PMID- 30315079
OWN - NLM
STAT- MEDLINE
DCOM- 20191011
LR  - 20231004
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 84
IP  - 24
DP  - 2018 Dec 15
TI  - Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox).
LID - 10.1128/AEM.01390-18 [doi]
LID - e01390-18
AB  - The discovery of complete ammonia oxidizers (comammox) refutes the century-old 
      paradigm that nitrification requires the activity of two types of microbes. 
      Determining the distribution and abundance of comammox in various environments is 
      important for revealing the ecology of microbial nitrification within the global 
      nitrogen cycle. In this study, the ubiquity and diversity of comammox were 
      analyzed for samples from different types of environments, including soil, 
      sediment, sludge, and water. The results of a two-step PCR using highly 
      degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the 
      relatively high abundance of comammox in nearly half of all samples tested, 
      sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In 
      addition, a relatively high proportion of comammox in tap and coastal water 
      samples was confirmed via analysis of metagenomic data sets in public databases. 
      The diversity of comammox was estimated by comammox-specific partial nested PCR 
      amplification of the ammonia monooxygenase subunit A (amoA) gene, and 
      phylogenetic analysis of comammox AmoA clearly showed a split of clade A into 
      clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing 
      among the various environmental samples. Moreover, compared to the amoA genes of 
      AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher 
      diversity indices. The ubiquitous distribution and high diversity of comammox 
      indicate that they are likely overlooked contributors to nitrification in various 
      ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), 
      which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm 
      that nitrification requires the activity of two types of microbes and redefines a 
      key process in the biogeochemical nitrogen cycle. Understanding the functional 
      relationships between comammox and other nitrifiers is important for ecological 
      studies on the nitrogen cycle. Therefore, the diversity and contribution of 
      comammox should be considered during ecological analyses of nitrifying 
      microorganisms. In this study, a ubiquitous and highly diverse distribution of 
      comammox was observed in various environmental samples, similar to the 
      distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox 
      was relatively high in coastal water and sediment samples, whereas it was nearly 
      undetectable in open-ocean samples. The ubiquitous distribution and high 
      diversity of comammox indicate that these microorganisms might be important 
      contributors to nitrification.
CI  - Copyright (c) 2018 American Society for Microbiology.
FAU - Xia, Fei
AU  - Xia F
AD  - Ministry of Education Key Laboratory for Biodiversity Science and Ecological 
      Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan 
      University, Shanghai, China.
AD  - School of Food and Biological Engineering, Shaanxi University of Science and 
      Technology, Xi'an, China.
FAU - Wang, Jian-Gong
AU  - Wang JG
AD  - Ministry of Education Key Laboratory for Biodiversity Science and Ecological 
      Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan 
      University, Shanghai, China.
FAU - Zhu, Ting
AU  - Zhu T
AD  - Ministry of Education Key Laboratory for Biodiversity Science and Ecological 
      Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan 
      University, Shanghai, China.
FAU - Zou, Bin
AU  - Zou B
AD  - Ministry of Education Key Laboratory for Biodiversity Science and Ecological 
      Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan 
      University, Shanghai, China.
FAU - Rhee, Sung-Keun
AU  - Rhee SK
AD  - Department of Microbiology, Chungbuk National University, Cheongju, Republic of 
      Korea.
FAU - Quan, Zhe-Xue
AU  - Quan ZX
AUID- ORCID: 0000-0002-7561-8572
AD  - Ministry of Education Key Laboratory for Biodiversity Science and Ecological 
      Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan 
      University, Shanghai, China quanzx@fudan.edu.cn.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20181130
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
RN  - 0 (Nitrates)
RN  - 0 (Nitrites)
RN  - 0 (Sewage)
RN  - 0 (Soil)
RN  - 059QF0KO0R (Water)
RN  - 7664-41-7 (Ammonia)
RN  - EC 1.- (Oxidoreductases)
RN  - EC 1.7.3.- (ammonia monooxygenase)
SB  - IM
MH  - Ammonia/*metabolism
MH  - Archaea/genetics/*metabolism
MH  - Bacteria/genetics/*metabolism
MH  - Geologic Sediments/chemistry
MH  - Metagenomics
MH  - Nitrates/metabolism
MH  - Nitrification
MH  - Nitrites/metabolism
MH  - Nitrogen Cycle
MH  - Oxidation-Reduction
MH  - Oxidoreductases/genetics
MH  - Phylogeny
MH  - Sewage/chemistry
MH  - Soil/chemistry
MH  - Soil Microbiology
MH  - Water/chemistry
PMC - PMC6275355
OTO - NOTNLM
OT  - AOA
OT  - AOB
OT  - comammox
OT  - diversity
OT  - metagenome
OT  - partial nested PCR
EDAT- 2018/10/14 06:00
MHDA- 2019/10/12 06:00
PMCR- 2019/05/30
CRDT- 2018/10/14 06:00
PHST- 2018/06/08 00:00 [received]
PHST- 2018/10/03 00:00 [accepted]
PHST- 2018/10/14 06:00 [pubmed]
PHST- 2019/10/12 06:00 [medline]
PHST- 2018/10/14 06:00 [entrez]
PHST- 2019/05/30 00:00 [pmc-release]
AID - AEM.01390-18 [pii]
AID - AEM01390-18 [pii]
AID - 10.1128/AEM.01390-18 [doi]
PST - epublish
SO  - Appl Environ Microbiol. 2018 Nov 30;84(24):e01390-18. doi: 10.1128/AEM.01390-18. 
      Print 2018 Dec 15.