PMID- 18200070
OWN - NLM
STAT- MEDLINE
DCOM- 20080520
LR  - 20131121
IS  - 1751-7362 (Print)
IS  - 1751-7362 (Linking)
VI  - 2
IP  - 4
DP  - 2008 Apr
TI  - Molecular and biogeochemical evidence for ammonia oxidation by marine 
      Crenarchaeota in the Gulf of California.
PG  - 429-41
LID - 10.1038/ismej.2007.118 [doi]
AB  - Nitrification plays an important role in marine biogeochemistry, yet efforts to 
      link this process to the microorganisms that mediate it are surprisingly limited. 
      In particular, ammonia oxidation is the first and rate-limiting step of 
      nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing 
      bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have 
      not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), 
      although mounting evidence indicates that marine Crenarchaeota are capable of 
      ammonia oxidation, and they are among the most abundant microbial groups in the 
      ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, 
      and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase 
      subunit A (amoA) genes, in the Gulf of California. Based on markedly different 
      archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum 
      zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target 
      and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers 
      recovered extensive variability with depth. Within the OMZ, AOA were most 
      abundant where nitrification may be coupled to denitrification. In the upper 
      water column, group A tracked variations in nitrogen biogeochemistry with depth 
      and between basins, whereas AOB were present in relatively low numbers or 
      undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated 
      with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene 
      copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent 
      compelling evidence for an archaeal role in oceanic nitrification.
FAU - Beman, J Michael
AU  - Beman JM
AD  - Department of Geological and Environmental Sciences, Stanford University, 
      Stanford, CA, USA. jmbeman@gmail.com
FAU - Popp, Brian N
AU  - Popp BN
FAU - Francis, Christopher A
AU  - Francis CA
LA  - eng
SI  - GENBANK/EU340464
SI  - GENBANK/EU340465
SI  - GENBANK/EU340466
SI  - GENBANK/EU340467
SI  - GENBANK/EU340468
SI  - GENBANK/EU340469
SI  - GENBANK/EU340470
SI  - GENBANK/EU340471
SI  - GENBANK/EU340472
SI  - GENBANK/EU340473
SI  - GENBANK/EU340474
SI  - GENBANK/EU340475
SI  - GENBANK/EU340476
SI  - GENBANK/EU340477
SI  - GENBANK/EU340478
SI  - GENBANK/EU340479
SI  - GENBANK/EU340480
SI  - GENBANK/EU340481
SI  - GENBANK/EU340482
SI  - GENBANK/EU340483
SI  - GENBANK/EU340484
SI  - GENBANK/EU340485
SI  - GENBANK/EU340486
SI  - GENBANK/EU340487
SI  - GENBANK/EU340488
SI  - GENBANK/EU340489
SI  - GENBANK/EU340490
SI  - GENBANK/EU340491
SI  - GENBANK/EU340492
SI  - GENBANK/EU340493
SI  - GENBANK/EU340494
SI  - GENBANK/EU340495
SI  - GENBANK/EU340496
SI  - GENBANK/EU340497
SI  - GENBANK/EU340498
SI  - GENBANK/EU340499
SI  - GENBANK/EU340500
SI  - GENBANK/EU340501
SI  - GENBANK/EU340502
SI  - GENBANK/EU340503
SI  - GENBANK/EU340504
SI  - GENBANK/EU340505
SI  - GENBANK/EU340506
SI  - GENBANK/EU340507
SI  - GENBANK/EU340508
SI  - GENBANK/EU340509
SI  - GENBANK/EU340510
SI  - GENBANK/EU340511
SI  - GENBANK/EU340512
SI  - GENBANK/EU340513
SI  - GENBANK/EU340514
SI  - GENBANK/EU340515
SI  - GENBANK/EU340516
SI  - GENBANK/EU340517
SI  - GENBANK/EU340518
SI  - GENBANK/EU340519
SI  - GENBANK/EU340520
SI  - GENBANK/EU340521
SI  - GENBANK/EU340522
SI  - GENBANK/EU340523
SI  - GENBANK/EU340524
SI  - GENBANK/EU340525
SI  - GENBANK/EU340526
SI  - GENBANK/EU340527
SI  - GENBANK/EU340528
SI  - GENBANK/EU340529
SI  - GENBANK/EU340530
SI  - GENBANK/EU340531
SI  - GENBANK/EU340532
SI  - GENBANK/EU340533
SI  - GENBANK/EU340534
SI  - GENBANK/EU340535
SI  - GENBANK/EU340536
SI  - GENBANK/EU340537
SI  - GENBANK/EU340538
SI  - GENBANK/EU340539
SI  - GENBANK/EU340540
SI  - GENBANK/EU340541
SI  - GENBANK/EU340542
SI  - GENBANK/EU340543
SI  - GENBANK/EU340544
SI  - GENBANK/EU340545
SI  - GENBANK/EU340546
SI  - GENBANK/EU340547
SI  - GENBANK/EU340548
SI  - GENBANK/EU340549
SI  - GENBANK/EU340550
SI  - GENBANK/EU340551
SI  - GENBANK/EU340552
SI  - GENBANK/EU340553
SI  - GENBANK/EU340554
SI  - GENBANK/EU340555
SI  - GENBANK/EU340556
PT  - Journal Article
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20080117
PL  - England
TA  - ISME J
JT  - The ISME journal
JID - 101301086
RN  - 0 (DNA, Archaeal)
RN  - 0 (Nitrogen Isotopes)
RN  - 7664-41-7 (Ammonia)
RN  - EC 1.- (Oxidoreductases)
RN  - EC 1.7.3.- (ammonia monooxygenase)
RN  - N762921K75 (Nitrogen)
SB  - IM
EIN - ISME J. 2008 Apr;2(4):453
MH  - Ammonia/*metabolism
MH  - California
MH  - Crenarchaeota/*genetics/metabolism
MH  - DNA, Archaeal/analysis/isolation & purification
MH  - Molecular Sequence Data
MH  - Nitrogen/chemistry/metabolism
MH  - Nitrogen Isotopes/metabolism
MH  - Oxidation-Reduction
MH  - Oxidoreductases/genetics/metabolism
MH  - Seawater/*microbiology
MH  - Sequence Analysis, DNA
EDAT- 2008/01/18 09:00
MHDA- 2008/05/21 09:00
CRDT- 2008/01/18 09:00
PHST- 2008/01/18 09:00 [pubmed]
PHST- 2008/05/21 09:00 [medline]
PHST- 2008/01/18 09:00 [entrez]
AID - ismej2007118 [pii]
AID - 10.1038/ismej.2007.118 [doi]
PST - ppublish
SO  - ISME J. 2008 Apr;2(4):429-41. doi: 10.1038/ismej.2007.118. Epub 2008 Jan 17.