Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia‐oxidizing archaea and bacteria. Issue 2 (12th February 2015)

• Record Type: Journal Article
• Authors: Meinhardt, Kelley A.; Bertagnolli, Anthony; Pannu, Manmeet W.; Strand, Stuart E.; Brown, Sally L.; Stahl, David A.
• Is Part Of: Environmental microbiology reports. Volume 7:Issue 2(2015)
• Page Start: 354
• Page End: 363
• Publication Date: 2015-02-12
• Subjects: Microbial ecology -- Periodicals; Environmental Microbiology -- Periodicals; Electronic journals; 579.17
• DOI: 10.1111/1758-2229.12259
• Languages: English
• ISSNs: 1758-2229

Abstract

<abstract abstract-type="main"> <title>Summary</title> <p>Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) fill key roles in the nitrogen cycle. Thus, well‐vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase (<italic>amoA</italic>) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within‐ and between‐system comparisons. We compared the performance of newly designed non‐degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the <italic>amoA</italic> of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different <italic>amoA</italic> sequence variants and increased detection of <italic>amoA</italic> in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB.</p> </abstract>