Lost in translation: the quest for Nitrosomonas cluster 7-specific amoA primers and TaqMan probes.
Journal
Microbial biotechnology
ISSN: 1751-7915
Titre abrégé: Microb Biotechnol
Pays: United States
ID NLM: 101316335
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
12
11
2019
revised:
22
06
2020
accepted:
24
06
2020
pubmed:
21
7
2020
medline:
15
5
2021
entrez:
21
7
2020
Statut:
ppublish
Résumé
The choice of primer and TaqMan probes to quantify ammonia-oxidizing bacteria (AOB) in environmental samples is of crucial importance. The re-evaluation of primer pairs based on current genomic sequences used for quantification of the amoA gene revealed (1) significant misrepresentations of the AOB population in environmental samples, (2) and a lack of perfect match primer pairs for Nitrosomonas europaea and Nitrosomonas eutropha. We designed two new amoA cluster 7-specific primer pairs and TaqMan probes to quantify N. europaea (nerF/nerR/nerTaq) and N. eutropha (netF/netR/netTaq). Specificity and quantification biases of the newly designed primer sets were compared with the most popular primer pair (amoA1f/amoA2r) using DNA from various AOB cultures as individual templates as well as DNA mixtures and environmental samples. Based on the qPCR results, we found that the newly designed primer pairs and the most popular one performed similarly for individual templates but differed for the DNA mixtures and environmental samples. Using the popular primer pair introduced a high underestimation of AOB in environmental samples, especially for N. eutropha. Thus, there is a strong need for more specific primers and probes to understand the occurrence and competition between N. europaea and N. eutropha in different environments.
Identifiants
pubmed: 32686322
doi: 10.1111/1751-7915.13627
pmc: PMC7533338
doi:
Substances chimiques
Ammonia
7664-41-7
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2069-2076Informations de copyright
© 2020 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
Références
Environ Microbiol Rep. 2015 Apr;7(2):354-63
pubmed: 25534249
Appl Environ Microbiol. 2005 Feb;71(2):1105-8
pubmed: 15691975
PLoS One. 2014 May 12;9(5):e97068
pubmed: 24819357
Appl Environ Microbiol. 2002 Jan;68(1):245-53
pubmed: 11772633
Microb Biotechnol. 2016 Jul;9(4):519-24
pubmed: 27166579
Water Res. 2007 Mar;41(5):1110-20
pubmed: 17254627
Appl Environ Microbiol. 1997 Dec;63(12):4704-12
pubmed: 9406389
Environ Sci Technol. 2003 Jan 15;37(2):343-51
pubmed: 12564907
Appl Environ Microbiol. 2000 Dec;66(12):5368-82
pubmed: 11097916
Appl Environ Microbiol. 2002 Oct;68(10):4751-7
pubmed: 12324316
Appl Microbiol Biotechnol. 2009 May;83(1):175-88
pubmed: 19274459
J Microbiol Methods. 2007 Mar;68(3):445-52
pubmed: 17126937
Nature. 2006 Aug 17;442(7104):806-9
pubmed: 16915287
Appl Environ Microbiol. 2008 Mar;74(5):1660-3
pubmed: 18192413
Arch Microbiol. 1998 Apr;169(4):282-6
pubmed: 9531628
Appl Environ Microbiol. 2004 Feb;70(2):1008-16
pubmed: 14766583
Appl Environ Microbiol. 2010 Feb;76(3):900-9
pubmed: 19948857
FEMS Microbiol Lett. 2001 Dec 18;205(2):237-42
pubmed: 11750809
Curr Microbiol. 2009 Aug;59(2):130-8
pubmed: 19452213
Water Res. 2008 Feb;42(4-5):1093-101
pubmed: 17889247
Environ Microbiol. 2007 Dec;9(12):2993-3007
pubmed: 17991028
FEMS Microbiol Lett. 2011 Jun;319(2):169-75
pubmed: 21470297
ISME J. 2020 Feb;14(2):335-346
pubmed: 31624348
Biotechnol Bioeng. 2008 Apr 15;99(6):1374-83
pubmed: 18023051
PLoS One. 2015 May 21;10(5):e0128122
pubmed: 25996930
Syst Appl Microbiol. 2008 Jun;31(2):114-25
pubmed: 18289820
Sci Rep. 2019 May 6;9(1):6954
pubmed: 31061389
J Microbiol Methods. 2006 Jul;66(1):147-55
pubmed: 16343671
Appl Environ Microbiol. 2014 Oct;80(19):5901-10
pubmed: 25002435