Publications

Export 102 results:
Sort by: Author Title [ Type  (Asc)] Year
Book Chapter
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
n/a
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
n/a
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, 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
n/a
Swift, H, Palenik B.  1993.  Prochlorophyte evolution and the origin of chloroplasts: Morphological and molecular evidence. Origins of plastids : symbiogenesis, prochlorophytes, and the origins of chloroplasts. ( Lewin RA, Ed.).:123-139., New York: Chapman & Hall Abstract
n/a
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.

Palenik, B, Dyhrman ST.  1998.  Recent progress in understanding the regulation of marine primary productivity by phosphorus. Phosphorus in Plant Biology: Regulating Roles in Molecular, Cellular, Organismic and Ecosystem Processe. ( Lynch JP, Deikman J, Eds.).:26-38., Rockville, MD: American Society of Plant Physiologists Abstract
n/a
Conference Proceedings
Palenik, B.  1998.  Why do isolates of eubacterial species have different growth rates under hte same conditions, in Microbial biosystems: new frontiers. 8th International Symposium on Microbial Ecology. ( Bell C, Brylinsky M, Johnson-Green PC, Eds.).:611-616., Halifax, Canada: Atlantic Canada Society for Microbial Ecology Abstract
n/a
Journal Article
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.

Toledo, G, Palenik B.  1997.  Synechococcus diversity in the California Current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Applied and Environmental Microbiology. 63:4298-4303. AbstractWebsite

Because they are ubiquitous in a range of aquatic environments and culture methods are relatively advanced, cyanobacteria may be useful models for understanding the extent of evolutionary adaptation of prokaryotes in general to environmental gradients. The roles of environmental variables such as light and nutrients in influencing cyanobacterial genetic diversity are still poorly characterized, however, In this study, a total of 15 Synechococcus strains were isolated from the oligotrophic edge of the California Current from two depths (5 and 95 m) with large differences in fight intensity, light quality, and nutrient concentrations. RNA polymerase gene (rpoC1) fragment sequences of the strains revealed two major genetic lineages, distinct from other marine or freshwater cyanobacterial isolates or groups seen in shotgun-cloned sequences from the oligotrophic Atlantic Ocean. The California Current low-phycourobilin (CCLPUB) group represented by six isolates in a single lineage was less diverse than the California Current high-phycourobilin (CCHPUB) group with nine isolates in three relatively divergent lineages. The former,vas found to be the closest known genetic group to Prochlorococcus spp., a chlorophyll b-containing cyanobacterial group, Having an isolate from this group will be valuable for looking at the molecular changes necessary for the transition from the use of phycobiliproteins to chlorophyll b as light-harvesting pigments. Both of the CCHPUB and CCLPUB groups included strains obtained from surface (5 m) and deep (95 m) samples, Thus, contrary to expectations, there was no clear correlation between sampling depth and isolation of genetic groups, despite the large environmental gradients present, To our knowledge, this is the first demonstration with isolates that genetically divergent Synechococcus groups coexist in the same seawater sample.

Toledo, G, Palenik B.  2003.  A Synechococcus serotype is found preferentially in surface marine waters. Limnology and Oceanography. 48:1744-1755. AbstractWebsite

In marine ecosystems, gradients of light, temperature, and nutrients occur horizontally (coastal to offshore) and vertically. The extent to which microorganisms acclimate or speciate in response to these gradients is under active investigation. Strain isolation data (e.g., site or depth), environmental DNA clone libraries, and preliminary physiology experiments have indicated that marine Synechococcus strain CC9605 might be adapted to the surface oligotrophic ocean. In the present work, we used an immunofluorescent approach to detect the CC9605 serotype in the California Current during September 1998. At two offshore stations, samples were collected along vertical profiles. The relative abundance of the CC9605 serotype was significantly higher in shallow depths within the mixed layer than in deeper depths at the two stations, with maximum values (+/- standard deviation) of 10.3% +/- 6.4 and 28.7% +/- 9.5. Surface samples along an offshore-inshore transect showed higher abundance in the most oligotrophic site (8% +/- 3), compared with almost 1% inshore, but one coastal site also had high relative abundance of the CC9605 serotype (7% +/- 0.5). These data indicate that Synechococcus strains are not uniformly distributed and that some strains, such as CC9605, are more abundant in the mixed layer of the euphotic zone than below the mixed layer.

Palenik, B, Morel FMM.  1991.  Amine Oxidases of Marine-Phytoplankton. Applied and Environmental Microbiology. 57:2440-2443. AbstractWebsite

Some phytoplankton utilized a novel mechanism for obtaining nitrogen from primary amines. They oxidized the primary amines to produce extracellular hydrogen peroxide and aldehydes and used the third reaction product, ammonium, as a nitrogen source. The specificity, regulation, inhibition by bromoethylamine, and potential dependence on copper of this process are described.

Palenik, B, Morel FMM.  1990.  Amino acid utilization by a marine phytoplankton: A novel mechanism. Limnology and Oceanography. 35:260-269. AbstractWebsite
n/a
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.

Worden, AZ, Nolan JK, Palenik B.  2004.  Assessing the dynamics and ecology of marine picophytoplankton: The importance of the eukaryotic component. Limnology and Oceanography. 49:168-179. AbstractWebsite
n/a
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.

Taton, A, Unglaub F, Wright NE, Zeng WY, Paz-Yepes J, Brahamsha B, Palenik B, Peterson TC, Haerizadeh F, Golden SS, Golden JW.  2014.  Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. Nucleic Acids Research. 42   10.1093/nar/gku673   AbstractWebsite

Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bio-products, we developed a versatile platform for the construction of broad-host-range vector systems. This platform includes the following features: (i) an efficient assembly strategy in which modules released from 3 to 4 donor plasmids or produced by polymerase chain reaction are assembled by isothermal assembly guided by short GC-rich overlap sequences. (ii) A growing library of molecular devices categorized in three major groups: (a) replication and chromosomal integration; (b) antibiotic resistance; (c) functional modules. These modules can be assembled in different combinations to construct a variety of autonomously replicating plasmids and suicide plasmids for gene knockout and knockin. (iii) A web service, the CYANO-VECTOR assembly portal, which was built to organize the various modules, facilitate the in silico construction of plasmids, and encourage the use of this system. This work also resulted in the construction of an improved broad-host-range replicon derived from RSF1010, which replicates in several phylogenetically distinct strains including a new experimental model strain Synechocystis sp. WHSyn, and the characterization of nine antibiotic cassettes, four reporter genes, four promoters, and a ribozyme-based insulator in several diverse cyanobacterial strains.

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.

Davis, AK, Palenik B.  2008.  Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana. Protist. 159:195-207.   10.1016/j.protis.2007.09.006   AbstractWebsite

We report the characterization of a cell-surface protein isolated from copper-stressed cells of the centric diatom Thalassiosira pseudonana Hasle and Heimdal (CCMP 1335). This protein has an apparent molecular weight of 100kDa and is highly acidic. The 100kDa protein (p100) sequence is comprised almost entirely of a novel domain termed TpRCR for T pseudonana repetitive cysteine-rich domain, that is repeated 8 times and that contains conserved aromatic, acidic, and potential metal-binding amino acids. The analysis of the T pseudonana genome suggests that p100 belongs to a large family of modular proteins that consist of a variable number of TpRCR domain repeats. Based on cell surface biotinylation and antibody data, p100 appears to migrate more rapidly with SDS-PAGE when extracted from cells exposed to high levels of copper; however, the discovery of a large family of TpRCR domain-containing proteins leaves open the possibility that the antibody may be crossreacting with members of this protein family that are responding differently to copper. The response of the gene encoding p100 at the mRNA level during synchronized progression through the normal cell cycle is similar to previously characterized genes in T pseudonana encoding cell wall proteins called silaffins. (c) 2007 Elsevier GmbH. All rights reserved.

Palenik, B, Koke JA.  1995.  Characterization of a nitrogen-regulated protein identified by cell-surface biotinylation of a marine-phytoplankton. Applied and Environmental Microbiology. 61:3311-3315. AbstractWebsite

The biotinylating reagent succinimidyl 6-(biotinamido)hexanoate was used to label the cell surfaces of the cosmopolitan, marine, eukaryotic microorganism Emiliania huxleyi under different growth conditions. Proteins characteristic of different nutrient conditions could be identified. In particular, a nitrogen-regulated protein, nrp1, has an 82-kDa subunit that is present under nitrogen limitation and during growth on urea, It is absent under phosphate limitation or during exponential growth on nitrate or ammonia. nrp1 is the major membrane or wall protein in nitrogen-limited cells and is found in several strains of E, huxleyi, It may be a useful biomarker for examining the physiological state of E. huxleyi cells in their environment.

Dyhrman, ST, Palenik B.  2003.  Characterization of ectoenzyme activity and phosphate-regulated proteins in the coccolithophorid Emiliania huxleyi. Journal of Plankton Research. 25:1215-1225.   10.1093/plankt/fbg086   AbstractWebsite

Three phosphate-regulated proteins in the coccolithophorid Emiliania huxleyi were detected by the biotinylation of cell-surface proteins. Two of these phosphate-regulated proteins have reduced denatured molecular weights near I 10 000 Do (118 078 and 110 541, respectively), while the third, and most abundant, is 69 087 Da. Induction of the three proteins and the common marker of phosphate stress, alkaline phosphatase activity, occur in the presence of <0.25 mu M inorganic phosphate in batch culture. Phosphate-regulated proteins and enzyme activity differed among E. huxleyi strains. Alkaline phosphatase is an enzyme commonly induced by phytoplankton in response to phosphate stress in order for cells to scavenge inorganic phosphate from organic sources. In E. huxleyi, this enzyme activity and the phosphate-regulated proteins are rapidly lost when phosphate is added back to phosphate-stressed cultures. This contrasts with the slower loss of alkaline phosphatase activity in the dinoflagellate Prorocentrum minimum. The presence of the three phosphate-regulated proteins and enzyme activity appear to differ somewhat among E. huxleyi strains. Based on these differences between strains, kinetic data, growth experiments and enzyme activities, the 69 087 Da protein may be a phosphatase with a high specificity for 5'-nucleotides.

Wang, SY, Shi XG, Palenik B.  2016.  Characterization of Picochlorum sp use of wastewater generated from hydrothermal liquefaction as a nitrogen source. Algal Research-Biomass Biofuels and Bioproducts. 13:311-317.   10.1016/j.algal.2015.11.015   AbstractWebsite

Picochlorumsp. strain SENEW3 is a halotolerant green algawith high growth rates and the ability to utilize organic nitrogen sources including wastewater generated from hydrothermal liquefaction (HTL-WW). Picochlorum acclimates to the presence of HTL-WW. In a photosynthesis/respiration rate test, Picochlorum SENEW3 showed a stress response to HTL-WW additions in a dose-dependent manner while cells pre-grown with HTL-WW had a greatly reduced response to additions. A quantitative proteomics tool, iTRAQ, was applied to assess Picochlorum global proteome changes in response to HTL-WWas a nitrogen source. From this approach, a total of 350 different proteins were identified across 2 biological replicates which were significantly up-regulated or down-regulated (average ratio of more than 1.2 or less than 0.8, at least one p-value of <0.05). Protease and oxidative stress enzymes were notably up-regulated. An aminopeptidase enzyme assay showed that, compared to controls, cells grown with 0.1% (vol) HTL-WW had 2.1-fold higher protease activity. An ascorbate peroxidase assay showed an 8.6-fold increase in exponential cells grown with 0.1% HTL-WW compared to controls. This study provides insights into the development of microalgae for algal biofuel production using HTL wastewater recycling [1]. (C) 2015 Elsevier B.V. All rights reserved.

Palenik, B.  2001.  Chromatic adaptation in marine Synechococcus strains. Applied and Environmental Microbiology. 67:991-994.   10.1128/aem.67.2.991-994.2001   AbstractWebsite

Characterization of two genetically distinct groups of marine Synechococcus sp. strains shows that one, but not the other, increases its phycourobilin/phycoerythrobilin chromophore ratio when growing in blue light. This ability of at least some marine Synechococcus strains to chromatically adapt may help explain their greater abundance in particular ocean environments than cyanobacteria of the genus Prochlorococcus.

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.

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.