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Nagarkar, M, Countway PD, Du Yoo Y, Daniels E, Poulton NJ, Palenik B.  2018.  Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site. The ISME Journal.   10.1038/s41396-018-0172-3   Abstract

High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a significant proportion of which remains uncharacterized. Here we use a temporal approach to understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our ability to track operational taxonomic units (OTUs) temporally to evaluate the ability of 18S sequence-based OTU assignments to meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic in terms of both species richness and composition, although proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughout the year. OTUs unique to dates of Synechococcus blooms and crashes or enriched in Synechococcus addition incubation experiments suggest that the prasinophyte Tetraselmis sp. and Gymnodinium-like dinoflagellates are likely Synechococcus grazers under certain conditions, and may play an important role in their population fluctuations.

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.

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.

Chen, X, Su Z, Dam P, Palenik B, Xu Y, Jiang T.  2004.  Operon prediction by comparative genomics: an application to the Synechococcus sp WH8102 genome. Nucleic Acids Research. 32:2147-2157.   10.1093/nar/gkh510   AbstractWebsite

We present a computational method for operon prediction based on a comparative genomics approach. A group of consecutive genes is considered as a candidate operon if both their gene sequences and functions are conserved across several phylogenetically related genomes. In addition, various supporting data for operons are also collected through the application of public domain computer programs, and used in our prediction method. These include the prediction of conserved gene functions, promoter motifs and terminators. An apparent advantage of our approach over other operon prediction methods is that it does not require many experimental data (such as gene expression data and pathway data) as input. This feature makes it applicable to many newly sequenced genomes that do not have extensive experimental information. In order to validate our prediction, we have tested the method on Escherichia coli K12, in which operon structures have been extensively studied, through a comparative analysis against Haemophilus influenzae Rd and Salmonella typhimurium LT2. Our method successfully predicted most of the 237 known operons. After this initial validation, we then applied the method to a newly sequenced and annotated microbial genome, Synechococcus sp. WH8102, through a comparative genome analysis with two other cyanobacterial genomes, Prochlorococcus marinus sp. MED4 and P.marinus sp. MIT9313. Our results are consistent with previously reported results and statistics on operons in the literature.

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.

Collier, JL, Palenik B.  2003.  Phycoerythrin-containing picoplankton in the Southern California Bight. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 50:2405-2422.   10.1016/s0967-0645(03)00127-9   AbstractWebsite

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. (C) 2003 Elsevier Ltd. All rights reserved.

Collier, JL, Brahamsha B, Palenik B.  1999.  The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme. Microbiology-Sgm. 145:447-459.   10.1099/13500872-145-2-447   AbstractWebsite

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 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.

Palenik, B, Wood MA.  1998.  Molecular markers of phytoplankton status and their application at the level of individual cells. Molecular Approaches To The Study Of The Ocean. ( Cooksey KL, Ed.).:187-205., New York: Chapman & Hall Abstract
Chisholm, SW, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury JB, Westjohnsrud L, Zettler ER.  1992.  Prochlorococcus marinus nov. gen. nov. sp.: An oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b . Archives of Microbiology. 157:297-300.   10.1007/bf00245165   AbstractWebsite

Several years ago, prochlorophyte picoplankton were discovered in the N. Atlantic. They have since been found to be abundant within the euphotic zone of the world's tropical and temperate oceans. The cells are extremely small, lack phycobiliproteins. and contain divinyl chlorophyll a and b as their primary photosynthetic pigments. Phylogenies constructed from DNA sequence data indicate that these cells are more closely related to a cluster of marine cyanobacteria than to their prochlorophyte 'relatives' Prochlorothrix and Prochloron. Several strains of this organism have recently been brought into culture, and herewith are given the name Prochlorococcus marinus.

Morel, FMM, Palenik B.  1989.  The aquatic chemistry of biofilms. Structure and Function of Biofilms. 50( Characklis WG, Wilderer PA, Eds.).:351-366., Chichester: John Wiley & Sons, Ltd.   10.1002/jctb.280500315   Abstract
Palenik, B, Block JC, Burns RG, Characklis WG, Christensen BE, Ghiorse WC, Gristina AG, Morel FMM, Nichols WW, Tuovinen OH, Tuschewitzki GJ, Videla HA.  1989.  Biofilms: Properties and processes. Structure and Function of Biofilms. 50( Characklis WG, Wilderer PA, Eds.).:351-366., Chichester: John Wiley & Sons, Ltd.   10.1002/jctb.280500315   Abstract