PMID- 32916620
OWN - NLM
STAT- MEDLINE
DCOM- 20201116
LR  - 20201116
IS  - 1879-2448 (Electronic)
IS  - 0043-1354 (Linking)
VI  - 186
DP  - 2020 Nov 1
TI  - A refined set of rRNA-targeted oligonucleotide probes for in situ detection and 
      quantification of ammonia-oxidizing bacteria.
PG  - 116372
LID - S0043-1354(20)30908-8 [pii]
LID - 10.1016/j.watres.2020.116372 [doi]
AB  - Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas 
      and Nitrosospira are key nitrifying microorganisms in many natural and engineered 
      ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization 
      (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely 
      used approaches to study the community composition, abundance, and other features 
      of AOB directly in environmental samples. However, the established and widely 
      used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades 
      ago, based on much smaller rRNA gene sequence datasets than available today. 
      Several of these probes cover their target AOB lineages incompletely and suffer 
      from a weak target specificity, which causes cross-hybridization of probes that 
      should detect different AOB lineages. Here, a set of new highly specific 16S 
      rRNA-targeted oligonucleotide probes was developed and experimentally evaluated 
      that complements the existing probes and enables the specific detection and 
      differentiation of the known, major phylogenetic clusters of betaproteobacterial 
      AOB. The new probes were successfully applied to visualize and quantify AOB in 
      activated sludge and biofilm samples from seven pilot- and full-scale wastewater 
      treatment systems. Based on its improved target group coverage and specificity, 
      the refined probe set will facilitate future in situ analyses of AOB.
CI  - Copyright (c) 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.
FAU - Lukumbuzya, Michael
AU  - Lukumbuzya M
AD  - University of Vienna, Centre for Microbiology and Environmental Systems Science, 
      Division of Microbial Ecology, Vienna, Austria.
FAU - Kristensen, Jannie Munk
AU  - Kristensen JM
AD  - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg 
      University, Aalborg, Denmark.
FAU - Kitzinger, Katharina
AU  - Kitzinger K
AD  - University of Vienna, Centre for Microbiology and Environmental Systems Science, 
      Division of Microbial Ecology, Vienna, Austria; Max Planck Institute for Marine 
      Microbiology, Bremen, Germany.
FAU - Pommerening-Roser, Andreas
AU  - Pommerening-Roser A
AD  - University of Hamburg, Institute of Plant Science and Microbiology, Microbiology 
      and Biotechnology, Hamburg, Germany.
FAU - Nielsen, Per Halkjaer
AU  - Nielsen PH
AD  - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg 
      University, Aalborg, Denmark.
FAU - Wagner, Michael
AU  - Wagner M
AD  - University of Vienna, Centre for Microbiology and Environmental Systems Science, 
      Division of Microbial Ecology, Vienna, Austria; Center for Microbial Communities, 
      Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; 
      Joint Microbiome Facility of the Medical University of Vienna and the University 
      of Vienna, Vienna, Austria; University of Vienna, The Comammox Research Platform, 
      Vienna, Austria.
FAU - Daims, Holger
AU  - Daims H
AD  - University of Vienna, Centre for Microbiology and Environmental Systems Science, 
      Division of Microbial Ecology, Vienna, Austria; University of Vienna, The 
      Comammox Research Platform, Vienna, Austria. Electronic address: 
      holger.daims@univie.ac.at.
FAU - Pjevac, Petra
AU  - Pjevac P
AD  - University of Vienna, Centre for Microbiology and Environmental Systems Science, 
      Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the 
      Medical University of Vienna and the University of Vienna, Vienna, Austria.
LA  - eng
PT  - Journal Article
DEP - 20200901
PL  - England
TA  - Water Res
JT  - Water research
JID - 0105072
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 7664-41-7 (Ammonia)
SB  - IM
MH  - *Ammonia
MH  - *Ecosystem
MH  - In Situ Hybridization, Fluorescence
MH  - Oligonucleotide Probes/genetics
MH  - Oxidation-Reduction
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
OTO - NOTNLM
OT  - Ammonia-oxidizing bacteria
OT  - Fluorescence in situ hybridization
OT  - Nitrification
OT  - Oligonucleotide probes
OT  - Wastewater treatment plants
COIS- Declaration of Competing Interest The authors declare that they have no known 
      competing financial interests or personal relationships that could have appeared 
      to influence the work reported in this paper.
EDAT- 2020/09/12 06:00
MHDA- 2020/11/18 06:00
CRDT- 2020/09/11 20:22
PHST- 2020/05/26 00:00 [received]
PHST- 2020/08/12 00:00 [revised]
PHST- 2020/08/31 00:00 [accepted]
PHST- 2020/09/12 06:00 [pubmed]
PHST- 2020/11/18 06:00 [medline]
PHST- 2020/09/11 20:22 [entrez]
AID - S0043-1354(20)30908-8 [pii]
AID - 10.1016/j.watres.2020.116372 [doi]
PST - ppublish
SO  - Water Res. 2020 Nov 1;186:116372. doi: 10.1016/j.watres.2020.116372. Epub 2020 
      Sep 1.