Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean

Abstract

The in situ community structure of Prochlorococcus populations in the eastern North Atlantic Ocean was examined by analysis of Prochlorococcus 16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL) Prochlorococcus genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning of Prochlorococcus genotypes occurred. In each water column a shift from the HL to the LL genotype was observed, a transition correlating with the depth of the surface mixed layer (SML). Only the HL genotype was found in the SML in each water column, whereas the LL genotype was distributed below the SML. The range of in situ irradiance to which each genotype was subjected within these distinct niches was consistent with growth irradiance studies of cultured HL- and LL-adapted Prochlorococcus strains. DGGE analysis and the sequencing of Prochlorococcus 16S rDNA clones were in full agreement with the genotype-specific oligonucleotide probe hybridization data. These observations of a partitioning of Prochlorococcus genotypes in a stratified water column provide a genetic basis for the dim and bright Prochlorococcus populations observed in flow cytometric signatures in several oceanic provinces.

FIG. 1

Water column properties and picophytoplankton cell abundances of two vertical profiles in the eastern North Atlantic. Temperature and fluorescence profiles (A and B), flow cytometry data of picophytoplankton cell abundance (C and D), and nutrient concentrations (E and F) for profile 1 at 36.99°N, 19.68°W (A, C, and E) and profile 2 at 36.47°N, 19.2°W (B, D, and F).

FIG. 2

Phylogenetic tree showing the relationships of surface and deep Prochlorococcus environmental sequences and cultured Prochlorococcus and Synechococcus strains, inferred from 16S rRNA sequences. The tree was constructed from 1,114 unambiguously aligned bases by the neighbor-joining method. The number of bootstrap replicates supporting the branching order, of a total of 100, is shown at each node. Bootstrap values below 50 are not shown. The 16S rRNA sequence of the cyanobacterium Synechococcus sp. strain PCC6301 was used to root the tree.

FIG. 3

Representative dot blots showing the specificity of hybridization of each genotype-specific oligonucleotide (HLI, HLII, LL, MIT9303, and SS120) to arrays of control DNA samples (E. coli, Prochlorococcus sp. strains MED4, NATL1, TATL2, MIT9303, and SS120, Prochlorococcus 16S rDNA clone ENATL4, and Synechococcus sp. strain WH8103). EUB, eubacterial probe.

FIG. 4

Vertical distribution of the HLI- and LL-adapted Prochlorococcus 16S rDNA genotypes in two different water columns in the eastern North Atlantic, revealed by dot blot hybridization. In the upper panels are graphs showing the differential hybridization of the HLI and LL probes to oxygenic phototroph 16S rDNA sequences PCR amplified from different depths in depth profiles 1 (A) and 2 (B), together with the temperature and fluorescence data. Dot blots corresponding to the graphs from which the relative hybridization of each genotype-specific probe was quantified are shown in the lower panels, together with the PAR measured at each depth. EUB, eubacterial probe.

FIG. 5

DGGE analysis of the distribution of Prochlorococcus 16S rDNA genotypes in depth profiles 1 (A) and 2 (B). 16S rDNA sequences amplified from cultured Prochlorococcus strains were used as controls: panel A, lane 1, MED4; lane 2, ENATL4; lane 3, SS120; lane 4, TATL2; lane 5, mixture of MED4, SS120, ENATL4, and TATL2; lane 6, 10 m; lane 7, 20 m; lane 8, 30 m; lane 9, 40 m; lane 10, 50 m; lane 11, 60 m; and lane 12, 70 m; panel B, lane 1, MED4; lane 2, ENATL4; lane 3, SS120; lane 4, NATL1; lane 5, TATL1; lane 6, TATL2; lane 7, 10 m; lane 8, 30 m; lane 9, 40 m; lane 10, 50 m; lane 11, 60 m; lane 12, 70 m; lane 13, 90 m; and lane 14, 110 m.