Abstract
Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2–8 × 107 16S rRNA gene copies cm−3) than the high-salinity marine sites from BR and AR (2 × 104–2 × 107 and 4 × 106–2 × 107 16S rRNA gene copies cm−3, respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the ‘Bathyarchaeota’ (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only ‘marine’ group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.
Highlights
Estuaries are semi-enclosed coastal bodies of water where rivers meet the sea, and because estuaries are interfaces between riverine and marine habitats, they are extremely dynamic, with steep physico-chemical gradients due to variability of freshwater input, geomorphology and tidal heights (Meire et al, 2005; Bernhard and Bollmann 2010)
This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses
Phylogenetic analysis showed that members of the ‘Bathyarchaeota’ (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea
Summary
Estuaries are semi-enclosed coastal bodies of water where rivers meet the sea, and because estuaries are interfaces between riverine and marine habitats, they are extremely dynamic, with steep physico-chemical gradients due to variability of freshwater input, geomorphology and tidal heights (Meire et al, 2005; Bernhard and Bollmann 2010). Estuaries exhibit strong gradients along their course with organic matter and nitrogen concentrations normally decreasing away from the estuary head, and chloride and sulphate increasing towards the estuary mouth. The resulting gradients in salinity, turbidity, nutrients and organic matter influence the composition of the estuarine prokaryotic community (Crump et al, 2004; Freitag, Chang and Prosser 2006; Bernhard and Bollmann 2010), and this community, in turn, is critical in controlling the function and structure of estuarine ecosystems (Day et al, 1989). Since estuaries tend to have high concentrations of nutrients, they exhibit elevated primary production and heterotrophic activity that result in high levels of microbial activity in the upper sediment layers, which subsequently generate steep biogeochemical gradients with depth (Canfield and Thamdrup 2009). Relatively little is known about the diversity of the estuarine sediment prokaryotic community, and in particular the Archaea
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