Publications

Export 6 results:
Sort by: Author Title Type [ Year  (Desc)]
2018
Yoo, YD, Seong KA, Kim HS, Jeong HJ, Yoon EY, Park J, Kim JI, Shin W, Palenik B.  2018.  Feeding and grazing impact by the bloom-forming euglenophyte Eutreptiella eupharyngea on marine eubacteria and cyanobacteria. Harmful Algae. 73:98-109.   10.1016/j.hal.2018.02.003   AbstractWebsite

The phototrophic euglenophyte Eutreptiella eupharyngea often causes blooms in the coastal waters of many countries, but its mode of nutrition has not been assessed. This species has previously been considered as exclusively auxotrophic. To explore whether E. eupharyngea is a mixotrophic species, the protoplasm of E. eupharyngea cells were examined using light, epifluorescence, and transmission electron microscopy after eubacteria, the cyanobacterium Synechococcus sp., and diverse algal species were provided as potential prey. Furthermore, the ingestion rates of E. eupharyngea KR on eubacteria or Synechococcus sp. as a function of prey concentration were measured. In addition, grazing by natural populations of euglenophytes on natural populations of eubacteria in Masan Bay was investigated. This study is the first to report that E eupharyngea is a mixotrophic species. Among the potential prey organisms offered, E. eupharyngea fed only on eubacteria and Synechococcus sp., and the maximum ingestion rates of these two organisms measured in the laboratory were 5.7 and 0.7 cells predator(-1) h(-1), respectively. During the field experiments, the maximum ingestion rates and grazing impacts of euglenophytes, including E. eupharyngea, on natural populations of eubacteria were 11.8 cells predator(-1) h(-1) and 1.228 d(-1), respectively. Therefore, euglenophytes could potentially have a considerable grazing impact on marine bacterial populations. (C) 2018 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.

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.

2013
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.

2011
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.