Lisa Campbell

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the worlds oceans.

Photosynthetic picoplankton community structure in the subtropical North Pacific Ocean near Hawaii (station ALOHA)

The structure of the picoplankton community in the subtropical Pacific was examined on four depth profiles, one from each season, sampled at the Hawaii Ocean Time-series station ALOHA (22°45′N, 158°W). Three cell populations were discriminated by flow cytometry: Prochlorococcus prochlorophytes, Synechococcus cyanobacteria, and picoeukaryotes. Prochlorococcus were the most abundant component (maximum ca 2 × 105 cells ml−1). Unlike previous reports, their concentration was almost constant down to roughly 100 m, with a slight maximum at the surface or near the chlorophyll maximum. Cellular chlorophyll fluorescence increased 50-fold between surface and deep populations. One distinguishing feature of the community off Hawaii was the co-occurrence near the chlorophyll maximum of at least two distinct Prochlorococcus populations with different chlorophyll and DNA contents. Throughout the year, Synechococcus abundance was two orders of magnitude lower and there was no seasonal alteration between Prochlorococcus and Synechococcus, as observed in the northern Sargasso Sea. Synechococcus populations did not extend below 120 m and were dominated by high phycourobilin cell types. Picoeukaryote abundance was quite similar to that of Synechococcus, but these cells extended deeper in the water column. Their chlorophyll fluorescence exhibited much less depth variation than Prochlorococcus or Synechococcus. Seasonal variability was small (<2- to 3-fold) for all three components of the picoplankton, not only for cell abundance but also for cellular parameters such as light scatter or pigment fluorescence. Synechococcus populations exhibited the largest seasonal changes (e.g. abundance maximum and chlorophyll fluorescence varied 3-fold). Picoplankton community structure in the Pacific Ocean appears to be distinct from previous reports for other areas. In comparing station ALOHA to the Atlantic Ocean (especially the Sargasso Sea) and the Mediterranean Sea, depth-integrated abundances of Prochlorococcus were higher, that of Synechococcus were lower, and that of picoeukaryotes were similar. We believe this structure, dominated by Prochlorococcus, may be typical for subtropical open-ocean regions.

Annual variability of phytoplankton and bacteria in the subtropical North Pacific Ocean at Station ALOHA during the 1991–1994 ENSO event

Time-series data on community structure in the upper 200 m at Station ALOHA in the subtropical North Pacific were collected at approximately monthly intervals from December 1990 through to March 1994 during an extended El Niiio-Southern Oscillation (ENSO) event. Samples were analyzed by flow cytometry to enumerate Prochlorococcus, Synechococcus, picoeucaryotes, 3–20 μm algae, and heterotrophic bacteria, as well as to quantify cellular chlorophyll fluorescence for the autotrophic components. A significant seasonal cycle was evident in cellular chlorophyll fluorescence for each of the autotrophic components, with maxima occurring each winter as a consequence of photoacclimation. Abundance of each picophytoplankton component exhibited temporal variability on both seasonal and interannual scales. Although the magnitude of the seasonal cycles in the abundance was relatively small, the cycles appeared to be out of phase. Typically, abundance maxima of Synechococcus occurred in winter, of picoeucaryotes in spring, and of Prochlorococcus during summer/fall. The different timing in these cycles may explain why the presence of a seasonal pattern in total phytoplankton biomass has been difficult to establish. Abundance of the larger 3–20 μm algae varied over two orders of magnitude during the time series, with no obvious seasonal pattern. The 3–20 μm algae were a small percentage of the total estimated carbon biomass (∼8%). Heterotrophic bacteria were the most numerous of the picoplankton, and the seasonal pattern in their 200-m integrated abundance paralleled Prochlorococcus over the time series. Together, the procaryotes contributed 60–90% of the total estimated microbial carbon. Significant interannual variation in the total 200-m integrated microbial carbon estimates may be related to the effects of the extended ENSO event, which began in 1991.

Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization.

Abstract Photosynthetic pico- and nanoplankton dominate phytoplankton biomass and primary production in the oligotrophic open ocean. Species composition, community structure, and dynamics of the eukaryotic components of these size classes are poorly known primarily because of the difficulties associated with their preservation and identification. Molecular techniques utilizing 18S rRNA sequences offer a number of new and rapid means of identifying the picoplankton. From the available 18S rRNA sequence data for the algae, we designed new group-specific oligonucleotide probes for the division Chlorophyta, the division Haptophyta, and the class Pelagophyceae (division Heterokonta). Dot blot hybridization with polymerase chain reaction amplified target rDNA and whole-cell hybridization assays with fluorescence microscopy and flow cytometry were used to demonstrate probe specificity. Hybridization results with representatives from seven algal classes supported the phylogenetic affinities of the cells. Such group- or taxon-specific probes will be useful in examining community structure, for identifying new algal isolates, and for in situ detection of these three groups, which are thought to be the dominant algal taxa in the oligotrophic regions of the ocean.

Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes

Abstract Horizontal and vertical variations in bacterial community composition were examined in samples collected during two Joint Global Ocean Flux Study (JGOFS) Arabian Sea cruises in 1995. The cruises, 11 months apart, took place during two consecutive NE Monsoon periods (January and December). Bacteria were harvested by filtration from samples collected in the mixed layer, mid-water, and deep sea at stations across the study area. Total bacterial community genomic DNA was analyzed by PCR amplification of 16S rRNA gene fragments, followed by denaturing gradient gel electrophoresis (DGGE). In total, 20 DGGE bands reflecting unique or varying phylotypes were excised, cloned and sequenced. Amplicons were dominated by bacterial groups commonly found in oceanic waters (e.g., the SAR11 cluster of α -Proteobacteria and cyanobacteria), but surprisingly none of the sequenced amplicons were related to γ -Proteobacteria or to members of the Cytophaga-Flavobacter-Bacteroides phylum. Amplicons related to magnetotactic bacteria were found for the first time in pelagic oceanic waters. The DGGE banding patterns revealed a dominance of ≈15 distinguishable amplicons in all samples. In the mixed layer the bacterial community was dominated by the same ≈15 phylotypes at all stations, but unique phylotypes were found with increasing depth. Except for cyanobacteria, comparison of the bacterial community composition in surface waters from January and December 1995 showed only minor differences, despite significant differences in environmental parameters. These data suggest a horizontal homogeneity and some degree of seasonal predictability of bacterial community composition in the Arabian Sea.

A nitrate-dependent Synechococcus bloom in surface Sargasso Sea water

Considerable debate exists concerning the magnitude of oceanic primary production, its rate of transfer to other trophic levels and turnover times of carbon and nitrogen1–5. In nitrogen-limited ocean systems, episodic increases in nitrate concentrations can support a significant fraction of annual phytoplankton production5. Yet little information is available regarding the distribution of nitrate in seasonally stratified oceanic surface waters, because concentrations are below the 0.03 μM detection limit of colorimetric methods6. We present the first evidence that high surface productivity in stratified Sargasso Sea water was supported by nanomolar changes in nitrate concentrations. This change was stoichiometrically consistent with the subsequent cellular production of a cyanobacterial (Synechococcus) bloom. Initially, cellular phycoerythrin and chlorophyll pigments increased, after which growth was enhanced to near maximum rates, and grazing was closely coupled to production. These observations suggest that Synechococcus occupies an important trophic position in the transfer of new nitrogen into the oceanic food web.

FIRST HARMFUL DINOPHYSIS (DINOPHYCEAE, DINOPHYSIALES) BLOOM IN THE U.S. IS REVEALED BY AUTOMATED IMAGING FLOW CYTOMETRY1

Imaging FlowCytobot (IFCB) combines video and flow cytometric technology to capture images of nano‐ and microplankton (∼10 to >100 μm) and to measure the chlorophyll fluorescence associated with each image. The images are of sufficient resolution to identify many organisms to genus or even species level. IFCB has provided >200 million images since its installation at the entrance to the Mission‐Aransas estuary (Port Aransas, TX, USA) in September 2007. In early February 2008, Dinophysis cells (1–5 · mL−1) were detected by manual inspection of images; by late February, abundance estimates exceeded 200 cells · mL−1. Manual microscopy of water samples from the site confirmed that D. cf. ovum F. Schütt was the dominant species, with cell concentrations similar to those calculated from IFCB data, and toxin analyses showed that okadaic acid was present, which led to closing of shellfish harvesting. Analysis of the time series using automated image classification (extraction of image features and supervised machine learning algorithms) revealed a dynamic phytoplankton community composition. Before the Dinophysis bloom, Myrionecta rubra (a prey item of Dinophysis) was observed, and another potentially toxic dinoflagellate, Prorocentrum, was observed after the bloom. Dinophysis cell‐division rates, as estimated from the frequency of dividing cells, were the highest at the beginning of the bloom. Considered on a daily basis, cell concentration increased roughly exponentially up to the bloom peak, but closer inspection revealed that the increases generally occurred when the direction of water flow was into the estuary, suggesting the source of the bloom was offshore.

Genetic characterisation of Emiliania huxleyi (Haptophyta)

Amongst the coccolithophorids, Emiliania huxleyi is the most successful and can form large scale blooms under a variety of environmental conditions. This implies extensive genetic variation within this taxon. Physiological, morphological and antigenic differences between clonal isolates support this suggestion. Our investigations into the level of genetic variation within the morphological species concept of E. huxleyi indicate that it is such a young taxon that sequence comparisons of both coding and non-coding regions cannot resolve the issue of how many separate taxonomic entities are involved. However, PCR-based genetic fingerprinting techniques do reveal extensive genetic diversity, both on a global scale and within major bloom populations in both space and time. Cell DNA content can also separate cells with morphotype A coccoliths from those with morphotype B coccoliths. Taken together with physiological and morphological evidence, these data suggest that the morphotypes of E. huxleyi should be separated at the variety level. We have used both nuclear and plastid rRNA sequence comparisons to confirm the place of E. huxleyi within the Haptophyta.

Marine ecology: Microbial microdiversity

Analysis of 16S ribosomal RNA from samples of the bacterial groupProchlorococcus (a component of phytoplankton) shows that closely related Prochlorococcus populations that are genetically adapted to different levels of light coexist. This technique has been used to study genetic diversity in samples that are difficult to culture in the laboratory. But the technique is not perfect and leads to a tendency to group together organisms that appear very similar genetically but may be different physiologically — such as the Prochlorococcusecotypes.

Seasonal variability in the phytoplankton community of the North Pacific Subtropical Gyre

Time series measurements of in situ fluorescence, extracted particulate chlorophyll a, primary productivity, extracted adenosine 5′-triphosphate, and fluorescence per cell, as measured by flow cytometry, demonstrate seasonal cycles in fluorescence and chlorophyll concentrations in the North Pacific Subtropical Gyre (22° 45′N, 158° 00′W). Two opposing cycles are evident. In the upper euphotic zone (0–50 m), chlorophyll a concentrations increase in winter, with a maximum in December, and decrease each summer, with a minimum in June or July. In contrast, chlorophyll a concentrations in the lower euphotic zone (100–175 m) increase in spring, with a maximum in May, and decline in fall, with a minimum in October or November. The winter increase in chlorophyll a concentration in the upper 50 m of the water column appears to be a consequence of photoadaptation in response to decreased average mixed-layer light intensity rather than a change in phytoplankton biomass. In the lower euphotic zone, however, the seasonal cycle in pigment concentration does reflect a change in the rate of primary production and in phytoplankton biomass as a consequence of increased light intensity in summer. These observations have important implications for phytoplankton dynamics in the subtropical oceans and for remote sensing of phytoplankton biomass.