Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate

Abstract

The Roseobacter group and SAR11 clade constitute high proportions of the marine bacterioplankton, but only scarce information exists on the abundance of distinct populations of either lineage. Therefore, we quantified the abundance of the largest cluster of the Roseobacter group, the RCA (Roseobacter clade affiliated) cluster together with the SAR11 clade by quantitative PCR in the southern and eastern North Sea. The RCA cluster constituted up to 15 and 21% of total bacterial 16S ribosomal RNA (rRNA) genes in September 2005 and May 2006, respectively. At a few stations, the RCA cluster exceeded the SAR11 clade, whereas at most stations, SAR11 constituted higher fractions with maxima of 37%. In most samples, only one RCA ribotype was detected. RCA abundance was positively correlated with phaeopigments, chlorophyll, dissolved and particulate organic carbon (POC), turnover rates of dissolved free amino acids (DFAAs), temperature, and negatively correlated with salinity. The SAR11 clade was only correlated with POC (negatively, May) and with DFAA turnover rates (positively, September). An abundant RCA strain, 'Candidatus Planktomarina temperata', was isolated from the southern North Sea. This strain has an identical 16S rRNA gene sequence to the dominant RCA ribotype. Detection of the pufM gene, coding for a subunit of the reaction center of bacteriochlorophyll a, indicates the potential of the isolate for aerobic anoxygenic photosynthesis. Our study shows that a distinct population of the RCA cluster constitutes an abundant bacterioplankton group in a neritic sea of the temperate zone and indicates that this population has an important role during decaying phytoplankton blooms.

Figure 1

Bathymetry and sampling locations in the North Sea during cruises HE-238 (September 2005) and HE-249 (May 2006) with RV Heincke. For exact locations of the stations and dates of sampling, see Supplementary Table S1.

Figure 2

Abundance of the RCA cluster and SAR11 clade and various hydrographic and biological parameters assessed in the North Sea surface waters during cruises HE-238 in September 2005 and HE-249 in May 2006. (a, b) Abundances of the RCA cluster and SAR11 clade, salinity and temperature (the different scales must be noted); (c, d) Concentrations of chlorophyll a (Chl a) and phaeopigments; ^*RCA phylotypes detected but abundance below the resolution of the y axis. For exact locations of the stations and dates of sampling, see Supplementary Table S1.

Figure 3

Growth of strain RCA23 at pH values between 6.3 and 8.8, measured as change in optical density at 600 nm (OD₆₀₀). The mean of triplicate cultures is shown.

Figure 4

Neighbor-joining tree showing the phylogeny of the three RCA ribotypes (NSI, NSII, NSIII, bold type) of the North Sea transects and strain RCA23 (bold type) within the RCA cluster based on 16S rRNA gene sequence similarity. NSI, NSII and NSIII were represented by longest sequences of each ribotype and added later to the final tree using the maximum parsimony option of the ARB program. The backbone tree considered only sequences >1300 bp and from different locations. Several sequences from the same location were only included if they show sequence variations. Filled circles indicate nodes also recovered reproducibly with maximum-likelihood calculation. Numbers at the nodes are bootstrap values (only >50% are shown) from 1500 replicates. Methylococcus capsulatus ACM1292 (X72770) and Thiotrix nivea JP2 (L40993) were used as outgroup (not shown) to define the root of the tree. GenBank accession numbers are given in parentheses. Bar, 0.1 substitutions per nucleotide position. ^*, isolated strains.