期刊
ENVIRONMENTAL MICROBIOLOGY
卷 20, 期 8, 页码 2709-2726出版社
WILEY
DOI: 10.1111/1462-2920.14091
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资金
- National Aeronautics and Space Administration Biodiversity and Ecological Forecasting program [NNX14AR62A]
- Bureau of Ocean and Energy Management Ecosystem Studies program (BOEM award) [MC15AC00006]
- National Oceanic and Atmospheric Administration
- NASA Earth and Space Science Fellowship Program [NNX12AO13H]
- National Science Foundation [OCE-0850857]
- NASA Postdoctoral Fellowship
- NSF [OCE-1538428, OCE-1232779]
- NIH [1S10OD010786-01]
- National Oceanic and Atmospheric Administration, Project A/AS-1 - University of Hawai'i Sea Grant College Program, SOEST from NOAA Office of Sea Grant, Department of Commerce [NA14OAR4170071]
- University of Hawai'i Sea Grant College Program [UNIHI-SEAGRANT-JC-16-17]
- Directorate For Geosciences [1538428] Funding Source: National Science Foundation
- Division Of Ocean Sciences [1538428] Funding Source: National Science Foundation
- NASA [NNX12AO13H, 12344] Funding Source: Federal RePORTER
Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers.
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