title: Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.
abstract: Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible.
authors: Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark.
authors: Bärbel U
authors: BU
authors: Foesel
authors: Armin
authors: A
authors: Gieseke
authors: Carsten
authors: C
authors: Schwermer
authors: Peter
authors: P
authors: Stief
authors: Liat
authors: L
authors: Koch
authors: Eddie
authors: E
authors: Cytryn
authors: José R
authors: JR
authors: de la Torré
authors: Jaap
authors: J
authors: van Rijn
authors: Dror
authors: D
authors: Minz
authors: Harold L
authors: HL
authors: Drake
authors: Andreas
authors: A
authors: Schramm
mesh_terms: D000641:Ammonia / Q000378:metabolism; D017756:Aquaculture; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D001483:Base Sequence; D018441:Biofilms; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater; D017423:Sequence Analysis, RNA
chemical_list: D009573:Nitrites; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase