Jackie L. Collier

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.

A small polypeptide triggers complete degradation of light-harvesting phycobiliproteins in nutrient-deprived cyanobacteria

Phycobilisomes are the multiprotein complexes predominantly responsible for harvesting light energy in cyanobacteria and some eukaryotic algae. When the cyanobacterium Synechococcus sp. strain PCC 7942 is deprived of an essential nutrient, the phycobilisomes are specifically and rapidly degraded. Degradation may be either partial (after phosphorus deprivation) or complete (after sulfur or nitrogen deprivation). We have developed a visual screen to obtain mutants unable to degrade their phycobilisomes upon nutrient starvation. Complementation of one of these mutants led to the identification of a gene, designated nblA, that encodes a 59 amino acid polypeptide essential for phycobilisome degradation. Transcription of nblA increases dramatically in sulfur‐ or nitrogen‐deprived cells and moderately in phosphorus‐deprived cells. Using the phosphorus‐regulated alkaline phosphatase (phoA) promoter as a tool, we engineered constructs from which we could control the expression of either sense or antisense nblA. Increased expression of sense nbLA caused complete phycobilisome degradation during phosphorus deprivation, while expression of antisense nblA prevented phycobilisome degradation. Hence, nblA is necessary, and may be sufficient, for the degradation of phycobilisomes under adverse environmental conditions. Further investigation of the mechanism by which nblA causes phycobilisome destruction may reveal general principles that govern the specificity of macromolecular complex degradation.

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.

The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC 3.5.1.5) to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme.

Cyanobacteria assigned to the genus Synechococcus are an important component of oligotrophic marine ecosystems, where their growth may be constrained by low availability of fixed nitrogen. Urea appears to be a major nitrogen resource in the sea, but little molecular information exists about its utilization by marine organisms, including Synechococcus. Oligonucleotide primers were used to amplify a conserved fragment of the urease (urea amidohydrolase, EC 3.5.1.5) coding region from cyanobacteria. A 5.7 kbp region of the genome of the unicellular marine cyanobacterium Synechococcus sp. strain WH7805 was then cloned, and genes encoding three urease structural subunits and four urease accessory proteins were sequenced and identified by homology. The WH7805 urease had a predicted subunit composition typical of bacterial ureases, but the organization of the WH7805 urease genes was unique. Biochemical characteristics of the WH7805 urease enzyme were consistent with the predictions of the sequence data. Physiological data and sequence analysis both suggested that the urease operon may be nitrogen-regulated by the ntcA system in WH7805. Inactivation of the large subunit of urease, ureC, prevented WH7805 and Synechococcus WH8102 from growing on urea, demonstrating that the urease genes cloned are essential to the ability of these cyanobacteria to utilize urea as a nitrogen source.

FLOW CYTOMETRY AND THE SINGLE CELL IN PHYCOLOGY

Flow cytometers measure light scattering and fluorescence characteristics from individual particles in a fluid stream as they cross one or more light beams at rates of up to thousands of events per second. Flow cytometrically detectable optical signals may arise naturally from algae, reflecting cell size, structure, and endogenous pigmentation, or may be generated by fluorescent stains that report the presence of otherwise undetected cellular constituents. Some flow cytometers can physically sort particles with desired optical characteristics out of the flow stream and collect them for subsequent culture or other analyses. The statistically rigorous, cell‐level perspective provided by flow cytometry has been advantageous in experimental investigations of phycological problems, such as the regulation of cell cycle progression. The capacity of flow cytometry to measure large numbers of cells in large numbers of samples rapidly and quantitatively has been used extensively by biological oceanographers to define the distributions and dynamics of marine picophytoplankton. Recent work has shown that flow cytometry can be used to elucidate relationships between the optical properties of individual cells and the bulk optical properties of the water they live in, and thereby may provide an explicit link between algal physiology and global biogeochemistry. Unfortunately, commercially available flow cytometers that are optimized for biomedical applications have a limited capacity to analyze larger phytoplankton. To circumvent these limitations, many investigators are developing flow cytometers specifically designed for analyzing the broad range of sizes, shapes, and pigments found among algae. These new instruments can perform some novel measurements, including simple fluorescence excitation spectra, detailed angular scattering measurements, and in‐flow digital imaging. The growing accessibility and power of flow cytometers may allow the technology to be applied to a wider array of problems in phycology, including investigations of nonplanktonic and multicellular algae, but also presents new challenges for effectively analyzing the large quantity of multiparameter data produced. Ultimately, the detection of molecular probes by flow cytometry may allow single‐cell taxonomic and physiological information to be garnered for a variety of algae, both in culture and in nature.

The Responses of Cyanobacteria to Environmental Conditions: Light and Nutrients

Cyanobacteria are found in virtually all terrestrial niches and can be found in locations which exhibit widely fluctuating chemical and physical parameters including nutrient availability, light intensity, light wavelength, temperature, and water activity. Described throughout this volume are ways in which cyanobacteria respond to changes in their environment, and examples of the insights that molecular genetic analyses have provided into acclimation processes. This chapter will discuss the modification of the cyanobacterial light-harvesting apparatus in response to light quality and nutrient availability. Recent advances in understanding the regulation of nutrient acquisition systems during nutrient-limited growth will also be summarized.

Changes in the cyanobacterial photosynthetic apparatus during acclimation to macronutrient deprivation.

When the cyanobacterium Synechococcus sp. Strain PCC 7942 is deprived of an essential macronutrient such as nitrogen, sulfur or phosphorus, cellular phycobiliprotein and chlorophyll contents decline. The level of β-carotene declines proportionately to chlorophyll, but the level of zeaxanthin increases relative to chlorophyll. In nitrogen- or sulfur-deprived cells there is a net degradation of phycobiliproteins. Otherwise, the declines in cellular pigmentation are due largely to the diluting effect of continued cell division after new pigment synthesis ceases and not to net pigment degradation. There was also a rapid decrease in O2 evolution when Synechococcus sp. Strain PCC 7942 was deprived of macronutrients. The rate of O2 evolution declined by more than 90% in nitrogen- or sulfur-deprived cells, and by approximately 40% in phosphorus-deprived cells. In addition, in all three cases the fluorescence emissions from Photosystem II and its antennae were reduced relative to that of Photosystem I and the remaining phycobilisomes. Furthermore, state transitions were not observed in cells deprived of sulfur or nitrogen and were greatly reduced in cells deprived of phosphorus. Photoacoustic measurements of the energy storage capacity of photosynthesis also showed that Photosystem II activity declined in nutrient-deprived cells. In contrast, energy storage by Photosystem I was unaffected, suggesting that Photosystem I-driven cyclic electron flow persisted in nutrient-deprived cells. These results indicate that in the modified photosynthetic apparatus of nutrient-deprived cells, a much larger fraction of the photosynthetic activity is driven by Photosystem I than in nutrient-replete cells.

Ocean urea fertilization for carbon credits poses high ecological risks

The proposed plan for enrichment of the Sulu Sea, Philippines, a region of rich marine biodiversity, with thousands of tonnes of urea in order to stimulate algal blooms and sequester carbon is flawed for multiple reasons. Urea is preferentially used as a nitrogen source by some cyanobacteria and dinoflagellates, many of which are neutrally or positively buoyant. Biological pumps to the deep sea are classically leaky, and the inefficient burial of new biomass makes the estimation of a net loss of carbon from the atmosphere questionable at best. The potential for growth of toxic dinoflagellates is also high, as many grow well on urea and some even increase their toxicity when grown on urea. Many toxic dinoflagellates form cysts which can settle to the sediment and germinate in subsequent years, forming new blooms even without further fertilization. If large-scale blooms do occur, it is likely that they will contribute to hypoxia in the bottom waters upon decomposition. Lastly, urea production requires fossil fuel usage, further limiting the potential for net carbon sequestration. The environmental and economic impacts are potentially great and need to be rigorously assessed.

Flow cytometry in molecular aquatic ecology

In working towards understanding ecosystems that are often dominated by microorganisms, aquatic ecologists have historically relied on measuring bulk, community-level properties and synecological processes. However, developing a mechanistic and predictive explanation for the factors structuring aquatic ecosystems will require understanding the roles that individual microorganisms play in these higher-order phenomena. The application of molecular biological techniques to examine nucleic acids extracted in bulk from microbial communities can provide information about the taxonomic structure of microbial communities and the physiological ecology of particular types of organisms at various levels of specificity. Yet, even if accomplished at the ‘species’ level, these data still represent bulk parameters because they can reveal only an average value for the organisms and community of interest. A more detailed view may be gained by investigations performed at a single-cell level. Flow cytometry allows the measurement of one cell at a time, at a rate of thousands of cells per second. When combined with fluorescent stains, including nucleic acid and antibody-based molecular probes, flow cytometry permits rapid analysis of cell-specific information for particular types of microbes within complex microbial assemblages. Thus, the autecology of microbial populations and structure of microbial communities can be examined from the vantage point of the individual cells comprising them. By bringing the level of analysis closer to the relevant scale of the organisms being investigated, the combination of molecular tools and flow cytometry will bring powerful new insights into the autecology of aquatic microorganisms.

Phycoerythrin-containing picoplankton in the Southern California Bight

Abstract Flow cytometry was used to examine the distribution of phycoerythrin-rich picophytoplankton, referred to here as Synechococcus , off the Southern California coast during six California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises. Depth profiles revealed that Synechococcus was most abundant in the surface mixed layer, gradually disappearing with depth below the thermocline. Within the surface mixed layer, Synechococcus abundance was generally greater and more variable at stations shoreward of the California Current than at stations offshore of it. In waters associated with the California Current not impacted by upwelling, Synechococcus abundance increased with increasing bulk chlorophyll. In contrast, Synechococcus abundance declined with increasing bulk chlorophyll at stations that were impacted by upwelling. Synechococcus at stations impacted by upwelling also had more phycoerythrin per cell than at non-upwelling stations. Offshore of the California Current, Synechococcus cells in waters intruding from the Central North Pacific displayed higher side-scatter relative to forward scatter than did Synechococcus cells elsewhere in the region. Flow cytometrically distinct Synechococcus cell types were also detected below the thermocline at most of the stations where depth profiles were analyzed. These patterns in Synechococcus abundance and cellular characteristics might reflect physiological and/or genetic differences among Synechococcus associated with the various water masses that comprise the CalCOFI region. The data presented here provide a framework from which to launch more detailed and mechanistic studies examining the role of Synechococcus in the CalCOFI ecosystem.