PMID- 26140533
OWN - NLM
STAT- MEDLINE
DCOM- 20160823
LR  - 20220129
IS  - 1751-7370 (Electronic)
IS  - 1751-7362 (Print)
IS  - 1751-7362 (Linking)
VI  - 10
IP  - 1
DP  - 2016 Jan
TI  - Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.
PG  - 85-96
LID - 10.1038/ismej.2015.101 [doi]
AB  - Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both 
      the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia 
      oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The 
      ecology of AOA in terrestrial environments has been extensively studied using 
      either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S 
      ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to 
      soil pH. To test phylogenetic congruence between these two markers and to 
      determine ecological coherence in all Thaumarchaeota, we performed 
      high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 
      29 available contextual soil characteristics. Adaptation to pH and organic matter 
      content reflected strong ecological coherence at various levels of taxonomic 
      resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total 
      mineralisable nitrogen and zinc concentration were also important factors 
      associated with AOA thaumarchaeotal community distribution. Other significant 
      associations with environmental factors were also detected for amoA and 16S rRNA 
      genes, reflecting different diversity characteristics between these two markers. 
      Nonetheless, there was significant statistical congruence between the markers at 
      fine phylogenetic resolution, supporting the hypothesis of low horizontal gene 
      transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely 
      distributed, with two clusters predominating, particularly in environments with 
      higher moisture content and organic matter, whereas a similar ecological pattern 
      was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic 
      congruence identified is fundamental to understand better the life strategies, 
      evolutionary history and ecosystem function of the Thaumarchaeota.
FAU - Oton, Eduard Vico
AU  - Oton EV
AD  - Institute of Biological and Environmental Sciences, University of Aberdeen, 
      Cruickshank Building, Aberdeen, UK.
AD  - School of Life Sciences, Centre for Biomolecular Sciences, University of 
      Nottingham, Nottingham, UK.
FAU - Quince, Christopher
AU  - Quince C
AD  - Warwick Medical School, University of Warwick, Warwick, UK.
FAU - Nicol, Graeme W
AU  - Nicol GW
AD  - Institute of Biological and Environmental Sciences, University of Aberdeen, 
      Cruickshank Building, Aberdeen, UK.
AD  - Laboratoire Ampere UMR CNRS 5005, Ecole Centrale de Lyon, Universite de Lyon, 
      Ecully CEDEX, France.
FAU - Prosser, James I
AU  - Prosser JI
AD  - Institute of Biological and Environmental Sciences, University of Aberdeen, 
      Cruickshank Building, Aberdeen, UK.
FAU - Gubry-Rangin, Cecile
AU  - Gubry-Rangin C
AD  - Institute of Biological and Environmental Sciences, University of Aberdeen, 
      Cruickshank Building, Aberdeen, UK.
LA  - eng
GR  - MR/L015080/1/MRC_/Medical Research Council/United Kingdom
GR  - MR/M50161X/1/MRC_/Medical Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150703
PL  - England
TA  - ISME J
JT  - The ISME journal
JID - 101301086
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Soil)
RN  - 7664-41-7 (Ammonia)
RN  - EC 1.- (Oxidoreductases)
RN  - EC 1.7.3.- (ammonia monooxygenase)
RN  - N762921K75 (Nitrogen)
SB  - IM
MH  - Adaptation, Biological
MH  - Ammonia/analysis
MH  - Archaea/*genetics
MH  - *Biodiversity
MH  - Biological Evolution
MH  - DNA, Bacterial/genetics
MH  - Ecology
MH  - Ecosystem
MH  - Multivariate Analysis
MH  - Nitrogen/analysis
MH  - Oxidation-Reduction
MH  - Oxidoreductases
MH  - *Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
MH  - Soil/*chemistry
MH  - *Soil Microbiology
PMC - PMC4604658
MID - EMS63403
EDAT- 2015/07/04 06:00
MHDA- 2016/08/24 06:00
PMCR- 2016/01/01
CRDT- 2015/07/04 06:00
PHST- 2015/01/27 00:00 [received]
PHST- 2015/04/13 00:00 [revised]
PHST- 2015/05/08 00:00 [accepted]
PHST- 2015/07/04 06:00 [entrez]
PHST- 2015/07/04 06:00 [pubmed]
PHST- 2016/08/24 06:00 [medline]
PHST- 2016/01/01 00:00 [pmc-release]
AID - ismej2015101 [pii]
AID - 10.1038/ismej.2015.101 [doi]
PST - ppublish
SO  - ISME J. 2016 Jan;10(1):85-96. doi: 10.1038/ismej.2015.101. Epub 2015 Jul 3.