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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.

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.

Mao, X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y.  2010.  Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. Bmc Genomics. 11   10.1186/1471-2164-11-291   AbstractWebsite

Background: Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO(2) fixation. Results: We present here a computational study of the osmoregulation network in response to hyperosmotic stress of Synechococcus sp strain WH8102 using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress. Conclusions: From the predicted network model, we have made a number of interesting observations about WH8102. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma(38), one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

Mayali, X, Palenik B, Burton RS.  2010.  Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environmental Microbiology. 12:975-989.   10.1111/j.1462-2920.2009.02142.x   AbstractWebsite

Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate.

Moore, MJK, Furutani H, Roberts GC, Moffet RC, Gilles MK, Palenik B, Prather KA.  2011.  Effect of organic compounds on cloud condensation nuclei (CCN) activity of sea spray aerosol produced by bubble bursting. Atmospheric Environment. 45:7462-7469.   10.1016/j.atmosenv.2011.04.034   AbstractWebsite

The ocean comprises over 70% of the surface of the earth and thus sea spray aerosols generated by wave processes represent a critical component of our climate system. The manner in which different complex oceanic mixtures of organic species and inorganic salts are distributed between individual particles in sea spray directly determines which particles will effectively form cloud nuclei. Controlled laboratory experiments were undertaken to better understand the full range of particle properties produced by bubbling solutions composed of simplistic model organic species, oleic acid and sodium dodecyl sulfate (SDS), mixed with NaCl to more complex artificial seawater mixed with complex organic mixtures produced by common oceanic microorganisms. Simple mixtures of NaCl and oleic acid or SDS had a significant effect on CCN activity, even in relatively small amounts. However, an artificial seawater (ASW) solution containing microorganisms, the common cyanobacteria (Synechococcus) and DMS-producing green algae (Ostreococcus), produced particles containing similar to 34 times more carbon than the particles produced from pure ASW, yet no significant change was observed in the overall CCN activity. We hypothesize that these microorganisms produce diverse mixtures of organic species with a wide range of properties that produced offsetting effects, leading to no net change in the overall average measured hygroscopicity of the collection of sea spray particles. Based on these observations, changes in CCN activity due to "bloom" conditions would be predicted to lead to small changes in the average CCN activity, and thus have a negligible impact on cloud formation. However, each sea spray particle will contain a broad spectrum of different species, and thus further studies are needed of the CCN activity of individual sea spray particles and biological processes under a wide range of controllable conditions. (C) 2011 Published by Elsevier Ltd.

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