Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

Abstract

Microorganisms remineralize and respire half of marine primary production, yet the niches occupied by specific microbial groups, and how these different groups may interact, are poorly understood. In this study, we identify co-occurrence patterns for marine Archaea and specific bacterial groups in the chlorophyll maximum of the Southern California Bight. Quantitative PCR time series of marine group 1 (MG1) Crenarchaeota 16S rRNA genes varied substantially over time but were well-correlated (r(2)=0.94, P<0.001) with ammonia monooxygenase subunit A (amoA) genes, and were more weakly related to 16S rRNA genes for all Archaea (r(2)=0.39), indicating that other archaeal groups (for example, Euryarchaeota) were numerically important. These data sets were compared with variability in bacterial community composition based on automated ribosomal intergenic spacer analysis (ARISA). We found that archaeal amoA gene copies and a SAR11 (or Pelagibacter) group Ib operational taxonomic unit (OTU) displayed strong co-variation through time (r(2)=0.55, P<0.05), and archaeal amoA and MG1 16S rRNA genes also co-occurred with two SAR86 and two Bacteroidetes OTUs. The relative abundance of these groups increased and decreased in synchrony over the course of the time series, and peaked during periods of seasonal transition. By using a combination of quantitative and relative abundance estimates, our findings show that abundant microbial OTUs-including the marine Crenarchaeota, SAR11, SAR86 and the Bacteroidetes-co-occur non-randomly; they consequently have important implications for our understanding of microbial community ecology in the sea.

Figure 1

Times series from 2000–2004 of (a) chlorophyll from 0 to 100 m; (b) all archaeal 16S rRNA genes in the DCM; (c) MG1 16S rRNA genes in the DCM; and (d) archaeal amoA genes in the DCM. Shaded regions indicate the months from July to December.

Figure 2

MG1 Crenarchaeota time series compared with (a) SAR11 OTU 684; (b) SAR86 OTUs 525 and 528; and (c) Bacteroidetes OTUs 709 and 779. MG1 Crenarchaeota data are expressed in 16 rRNA genes ng DNA⁻¹ (left axis), and bacterial OTUs are expressed as percent of total ARISA peak area (right axis). Shaded regions correspond the months from September to March.

Figure 3

Time series for SAR11 OTU 684 (a) compared with (b) cell counts and (c) nitrate concentrations for each month of the year at SPOT. Smaller gray symbols show the mean values averaged for each month; values for individual months in each year are shown in different colors.