PMID- 23577005
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20130412
LR  - 20220409
IS  - 1664-302X (Print)
IS  - 1664-302X (Electronic)
IS  - 1664-302X (Linking)
VI  - 4
DP  - 2013
TI  - An analysis of thaumarchaeota populations from the northern gulf of Mexico.
PG  - 72
LID - 10.3389/fmicb.2013.00072 [doi]
LID - 72
AB  - We sampled Thaumarchaeota populations in the northern Gulf of Mexico, including 
      shelf waters under the Mississippi River outflow plume that are subject to 
      recurrent hypoxia. Data from this study allowed us to: (1) test the hypothesis 
      that Thaumarchaeota would be abundant in this region; (2) assess phylogenetic 
      composition of these populations for comparison with other regions; (3) compare 
      the efficacy of quantitative PCR (qPCR) based on primers for 16S rRNA genes (rrs) 
      with primers for genes in the ammonia oxidation (amoA) and carbon fixation (accA, 
      hcd) pathways; (4) compare distributions obtained by qPCR with the relative 
      abundance of Thaumarchaeota rrs in pyrosequenced libraries; (5) compare 
      Thaumarchaeota distributions with environmental variables to help us elucidate 
      the factors responsible for the distributions; (6) compare the distribution of 
      Thaumarchaeota with Nitrite-Oxidizing Bacteria (NOB) to gain insight into the 
      coupling between ammonia and nitrite oxidation. We found up to 10(8) copies L(-1) 
      of Thaumarchaeota rrs in our samples (up to 40% of prokaryotes) by qPCR, with 
      maximum abundance in slope waters at 200-800 m. Thaumarchaeota rrs were also 
      abundant in pyrosequenced libraries and their relative abundance correlated well 
      with values determined by qPCR (r (2) = 0.82). Thaumarchaeota populations were 
      strongly stratified by depth. Canonical correspondence analysis using a suite of 
      environmental variables explained 92% of the variance in qPCR-estimated gene 
      abundances. Thaumarchaeota rrs abundance was correlated with salinity and depth, 
      while accA abundance correlated with fluorescence and pH. Correlations of 
      Archaeal amoA abundance with environmental variables were primer-dependent, 
      suggesting differential responses of sub-populations to environmental variables. 
      Bacterial amoA was at the limit of qPCR detection in most samples. NOB and 
      Euryarchaeota rrs were found in the pyrosequenced libraries; NOB distribution was 
      correlated with that of Thaumarchaeota (r (2) = 0.49).
FAU - Tolar, Bradley B
AU  - Tolar BB
AD  - Department of Marine Sciences, University of Georgia Athens, GA, USA ; Department 
      of Microbiology, University of Georgia Athens, GA, USA.
FAU - King, Gary M
AU  - King GM
FAU - Hollibaugh, James T
AU  - Hollibaugh JT
LA  - eng
PT  - Journal Article
DEP - 20130409
PL  - Switzerland
TA  - Front Microbiol
JT  - Frontiers in microbiology
JID - 101548977
PMC - PMC3620491
OTO - NOTNLM
OT  - 4-hydroxybutyryl-CoA dehydratase
OT  - Gulf of Mexico
OT  - acetyl-CoA/propionyl-CoA carboxylase
OT  - ammonia monooxygenase
OT  - euryarchaeota
OT  - hypoxia
OT  - nitrite-oxidizing Bacteria
OT  - thaumarchaeota
EDAT- 2013/04/12 06:00
MHDA- 2013/04/12 06:01
PMCR- 2013/04/09
CRDT- 2013/04/12 06:00
PHST- 2012/11/16 00:00 [received]
PHST- 2013/03/14 00:00 [accepted]
PHST- 2013/04/12 06:00 [entrez]
PHST- 2013/04/12 06:00 [pubmed]
PHST- 2013/04/12 06:01 [medline]
PHST- 2013/04/09 00:00 [pmc-release]
AID - 10.3389/fmicb.2013.00072 [doi]
PST - epublish
SO  - Front Microbiol. 2013 Apr 9;4:72. doi: 10.3389/fmicb.2013.00072. eCollection 
      2013.