title: Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments.
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 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 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.
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK websterg@cardiff.ac.uk.
authors.forename: Gordon
authors.initials: G
authors.lastname: Webster
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Louise A
authors.initials: LA
authors.lastname: O'Sullivan
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Yiyu
authors.initials: Y
authors.lastname: Meng
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Angharad S
authors.initials: AS
authors.lastname: Williams
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Sass
authors.affiliation: School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Watkins
authors.affiliation: School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: R John
authors.initials: RJ
authors.lastname: Parkes
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, Cardiff, Wales, CF10 3AT, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Weightman
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D044822:Biodiversity; D004262:DNA Restriction Enzymes / Q000235:genetics; D019641:DNA, Archaeal / Q000235:genetics*; D063366:Estuaries; D020459:Genes, rRNA; D019015:Geologic Sediments / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D054712:Salinity; D017422:Sequence Analysis, DNA
chemical_list: D019641:DNA, Archaeal; D012336:RNA, Ribosomal, 16S; D004262:DNA Restriction Enzymes; C060629:endodeoxyribonuclease McrA
keywords: Archaea; estuarine sediment; methanogens; pyrosequencing; qPCR; salinity gradient