Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (q ¼ À 0.664) and residence time (q ¼ 0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

For several decades, annually recurring blooms of the photosynthetic ciliate Myrionecta rubra have been observed in the Columbia River estuary in late summer. In an effort to understand the dynamics of these blooms, we investigated the genetic variability of M. rubra and its cryptophyte plastids within 3 large estuarine blooms formed in consecutive years (2007 to 2009), and conducted a broader spatial survey along the coasts of Oregon and Washington. Analysis of the '18S-28S' sequences specific for Mesodiniidae uncovered at least 5 variants of M. rubra within the Columbia River coastal margin in spring and summer, but only one of these M. rubra variants was implicated in estuary bloom formation. Using a multigene approach, we show that the bloom-forming variant of M. rubra appears to harbor the same cryptophyte chloroplast in recurring blooms. Analyses of chloroplast 16S rRNA, cryptophyte RuBisCO and Photosystem II D2 genes together suggest that the plastid is derived from Teleaulax amphioxeia. Free-living cells of this species and of other cryptophytes were practically absent from the bloom patches in the estuary main channels based on 18S rDNA sequence analyses. The respectively low and high proportions of T. amphioxeia nuclei and chloroplast signals found in the M. rubra bloom of the Columbia River estuary in successive years supports the notion of an association (either endosymbiosis or kleptoplastidy) between T. amphioxeia and the bloom-forming M. rubra variant, with loss of cryptophyte nuclei. The genetic variability of M. rubra uncovered here is relevant to the controversy in the literature regarding the cryptophyte/M. rubra association.

Near-surface seawater from the northeastern subarctic Pacific was incubated on deck for 8 d, supplemented with (1) control, no additions (2) ϩZn (3) ϩFe (4) ϩZnϩFe. Concentrations of total Zn and Fe at time zero (t 0 ) and in the control remained at ϳ0.1-0.2 nmol L Ϫ1. In the control, chlorophyll (Ͻ0.3 mg m Ϫ3 ), 14 C uptake into POC and PIC, and inorganic nutrients all remained relatively constant. Addition of Zn slightly but significantly increased chlorophyll (p Ͻ 0.05), decreased phosphate (p Ͻ 0.01) and nitrate (p Ͻ 0.05), and in P versus E experiments, increased P m Ͼ10-fold and P 2-3-fold. The abundance of small diatoms and coccolithophores was higher in the chl m ϩZn treatment compared to the control. The ϩFe and ϩZnϩFe treatments, compared to the control, both showed Ͼ10-fold increases in chlorophyll and 14 C uptake into POC and PIC and complete removal of nitrate (Յ0.2 mmol m Ϫ3 ). However, differences were observed in size-fractionated data; the ϩZnϩFe treatment had significantly lower percent chlorophyll in the Ͼ20-m fraction (p Ͻ 0.01) and a higher percentage in the 0.2-5-m fraction (p Ͻ 0.01) than the ϩFe treatment. In P versus E experiments, both ϩFe treatments increased P m and ␣ around 100-fold and P and ␣ chl by 5-10-fold compared to the control. The ϩFe treatment showed a slightly higher ␣ chl and slightly chl m lower P than the ϩZnϩFe treatment. Abundance of large diatoms, small diatoms, small flagellates, and coccolchl m ithophores all increased substantially (ϳ7-1,000-fold) in response to Fe addition, whereas dinoflagellate abundance only doubled. The ϩZnϩFe treatment had higher abundances of small diatoms and small flagellates than the ϩFe treatment. We conclude that Zn additions had limited influence on conventional indices of phytoplankton growth compared to Fe, but that there might be subtle influences of Zn that require further attention.

No abstract

Frequent blooms of phytoplankton occur in coastal upwelling zones creating hotspots of biological productivity in the ocean. As cold, nutrient-rich water is brought up to sunlit layers from depth, phytoplankton are also transported upwards to seed surface blooms that are often dominated by diatoms. The physiological response of phytoplankton to this process, commonly referred to as shift-up, is characterized by increases in nitrate assimilation and rapid growth rates. To examine the molecular underpinnings behind this phenomenon, metatranscriptomics was applied to a simulated upwelling experiment using natural phytoplankton communities from the California Upwelling Zone. An increase in diatom growth following 5 days of incubation was attributed to the genera Chaetoceros and Pseudo-nitzschia. Here, we show that certain bloom-forming diatoms exhibit a distinct transcriptional response that coordinates shift-up where diatoms exhibited the greatest transcriptional change following upwelling; however, comparison of co-expressed genes exposed overrepresentation of distinct sets within each of the dominant phytoplankton groups. The analysis revealed that diatoms frontload genes involved in nitrogen assimilation likely in order to outcompete other groups for available nitrogen during upwelling events. We speculate that the evolutionary success of diatoms may be due, in part, to this proactive response to frequently encountered changes in their environment.