Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
10223898 | Marine Environmental Research | 2018 | 6 Pages |
Abstract
Quantification of the α-subunit of ammonia monooxygenase (amoA) through PCR is an established technique for estimating the abundance of ammonia oxidizing archaea (AOA) in environmental samples. This study quantified AOA with two established primer sets in 1â¯cm increments from the sediment surface (0-1â¯cm) to a depth of 10â¯cmâ¯at two locations within Port Phillip Bay (PPB), Australia. Primer choice had a significant effect on within sample estimates of AOA with copy numbers ranging from 102 to 104 copies per ng DNA. Variation in AOA abundance patterns with increasing sediment depth were site and primer specific. Sequence mismatches between the primer binding region of the isolated amoA sequences from PPB and Nitrosopumilus maritimus SCM1 were identified and may explain the high variation identified between primer estimates. Our results highlight the need for testing multiple primer pairs that target different regions of the AOA amoA sequence prior to large-scale marine sediment environmental studies.
Related Topics
Physical Sciences and Engineering
Earth and Planetary Sciences
Oceanography
Authors
Alexis Marshall, Lori Phillips, Andrew Longmore, Caixian Tang, Karla Heidelberg, Pauline Mele,