Distribution of denitrification and nitrogen fixation genes in<i>Hyphomicrobium</i>spp. and other budding bacteria

Fesefeldt, Andreas; Kloos, Karin; Bothe, Hermann; Lemmer, Hilde; Gliesche, Christian G.

doi:10.1139/w97-139

Cited by 29 publications

(15 citation statements)

References 19 publications

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“…Most of hyphomicrobia are appendaged bacteria that multiply by budding, with the ability of nitrogen-fixing and denitrifying (Fesefeldt et al, 1998). In terms of carbon utilization, members of Hyphomicrobium are restricted facultative methylotrophs, growing on C1 components, such as methanol, methylated amines, and formate etc, but not compounds with three or more carbon atoms.…”

Section: Bacterial Communitiesmentioning

confidence: 99%

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system

Liu

Zhu

et al. 2014

Journal of Environmental Sciences

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a b s t r a c tTo understand the impacts of different plumbing materials on long-term biofilm formation in water supply system, we analyzed microbial community compositions in the bulk water and biofilms on faucets with two different materials-polyvinyl chloride (PVC) and cast iron, which have been frequently used for more than10 years. Pyrosequencing was employed to describe both bacterial and eukaryotic microbial compositions. Bacterial communities in the bulk water and biofilm samples were significantly different from each other. Specific bacterial populations colonized on the surface of different materials. Hyphomicrobia and corrosion associated bacteria, such as Acidithiobacillus spp., Aquabacterium spp., Limnobacter thiooxidans, and Thiocapsa spp., were the most dominant bacteria identified in the PVC and cast iron biofilms, respectively, suggesting that bacterial colonization on the material surfaces was selective. Mycobacteria and Legionella spp. were common potential pathogenic bacteria occurred in the biofilm samples, but their abundance was different in the two biofilm bacterial communities. In contrast, the biofilm samples showed more similar eukaryotic communities than the bulk water. Notably, potential pathogenic fungi, i.e., Aspergillus spp. and Candida parapsilosis, occurred in similar abundance in both biofilms. These results indicated that microbial community, especially bacterial composition was remarkably affected by the different pipe materials (PVC and cast iron).

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Section: Bacterial Communitiesmentioning

confidence: 99%

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system

Liu

Zhu

et al. 2014

Journal of Environmental Sciences

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“…They are ubiquitous in water and soil but can also be found in sewage treatment plants (1). Some strains have been characterized by their denitrification capacities (2)(3)(4)(5). They have often been identified as major players in denitrification systems supplemented with methanol (4,(6)(7)(8), and their presence has been associated with high denitrification rates (9,10).…”

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confidence: 99%

“…Previous studies using DNA hybridization with probes targeting genes encoding the catalytic subunit of denitrification reductases (narG, nirK, nirS, and nosZ) detected denitrification genes in several members of the genus Hyphomicrobium, including H. denitrificans and H. zavarzinii (2,3). H. denitrificans (5) is commonly found in soils, freshwater environments, and activated sludge.…”

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confidence: 99%

“…H. denitrificans (5) is commonly found in soils, freshwater environments, and activated sludge. This bacterium has the capacity to denitrify (2), and its nitrite and nitrous oxide reductases were previously characterized (15)(16)(17)(18). H. zavarzinii is a soil bacterium that has been studied mainly for the biotechnological potential of the exceptional formaldehyde dehydrogenase found in strain ZV580 (19,20).…”

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Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii

Martineau

Mauffrey

Villemur

2015

Appl Environ Microbiol

130

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Hyphomicrobium spp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. However, denitrifying Hyphomicrobium species are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. This is a comparative study of three denitrifying Hyphomicrobium species, H. denitrificans ATCC 51888, H. zavarzinii ZV622, and a newly described species, H. nitrativorans NL23, which was isolated from a denitrification system treating seawater. Whole-genome sequence analyses revealed that although they share numerous orthologous genes, these three species differ greatly in their nitrate reductases, with gene clusters encoding a periplasmic nitrate reductase (Nap) in H. nitrativorans, a membrane-bound nitrate reductase (Nar) in H. denitrificans, and one Nap and two Nar enzymes in H. zavarzinii. Concurrently with these differences observed at the genetic level, important differences in the denitrification capacities of these Hyphomicrobium species were determined. H. nitrativorans grew and denitrified at higher nitrate and NaCl concentrations than did the two other species, without significant nitrite accumulation. Significant increases in the relative gene expression levels of the nitrate (napA) and nitrite (nirK) reductase genes were also noted for H. nitrativorans at higher nitrate and NaCl concentrations. Oxygen was also found to be a strong regulator of denitrification gene expression in both H. nitrativorans and H. zavarzinii, although individual genes responded differently in these two species. Taken together, the results presented in this study highlight the potential of H. nitrativorans as an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions. H yphomicrobium spp. are restricted facultative methylotrophs that reproduce by budding at the tip of a polar prostheca. They are ubiquitous in water and soil but can also be found in sewage treatment plants (1). Some strains have been characterized by their denitrification capacities (2-5). They have often been identified as major players in denitrification systems supplemented with methanol (4, 6-8), and their presence has been associated with high denitrification rates (9, 10).Denitrification takes place in bacterial cells where N-oxides and/or N-oxyanions serve as the terminal electron acceptor instead of oxygen (O 2 ) for energy production when oxygen depletion occurs, leading to the production of gaseous nitrogen (N 2 ) (11). Four sequential reactions are essential for the reduction of nitrate to gaseous nitrogen via nitrite, nitric oxide, and nitrous oxide intermediates, and each of these reactions is catalyzed by different enzymes, namely, nitrate reductases (Nar and Nap), nitrite reductase (Nir), nitric oxide reductase (Nor), and nitrous oxide reductase (Nos) (12)(13)(14).Previous studies using DNA hybridization with probes targeting genes encoding the catalytic...

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“…Unlabelled DNA was also isolated and extracted using the Puregene DNA-purification kit. The DNA was transferred to a Hybond-N + membrane (Amersham Pharmacia Biotech) and dot-blot hybridization was done as described by Fesefeldt et al (1998). Total DNA of strain VR1 T labelled with a DIG DNA labelling kit (Roche Diagnostics) was used as a probe.…”

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Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water

Shieh

2003

International Journal of Systematic and Evolutionary Microbiology

149

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NoteVibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water Institute of Botany, Academy Sinica, Nankang, Taipei, Taiwan A red, heterotrophic, marine bacterium, designated strain VR1 T , was isolated from a sea-water sample collected in the shallow coastal region of Keelung, Taiwan. Cells of the novel strain were facultatively anaerobic, Gram-negative rods that were motile by means of a polar flagellum. The strain grew optimally at 25-30˚C and pH 6-7. Growth required the presence of NaCl, the optimal concentration being about 2 %. The red pigment produced by the cells was identified as prodigiosin. Strain VR1 T grew anaerobically by fermenting glucose and other carbohydrates and producing acids and gases. The strain did not require either vitamins or other organic growth factors for growth. It contained 2-OH-16 : 0 and 3-OH-14 : 0 as the major cellular fatty acids. The DNA G+C content was 45?8 mol%. Phenotypic and chemotaxonomic characterization indicated that strain VR1 T represents a novel species in the genus Vibrio. Strain VR1 T is phenotypically similar to Vibrio gazogenes. However, the reduction of nitrate to nitrite, the ability to utilize D-arabinose, melibiose and L-glycine as sole carbon sources, the inability to utilize sorbitol as a sole carbon source, resistance to O/129 and susceptibility to erythromycin and novobiocin allow differentiation between V. gazogenes and strain VR1 T . The name Vibrio ruber sp. nov. is proposed for the novel species, with strain VR1 T (=CCRC 17186 T =JCM 11486 T ) as the type strain.Marine, halophilic, facultatively anaerobic, Gram-negative, rod-shaped bacteria are currently placed in the genera Vibrio , Photobacterium , Listonella (MacDonell & Colwell, 1985) and Moritella (Urakawa et al., 1998) of the family Vibrionaceae. They are ubiquitous in estuarine, coastal and oceanic waters and in marine sediments (Huq & Colwell, 1995;Simidu & Tsukamoto, 1985;Simidu et al., 1982). They are closely associated with many kinds of marine organisms, from plankton to fish (Cerdà-Cuéllar et al., 1997;MacDonald et al., 1986;Nair et al., 1988;Onarheim et al., 1994;Simidu et al., 1969Simidu et al., , 1971Sochard et al., 1979). Some species are found as symbionts in specialized luminous organs of marine fish and invertebrates (Lee & Ruby, 1994;Leisman et al., 1980;Reichelt et al., 1977;Ruby & Asato, 1993;Ruby & Morin, 1978), whereas many other species are pathogens of humans or marine animals (Blake et al., 1980;Borrego et al., 1996;Egidius et al., 1986;Hada et al., 1984;Ishimaru et al., 1996;Schiewe et al., 1981). These halophilic, facultatively anaerobic, Gram-negative rods are known to include both nitrogen-fixers and denitrifiers (Guerinot & Colwell, 1985;Guerinot et al., 1982;Shieh & Lin, 1992Shieh & Liu, 1996;Shieh & Yang, 1997;Shieh et al., 1989), though the definitions given in Bergey's Manual of Systematic Bacteriology in 1984 indicated that these bacteria include neither nitrogen-fixers nor denitrifiers Baumann & Schubert, 1984;.Vibrio a...

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Distribution of denitrification and nitrogen fixation genes inHyphomicrobiumspp. and other budding bacteria

Cited by 29 publications

References 19 publications

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system

Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii

Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water

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