Periodic Report Summary 1 - GENMARPHYTO (FUNCTIONAL GENOMICS STUDIES IN MARINE PRIMARY PRODUCTIVITY: ENVIRONMENTAL AND POLUTION EFFECTS ON PHYTOPLANKTON)
Marine cyanobacteria are an ecologically relevant group within marine phytoplankton. They highly contribute to the global carbon fixation in the marine environments and occupy a key position at the base of the marine food web. Our understanding of gene regulation in marine phytoplankton, in particular with respect to the response to various significant environmental parameters, as competitor strains or nutrients, is very limited yet. Therefore, one goal of the outgoing phase was to carry out functional transcriptomics studies in marine Synechococcus to compare the global responses between them and with other available microbial data. Additionally, we wanted to understand how marine Synechococcus interacts with its biotic environment. With all this information we can better understand why this cyanobacterial group is so abundant and successful in the environment. This phase of the project (outgoing phase) has been developed in the Scripps Institution of Oceanography at the University of California San Diego. The following main scientific objectives were planned for the outgoing phase: 1) Determine which genes are involved in stress responses under different stress conditions; 2) Compare the response of genes involved in different stress conditions. 3) Find connections between metabolic regulators. 4) Find defence mechanisms of marine Synechococcus under environmental competition or predation pressure. Several axenic model Synechococcus strains with the genomes available were used to carry out the laboratory experiments.
Multiple incubation analyses have been carried out to determine when Synechococcus sp. CC9311 reaches nitrogen limitation and phosphate limitation. The fellow has discovered that this strain is able to take up DNA and use it as a phosphate source under phosphate limited conditions. The fellow has shown that there is an ORF that is involved in this process since when it is disrupted the growth of Synechococcus sp. CC9311 on DNA is impaired (work to be submitted).
RNA-seq has been used to study the transcriptomic response of Synechococcus. We have analyzed differential gene expression when two Synechococcus strains are mixed. It has been done in triplicate taking samples before mixing and after mixing both strains (times 0, 3, 6, 12, 24, 48 hours). We have found that both strains enrich the same specific biological functions and many of the up-regulated genes are predicted to be involved in toxicity, defense and interspecific competition in general. Very interestingly both strains also induce the gene expression of multiple genes from nutrient metabolisms as a competitive response. Curiously Synechococcus sp. CC9311, strain known to be impared by toxins that CC9605 produces, shows a higher global change in gene expression than CC9605 (work to be submitted).
We have studied the interactions of several marine Synechococcus strains with its biotic environment (from other Synechococcus strains to fish or heterotrophic nanoflagellates that feed on them). We have discovered the occurrence of allelopathic interactions between different marine Synechococcus strains (Paz-Yepes et al., 2013). This finding increases our understanding of how marine Synechococcus communities are structured in the marine environments. We have also reported recently that exposure to bloom-like concentrations of two coastal marine Synechococcus alters the behavior of the Californian black perch (Embiotoca jacksoni) (Hamilton, Paz-Yepes et al., 2014). Our results demonstrate, for the first time, that blooms of specific Synechococcus strains can induce sub-lethal effects on fish, namely alterations in basic motor control and preference behavior. Additionally, we have characterized prey-predator interactions between marine Synechococcus strains and new heterotrophic nanoflagellates. To do this, the fellow has performed laboratory incubations mixing different Synechococcus strains with new heterotrophic nanoflagellates isolates from the Scripps Institution of Oceanography pier (La Jolla, CA, USA) from the highly divergent genera Acanthoeca, Mataza, Paraphysomonas and Pteridomonas. Including as well the well-known nanoflagellate Goniomonas pacifica. Thus, we have calculated the growth rate for each microorganism and we have studied defense mechanisms of diverse marine Synechococcus strains under grazing pressure (Paz-Yepes et al, in review. ISME J).
The previous results increase our knowledge of marine Synechococcus adaptation to changing environment conditions. This also gives us hints of the microbial community adaptability to future changing conditions and how it might react. We have also characterized how this group of microorganisms interacts with its biotic environment, as for example affecting the behaviour of local fish from the coast of California. This new knowledge is crucial if we consider the key role played by this group of microorganisms in both, the planetary CO2 capture and the marine trophic webs.
The fellow has also contributed in the development of a broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. This work provides an integrated and expandable platform for the efficient construction of vectors and finished plasmids from in silico design to laboratory protocols. It will greatly benefit the research and industrial communities (Taton et al., 2014).
- Hamilton T, Paz-Yepes J (Co-first author), Morrison R, Palenik B, Tresguerres M (2014). Exposure to a bloom-like concentration of the marine cyanobacterium Synechococcus sp. CC9311 (but not strain CC9902) alters fish behaviour. Coservation Physiology 2: doi:10.1093/conphys/cou020.
- Paz-Yepes J, Brahamsha B, Palenik B (2013). The role of a Microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proceedings of the National Academy of Sciences of the U S A 110:12030-5.
- Paz-Yepes J, Beld J, Burkart MC, Palenik B. Grazing on marine Synechococcus by new marine heterotrophic nanoflagellate isolates. ISME J In Review.
- Taton A, Unglaub F, Wright NE, Zeng WY, Paz-Yepez 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. doi: 10.1093/nar/gku673.
Multiple incubation analyses have been carried out to determine when Synechococcus sp. CC9311 reaches nitrogen limitation and phosphate limitation. The fellow has discovered that this strain is able to take up DNA and use it as a phosphate source under phosphate limited conditions. The fellow has shown that there is an ORF that is involved in this process since when it is disrupted the growth of Synechococcus sp. CC9311 on DNA is impaired (work to be submitted).
RNA-seq has been used to study the transcriptomic response of Synechococcus. We have analyzed differential gene expression when two Synechococcus strains are mixed. It has been done in triplicate taking samples before mixing and after mixing both strains (times 0, 3, 6, 12, 24, 48 hours). We have found that both strains enrich the same specific biological functions and many of the up-regulated genes are predicted to be involved in toxicity, defense and interspecific competition in general. Very interestingly both strains also induce the gene expression of multiple genes from nutrient metabolisms as a competitive response. Curiously Synechococcus sp. CC9311, strain known to be impared by toxins that CC9605 produces, shows a higher global change in gene expression than CC9605 (work to be submitted).
We have studied the interactions of several marine Synechococcus strains with its biotic environment (from other Synechococcus strains to fish or heterotrophic nanoflagellates that feed on them). We have discovered the occurrence of allelopathic interactions between different marine Synechococcus strains (Paz-Yepes et al., 2013). This finding increases our understanding of how marine Synechococcus communities are structured in the marine environments. We have also reported recently that exposure to bloom-like concentrations of two coastal marine Synechococcus alters the behavior of the Californian black perch (Embiotoca jacksoni) (Hamilton, Paz-Yepes et al., 2014). Our results demonstrate, for the first time, that blooms of specific Synechococcus strains can induce sub-lethal effects on fish, namely alterations in basic motor control and preference behavior. Additionally, we have characterized prey-predator interactions between marine Synechococcus strains and new heterotrophic nanoflagellates. To do this, the fellow has performed laboratory incubations mixing different Synechococcus strains with new heterotrophic nanoflagellates isolates from the Scripps Institution of Oceanography pier (La Jolla, CA, USA) from the highly divergent genera Acanthoeca, Mataza, Paraphysomonas and Pteridomonas. Including as well the well-known nanoflagellate Goniomonas pacifica. Thus, we have calculated the growth rate for each microorganism and we have studied defense mechanisms of diverse marine Synechococcus strains under grazing pressure (Paz-Yepes et al, in review. ISME J).
The previous results increase our knowledge of marine Synechococcus adaptation to changing environment conditions. This also gives us hints of the microbial community adaptability to future changing conditions and how it might react. We have also characterized how this group of microorganisms interacts with its biotic environment, as for example affecting the behaviour of local fish from the coast of California. This new knowledge is crucial if we consider the key role played by this group of microorganisms in both, the planetary CO2 capture and the marine trophic webs.
The fellow has also contributed in the development of a broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. This work provides an integrated and expandable platform for the efficient construction of vectors and finished plasmids from in silico design to laboratory protocols. It will greatly benefit the research and industrial communities (Taton et al., 2014).
- Hamilton T, Paz-Yepes J (Co-first author), Morrison R, Palenik B, Tresguerres M (2014). Exposure to a bloom-like concentration of the marine cyanobacterium Synechococcus sp. CC9311 (but not strain CC9902) alters fish behaviour. Coservation Physiology 2: doi:10.1093/conphys/cou020.
- Paz-Yepes J, Brahamsha B, Palenik B (2013). The role of a Microcin-C-like biosynthetic gene cluster in allelopathic interactions in marine Synechococcus. Proceedings of the National Academy of Sciences of the U S A 110:12030-5.
- Paz-Yepes J, Beld J, Burkart MC, Palenik B. Grazing on marine Synechococcus by new marine heterotrophic nanoflagellate isolates. ISME J In Review.
- Taton A, Unglaub F, Wright NE, Zeng WY, Paz-Yepez 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. doi: 10.1093/nar/gku673.