RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis

Background Mean phosphorous:nitrogen (P:N) ratios and relationships of P:N ratios with the growth rate of organisms indicate a surprising similarity among and within microbial species, plants, and insect herbivores. To reveal the cellular mechanisms underling this similarity, the macromolecular composition of seven microorganisms and the effect of specific growth rate (SGR) on RNA:protein ratio, the number of ribosomes, and peptide elongation rate (PER) were analyzed under different conditions of exponential growth. Results It was found that P:N ratios calculated from RNA and protein contents in these particular organisms were in the same range as the mean ratios reported for diverse organisms and had similar positive relationships with growth rate, consistent with the growth-rate hypothesis. The efficiency of protein synthesis in microorganisms is estimated as the number of active ribosomes required for the incorporation of one amino acid into the synthesized protein. This parameter is calculated as the SGR:PER ratio. Experimental and theoretical evidence indicated that the requirement of ribosomes for protein synthesis is proportional to the RNA:protein ratio. The constant of proportionality had the same values for all organisms, and was derived mechanistically from the characteristics of the protein-synthesis machinery of the cell (the number of nucleotides per ribosome, the average masses of nucleotides and amino acids, the fraction of ribosomal RNA in the total RNA, and the fraction of active ribosomes). Impairment of the growth conditions decreased the RNA:protein ratio and increased the overall efficiency of protein synthesis in the microorganisms. Conclusion Our results suggest that the decrease in RNA:protein and estimated P:N ratios with decrease in the growth rate of the microorganism is a consequence of an increased overall efficiency of protein synthesis in the cell resulting from activation of the general stress response and increased transcription of cellular maintenance genes at the expense of growth related genes. The strong link between P:N stoichiometry, RNA:protein ratio, ribosomal requirement for protein synthesis, and growth rate of microorganisms indicated by the study could be used to characterize the N and P economy of complex ecosystems such as soils and the oceans

Role of zooplankton dynamics for Southern Ocean phytoplankton biomass and global biogeochemical cycles

Global ocean biogeochemistry models currently employed in climate change projections use highly simplified representations of pelagic food webs. These food webs do not necessarily include critical pathways by which ecosystems interact with ocean biogeochemistry and climate. Here we present a global biogeochemical model which incorporates ecosystem dynamics based on the representation of ten plankton functional types (PFTs); six types of phytoplankton, three types of zooplankton, and heterotrophic bacteria. We improved the representation of zooplankton dynamics in our model through (a) the explicit inclusion of large, slow-growing zooplankton, and (b) the introduction of trophic cascades among the three zooplankton types. We use the model to quantitatively assess the relative roles of iron vs. grazing in determining phytoplankton biomass in the Southern Ocean High Nutrient Low Chlorophyll (HNLC) region during summer. When model simulations do not represent crustacean macrozooplankton grazing, they systematically overestimate Southern Ocean chlorophyll biomass during the summer, even when there was no iron deposition from dust. When model simulations included the developments of the zooplankton component, the simulation of phytoplankton biomass improved and the high chlorophyll summer bias in the Southern Ocean HNLC region largely disappeared. Our model results suggest that the observed low phytoplankton biomass in the Southern Ocean during summer is primarily explained by the dynamics of the Southern Ocean zooplankton community rather than iron limitation. This result has implications for the representation of global biogeochemical cycles in models as zooplankton faecal pellets sink rapidly and partly control the carbon export to the intermediate and deep ocean

Photosynthetic responses in Phaeocystis antarctica towards varying light and iron conditions

The effects of iron limitation on photoacclimation to a dynamic light regime were studied in Phaeocystis antarctica. Batch cultures were grown under a sinusoidal light regime, mimicking vertical mixing, under both iron-sufficient and -limiting conditions. Iron-replete cells responded to changes in light intensity by rapid xanthophyll cycling. Maximum irradiance coincided with maximum ratios of diatoxanthin/diadinoxanthin (dt/dd). The maximum quantum yield of photosynthesis (F-v /F-m) was negatively related to both irradiance and dt/dd. Full recovery of F-v /F-m by the end of the light period suggested successful photoacclimation. Iron-limited cells displayed characteristics of high light acclimation. The ratio of xanthophyll pigments to chlorophyll a was three times higher compared to iron-replete cells. Down-regulation of photosynthetic activity was moderated. It is argued that under iron limitation cells maintain a permanent state of high energy quenching to avoid photoinhibition during exposure to high irradiance. Iron-limited cells could maintain a high growth potential due to an increased absorption capacity as recorded by in vivo absorption, which balanced a decrease in F-v/F-m . The increase in the chlorophyll a-specific absorption cross section was related to an increase in carotenoid pigments and a reduction in the package effect. These experiments show that P. antarctica can acclimate successfully to conditions as they prevail in the Antarctic ocean, which may explain the success of this species

Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

Background: In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications. Methodology: We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection. Conclusions: With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approac

Eddy-resolving simulation of plankton ecosystem dynamics in the California Current System

Author Posting. © Elsevier B.V., 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 53 (2006): 1483-1516, doi:10.1016/j.dsr.2006.06.005.We study the dynamics of the planktonic ecosystem in the coastal upwelling zone within the California Current System using a three-dimensional, eddy-resolving circulation model coupled to an ecosystem/biogeochemistry model. The physical model is based on the Regional Oceanic Modeling System (ROMS), configured at a resolution of 15 km for a domain covering the entire U.S. West Coast, with an embedded child grid covering the central California upwelling region at a resolution of 5 km. The model is forced with monthly mean boundary conditions at the open lateral boundaries as well as at the surface. The ecological/biogeochemical model is nitrogen based, includes single classes for phytoplankton and zooplankton, and considers two detrital pools with different sinking speeds. The model also explicitly simulates a variable chlorophyll-to-carbon ratio. Comparisons of model results with either remote sensing observations (AVHRR, SeaWiFS) or in situ measurements from the CalCOFI program indicate that our model is capable of replicating many of the large-scale, time averaged features of the coastal upwelling system. An exception is the underestimation of the chlorophyll levels in the northern part of the domain, perhaps because of the lack of short-term variations in the forcing from the atmosphere. Another shortcoming is that the modeled thermocline is too diffuse, and that the upward slope of the isolines toward the coast is too small. Detailed time-series comparisons with observations from Monterey Bay reveal similar agreements and discrepancies. We attribute the good agreement between the modeled and observed ecological properties in large part to the accuracy of the physical fields. In turn, many of the discrepancies can be traced back to our use of monthly mean forcing. Analysis of the ecosystem structure and dynamics reveal that the magnitude and pattern of phytoplankton biomass in the nearshore region are determined largely by the balance of growth and zooplankton grazing, while in the offshore region, growth is balanced by mortality. The latter appears to be inconsistent with in situ observations and is a result of our consideration of only one zooplankton size class (mesozooplankton), neglecting the importance of microzooplankton grazing in the offshore region. A comparison of the allocation of nitrogen into the different pools of the ecosystem in the 3-D results with those obtained from a box model configuration of the same ecosystem model reveals that only a few components of the ecosystem reach a local steady-state, i.e. where biological sources and sinks balance each other. The balances for the majority of the components are achieved by local biological source and sink terms balancing the net physical divergence, confirming the importance of the 3-D nature of circulation and mixing in a coastal upwelling system.Most of this work has been made possible by two grants from NASA. Additional support is acknowledged from NSF’s ITR program

Toward autonomous measurements of photosynthetic electron transport rates: An evaluation of active fluorescence-based measurements of photochemistry

This study presents a methods evaluation and intercalibration of active fluorescence-based measurements of the quantum yield (ϕʹ 0 PSII) and absorption coefficient (aPSII) of photosystem II (PSII) photochemistry. Measurements of ϕʹ PSII , aPSII, and irradiance (E) can be scaled to derive photosynthetic electron transport rates (P e ), the process that fuels phytoplankton carbon fixation and growth. Bio-optical estimates of ϕ PSII and aPSII were evaluated using 10 phytoplankton cultures across different pigment groups with varying bio-optical absorption characteristics on six different fast-repetition rate fluorometers that span two different manufacturers and four different models. Culture measurements of ϕʹ PSII and the effective absorption cross section of PSII photochemistry (σPSII, a constituent of aPSII) showed a high degree of correspondence across instruments, although some instrument-specific biases are identified. A range of approaches have been used in the literature to estimate aPSII(λ) and are evaluated here.With the exception of ex situ aPSII(λ) estimates from paired σPSII and PSII reaction center concentration ([RCII]) measurements, the accuracy and precision of in situ aPSII(λ) methodologies are largely determined by the variance of method-specific coefficients. The accuracy and precision of these coefficients are evaluated, compared to literature data, and discussed within a framework of autonomous P e measurements. This study supports the application of an instrument-specific calibration coefficient (KR) that scales minimum fluorescence in the dark (F 0 ) to aPSII as both the most accurate in situ measurement of aPSII, and the methodology best suited for highly resolved autonomous P e measurements

Distributions of phytoplankton carbohydrate, protein and lipid in the world oceans from satellite ocean colour

Energy value of phytoplankton regulates the growth of higher trophic species, affecting the tropic balance and sustainability of marine food webs. Therefore, developing our capability to estimate and monitor, on a global scale, the concentrations of macromolecules that determine phytoplankton energy value, would be invaluable. Reported here are the first estimates of carbohydrate, protein, lipid, and overall energy value of phytoplankton in the world oceans, using ocean-colour data from satellites. The estimates are based on a novel bio-optical method that utilises satellite-derived bio-optical fingerprints of living phytoplankton combined with allometric relationships between phytoplankton cells and cellular macromolecular contents. The annually-averaged phytoplankton energy value, per cubic meter of sub-surface ocean, varied from less than 0.1 kJ in subtropical gyres, to 0.5–1.0 kJ in parts of the equatorial, northern and southern latitudes, and rising to more than 10 kJ in certain coastal and optically complex waters. The annually-averaged global stocks of carbohydrate, protein and lipid were 0.044, 0.17 and 0.108 gigatonnes, respectively, with monthly stocks highest in September and lowest in June, over 1997-2013. The fractional contributions of phytoplankton size classes e.g., picoplankton, nanoplankton and microplankton to surface concentrations and global stocks of macromolecules varied considerably across marine biomes classified as Longhurst provinces. Among these provinces, the highest annually-averaged surface concentrations of carbohydrate, protein, and lipid were in North-East Atlantic Coastal Shelves, whereas, the lowest concentration of carbohydrate or lipid were in North Atlantic Tropical Gyral, and that of protein was in North Pacific Subtropical Gyre West. The regional accuracy of the estimates and their sensitivity to satellite inputs are quantified from the bio-optical model, which show promise for possible operational monitoring of phytoplankton energy value from satellite ocean colour. Adequate in situ measurements of macromolecules and improved retrievals of inherent optical properties from high-resolution satellite images, would be required to validate these estimates at local sites, and to further improve their accuracy in the world oceans

Tracer-based assessment of the origin and biogeochemical transformation of a cyclonic eddy in the Sargasso Sea

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C10006, doi:10.1029/2008JC004840.Mechanisms of nutrient supply in oligotrophic ocean systems remain inadequately understood and quantified. In the North Atlantic Subtropical Gyre, for example, the observed rates of new production are apparently not balanced by nutrient supply via vertical mixing. Mesoscale eddies have been hypothesized as a mechanism for vertical nutrient pumping into the euphotic zone, but the full range and magnitude of biogeochemical impacts by eddies remain uncertain. We evaluated a cyclonic eddy located near Bermuda for its effect on water column biogeochemistry. In the density range σ θ 26.1 to 26.7, an eddy core with anomalous salinity, temperature, and biogeochemical properties was observed, suggesting that the eddy was not formed with local water (i.e., not formed of the waters surrounding the eddy at the time of observations), hence complicating efforts to quantify biogeochemical processes in the eddy. We combined conservative hydrographic tracers (density versus potential temperature and salinity) and quasi-conservative biogeochemical tracers (density versus NO, PO, and total organic carbon) to propose the origin of the eddy core water to have been several hundred kilometers to the southeast of the eddy location at sampling. By comparing the observed eddy core's biogeochemical properties with those near the proposed origin, we estimate the net changes in biogeochemical properties that occurred. A conservative estimate of export was 0.5 ± 0.34 mol N m−2 via sinking particles, with export occurring prior to our period of direct observation. Our results suggest that biogeochemical signals induced by mesoscale eddies could survive to be transported over long distances, thus providing a mechanism for lateral fluxes of nutrients and AOU (apparent oxygen utilization). Given that the proposed source area of this eddy is relatively broad, and the eddy-mixing history before our sampling is unknown, uncertainty remains in our assessment of the true biogeochemical impact of mesoscale eddies in the gyre.Support for the EDDIES project came from the U.S. National Science Foundation. D.J.M. was also partially supported by NASA