Abstract
The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.
Highlights
The Elbe Estuary is a highly dynamic environment
The population structure of ß-ammonia-oxidizing bacteria (AOB) was analyzed by deep sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons
The aim of the present study was to prove the assumption that the community composition of ß-AOB might indicate the environmental dynamics of river habitats, exemplarily examined at the freshwater region of the Elbe Estuary
Summary
The Elbe Estuary is a highly dynamic environment. Its particular complexity results from both natural forces and anthropogenic influences. The present study is consciously limited to the bacterial ammonia oxidizers (AOB) which are considered to belong to the most thoroughly investigated nitrifiers[15]. They can be regarded as one of the few cases in microbial ecology where pure cultures of most recognized lineages of descent are available[16]. With the exception of the halophilic Nitrosococcus species[17,18,19,20] and the recently proposed Candidatus Nitrosoglobus terrae isolated from acidic s oils[19] all AOB belong to the family N itrosomonadaceae[21] within the (recently proposed to be obsolete22) class Betaproteobacteria These organisms are hereinafter designated as ß-AOB. This provides the opportunity for comparisons to reveal causal relations between abundance of certain AOB-lineages and the environmental situation at specific sites
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