Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats.
In order to study the diversity of ammonia-oxidising bacteria in freshwater habitats, including sediments, a molecular approach focused on the sequencing of 16S rDNA was adopted. 16S rDNA sequences showing affinity with the beta-subgroup of ammonia-oxidising bacteria were recovered by specific PCR of directly isolated DNA from freshwater samples, and samples from brackish water and Glyceria maxima rhizosphere were included in the analysis for comparison. The ammonia oxidiser-like sequences recovered from several locations, which exhibit differences in the composition of their total microbial communities as indicated by denaturing gradient gel electrophoresis, formed a strong monophyletic cluster including Nitrosomonas ureae. This is the first report presenting sequences from an apparently dominant group of Nitrosomonas-like organisms among the beta-subdivision of ammonia-oxidising bacteria in freshwater environments. This group of sequences extends the known diversity within the beta-subgroup of ammonia-oxidisers. The new sequences related to Nitrosomonas ureae do not match with some published primers and probes designed for the detection of Nitrosomonas species, which may explain why these sequences have not previously been detected in freshwater habitats. The sequence diversity detected within this group of sequences was minimal across the environments examined, and no patterns of distribution were indicated with respect to environmental factors such as sediment depth or location.
Speksnijder
A G
AG
Netherlands Institute of Ecology-Centre for Limnology, Department of Microbial Ecology, Nieuwersluis, The Netherlands.
Kowalchuk
G A
GA
Roest
K
K
Laanbroek
H J
HJ
D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry; D004275:DNA, Ribosomal / Q000737:chemistry*; D004587:Electrophoresis, Agar Gel; D005618:Fresh Water / Q000737:chemistry / Q000382:microbiology*; D015723:Gene Library; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology*; D008969:Molecular Sequence Data; D009426:Netherlands; D009606:Nitrosomonas / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014871:Water Microbiology
D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S