Whitby, Corinne B and Saunders, Jon R and Rodriguez, Juana and Pickup, Roger W and McCarthy, Alan (1999) Phylogenetic Differentiation of Two Closely Related <i>Nitrosomonas</i> spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake. Applied and Environmental Microbiology, 65 (11). pp. 4855-4862. DOI https://doi.org/10.1128/aem.65.11.4855-4862.1999
Whitby, Corinne B and Saunders, Jon R and Rodriguez, Juana and Pickup, Roger W and McCarthy, Alan (1999) Phylogenetic Differentiation of Two Closely Related <i>Nitrosomonas</i> spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake. Applied and Environmental Microbiology, 65 (11). pp. 4855-4862. DOI https://doi.org/10.1128/aem.65.11.4855-4862.1999
Whitby, Corinne B and Saunders, Jon R and Rodriguez, Juana and Pickup, Roger W and McCarthy, Alan (1999) Phylogenetic Differentiation of Two Closely Related <i>Nitrosomonas</i> spp. That Inhabit Different Sediment Environments in an Oligotrophic Freshwater Lake. Applied and Environmental Microbiology, 65 (11). pp. 4855-4862. DOI https://doi.org/10.1128/aem.65.11.4855-4862.1999
Abstract
<jats:title>ABSTRACT</jats:title> <jats:p> The population of ammonia-oxidizing bacteria in a temperate oligotrophic freshwater lake was analyzed by recovering 16S ribosomal DNA (rDNA) from lakewater and sediment samples taken throughout a seasonal cycle. <jats:italic>Nitrosospira</jats:italic> and <jats:italic>Nitrosomonas</jats:italic> 16S rRNA genes were amplified in a nested PCR, and the identity of the products was confirmed by oligonucleotide hybridization. <jats:italic>Nitrosospira</jats:italic> DNA was readily identified in all samples, and nitrosomonad DNA of the <jats:italic>Nitrosomonas europaea-Nitrosomonas eutropha</jats:italic> lineage was also directly detected, but during the summer months only. Phylogenetic delineation with partial (345 bp) 16S rRNA gene sequences of clones obtained from sediments confirmed the fidelity of the amplified nitrosomonad DNA and identified two sequence clusters closely related to either <jats:italic>N. europaea</jats:italic> or <jats:italic>N. eutropha</jats:italic> that were equated with the littoral and profundal sediment sites, respectively. Determination of 701-bp sequences for 16S rDNA clones representing each cluster confirmed this delineation. A PCR-restriction fragment length polymorphism (RFLP) system was developed that enabled identification of clones containing <jats:italic>N. europaea</jats:italic> and <jats:italic>N. eutropha</jats:italic> 16S rDNA sequences, including subclasses therein. It proved possible to analyze 16S rDNA amplified directly from sediment samples to determine the relative abundance of each species compared with that of the other. <jats:italic>N. europaea</jats:italic> and <jats:italic>N. eutropha</jats:italic> are very closely related, and direct evidence for their presence in lake systems is limited. The correlation of each species with a distinct spatial location in sediment is an unusual example of niche adaptation by two genotypically similar bacteria. Their occurrence and relative distribution can now be routinely monitored in relation to environmental variation by the application of PCR-RFLP analysis. </jats:p>
Item Type: | Article |
---|---|
Uncontrolled Keywords: | Nitrosomonas; DNA, Bacterial; DNA, Ribosomal; RNA, Bacterial; RNA, Ribosomal, 16S; Cloning, Molecular; Polymerase Chain Reaction; Fresh Water; Phylogeny; Polymorphism, Restriction Fragment Length; Geologic Sediments |
Subjects: | Q Science > QH Natural history > QH301 Biology |
Divisions: | Faculty of Science and Health Faculty of Science and Health > Life Sciences, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 27 Jul 2017 13:23 |
Last Modified: | 11 Dec 2024 12:39 |
URI: | http://repository.essex.ac.uk/id/eprint/15843 |