Assessment of Changes in Microbial Community Structure during Operation of an Ammonia Biofilter with Molecular Tools

Sakano, Yuko; Kerkhof, Lee J.

doi:10.1128/aem.64.12.4877-4882.1998

Cited by 89 publications

(44 citation statements)

References 30 publications

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“…4a). The majority of the clones were most closely related to uncultivated marine bacterioplankton, including the SAR11 cluster from coastal California waters [53], the Sargasso Sea [54], an ammonia bio¢lter [55], and the North Sea (unpublished). Additionally, a number of clones from this study were closely related to the cultured marine bacterium Sphingomonas spp.…”

Section: The K-proteobacteria Groupmentioning

confidence: 98%

Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption

Huber

2003

FEMS Microbiology Ecology

140

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The bacterial diversity in a diffuse flow hydrothermal vent habitat at Axial Volcano, Juan de Fuca Ridge was examined shortly after an eruptive event in 1998 and again in 1999 and 2000 using PCR-amplified 16S rRNA gene sequence analyses. While considerable overlap with deep-sea background seawater was found within the K-and Q-proteobacteria, unique subseafloor phylotypes were distinguishable. These included diverse members of the O-proteobacteria, high temperature groups such as Desulfurobacterium, Gram-positive bacteria, and members of novel candidate divisions WS6 and ABY1. Phylotype richness was highest in the particle-attached populations from all three sampling periods, and diversity appeared to increase over that time, particularly among the O-proteobacteria. A preliminary model of the subseafloor is presented that relates microbial diversity to temperature, chemical characteristics of diffuse flow fluids and the degree of mixing with seawater.

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Section: The K-proteobacteria Groupmentioning

confidence: 98%

Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption

Huber

2003

FEMS Microbiology Ecology

140

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“…Only a few cultivation-independent studies of microbial diversity in biofilters have been conducted (Sakano and Kerkhof, 1998;Friedrich et al ., 1999;von Keitz et al ., 1999). In only one of these studies were 16S rDNA gene sequences retrieved.…”

Section: Introductionmentioning

confidence: 99%

High bacterial diversity of a waste gas‐degrading community in an industrial biofilter as shown by a 16S rDNA clone library

Friedrich

Prior

Altendorf

et al. 2002

Environmental Microbiology

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The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal-rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer-aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA patterns and the remaining 174 clones were clustered into 65 groups. Almost full-length 16S rDNA sequences of 106 clones were determined and 90.5% of the clones were affiliated with the two phyla Proteobacteria and Bacteroidetes. Alpha-, Beta-, and Gammaproteobacteria accounted for 22.1, 17.6 and 18.6% respectively. Minor portions were affiliated with the Actinobacteria (2.0%), Firmicutes and Verrucomicrobia (both 1.0%), and the Deltaproteobacteria and Thermomicrobia (each 0.5%). Only six out of the 106 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species indicating that a substantial fraction of the clone sequences were derived from unknown taxa. It was also evaluated whether a database containing 281 computer-simulated bacterial rDNA fragment patterns generated from published reference sequences can be used for identification purposes. The data analysis demonstrated that this was possible only for a small number of clones, which were closely related to described bacterial strains. Rarefaction analysis of ARDRA clusters demonstrated that the 444 clones screened are insufficient to describe the entire diversity of the clone library.

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“…Ammonia oxidation in RAS is generally associated with two specific bacterial genera identified as Nitrosomonas and Nitrosospira (Sakano & Kerkhof, 1998;Foesel et al, 2008). The elevated proportion of Nitrosospira compared with other nitrifying bacteria populations in unit 2 early during operation may be due to the higher concentrations of TOC and increased turbidity that inhibited the growth of Nitrosomonas (Kr€ ummel & Harms, 1982) and supported the growth of heterotrophic bacteria in the biofilter (Nogueira et al, 2002;Michaud et al, 2006).…”

mentioning

confidence: 99%

Impact of water quality on the bacterial populations and off-flavours in recirculating aquaculture systems

Auffret

Yergeau

Pilote

et al. 2013

FEMS Microbiol Ecol

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A variety of factors affecting water quality in recirculating aquaculture systems (RAS) are associated with the occurrence of off-flavours. In this study, we report the impact of water quality on the bacterial diversity and the occurrence of the geosmin-synthesis gene (geoA) in two RAS units operated for 252 days. Unit 2 displayed a higher level of turbidity and phosphate, which affected the fresh water quality compared with unit 1. In the biofilter, nitrification is one of the major processes by which high water quality is maintained. The bacterial population observed in the unit 1 biofilter was more stable throughout the experiment, with a higher level of nitrifying bacteria compared with the unit 2 biofilter. Geosmin appeared in fish flesh after 84 days in unit 2, whereas it appeared in unit 1 after 168 days, but at a much lower level. The geoA gene was detected in both units, 28 days prior to the detection of geosmin in fish flesh. In addition, we detected sequences associated with Sorangium and Nannocystis (Myxococcales): members of these genera are known to produce geosmin. These sequences were observed at an earlier time in unit 2 and at a higher level than in unit 1. This study confirms the advantages of new molecular methods to understand the occurrence of geosmin production in RAS.

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Assessment of Changes in Microbial Community Structure during Operation of an Ammonia Biofilter with Molecular Tools

Cited by 89 publications

References 30 publications

Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption

Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption

High bacterial diversity of a waste gas‐degrading community in an industrial biofilter as shown by a 16S rDNA clone library

Impact of water quality on the bacterial populations and off-flavours in recirculating aquaculture systems

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