Publications

Export 102 results:
Sort by: Author Title Type [ Year  (Desc)]
2013
Prather, KA, Bertram TH, Grassian VH, Deane GB, Stokes MD, DeMott PJ, Aluwihare LI, Palenik BP, Azam F, Seinfeld JH, Moffet RC, Molina MJ, Cappa CD, Geiger FM, Roberts GC, Russell LM, Ault AP, Baltrusaitis J, Collins DB, Corrigan CE, Cuadra-Rodriguez LA, Ebben CJ, Forestieri SD, Guasco TL, Hersey SP, Kim MJ, Lambert WF, Modini RL, Mui W, Pedler BE, Ruppel MJ, Ryder OS, Schoepp NG, Sullivan RC, Zhao DF.  2013.  Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol. Proceedings of the National Academy of Sciences of the United States of America. 110:7550-7555.   10.1073/pnas.1300262110   AbstractWebsite

The production, size, and chemical composition of sea spray aerosol (SSA) particles strongly depend on seawater chemistry, which is controlled by physical, chemical, and biological processes. Despite decades of studies in marine environments, a direct relationship has yet to be established between ocean biology and the physicochemical properties of SSA. The ability to establish such relationships is hindered by the fact that SSA measurements are typically dominated by overwhelming background aerosol concentrations even in remote marine environments. Herein, we describe a newly developed approach for reproducing the chemical complexity of SSA in a laboratory setting, comprising a unique ocean-atmosphere facility equipped with actual breaking waves. A mesocosm experiment was performed in natural seawater, using controlled phytoplankton and heterotrophic bacteria concentrations, which showed SSA size and chemical mixing state are acutely sensitive to the aerosol production mechanism, as well as to the type of biological species present. The largest reduction in the hygroscopicity of SSA occurred as heterotrophic bacteria concentrations increased, whereas phytoplankton and chlorophyll-a concentrations decreased, directly corresponding to a change in mixing state in the smallest (60-180 nm) size range. Using this newly developed approach to generate realistic SSA, systematic studies can now be performed to advance our fundamental understanding of the impact of ocean biology on SSA chemical mixing state, heterogeneous reactivity, and the resulting climate-relevant properties.

2012
Dupont, CL, Johnson DA, Phillippy K, Paulsen IT, Brahamsha B, Palenik B.  2012.  Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102. Applied and Environmental Microbiology. 78:7822-7832.   10.1128/aem.01739-12   AbstractWebsite

One biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, including Synechococcus sp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded by sodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome with sodN, sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter gene sodT appeared to be lethal in WH8102, so the genes for sodT and sodN in WH8102 were interrupted with the gene for Fe-SOD, sodB, and its promoter from Synechococcus sp. strain WH7803. The sodT:: sodB exconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. The sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.

Ma, Y, Paulsen IT, Palenik B.  2012.  Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environmental Microbiology. 14:453-466.   10.1111/j.1462-2920.2011.02633.x   AbstractWebsite

Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.

Palenik, B.  2012.  Recent functional genomics studies in marine synechococcus. Functional Genomics and Evolution of Photosynthetic Systems. 33( Burnap VRLWFJ, Ed.).:103-118.   10.1007/978-94-007-1533-2_4   Abstract

Marine Synechoccocus are major contributors to global primary productivity. Genomics and metagenomics have revealed high levels of gene content diversity in these cyanobacteria, partly due to horizontal gene transfer. These differences would be extremely important for ecological niche adaptation. Functional genomics studies using microarrays are now revealing how gene expression in marine cyanobacteria is responding to common environmental stresses such as nutrient deprivation, metal stress, and even the presence of other microbes. Many genes highly expressed under environmental stresses seem to be clade - or even strain-specific, which may change our view of how microbes adapt to new environmental conditions.

2011
Apple, JK, Strom SL, Palenik B, Brahamsha B.  2011.  Variability in protist grazing and growth on different marine Synechococcus isolates. Applied and Environmental Microbiology. 77:3074-3084.   10.1128/aem.02241-10   AbstractWebsite

Grazing mortality of the marine phytoplankton Synechococcus is dominated by planktonic protists, yet rates of consumption and factors regulating grazer-Synechococcus interactions are poorly understood. One aspect of predator-prey interactions for which little is known are the mechanisms by which Synechococcus avoids or resists predation and, in turn, how this relates to the ability of Synechococcus to support growth of protist grazer populations. Grazing experiments conducted with the raptorial dinoflagellate Oxyrrhis marina and phylogenetically diverse Synechococcus isolates (strains WH8102, CC9605, CC9311, and CC9902) revealed marked differences in grazing rates-specifically that WH8102 was grazed at significantly lower rates than all other isolates. Additional experiments using the heterotrophic nanoflagellate Goniomonas pacifica and the filter-feeding tintinnid ciliate Eutintinnis sp. revealed that this pattern in grazing susceptibility among the isolates transcended feeding guilds and grazer taxon. Synechococcus cell size, elemental ratios, and motility were not able to explain differences in grazing rates, indicating that other features play a primary role in grazing resistance. Growth of heterotrophic protists was poorly coupled to prey ingestion and was influenced by the strain of Synechococcus being consumed. Although Synechococcus was generally a poor-quality food source, it tended to support higher growth and survival of G. pacifica and O. marina relative to Eutintinnis sp., indicating that suitability of Synechococcus varies among grazer taxa and may be a more suitable food source for the smaller protist grazers. This work has developed tractable model systems for further studies of grazer-Synechococcus interactions in marine microbial food webs.

Lucas, AJ, Dupont CL, Tai V, Largier JL, Palenik B, Franks PJS.  2011.  The green ribbon: Multiscale physical control of phytoplankton productivity and community structure over a narrow continental shelf. Limnology and Oceanography. 56:611-626.   10.4319/lo.2011.56.2.0611   AbstractWebsite

Chlorophyll concentration, phytoplankton biomass, and total and nitrate-fueled primary productivity increase toward the coast over the 12-km-wide continental shelf of the southern portion of the Southern California Bight. These gradients are accompanied by changes in phytoplankton community composition: the outer shelf is characterized by offshore assemblages including pelagophytes and oligotrophic Synechococcus ecotypes while the inner shelf is dominated by diatoms, coastal Synechococcus ecotypes, and the picoeukaryote Ostreococcus. Across the small horizontal scale of the shelf, large changes in the vertical distribution and flux of nitrate maintain elevated productivity, driving variability in the vertical distribution of biomass and the integrated biomass and productivity of the entire shelf. Temporal variability from hours to days in chlorophyll fluorescence as measured by an autonomous profiling vehicle demonstrates that phytoplankton respond vigorously and rapidly to physical variability. The interaction of physical processes at different temporal and spatial scales is responsible for the observed biological gradients. These dynamics include: (1) vertical shear in the alongshore currents, (2) local wind forcing, (3) the internal tide, and (4) remote, large-scale variability. Individually, these mechanisms rarely or never explain the phytoplankton community composition and metabolic rate gradients. These results and a reanalysis of historical data suggest that monitoring thermal stratification at the shelf break and the tilt of the thermocline across the shelf will augment our ability to predict phytoplankton productivity, community composition, and biomass, thereby improving our understanding of fisheries dynamics and carbon cycling in the coastal ocean.

Moore, MJK, Furutani H, Roberts GC, Moffet RC, Gilles MK, Palenik B, Prather KA.  2011.  Effect of organic compounds on cloud condensation nuclei (CCN) activity of sea spray aerosol produced by bubble bursting. Atmospheric Environment. 45:7462-7469.   10.1016/j.atmosenv.2011.04.034   AbstractWebsite

The ocean comprises over 70% of the surface of the earth and thus sea spray aerosols generated by wave processes represent a critical component of our climate system. The manner in which different complex oceanic mixtures of organic species and inorganic salts are distributed between individual particles in sea spray directly determines which particles will effectively form cloud nuclei. Controlled laboratory experiments were undertaken to better understand the full range of particle properties produced by bubbling solutions composed of simplistic model organic species, oleic acid and sodium dodecyl sulfate (SDS), mixed with NaCl to more complex artificial seawater mixed with complex organic mixtures produced by common oceanic microorganisms. Simple mixtures of NaCl and oleic acid or SDS had a significant effect on CCN activity, even in relatively small amounts. However, an artificial seawater (ASW) solution containing microorganisms, the common cyanobacteria (Synechococcus) and DMS-producing green algae (Ostreococcus), produced particles containing similar to 34 times more carbon than the particles produced from pure ASW, yet no significant change was observed in the overall CCN activity. We hypothesize that these microorganisms produce diverse mixtures of organic species with a wide range of properties that produced offsetting effects, leading to no net change in the overall average measured hygroscopicity of the collection of sea spray particles. Based on these observations, changes in CCN activity due to "bloom" conditions would be predicted to lead to small changes in the average CCN activity, and thus have a negligible impact on cloud formation. However, each sea spray particle will contain a broad spectrum of different species, and thus further studies are needed of the CCN activity of individual sea spray particles and biological processes under a wide range of controllable conditions. (C) 2011 Published by Elsevier Ltd.

Johnson, TL, Palenik B, Brahamsha B.  2011.  Characterization of a functional vanadium-dependent bromoperoxidase in the marine cyanobacterium Synechococcus sp. CC9311. Journal of Phycology. 47:792-801.   10.1111/j.1529-8817.2011.01007.x   AbstractWebsite

Vanadium-dependent bromoperoxidases (VBPOs) are characterized by the ability to oxidize halides using hydrogen peroxide. These enzymes are well-studied in eukaryotic macroalgae and are known to produce a variety of brominated secondary metabolites. Though genes have been annotated as VBPO in multiple prokaryotic genomes, they remain un-characterized. The genome of the coastal marine cyanobacterium Synechococcus sp. CC9311 encodes a predicted VBPO (YP_731869.1, sync_2681), and in this study, we show that protein extracts from axenic cultures of Synechococcus possess bromoperoxidase activity, oxidizing bromide and iodide, but not chloride. In-gel activity assays of Synechococcus proteins separated using PAGE reveal a single band having VBPO activity. When sequenced via liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS), peptides from the band aligned to the VBPO sequence predicted by the open reading frame (ORF) sync_2681. We show that a VBPO gene is present in a closely related strain, Synechococcus sp. WH8020, but not other clade I Synechococcus strains, consistent with recent horizontal transfer of the gene into Synechococcus. Diverse cyanobacterial-like VBPO genes were detected in a pelagic environment off the California coast using PCR. Investigation of functional VBPOs in unicellular cyanobacteria may lead to discovery of novel halogenated molecules and a better understanding of these organisms' chemical ecology and physiology.

Urbano, R, Palenik B, Gaston CJ, Prather KA.  2011.  Detection and phylogenetic analysis of coastal bioaerosols using culture dependent and independent techniques. Biogeosciences. 8:301-309.   10.5194/bg-8-301-2011   AbstractWebsite

Bioaerosols are emerging as important yet poorly understood players in atmospheric processes. Microorganisms can impact atmospheric chemistry through metabolic reactions and can potentially influence physical processes by participating in ice nucleation and cloud droplet formation. Microbial roles in atmospheric processes are thought to be species-specific and potentially dependent on cell viability. Using a coastal pier monitoring site as a sampling platform, culture-dependent (i.e. agar plates) and culture-independent (i.e. DNA clone libraries from filters) approaches were combined with 18S rRNA and 16S rRNA gene targeting to obtain insight into the local atmospheric microbial composition. From 13 microbial isolates and 42 DNA library clones, a total of 55 sequences were obtained representing four independent sampling events. Sequence analysis revealed that in these coastal samples two fungal phyla, Ascomycota and Basidiomycota, predominate among eukaryotes while Firmicutes and Proteobacteria predominate among bacteria. Furthermore, our culture-dependent study verifies the viability of microbes from all four phyla detected through our culture-independent study. Contrary to our expectations and despite oceanic air mass sources, common marine planktonic bacteria and phytoplankton were not typically found. The abundance of terrestrial and marine sediment-associated microorganisms suggests a potential importance for bioaerosols derived from beaches and/or coastal erosion processes.

Tai, V, Poon AFY, Paulsen IT, Palenik B.  2011.  Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes. Plos One. 6:e24249. AbstractWebsite

Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, particularly of short, unlinked sequences. A custom analytical pipeline was developed to calculate dN/dS ratios, a common metric to evaluate the role of selection in the evolution of a gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine Synechococcus, the dominant cyanobacteria in coastal environments. The large majority of genes (98%) have evolved under purifying selection (dN/dS<1). The metagenome sequence coverage of the reference genomes was not uniform and genes that were highly represented in the environment (i.e. high read coverage) tended to be more evolutionarily conserved. Of the genes that may have evolved under positive selection (dN/dS>1), 77 out of 83 (93%) were hypothetical. Notable among annotated genes, ribosomal protein L35 appears to be under positive selection in one Synechococcus population. Other annotated genes, in particular a possible porin, a large-conductance mechanosensitive channel, an ATP binding component of an ABC transporter, and a homologue of a pilus retraction protein had regions of the gene with elevated dN/dS. With the increasing use of next-generation sequencing in metagenomic investigations of microbial diversity and ecology, analytical methods need to accommodate the peculiarities of these data streams. By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer.

Tai, V, Burton RS, Palenik B.  2011.  Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays. Marine Ecology-Progress Series. 426:133-U164.   10.3354/meps09030   AbstractWebsite

Marine Synechococcus diversity has been previously described using multi-locus gene sequence phylogenies and the identification of distinct clades. Synechococcus from Clades I, II, III, and IV and from sub-clades within Clades I and IV were enumerated from environmental samples by developing a hybridization assay to liquid bead-arrays (Luminex). Oligonucleotide probes targeting a gene encoding a subunit of RNA polymerase (rpoC1) were used simultaneously in multiplexed assays to track Synechococcus diversity from a Pacific Ocean coastal monitoring site and along a coastal to open-ocean transect in the Southern California Bight. The Luminex assay demonstrated that Synechococcus from Clades I and IV were the dominant types at the coastal site throughout the year. Synechococcus from Clades II and III were not detected except during the late summer or early winter. Within the dominant Clades I and IV, rpoC1-defined sub-clades of Synechococcus showed distinct spatial distributions along the coastal to open-ocean transect, coinciding with changes in the nitricline, thermocline, and fluorescence (chlorophyll) maximum depths. In coastal waters, Synechococcus targeted by 2 sub-clade IV probes were dominant at the surface, whereas 2 sub-clade I probes and a third sub-clade IV probe had increased signals in deeper water near the fluorescence maximum. In mesotrophic waters, this third sub-clade IV probe dominated at the fluorescence maximum (depth of 50 to 70 m), whereas all other sub-clade probes were below detection limits. The differing distributions of sub-clades within the dominant Synechococcus clades indicate that the sub-clades likely have adapted to distinct ecological niches found within the Southern California Bight.

Rynearson, TA, Palenik B.  2011.  Learning to read the oceans: Genomics of marine phytoplankton. Advances in Marine Biology, Vol 60. 60( Lesser M, Ed.).:1-39.   10.1016/b978-0-12-385529-9.00001-9   Abstract

The phytoplankton are key members of marine ecosystems, generating about half of global primary productivity, supporting valuable fisheries and regulating global biogeochemical cycles. Marine phytoplankton are phylogenetically diverse and are comprised of both prokaryotic and eukaryotic species. In the last decade, new insights have been gained into the ecology and evolution of these important organisms through whole genome sequencing projects and more recently, through both transcriptomics and targeted metagenomics approaches. Sequenced genomes of cyanobacteria are generally small, ranging in size from 1.8 to 9 million base pairs (Mbp). Eukaryotic genomes, in general, have a much larger size range and those that have been sequenced range from 12 to 57 Mbp. Whole genome sequencing projects have revealed key features of the evolutionary history of marine phytoplankton, their varied responses to environmental stress, their ability to scavenge and store nutrients and their unique ability to form elaborate cellular coverings. We have begun to learn how to read the 'language' of marine phytoplankton, as written in their DNA. Here, we review the ecological and evolutionary insights gained from whole genome sequencing projects, illustrate how these genomes are yielding information on marine natural products and informing nanotechnology as well as make suggestions for future directions in the field of marine phytoplankton genomics.

2010
Mao, X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y.  2010.  Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. Bmc Genomics. 11   10.1186/1471-2164-11-291   AbstractWebsite

Background: Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO(2) fixation. Results: We present here a computational study of the osmoregulation network in response to hyperosmotic stress of Synechococcus sp strain WH8102 using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress. Conclusions: From the predicted network model, we have made a number of interesting observations about WH8102. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma(38), one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

Ostrowski, M, Mazard S, Tetu SG, Phillippy K, Johnson A, Palenik B, Paulsen IT, Scanlan DJ.  2010.  PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus. Isme Journal. 4:908-921.   10.1038/ismej.2010.24   AbstractWebsite

Previous microarray analyses have shown a key role for the two-component system PhoBR (SYNW0947, SYNW0948) in the regulation of P transport and metabolism in the marine cyanobacterium Synechococcus sp. WH8102. However, there is some evidence that another regulator, SYNW1019 (PtrA), probably under the control of PhoBR, is involved in the response to P depletion. PtrA is a member of the cAMP receptor protein transcriptional regulator family that shows homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the role of this regulator, we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-stress conditions. In response to P stress the ptrA mutant failed to upregulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is controlled by PtrA, including two phosphatases, a predicted phytase and a gene of unknown function psip1 (SYNW0165), all of which are highly upregulated during P limitation. Electrophoretic mobility shift assays indicate binding of overexpressed PtrA to promoter sequences upstream of the induced genes. This work suggests a two-tiered response to P depletion in this strain, the first being PhoB-dependent induction of high-affinity PO(4) transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly influenced by PtrA, including those involved in cell-surface modification, metal uptake, photosynthesis, stress responses and other metabolic processes, which may indicate a wider role for PtrA in cellular regulation in marine picocyanobacteria. The ISME Journal (2010) 4, 908-921; doi:10.1038/ismej.2010.24; published online 8 April 2010

Mayali, X, Palenik B, Burton RS.  2010.  Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environmental Microbiology. 12:975-989.   10.1111/j.1462-2920.2009.02142.x   AbstractWebsite

Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate.

Dupont, CL, Buck KN, Palenik B, Barbeau K.  2010.  Nickel utilization in phytoplankton assemblages from contrasting oceanic regimes. Deep-Sea Research Part I-Oceanographic Research Papers. 57:553-566.   10.1016/j.dsr.2009.12.014   AbstractWebsite

In most oceanic environments, dissolved nickel (Ni) concentrations are drawn clown in surface waters with increasing concentrations at depth, implying a role for biology in the geochemical distribution of Ni Studies with phytoplankton isolates from the surface ocean have established the biochemical roles of Ni in the assimilation of urea and oxidative defense To determine if these requirements are relevant in natural marine planktonic assemblages, bottle-based fertilization experiments were used to test the effects of low-level additions of Ni. urea, or both Ni and urea to surface waters at several locations offshore of Peru and California, as well as in the Gulf of California Urea and Ni(+) urea additions consistently promoted phytoplankton growth relative to control and +Ni treatments, except in a coastal upwelling site and Peruvian water. No effect was observed in the upwelling site, but in Peruvian waters urea additions resulted in increased phytoplankton pigments and phosphate drawdown only when Ni was added concurrently, suggesting a biochemically dependent Ni-urea colimitation In the Gulf of California, Ni additions without urea resulted in increased abundances of cyanobacteria, picoeukaryotes, and the corresponding pigments As urea additions showed the overall phytoplankton community was also urea-limited, it appears that the cyanobactena and potentially the picoeukaryotes were colimited by Ni and urea in a biochemically independent fashion. In parallel, radiotracer-based uptake experiments were used to study the kinetics and spatial variation of biological Ni assimilation. In these experiments, the added radiotracer rarely equilibrated with the natural Ni present, precluding estimates a determination of in situ Ni uptake rates and suggesting that much of the natural Ni was not bioavailable. The lack of equilibration likely did not preclude the measurement of community Ni uptake kinetics, nor the comparison of measured rates between locations The highest V(max)K(p)(-1) values, which reflect a competitive advantage in Ni acquisition at low concentrations, were observed in stratified nitrogen-deplete communities, potentially linking Ni and nitrogen biogeochemistry in a manner consistent with the biochemical utilization of Ni. Overall, uptake rates were higher in the euphotic rather than non-euphotic zone communities, directly reconciling the nutrient-like depth profile of Ni The Ni uptake rates observed at the nitrate-replete Fe-deplete Peru stations were an order of magnitude lower than the other sites This result agrees with calculations suggesting that saturation of the cell surface with Ni and iron (Fe) transporters may limit uptake rates in low Fe waters. (C) 2010 Elsevier Ltd. All rights reserved

2009
Snyder, DS, Brahamsha B, Azadi P, Palenik B.  2009.  Structure of compositionally simple lipopolysaccharide from marine Synechococcus. Journal of Bacteriology. 191:5499-5509.   10.1128/jb.00121-09   AbstractWebsite

Lipopolysaccharide (LPS) is the first defense against changing environmental factors for many bacteria. Here, we report the first structure of the LPS from cyanobacteria based on two strains of marine Synechococcus, WH8102 and CC9311. While enteric LPS contains some of the most complex carbohydrate residues in nature, the full-length versions of these cyanobacterial LPSs have neither heptose nor 3-deoxy-D-manno-octulosonic acid (Kdo) but instead 4-linked glucose as their main saccharide component, with low levels of glucosamine and galacturonic acid also present. Matrix-assisted laser desorption ionization mass spectrometry of the intact minimal core LPS reveals triacylated and tetraacylated structures having a heterogeneous mix of both hydroxylated and nonhydroxylated fatty acids connected to the diglucosamine backbone and a predominantly glucose outer core-like region for both strains. WH8102 incorporated rhamnose in this region as well, contributing to differences in sugar composition and possibly nutritional differences between the strains. In contrast to enteric lipid A, which can be liberated from LPS by mild acid hydrolysis, lipid A from these organisms could be produced by only two novel procedures: triethylamine-assisted periodate oxidation and acetolysis. The lipid A contains odd-chain hydroxylated fatty acids, lacks phosphate, and contains a single galacturonic acid. The LPS lacks any limulus amoebocyte lysate gelation activity. The highly simplified nature of LPSs from these organisms leads us to believe that they may represent either a primordial structure or an adaptation to the relatively higher salt and potentially growth-limiting phosphate levels in marine environments.

Tai, V, Paulsen IT, Phillippy K, Johnson AD, Palenik B.  2009.  Whole-genome microarray analyses of Synechococcus-Vibrio interactions. Environmental Microbiology. 11:2698-2709.   10.1111/j.1462-2920.2009.01997.x   AbstractWebsite

P>Microbes live in diverse communities yet their physiologies are typically studied in axenic culture. To begin to address this dichotomy, whole-genome microarray analyses were used and revealed that several major metabolic pathways were affected in Synechococcus sp. WH8102, a model phototroph, when grown with Vibrio parahaemolyticus, a model heterotroph. In co-cultures with V. parahaemolyticus, although phosphate was not depleted, Synechococcus sp. WH8102 may have experienced phosphate stress since the expression of phosphate acquisition genes increased and alkaline phosphatase activity was higher than in monocultures. Expression of cell wall synthesis genes and the components of a zinc transporter were also upregulated. In contrast, a ferric uptake regulation (Fur) family gene was downregulated as were genes that encode proteins rich in iron or involved in detoxifying oxygen radicals. Nitrogen use may also have been affected in co-cultures as the gene expression changes share similarities with ammonia-grown Synechococcus. This study demonstrates the multiple impacts that interspecific microbial interactions can have on the physiology of a major primary producer and the importance of investigating microbial physiology from a community perspective.

Landry, DM, Kristiansen S, Palenik BP.  2009.  Molecular characterization and antibody detection of a nitrogen-regulated cell-surface protein of the coccolithophore emiliania huxleyi (prymnesiophyceae). Journal of Phycology. 45:650-659.   10.1111/j.1529-8817.2009.00693.x   AbstractWebsite

Dissolved organic nitrogen (DON) can account for a significant portion of total nitrogen in some aquatic environments, and many species of phytoplankton are able to scavenge nitrogen from this pool especially when inorganic nitrogen is limiting. Emiliania huxleyi (Lohmann) H. W. Hay et H. Mohler is able to use various forms of DON for growth, including several amino acids, purines, and pyrimidines. A cell-surface protein up-regulated in the absence of inorganic nitrogen, NRP1, is hypothesized to play a role in the metabolism of one or more of these organic nitrogen forms. Here, the genomic and cDNA sequence of NRP1 is reported. Structural predictions based on the amino acid sequence suggest a pyridoxal-5'-phosphate-dependent enzyme that may have a role in acquiring nitrogen from amino acids. Further evidence for the function of NRP1 is measured in spent media from nitrogen-limited cultures, which contain NRP1 and have glutaminase and formamidase activity. Field studies using an antibody to NRP1 show that it is expressed in E. huxleyi during bloom conditions in a Norwegian fjord.

Tetu, SG, Brahamsha B, Johnson DA, Tai V, Phillippy K, Palenik B, Paulsen IT.  2009.  Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp WH8102. ISME Journal. 3:835-849.   10.1038/ismej.2009.31   AbstractWebsite

Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria, is often limited by low inorganic phosphate (P). To observe how these organisms cope with P starvation, we constructed a full genome microarray for Synechococcus sp. WH8102 and compared differences in gene expression under P-replete and P-limited growth conditions, including both early P stress, during extracellular alkaline phosphatase induction, and late P stress. A total of 36 genes showed significant upregulation (>log(2) fold) whereas 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained during late P stress for only 5 of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 and SYNW0948, comprising a two-component regulator hypothesized to have a key function in regulating P metabolism. A high degree of overlap in the sets of genes affected by P stress conditions and in the knockout mutants supports this hypothesis; however, there is some indication that other regulators may be involved in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria. The ISME Journal (2009) 3, 835-849; doi: 10.1038/ismej.2009.31; published online 2 April 2009

Palenik, B, Ren Q, Tai V, Paulsen IT.  2009.  Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology. 11:349-359.   10.1111/j.1462-2920.2008.01772.x   AbstractWebsite

The extent to which cultured strains represent the genetic diversity of a population of microorganisms is poorly understood. Because they do not require culturing, metagenomic approaches have the potential to reveal the genetic diversity of the microbes actually present in an environment. From coastal California seawater, a complex and diverse environment, the marine cyanobacteria of the genus Synechococcus were enriched by flow cytometry-based sorting and the population metagenome was analysed with 454 sequencing technology. The sequence data were compared with model Synechococcus genomes, including those of two coastal strains, one isolated from the same and one from a very similar environment. The natural population metagenome had high sequence identity to most genes from the coastal model strains but diverged greatly from these genomes in multiple regions of atypical trinucleotide content that encoded diverse functions. These results can be explained by extensive horizontal gene transfer presumably with large differences in horizontally transferred genetic material between different strains. Some assembled contigs showed the presence of novel open reading frames not found in the model genomes, but these could not yet be unambiguously assigned to a Synechococcus clade. At least three distinct mobile DNA elements (plasmids) not found in model strain genomes were detected in the assembled contigs, suggesting for the first time their likely importance in marine cyanobacterial populations and possible role in horizontal gene transfer.

Stuart, RK, Dupont CL, Johnson AD, Paulsen IT, Palenik B.  2009.  Coastal strains of marine synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. Applied and Environmental Microbiology. 75:5047-5057.   10.1128/aem.00271-09   AbstractWebsite

Copper appears to be influencing the distribution and abundance of phytoplankton in marine environments, and cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity. By using growth assays of phylogenetically divergent clades, we found that coastal strains of marine Synechococcus species were more tolerant to copper shock than open-ocean strains. The global transcriptional response to two levels of copper shock were determined for both a coastal strain and an open-ocean strain of marine Synechococcus species using whole-genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus species. The two strains additionally showed a common reduction in levels of photosynthesis-related gene transcripts. Contrastingly, the open-ocean strain showed a general stress response, whereas the coastal strain exhibited a more specifically oxidative or heavy-metal acclimation response that may be conferring tolerance. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus strains may in part be a result of a generally increased ability to sense and respond in a more stress-specific manner.

Tai, V, Palenik B.  2009.  Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site. Isme Journal. 3:903-915.   10.1038/ismej.2009.35   AbstractWebsite

Marine cyanobacteria from the genus Synechococcus are found throughout the world's oceans and are important contributors to global primary productivity and carbon cycling. Cultured isolates and environmental DNA clone libraries of Synechococcus have demonstrated the diversity of these microbes. However, the natural distribution of this diversity through space and time and the ecological significance of their distribution are still poorly understood. To understand the seasonal dynamics of Synechococcus diversity, we have developed a quantitative PCR strategy using the gene encoding as a subunit of DNA-dependent RNA polymerase (rpoC1) and applied it to a 3-year time series of surface samples from the Scripps Institution of Oceanography pier (La Jolla, CA, USA), a coastal site in the northeastern Pacific Ocean. Synechococcus from clades I and IV were dominant throughout the time series and correlated with total Synechococcus abundance. The relative abundance of these two dominant clades showed evidence of a seasonal cycle. Synechococcus from clade IV were typically more abundant, but those from clade I dominated during periods just before the annual spring bloom of Synechococcus. Synechococcus from clades II and III were absent during spring and early summer, but appeared at low abundances in late summer and winter possibly due to changes in circulation in the Southern California Bight. As the first long-term time series describing Synechococcus population diversity, these temporal dynamics were used to interpret the genetic/genomic diversity observed in the environment and the potential factors regulating their distribution. The ISME Journal (2009) 3, 903-915; doi: 10.1038/ismej.2009.35; published online 9 April 2009

Thomas, EV, Phillippy KH, Brahamsha B, Haaland DM, Timlin JA, Elbourne LDH, Palenik B, Paulsen IT.  2009.  Statistical analysis of microarray data with replicated spots: a case study with Synechococcus WH8102. Comparative and Functional Genomics.   10.1155/2009/950171   AbstractWebsite

Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition. Copyright (C) 2009 E. V. Thomas et al.

2008
Dupont, CL, Neupane K, Shearer J, Palenik B.  2008.  Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. Environmental Microbiology. 10:1831-1843.   10.1111/j.1462-2920.2008.01604.x   AbstractWebsite

We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.