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2017
Stuart, RK, Bundy R, Buck K, Ghassemain M, Barbeau K, Palenik B.  2017.  Copper toxicity response influences mesotrophic Synechococcus community structure. Environmental Microbiology. 19:756-769.   10.1111/1462-2920.13630   AbstractWebsite

Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, species', also known as clades. Here, we compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbour stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

2016
Paerl, RW, Bouget F-Y, Lozano J-C, Verge V, Schatt P, Allen EE, Palenik B, Azam F.  2016.  Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. : The Author(s)   10.1038/ismej.2016.145   Abstract

Several cosmopolitan marine picoeukaryotic phytoplankton are B1 auxotrophs requiring exogenous vitamin B1 or precursor to survive. From genomic evidence, representatives of picoeukaryotic phytoplankton (Ostreococcus and Micromonas spp.) were predicted to use known thiazole and pyrimidine B1 precursors to meet their B1 demands, however, recent culture-based experiments could not confirm this assumption. We hypothesized these phytoplankton strains could grow on precursors alone, but required a thiazole-related precursor other the well-known and extensively tested 4-methyl-5-thiazoleethanol. This hypothesis was tested using bioassays and co-cultures of picoeukaryotic phytoplankton and bacteria. We found that specific B1-synthesizing proteobacteria and phytoplankton are sources of a yet-to-be chemically identified thiazole-related precursor(s) that, along with pyrimidine B1 precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine, can support growth of Ostreococcus spp. (also Micromonas spp.) without B1. We additionally found that the B1-synthesizing plankton do not require contact with picoeukaryotic phytoplankton cells to produce thiazole-related precursor(s). Experiments with wild-type and genetically engineered Ostreococcus lines revealed that the thiazole kinase, ThiM, is required for growth on precursors, and that thiazole-related precursor(s) accumulate to appreciable levels in the euphotic ocean. Overall, our results point to thiazole-related B1 precursors as important micronutrients promoting the survival of abundant phytoplankton influencing surface ocean production and biogeochemical cycling.

Foflonker, F, Ananyev G, Qiu H, Morrison A, Palenik B, Dismukes GC, Bhattacharya D.  2016.  The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Research-Biomass Biofuels and Bioproducts. 16:465-472.   10.1016/j.algal.2016.04.003   AbstractWebsite

The broadly halotolerant green alga, Picochlorum strain SENEW3, has a highly reduced nuclear genome of 13.5 Mbp that encodes only 7367 genes. It was isolated from a shallow, mesophilic brackish-water lagoon that experiences extreme changes in temperature, light, and in particular, salinity (freshwater to 3-fold seawater). We challenged Picochlorum cells with high or low salinity shock and used transcriptomic and chlorophyll fluorescence analyses to elucidate tolerance to salinity fluctuation. The transcriptome analysis showed that one-half of the coding regions are differentially expressed in response to salinity changes. In addition, a significant number of co-expressed genes (usually from different metabolic pathways) are co-localized in the genome, forming 2-10 gene clusters. Whereas the overall salt stress response in Picochlorum SENEW3 is similar to that in other salt-tolerant algae, the "operon-like" structure in this species likely contributes to rapid recovery during salinity fluctuation. In summary, our work elucidates how evolutionary forces play out in a streamlined genome. Picochlorum SENEW3 relies on a broad array of adaptations from the reliance on horizontally transferred adaptive genes to the co-localization of stress response genes and a robust photosystem II to deal with a fluctuating environment. These attributes make Picochlorum SENEW3 of great biotechnological interest. (C) 2016 Elsevier B.V. All rights reserved.

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.

2015
Yoo, YD, Seong KA, Myung G, Kim HS, Jeong HJ, Palenik B, Yih W.  2015.  Ingestion of the unicellular cyanobacterium Synechococcus by the mixotrophic red tide ciliate Mesodinium rubrum. Algae. 30:281-290.   10.4490/algae.2015.30.4.281   AbstractWebsite

We explored phagotrophy of the phototrophic ciliate Mesodinium rubrum on the cyanobacterium Synechococcus. The ingestion and clearance rates of M. rubrum on Synechococcus as a function of prey concentration were measured. In addition, we calculated grazing coefficients by combining the field data on abundance of M. rubrum and co-occurring Synechococcus spp. with laboratory data on ingestion rates. The ingestion rate of M. rubrum on Synechococcus sp. linearly increased with increasing prey concentrations up to approximately 1.9 x 10(6) cells mL(-1), to exhibit sigmoidal saturation at higher concentrations. The maximum ingestion and clearance rates of M. rubrum on Synechococcus were 2.1 cells predator(-1) h(-1) and 4.2 nL predator(-1)h(-1), respectively. The calculated grazing coefficients attributable to M. rubrum on co-occurring Synechococcus spp. reached 0.04 day(-1). M. rubrum could thus sometimes be an effective protistan grazer of Synechococcus in marine planktonic food webs. M. rubrum might also be able to form recurrent and massive blooms in diverse marine environments supported by the unique and complex mixotrophic arrays including phagotrphy on hetrotrophic bacteria and Synecho coccus as well as digestion, kleptoplastidy and karyoklepty after the ingestion of cryptophyte prey.

Xia, XM, Vidyarathna NK, Palenik B, Lee P, Liu HB.  2015.  Comparison of the seasonal variations of synechococcus assemblage structures in estuarine waters and coastal waters of Hong Kong. Applied and Environmental Microbiology. 81:7644-7655.   10.1128/aem.01895-15   AbstractWebsite

Seasonal variation in the phylogenetic composition of Synechococcus assemblages in estuarine and coastal waters of Hong Kong was examined through pyrosequencing of the rpoC1 gene. Sixteen samples were collected in 2009 from two stations representing estuarine and ocean-influenced coastal waters, respectively. Synechococcus abundance in coastal waters gradually increased from 3.6 x 10(3) cells ml(-1) in March, reaching a peak value of 5.7 x 10(5) cells ml(-1) in July, and then gradually decreased to 9.3 x 10(3) cells ml(-1) in December. The changes in Synechococcus abundance in estuarine waters followed a pattern similar to that in coastal waters, whereas its composition shifted from being dominated by phycoerythrin-rich (PE-type) strains in winter to phycocyanin-only (PC-type) strains in summer owing to the increase in freshwater discharge from the Pearl River and higher water temperature. The high abundance of PC-type Synechococcus was composed of subcluster 5.2 marine Synechococcus, freshwater Synechococcus (F-PC), and Cyanobium. The Synechococcus assemblage in the coastal waters, on the other hand, was dominated by marine PE-type Synechococcus, with subcluster 5.1 clades II and VI as the major lineages from April to September, when the summer monsoon prevailed. Besides these two clades, clade III cooccurred with clade V at relatively high abundance in summer. During winter, the Synechococcus assemblage compositions at the two sites were similar and were dominated by subcluster 5.1 clades II and IX and an undescribed clade (represented by Synechococcus sp. strain miyav). Clade IX Synechococcus was a relatively ubiquitous PE-type Synechococcus found at both sites, and our study demonstrates that some strains of the clade have the ability to deal with large variation of salinity in subtropical estuarine environments. Our study suggests that changes in seawater temperature and salinity caused by the seasonal variation of monsoonal forcing are two major determinants of the community composition and abundance of Synechococcus assemblages in Hong Kong waters.

Johnson, TL, Brahamsha B, Palenik B, Muhle J.  2015.  Halomethane production by vanadium-dependent bromoperoxidase in marine Synechococcus. Limnology and Oceanography. 60:1823-1835.   10.1002/lno.10135   AbstractWebsite

To investigate the role of vanadium-dependent bromoperoxidase (VBPO) for the production of halogenated methanes in marine prokaryotes, we measured VBPO activity and halomethane production in two strains of Synechococcus; one with VBPO (strain CC9311) and one without VBPO (strain WH8102). A mutant strain of CC9311, VMUT2, in which the gene for VBPO is disrupted, was also tested. A suite of halomethanes was measured in the headspace above cultures as well as in the culture medium with a purge-and-trap method. Monohalomethanes were the most consistently produced molecules among the three strains tested. Additionally, CC9311 produced 301 +/- 109 molecules cell(-1) d(-1) of bromoform (CHBr3) when VBPO activity was detected, while production was not significantly different from zero when VBPO activity was not detected. VBPO activity and CHBr3 production were only detected when cultures of CC9311 were stirred, which may contribute to the often moderate to weak correlations between CHBr3 concentration and biological markers in the ocean. No production was seen by VMUT2 or WH8102. These data show that CHBr3 production rates are dramatically increased with or exclusive to the presence of VBPO, supporting its involvement in CHBr3 synthesis. This study thus provides genetic evidence that certain strains of marine Synechococcus, under particular conditions, can be a natural source of marine CHBr3, which contributes to ozone depletion in the stratosphere.

Foflonker, F, Price DC, Qiu H, Palenik B, Wang SY, Bhattacharya D.  2015.  Genome of the halotolerant green alga Picochlorum sp reveals strategies for thriving under fluctuating environmental conditions. Environmental Microbiology. 17:412-426.   10.1111/1462-2920.12541   AbstractWebsite

An expected outcome of climate change is intensification of the global water cycle, which magnifies surface water fluxes, and consequently alters salinity patterns. It is therefore important to understand the adaptations and limits of microalgae to survive changing salinities. To this end, we sequenced the 13.5Mbp genome of the halotolerant green alga PicochlorumSENEW3 (SE3) that was isolated from a brackish water pond subject to large seasonal salinity fluctuations. PicochlorumSE3 encodes 7367 genes, making it one of the smallest and most gene dense eukaryotic genomes known. Comparison with the pico-prasinophyte Ostreococcus tauri, a species with a limited range of salt tolerance, reveals the enrichment of transporters putatively involved in the salt stress response in PicochlorumSE3. Analysis of cultures and the protein complement highlight the metabolic flexibility of PicochlorumSE3 that encodes genes involved in urea metabolism, acetate assimilation and fermentation, acetoin production and glucose uptake, many of which form functional gene clusters. Twenty-four cases of horizontal gene transfer from bacterial sources were found in PicochlorumSE3 with these genes involved in stress adaptation including osmolyte production and growth promotion. Our results identify PicochlorumSE3 as a model for understanding microalgal adaptation to stressful, fluctuating environments.

Paerl, RW, Bertrand EM, Allen AE, Palenik B, Azam F.  2015.  Vitamin B1 ecophysiology of marine picoeukaryotic algae: Strain-specific differences and a new role for bacteria in vitamin cycling. Limnology and Oceanography. 60:215-228.   10.1002/lno.10009   AbstractWebsite

We confirmed multiple picoeukaryotic algae, Ostreococcus, Micromonas, and Pelagomonas spp., as thiamine (vitamin B1) auxotrophs in laboratory experiments with axenic cultures. Examined strains have half saturation growth constants (K-s) for B1 between 1.26 and 6.22 pmol B1 L-1, which is higher than reported seawater concentrations. Minimum B1 cell quotas for Ostreococcus and Micromonas spp. are high (2.20 x 10(-8)-4.46 x 10(-8) pmol B1 cell(-1)) relative to other B1 auxotrophic phytoplankton, potentially making them B1 rich prey for zooplankton and significant B1 reservoirs in oligotrophic marine habitats. Ostreococcus and Micromonas genomes are nonuniformly missing portions of the B1 biosynthesis pathway. Given their gene repertoires, Ostreococcus lucimarinus CCE9901 and Ostreococcus tauri OTH95 are expected to salvage B1 from externally provided 4-methyl-5-thiazoleethanol (HET) and 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). However, in culture, neither could use HET plus HMP instead of B1, highlighting current limitations of genome-based prediction of B1 salvaging by picoeukaryotic algae. HMP and phosphorylated B1 use varied amongst tested strains and notably all Prasinophytes tested could not use HMP. B1-limited O. lucimarinus CCE9901 could not grow on added thiamine diphosphate (TDP), a phosophorylated B1 form. However, in co-culture with Pseudoalteromonas sp. TW7, a bacterium known to exhibit phosphatase activity, O. lucimarinus CCE9901 exhibited increased growth following TDP additions. This demonstrates that bacteria influence vitamin B1 availability beyond de novo synthesis and consumption; they can also serve as conduits that chemically alter, but not completely degrade or retain B1 analogs (e.g., TDP), and make them accessible to a broader range of microbes.

Palenik, B.  2015.  Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment. Annual Review of Marine Science, Vol 7. 7:325-340.   10.1146/annurev-marine-010814-015639   AbstractWebsite

Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.

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.

2014
Ma, YF, Allen LZ, Palenik B.  2014.  Diversity and genome dynamics of marine cyanophages using metagenomic analyses. Environmental Microbiology Reports. 6:583-594.   10.1111/1758-2229.12160   AbstractWebsite

Cyanophages are abundant in the oceanic environment and directly impact cyanobacterial distributions, physiological processes and evolution. Two samples collected from coastal Maine in July and September 2009 were enriched for Synechococcus cells using flow cytometry and examined through metagenomic sequencing. Homology-based sequence prediction indicated cyanophages, largely myoviruses, accounted for almost half the reads and provided insights into environmental infection events. T4-phage core-gene phylogenetic reconstruction revealed unique diversity among uncultured cyanophages and reference isolates resulting in identification of a new phylogenetic cluster. Genomic comparison of reference cyanophage strains S-SM2 and Syn1 with putative homologous contigs recovered from metagenomes provided evidence that gene insertion, deletion and recombination have occurred among, and are likely important for diversification of, natural populations. Identification of putative genetic exchange between cyanophage and non-cyanophage viruses, i.e. Micromonas virus and Pelagibacter phage, supports hypotheses related to a significant role for viruses in mediating transfer of genetic material between taxonomically diverse organisms with overlapping ecological niches.

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.

Hamilton, TJ, Paz-Yepes J, Morrison RA, Palenik B, Tresguerres M.  2014.  Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour. Conservation Physiology. 2   10.1093/conphys/cou020   AbstractWebsite

Coastal California experiences large-scale blooms of Synechococcus cyanobacteria, which are predicted to become more prevalent by the end of the 21st century as a result of global climate change. This study investigated whether exposure to bloom-like concentrations of two Synechococcus strains, CC9311 and CC9902, alters fish behaviour. Black perch (Embiotoca jacksoni) were exposed to Synechococcus strain CC9311 or CC9902 (1.5 × 106 cells ml−1) or to control seawater in experimental aquaria for 3 days. Fish movement inside a testing arena was then recorded and analysed using video camera-based motion-tracking software. Compared with control fish, fish exposed to CC9311 demonstrated a significant preference for the dark zone of the tank in the light–dark test, which is an indication of increased anxiety. Furthermore, fish exposed to CC9311 also had a statistically significant decrease in velocity and increase in immobility and they meandered more in comparison to control fish. There was a similar trend in velocity, immobility and meandering in fish exposed to CC9902, but there were no significant differences in behaviour or locomotion between this group and control fish. Identical results were obtained with a second batch of fish. Additionally, in this second trial we also investigated whether fish would recover after a 3 day period in seawater without cyanobacteria. Indeed, there were no longer any significant differences in behaviour among treatments, demonstrating that the sp. CC9311-induced alteration of behaviour is reversible. These results demonstrate that blooms of specific marine Synechococcus strains can induce differential sublethal effects in fish, namely alterations light–dark preference behaviour and motility.

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.

Gutierrez-Rodriguez, A, Slack G, Daniels EF, Selph KE, Palenik B, Landry MR.  2014.  Fine spatial structure of genetically distinct picocyanobacterial populations across environmental gradients in the Costa Rica Dome. Limnology and Oceanography. 59:705-723.   10.4319/lo.2014.59.3.0705   AbstractWebsite

We investigated the spatial variability of picocyanobacterial community structure across the Costa Rica Dome (CRD), an offshore upwelling system characterized by high seasonal abundance of Synechococcus spp. We constructed clone libraries of the rpoC1 gene to survey picocyanobacterial diversity and developed specific real-time quantitative polymerase chain reaction assays to assess the distribution of genetically distinct Synechococcus (SYN) and Prochlorococcus (PRO) populations across vertical and horizontal physicochemical gradients. Flow cytometry data showed that cell abundances for both SYN and PRO were highest near the dome center. Phylogenetic analysis of rpoC1 sequences revealed a remarkably high and distinctive picocyanobacterial diversity (FLU1-3, CRD1, Clade II, XV, XVI) that included "novel'' SYN and PRO genotypes. Furthermore, genetically different populations exhibited vertical and horizontal spatial partitioning. Abundances of distinct SYN genotypes peaked at subsequent depth horizons, leading to a fine vertical structure with at least three populations stacked within the upper 30-40 m at the dome. Clade II and FLU1A peaked in surface waters, while maximum concentrations of CRD1, FLU1B, and Clade XVI occurred in the upper and lower thermocline, respectively. Horizontally, Clade II abundance in surface waters remained high across the entire region, while SYN genotypes CRD1 and FLU1A increased with shoaling of the thermo- and nutricline toward the center of the dome to become the dominant genotypes of the SYN assemblage in the dome. Below the mixed layer, Clade XVI and PRO genotype FLU2, virtually absent outside the dome, became abundant components of the picocyanobacterial assemblage. Despite their phylogenetic relatedness, FLU1A and FLU1B subclades followed different distributional patterns, suggesting ecological significance of the microdiversity within the clade. The unprecedented fine vertical structure demonstrated for SYN genotypes is driven by sharp physicochemical gradients (e.g., density, nutrient, oxygen, and trace metals) created by the dome and the presence of a shallow oxycline that enhances habitat diversification.

Wang, SY, Lambert W, Giang S, Goericke R, Palenik B.  2014.  Microalgal assemblages in a poikilohaline pond. Journal of Phycology. 50:303-309.   10.1111/jpy.12158   AbstractWebsite

Microalgal strains for algal biofuels production in outdoor ponds will need to have high net growth rates under diverse environmental conditions. A small, variable salinity pond in the San Elijo Lagoon estuary in southern California was chosen to serve as a model pond due to its routinely high chlorophyll content. Profiles of microalgal assemblages from water samples collected from April 2011 to January 2012 were obtained by constructing 18S rDNA environmental clone libraries. Pond assemblages were found to be dominated by green algae Picochlorum sp. and Picocystis sp. throughout the year. Pigment analysis suggested that the two species contributed most of the chlorophyll a of the pond, which ranged from 21.9 to 664.3 mu g center dot L-1 with the Picocystis contribution increasing at higher salinities. However, changes of temperature, salinity or irradiance may have enabled a bloom of the diatom Chaetoceros sp. in June 2011. Isolates of these microalgae were obtained and their growth rates characterized as a function of temperature and salinity. Chaetoceros sp. had the highest growth rate over the temperature test range while it showed the most sensitivity to high salinity. All three strains showed the presence of lipid bodies during nitrogen starvation, suggesting they have potential as future biofuels strains.

Bradley, JM, Hill N, Le Brun NE, Stuart RK, Palenik B.  2014.  Spectroscopic investigation of iron mineralisation by a cyanobacterial ferritin. Journal of Biological Inorganic Chemistry. 19:S291-S291. AbstractWebsite
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2013
Tetu, SG, Johnson DA, Varkey DR, Phillippy K, Stuart RK, Dupont C, Hassan KA, Palenik B, Paulsen IT.  2013.  Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Frontiers in Microbiology. 4   10.3389/fmicb.2013.00232   AbstractWebsite

Marine microorganisms, particularly those residing in coastal areas, may come in contact with any number of chemicals of environmental or xenobiotic origin. The sensitivity and response of marine cyanobacteria to such chemicals is, at present, poorly understood. We have looked at the transcriptional response of well characterised Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole-genome expression microarrays. The coastal strain showed differential regulation of a larger proportion of its genome following ëshockí treatment with each agent. Many of the orthologous genes in these strains, including those encoding sensor kinases, showed different transcriptional responses, with the CC9311 genes more likely to show significant changes in both treatments. While the overall response of each strain was considerably different, there were distinct transcriptional responses common to both strains observed for each DNA damaging agent, linked to the mode of action of each chemical. In both CC9311 and WH8102 there was evidence of SOS response induction under mitomycin C treatment, with genes recA, lexA and umuC significantly upregulated in this experiment but not under ethidium bromide treatment. Conversely, ethidium bromide treatment tended to result in upregulation of the DNA-directed RNA polymerase genes, not observed following mitomycin C treatment. Interestingly, a large number of genes residing on putative genomic island regions of each genome also showed significant upregulation under one or both chemical treatments.

Paz-Yepes, J, Brahamsha B, Palenik B.  2013.  Role of a Microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proceedings of the National Academy of Sciences of the United States of America. 110:12030-12035.   10.1073/pnas.1306260110   AbstractWebsite

Competition between phytoplankton species for nutrients and light has been studied for many years, but allelopathic interactions between them have been more difficult to characterize. We used liquid and plate assays to determine whether these interactions occur between marine unicellular cyanobacteria of the genus Synechococcus. We have found a clear growth impairment of Synechococcus sp. CC9311 and Synechococcus sp. WH8102 when they are cultured in the presence of Synechococcus sp. CC9605. The genome of CC9605 contains a region showing homology to genes of the Escherichia coli Microcin C (McC) biosynthetic pathway. McC is a ribosome-synthesized peptide that inhibits translation in susceptible strains. We show that the CC9605 McC gene cluster is expressed and that three genes (mccD, mccA, and mccB) are further induced by coculture with CC9311. CC9605 was resistant to McC purified from E. coli, whereas strains CC9311 and WH8102 were sensitive. Cloning the CC9605 McC biosynthetic gene cluster into sensitive CC9311 led this strain to become resistant to both purified E. coli McC and Synechococcus sp. CC9605. A CC9605 mutant lacking mccA1, mccA2, and the N-terminal domain of mccB did not inhibit CC9311 growth, whereas the inhibition of WH8102 was reduced. Our results suggest that an McC-like molecule is involved in the allelopathic interactions with CC9605.

Stuart, RK, Brahamsha B, Busby K, Palenik B.  2013.  Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress. Isme Journal. 7:1139-1149.   10.1038/ismej.2012.175   AbstractWebsite

Highly variable regions called genomic islands are found in the genomes of marine picocyano-bacteria, and have been predicted to be involved in niche adaptation and the ecological success of these microbes. These picocyanobacteria are typically highly sensitive to copper stress and thus, increased copper tolerance could confer a selective advantage under some conditions seen in the marine environment. Through targeted gene inactivation of genomic island genes that were known to be upregulated in response to copper stress in Synechococcus sp. strain CC9311, we found two genes (sync_1495 and sync_1217) conferred tolerance to both methyl viologen and copper stress in culture. The prevalence of one gene, sync_1495, was then investigated in natural samples, and had a predictable temporal variability in abundance at a coastal monitoring site with higher abundance in winter months. Together, this shows that genomic island genes can confer an adaptive advantage to specific stresses in marine Synechococcus, and may help structure their population diversity.

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.