Abstract
Bacteria play a pivotal role in shaping ecosystems and contributing to elemental cycling and energy flow in the oceans. However, few studies have focused on bacteria at a trans-basin scale, and studies across the subtropical Northwest Pacific Ocean (NWPO), one of the largest biomes on Earth, have been especially lacking. Although the recently developed high-throughput quantitative sequencing methodology can simultaneously provide information on relative abundance, quantitative abundance, and taxonomic affiliations, it has not been thoroughly evaluated. We collected surface seawater samples for high-throughput, quantitative sequencing of 16S rRNA genes on a transect across the subtropical NWPO to elucidate the distribution of bacterial taxa, patterns of their community structure, and the factors that are potentially important regulators of that structure. We used the quantitative and relative abundances of bacterial taxa to test hypotheses related to their ecology. Total 16S rRNA gene copies ranged from 1.86 × 108 to 1.14 × 109 copies L−1. Bacterial communities were distributed in distinct geographical patterns with spatially adjacent stations clustered together. Spatial considerations may be more important determinants of bacterial community structures than measured environmental variables. The quantitative and relative abundances of bacterial communities exhibited similar distribution patterns and potentially important determinants at the whole-community level, but inner-community connections and correlations with variables differed at subgroup levels. This study advanced understanding of the community structure and distribution patterns of marine bacteria as well as some potentially important determinants thereof in a subtropical oligotrophic ocean system. Results highlighted the importance of considering both the quantitative and relative abundances of members of marine bacterial communities.
Highlights
Bacteria play a pivotal role in shaping ecosystems and contributing to the cycling of elements and the flow of energy in the oceans (Ducklow, 2000; Kirchman, 2016; Steinberg and Landry, 2017)
A mean quantitative abundance of 2.6 × 108 copies L−1 has been reported for SAR11 in surface seawater of the western North Atlantic based on the HTQS method (Wang et al, 2018), and SAR11 gene abundances estimated by quantitative PCR have been reported to fall in the range 0.3 × 108−6.3 × 108 copies L−1 at Station ALOHA (Eiler et al, 2009)
Our results revealed that environmental variables such as salinity, dissolved reactive phosphorus (DRP), and Si(OH)4 concentrations were correlated with spatial factors (Figure 2A), and that correlation could explain their shared effect on the variations of bacterial community structure (Supplementary Figure 4)
Summary
Bacteria play a pivotal role in shaping ecosystems and contributing to the cycling of elements and the flow of energy in the oceans (Ducklow, 2000; Kirchman, 2016; Steinberg and Landry, 2017). Sequences obtained from HTS can provide both genetic (taxonomic) information and relative abundance. This information has dramatically expanded our understanding of the composition and biogeography of bacterial communities and the mechanisms by which they are assembled (Sunagawa et al, 2015; Goodwin et al, 2016; Lindh et al, 2018). The effects of PCR bias cannot be ruled out in HTQS and would impact estimates of microbial abundances, it has been shown that estimates of microbial community structure and composition are not perturbed by artificial standard spikeins, and even complex 16S rRNA gene pools do not affect quantification based on artificial standard spike-ins (Tourlousse et al, 2017). Little is known about the differences and similarities of the implications of relative and quantitative abundances in marine microbial ecology
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