Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis

Peer reviewe

Selection of Suitable Reference Genes for RT-qPCR Analyses in Cyanobacteria

Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR) is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works

Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes

Multicellular differentiated organisms are composed of cells that begin by developing from a single pluripotent germ cell. In many organisms, a proportion of cells differentiate into specialized somatic cells. Whether these cells lose their pluripotency or are able to reverse their differentiated state has important consequences. Reversibly differentiated cells can potentially regenerate parts of an organism and allow reproduction through fragmentation. In many organisms, however, somatic differentiation is terminal, thereby restricting the developmental paths to reproduction. The reason why terminal differentiation is a common developmental strategy remains unexplored. To understand the conditions that affect the evolution of terminal versus reversible differentiation, we developed a computational model inspired by differentiating cyanobacteria. We simulated the evolution of a population of two cell types –nitrogen fixing or photosynthetic– that exchange resources. The traits that control differentiation rates between cell types are allowed to evolve in the model. Although the topology of cell interactions and differentiation costs play a role in the evolution of terminal and reversible differentiation, the most important factor is the difference in division rates between cell types. Faster dividing cells always evolve to become the germ line. Our results explain why most multicellular differentiated cyanobacteria have terminally differentiated cells, while some have reversibly differentiated cells. We further observed that symbioses involving two cooperating lineages can evolve under conditions where aggregate size, connectivity, and differentiation costs are high. This may explain why plants engage in symbiotic interactions with diazotrophic bacteria

Slip and hall current effects on Jeffrey fluid suspension flow in a peristaltic hydromagnetic blood micropump

The magnetic properties of blood allow it to be manipulated with an electromagnetic field. Electromagnetic blood flow pumps are a robust technology which provide more elegant and sustainable performance compared with conventional medical pumps. Blood is a complex multi-phase suspension with non-Newtonian characteristics which are significant in micro-scale transport. Motivated by such applications, in the present article a mathematical model is developed for magnetohydrodynamic (MHD) pumping of blood in a deformable channel with peristaltic waves. A Jeffery’s viscoelastic formulation is employed for the rheology of blood. A twophase fluid-particle (“dusty”) model is utilized to better simulate suspension characteristics (plasma and erythrocytes). Hall current and wall slip effects are incorporated to achieve more realistic representation of actual systems. A two-dimensional asymmetric channel with dissimilar peristaltic wave trains propagating along the walls is considered. The governing conservation equations for mass, fluid and particle momentum are formulated with appropriate boundary conditions. The model is simplified using of long wavelength and creeping flow approximations. The model is also transformed from the fixed frame to the wave frame and rendered non-dimensional. Analytical solutions are derived. The resulting boundary value problem is solved analytically and exact expressions are derived for the fluid velocity, particulate velocity, fluid/particle fluid and particulate volumetric flow rates, axial pressure gradient, pressure rise and skin friction distributions are evaluated in detail. Increasing Hall current parameter reduces bolus growth in the channel, particle phase velocity and pressure difference in the augmented pumping region whereas it increases fluid phase velocity, axial pressure gradient and pressure difference in the pumping region. Increasing the hydrodynamic slip parameter accelerates both particulate and fluid phase flow at and close to the channel walls, enhances wall skin friction, boosts pressure difference in the augmented pumping region and increases bolus magnitudes. Increasing viscoelastic parameter (stress relaxation time to retardation time ratio) decelerates the fluid phase flow, accelerates the particle phase flow, decreases axial pressure gradient, elevates pressure difference in the augmented pumping region and reduces pressure difference in the pumping region. Increasing drag particulate suspension parameter decelerates the particle phase velocity, accelerates the fluid phase velocity, strongly elevates axial pressure gradient and reduces pressure difference (across one wavelength) in the augmented pumping region. Increasing particulate volume fraction density enhances bolus magnitudes in both the upper and lower zones of the channel and elevates pressure rise in the augmented pumping region

The Influence of pCO2 and Temperature on Gene Expression of Carbon and Nitrogen Pathways in Trichodesmium IMS101

Growth, protein amount, and activity levels of metabolic pathways in Trichodesmium are influenced by environmental changes such as elevated pCO2 and temperature. This study examines changes in the expression of essential metabolic genes in Trichodesmium grown under a matrix of pCO2 (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO2 concentrating mechanism (bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX), energy metabolism (atpB, sod, prx, glcD), nitrogen metabolism (glnA, hetR, nifH), and inorganic carbon fixation and photosynthesis (rbcL, rca, psaB, psaC, psbA). nifH and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for glnA and hetR only when both pCO2 and temperature were elevated. CO2 concentrating mechanism genes were not affected by pCO2 and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO2 concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in Trichodesmium, CO2 concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N2 fixation take place, pointing at the tight and complex regulation of gene expression in Trichodesmium. Here we provide new data linking environmental changes of pCO2 and temperature to gene expression in Trichodesmium. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity

Diurnal expression of hetR and diazocyte development in the filamentous non-heterocystous cyanobacterium Trichodesmium erythraeum

The marine non-heterocystous cyanobacterium Trichodesmium fixes atmospheric N2 aerobically in light. In situ immunolocalization/light microscopy of NifH revealed that lighter, non-granulated cell regions observed correspond to the nitrogenase-containing diazocyte clusters in Trichodesmium IMS101. The number of diazocyte clusters per trichome varied from 0 to 4 depending on trichome length. The constant percentage of diazocytes (approx. 15 %) in cultured strains and five natural populations suggests a developmentally regulated differentiation process. Real-time RT-PCR showed that ntcA, encoding the global nitrogen regulator in cyanobacteria, and hetR, the key regulatory gene in heterocyst differentiation, are both constitutively expressed during a 12 h/12 h light/dark cycle. hetR in addition showed a distinct peak in the dark (close to midnight) while nifH expression commenced 6–8 h later. The expression of all three genes was negatively affected by addition of ammonia. Some early heterocyst differentiation genes were also identified in the genome of Trichodesmium. The data suggest that hetR and ntcA may be required for development and function of diazocytes in Trichodesmium