containing mixed carbon substrates. The regulatory mechanism underpinning such a selection is unknown but is likely to be related to the mechanism which controls the transcription of the nap operon.
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Affiliation(s)
- M J K Ellington
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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26
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Bartosik D, Baj J, Sochacka M, Piechucka E, Wlodarczyk M. Molecular characterization of functional modules of plasmid pWKS1 of Paracoccus pantotrophus DSM 11072. Microbiology (Reading) 2002; 148:2847-2856. [PMID: 12213930 DOI: 10.1099/00221287-148-9-2847] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete nucleotide sequence of the small, cryptic plasmid pWKS1 (2697 bp) of Paracoccus pantotrophus DSM 11072 was determined. The G+C content of the sequence of this plasmid was 62 mol%. Analysis revealed that over 80% of the plasmid genome was covered by two ORFs, ORF1 and ORF2, which were capable of encoding putative peptides of 44.1 and 37.8 kDa, respectively. Mutational analysis showed that ORF2 was crucial for plasmid replication. The translational product of ORF2 shared local homologies with replication proteins of several theta-replicating lactococcal plasmids, as well as with the Rep proteins of plasmids residing in Gram-negative hosts. An A+T-rich region, located upstream of the rep gene and containing three tandemly repeated 21 bp long iteron-like sequences, served as the origin of replication (oriV). ORF1 encoded a putative mobilization protein with similarities to mobilization proteins (Mob) from the broad-host-range plasmid pBBR1 and plasmids of Gram-positive bacteria. A plasmid bearing the MOB module of pWKS1 (the mob gene and the oriT sequence) could be mobilized for transfer (by IncP RP4 transfer apparatus) at low frequency between different strains of Escherichia coli. MOB modules of pWKS1 and pBBR1 were functionally complementary to each other. Hybridization analysis revealed that only plasmid pSOV1 (6.5 kb), among all of the paracoccal plasmids identified so far, carries sequences related to pWKS1. Plasmid pWKS1 could replicate in 10 species of Paracoccus and in Agrobacterium tumefaciens, Rhizobium leguminosarum and Rhodobacter sphaeroides, but it could not replicate in E. coli.
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Affiliation(s)
- Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Jadwiga Baj
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Marta Sochacka
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Ewa Piechucka
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Miroslawa Wlodarczyk
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
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27
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Bartosik D, Baj J, Bartosik AA, Wlodarczyk M. Characterization of the replicator region of megaplasmid pTAV3 of Paracoccus versutus and search for plasmid-encoded traits. Microbiology (Reading) 2002; 148:871-881. [PMID: 11882723 DOI: 10.1099/00221287-148-3-871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The replicon of the pTAV3 megaplasmid (approx. 400 kb) of Paracoccus versutus has been localized to a 4center dot3 kb EcoRI restriction fragment and its entire nucleotide sequence determined. The G+C content of the entire sequence is 66 mol%, which is within the range (62-66 mol%) previously determined for P. versutus total DNA. ORF1 encodes a replication initiation protein Rep (47.2 kDa), which shares substantial similarity with putative proteins of the Coxiella burnetii plasmids QpH1 and QpDV, and the replication protein of Pseudomonas syringae plasmid pPS10. ORF2, located in the opposite transcriptional orientation to ORF1, encodes a putative protein that shares similarity to a subfamily of ATPases involved in plasmid partitioning. The highest similarity was observed with homologous proteins (RepA) encoded by the repABC family of replicons found in several plasmids of Agrobacterium, Rhizobium and Paracoccus spp. The predicted product of ORF3 was similar to AcoR, Nif and NtrC transcriptional activators. A strong incompatibility determinant (inc) was localized between ORF1 (rep) and ORF2 (parA). The origin of replication of pTAV400 contains a short A+T-rich region and several imperfect palindromic sequences. Curing experiments demonstrated that the megaplasmid bears genes required for growth in minimal media and can therefore be referred to as a mini-chromosome. Megaplasmids pTAV3 of P. versutus UW1 and pKLW2 of Paracoccus pantotrophus DSM 11073 were found to carry closely related, incompatible replicons. It has been shown that plasmid pORI6 (containing oriV of pTAV3 cloned into plasmid pABW1, which does not replicate in Paracoccus spp.) can be trans activated not only by pTAV3, but also by pKLW2. Using pORI6, it was demonstrated that replication systems related to pTAV3 are also present in the replicons of Paracoccus alcaliphilus JCM 7364, Paracoccus thiocyanatus IAM 12816 and Paracoccus methylutens DM 12.
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Affiliation(s)
- Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Jadwiga Baj
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Aneta A Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
| | - Miroslawa Wlodarczyk
- Department of Bacterial Genetics, Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland1
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28
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Abstract
Two relatively low-copy plasmids of 9 and 16 kb were found to comprise the extrachromosomal DNA of a Paracoccus strain. Reduction of nitrate by plasmid-cured cells resulted in a significant intermediate nitrite accumulation as compared to wild-type cells. By examining nitrate reduction by transformants containing one of the two plasmids, it was found that nitrite accumulation was influenced by the 9.0-kb plasmid, designated as pYR1. Subcloning analysis showed that a 1.8-kb fragment of this plasmid affected nitrite accumulation. Sequence analysis of this fragment revealed the presence of five open reading frames. One of the six deduced proteins showed a strong homology to ABC transporters.
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Affiliation(s)
- Yoram Barak
- Department of Animal Sciences, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12, 76100, Rehovot, Israel
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29
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Kim SG, Bae HS, Lee ST. A novel denitrifying bacterial isolate that degrades trimethylamine both aerobically and anaerobically via two different pathways. Arch Microbiol 2001; 176:271-7. [PMID: 11685371 DOI: 10.1007/s002030100319] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2001] [Accepted: 05/30/2001] [Indexed: 10/27/2022]
Abstract
The aerobic and anaerobic degradation of trimethylamine by a newly isolated denitrifying bacterium from an enrichment culture with trimethylamine inoculated with activated sludge was studied. Based on 16S rDNA analysis, this strain was identified as a Paracoccus sp. The isolate, strain T231, aerobically degraded trimethylamine, dimethylamine and methylamine and released a stoichiometric amount of ammonium ion into the culture fluid as a metabolic product, indicating that these methylated amines were completely degraded to formaldehyde and ammonia. The strain degraded trimethylamine also under denitrifying conditions and consumed a stoichiometric amount of nitrate, demonstrating that complete degradation of trimethylamine was coupled with nitrate reduction. Cell-free extract prepared from cells grown aerobically on trimethylamine exhibited activities of trimethylamine mono-oxygenase, trimethylamine N-oxide demethylase, dimethylamine mono-oxygenase, and methylamine mono-oxygenase. Cell-free extract from cells grown anaerobically on trimethylamine and nitrate exhibited activities of trimethylamine dehydrogenase and dimethylamine dehydrogenase. These results indicate that strain T231 had two different pathways for aerobic and anaerobic degradation of trimethylamine. This is a new feature for trimethylamine metabolism in denitrifying bacteria.
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Affiliation(s)
- S G Kim
- Environmental Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Kusung-Dong, Yusung-Gu, Taejon 305-701, Republic of Korea
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30
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Quentmeier A, Kraft R, Kostka S, Klockenkämper R, Friedrich CG. Characterization of a new type of sulfite dehydrogenase from Paracoccus pantotrophus GB17. Arch Microbiol 2000; 173:117-25. [PMID: 10795683 DOI: 10.1007/s002039900118] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The periplasmic sulfite dehydrogenase of Paracoccus pantotrophus GB17 was purified to homogeneity by a four-step procedure from cells grown lithoautotrophically with thiosulfate. The molecular mass of native sulfite dehydrogenase was 190 kDa as determined by native gradient PAGE. SDS-PAGE showed sulfite dehydrogenase to comprise two subunits with molecular masses of 47 kDa and 50 kDa, suggesting an alpha2beta2 structure. The N-terminal amino acid sequence and immunochemical analysis using SoxC-specific antibodies identified the 47-kDa protein as the soxC gene product. SoxD-specific antibodies identified the 50-kDa protein as SoxD. Based on the molecular masses deduced from the nucleotide sequence for mature SoxC (43,442 Da) and SoxD (37,637 Da) sulfite dehydrogenase contained 1.30 mol molybdenum/mol alpha2beta2 sulfite dehydrogenase. The iron content was 3.17 mol/mol alpha2beta2 sulfite dehydrogenase, and 3.53 mol heme/mol alpha2beta2 sulfite dehydrogenase was determined by pyridine hemochrome analysis. These data are consistent with the two heme-binding domains (CxxCH), characteristic for c-type cytochromes, deduced from the soxD nucleotide sequence. Electrospray ionization revealed two masses for SoxC of 43,503 and 43,897 Da. The difference in molecular mass was attributed to the molybdenum cofactor of SoxC. For SoxD a mass of 38,815 Da was determined; this accounted for the polypeptide and two covalently bound hemes. Reconstitution of the catalytic activity of sulfite dehydrogenase required additional fractions; these eluted from Q Sepharose at 0.05, 0.25, and 0.30 M NaCl. The K(m) of sulfite dehydrogenase for sulfite was 7.0 microM and for cytochrome c 19 microM. Sulfite dehydrogenase activity was inhibited by sulfate and phosphate. The structural and catalytic properties make sulfite dehydrogenase from P. denitrificans GB17 distinct from sulfite oxidases of other prokaryotic or eukaryotic sources.
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Affiliation(s)
- A Quentmeier
- Lehrstuhl für Technische Mikrobiologie, Fachbereich Chemietechnik, Universität Dortmund, Germany
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Mikosch CARM, Denger K, Schäfer EM, Cook AM. Anaerobic oxidations of cysteate: degradation via L-cysteate:2-oxoglutarate aminotransferase in Paracoccus pantotrophus. Microbiology (Reading) 1999; 145 ( Pt 5):1153-1160. [PMID: 10376831 DOI: 10.1099/13500872-145-5-1153] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Anoxic, fresh-water enrichment cultures to oxidize different organosulfonates were set up with nitrate, ferric iron or sulfate as electron acceptors. Pure cultures were easily obtained with two naturally occurring sulfonates, cysteate (2-amino-3-sulfopropionate) and taurine (2-aminoethanesulfonate), under nitrate-reducing conditions. These two sulfonates were also oxidized during reduction of iron(III), though isolation of pure cultures was not successful. One nitrate-reducing cysteate-oxidizing bacterium, strain NKNCYSA, was studied in detail. It was identified as Paracoccus pantotrophus. Eighteen sulfonates were tested, and the organism degraded cysteate, taurine, isethionate (2-hydroxyethanesulfonate), sulfoacetate or 3-aminopropanesulfonate with concomitant reduction of nitrate, presumably to molecular nitrogen. The carbon skeleton of these substrates was converted to cell material and, presumably, CO2. The amino group was released as ammonia and the sulfono moiety was recovered as sulfate. Cell-free extracts of P. pantotrophus NKNCYSA contained constitutive L-cysteate:2-oxoglutarate aminotransferase (EC 2.6.1.-) and glutamate dehydrogenase (EC 1.4.1.4). Taurine:pyruvate aminotransferase, in contrast, was inducible.
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Wee S, Wilkinson BJ. Increased outer membrane ornithine-containing lipid and lysozyme penetrability of Paracoccus denitrificans grown in a complex medium deficient in divalent cations. J Bacteriol 1988; 170:3283-6. [PMID: 3384812 PMCID: PMC211283 DOI: 10.1128/jb.170.7.3283-3286.1988] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Paracoccus denitrificans grown in a complex medium was highly susceptible to lysozyme, in contrast to cells grown in a complex medium supplemented with Mg2+ and Ca2+ or in a succinate-salts medium. The complex medium was deficient in divalent cations needed for optimum outer membrane stability. The major change in molecular compositions of outer membranes isolated from cells grown under the different conditions was a higher ratio of ornithine-containing lipid to phospholipid in complex-medium-grown cells (0.63) than in cells grown in complex medium with Mg2+ and Ca2+ (0.22) or in succinate-salts medium (0.14). We suggest that the dipolarionic ornithine-containing lipid is less dependent than acidic phospholipids on divalent cations for its incorporation into the outer membrane.
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Affiliation(s)
- S Wee
- Department of Biological Sciences, Illinois State University, Normal 61761
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Abstract
A synthetic medium, consisting of inorganic salts and any of a number of carbon sources, supported the aerobic growth of Paracoccus halodenitrificans when supplemented with thiamine. The same medium plus an appropriate nitrogenous oxide supported anaerobic growth when additionally supplemented with methionine. The observation that vitamin B12 or betaine replaced methionine suggested that P. halodenitrificans had a defect in the cobalamin-dependent pathway for methionine biosynthesis, as well as the inability to synthesize betaine when growing anaerobically.
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Affiliation(s)
- L I Hochstein
- Extraterrestrial Research Division, National Aeronautics and Space Administration, Ames Research Center, Moffett Field, CA 94035, USA
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Hochstein LI, Betlach M, Kritikos G. The effect of oxygen on denitrification during steady-state growth of Paracoccus halodenitrificans. Arch Microbiol 1984; 137:74-8. [PMID: 6712418 DOI: 10.1007/bf00425811] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Steady-state cultures of Paracoccus halodenitrificans were grown anaerobically prior to establishing steady states at different concentrations of oxygen. In the absence of oxygen, nitrate-limited cultures produced dinitrogen, and as the oxygen supply increased, these cultures produced nitrous oxide, then nitrite. These changes reflected two phenomena: the inactivation of nitrous oxide reductase by oxygen and the diversion of electrons from nitrite to oxygen.
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Savel'eva ND, El'-Registman GI, Zavarzin GA. [Inhibition of the autotrophic growth of hydrogen bacteria by the autoregulation factor]. Mikrobiologiia 1980; 49:373-6. [PMID: 7402116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The purpose of this work was to study the action of the autoregulation factor isolated from the organotrophous culture of Pseudomonas carboxydoflava Z-1107 on autotrophous growth of this organism and some other cultures of hydrogen bacteria. If a sufficient dose of this metabolite was added to the culture growing lithoautotrophously, the growth of Ps. carboxydoflava Z-1107 stopped completely after 24 hours. A curve of false diauxia was observed if an increase in the concentration of the autoregulation factor in the culture was not great enough. When the factor acted on the autotrophously growing cultures of Alcaligenes eutrophus, Pseudomonas pantotropha and Paracoccus denitrificans, it was established that this endogenous metabolite possessed group specificity, and was capable of inhibiting, more or less, autotrophous growth of this hydrogen bacterium.
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Sadler M, McAninch M, Alico R, Hochstein LI. The intracellular Na+ and K+ composition of the moderately halophilic bacterium, Paracoccus halodenitrificans. Can J Microbiol 1980; 26:496-502. [PMID: 6445774 DOI: 10.1139/m80-083] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The intracellular concentrations of Na+ and K+ in exponentially growing Paracoccus halodenitrificans were independent of the NaCl concentration of the growth medium. The observed values were approximately 100 and 300 mM for Na+ and K+, respectively. In stationary phase cells, the ultimate values for Na+ depended on the NaCl concentration of the growth medium. With cells grown in the presence of 1 M NaCl, the value was about 500 mM; for cells grown in the presence of 3 M NaCl, the value was about 1.1 M. The K+ concentration in stationary phase cells was unaffected by the NaCl concentration in the growth medium. The final value was about 100 mM. Associated with these changes were changes in the ATP pool and decreases in the activities of the NADH oxidase system and the membrane-bound ATPase. It is proposed that the decrease in the activities of these enzymes may account for the ion flows observed in stationary phase cells.
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Savel'eva ND. [Relationship of hydrogen bacteria to carbon monoxide]. Mikrobiologiia 1979; 48:360-2. [PMID: 440170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this work was to study the ability of various cultures of hydrogen bacteria to grow in a gaseous mixture containing, apart from H2, O2 and CO2, carbon monoxide at a concentration of 10% (v/v) and higher. In contrast to CO-oxidizing bacteria, these organisms could not use CO as a sole source of energy. Among 17 studied strains of hydrogen bacteria, only those belonging to the group Alcaligenes eutrophus could withstand 10% of CO (v/v) in a gaseous mixture.
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Abstract
Two out of eleven newly isolated strains of Paracoccus denitrificans were investigated by light and electron microscopic methods and compared with two strains of P. denitrificans already kept in culture collections. Samples were taken from different growth phases revealing short rods and nearly spherical cells in the exponential growth phase, and an increasing ratio of nearly spherical cells in the stationary growth phase. Cell division followed the binary fission mode; higher cell aggregates were not observed. Fine structural analysis revealed extracellular surface material stainable with Ruthenium red, a gram-negative cell wall and different storage material inclusions. Structural properties and variations within the four strains under investigation are discussed and compared with those of related bacteria.
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