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Dupont, CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Craig Venter J, Allen AE.  2015.  Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 9:1076-1092.: International Society for Microbial Ecology   10.1038/ismej.2014.198   Abstract

Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-[mu]m size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.

Keeling, PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust VE, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AGB, Slamovits CH, Smith DR, Smith JG, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ.  2014.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12:e1001889.: Public Library of Science   10.1371/journal.pbio.1001889   AbstractWebsite

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 world's oceans.

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.

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.

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.

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.

Palenik, B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV.  2007.  The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America. 104:7705-7710.   10.1073/pnas.0611046104   AbstractWebsite

The smallest known eukaryotes, at approximate to 1-mu m diameter, are ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.

Palenik, B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin SA, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT.  2006.  Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences of the United States of America. 103:13555-13559.   10.1073/pnas.0602963103   AbstractWebsite

Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.

Sandhage, KH, Allan SM, Dickerson MB, Gaddis CS, Shian S, Weatherspoon MR, Cai Y, Ahmad G, Haluska MS, Snyder RL, Unocic RR, Zalar FM, Zhang YS, Rapp RA, Hildebrand M, Palenik BP.  2005.  Merging biological self-assembly with synthetic chemical tailoring: The potential for 3-D genetically engineered micro/nano-devices (3-D GEMS). International Journal of Applied Ceramic Technology. 2:317-326.   10.1111/j.1744-7402.2005.02035.x   AbstractWebsite

Appreciable global efforts are underway to develop processes for fabricating three-dimensional (3-D) nanostructured assemblies for advanced devices. Widespread commercialization of such devices will require: (i) precise 3-D fabrication of chemically tailored structures on a fine scale and (ii) mass production of such structures on a large scale. These often-conflicting demands can be addressed with a revolutionary new paradigm that couples biological self-assembly with synthetic chemistry: Bioclastic and Shape-preserving Inorganic Conversion (BaSIC). Nature provides numerous examples of microorganisms that assemble biominerals into intricate 3-D structures. Among the most spectacular of these microorganisms are diatoms (unicellular algae). Each of the tens of thousands of diatom species assembles silica nanoparticles into a microshell with a distinct 3-D shape and pattern of fine (nanoscale) features. The repeated doubling associated with biological reproduction enables enormous numbers of such 3-D microshells to be generated (e.g., only 40 reproduction cycles can yield >1 trillion 3-D replicas!). Such generic precision and massive parallelism are highly attractive for device manufacturing. However, the natural chemistries assembled by diatoms (and other microorganisms) are rather limited. With BaSIC processes, biogenic assemblies can be converted into a wide variety of new functional chemistries, while preserving the 3-D morphologies. Ongoing advances in genetic engineering promise to yield microorganisms tailored to assemble nanoparticle structures with device-specific shapes. Large-scale culturing of such genetically tailored microorganisms, coupled with shape-preserving chemical conversion (via BaSIC processes), would then provide low-cost 3-D Genetically Engineered Micro/nano-devices (3-D GEMs).

Armbrust, EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou SG, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WWY, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS.  2004.  The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science. 306:79-86.   10.1126/science.1101156   AbstractWebsite

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for similar to20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair ptastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Palenik, B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J.  2003.  The genome of a motile marine Synechococcus. Nature. 424:1037.: Macmillan Magazines Ltd.   10.1038/nature01943   Abstract

Marine unicellular cyanobacteria are responsible for an estimated 20–40% of chlorophyll biomass and carbon fixation in the oceans1. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria2.

Roulier, MA, Palenik B, Morel FMM.  1990.  A method for the measurement of choline and hydrogen-peroxide in seawater. Marine Chemistry. 30:409-421.   10.1016/0304-4203(90)90084-p   AbstractWebsite

The horseradish peroxidase-mediated dimerization of hydroxyphenylpropionic acid can be used to measure hydrogen peroxide in seawater. The method was optimized and interferences investigated, and the method was then adapted to the measurement of choline in seawater. The enzyme choline oxidase is used specifically to oxidize choline to produce betaine and H2O2, and the latter is measured. Possible interferences with this method were investigated, and choline was measured in coastal seawater, where it varied from 0 to 45 nM.