Project description:BackgroundVariation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils.Methodology/ principal findingsTo determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability.Conclusions/ significanceOur findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.

Project description:Interest in exploiting algae as a biofuel source and the role of nutrient deficiency in inducing triacylglyceride (TAG) accumulation in cells necessitates a strategy to efficiently formulate species-specific culture media that can be easily manipulated. Using the reference organism Chlamydomonas reinhardtii, we tested the hypothesis that modeling trace element supplements on the ionomes of cells would result in optimized cell growth. We characterized the ionomes of multiple wild-type Chlamydomonas strains in various culture conditions and developed a revised trace element solution to parallel our measurements. Comparison of cells growing in the revised supplement versus a traditional trace element solution revealed faster growth rates and higher maximum cell densities with the revised recipe. RNA-seq analysis of cultures growing in the traditional versus revised medium suggest that the variation in transcriptomes was smaller than that found between laboratories using the same supplement. Visual observation did not reveal defects in cell motility or mating efficiency. Ni2+-inducible expression from the CYC6 promoter remained a useful tool, albeit with an increased amount of Ni2+ supplementation due to the introduction of an EDTA buffer system in the revised medium. Equilibrium modeling of the revised supplement predicts less metal precipitation in the revised medium. Other advantages include more facile preparation of trace element stock solutions that can readily be adapted for deficiency studies, a reduction in total chemical use, a more consistent batch-to-batch formulation, and long-term stability (up to 5 years). Under the new growth regime, we analyzed cells growing under different macro- and micronutrient-deficiencies. In N and S deficiency, cells accumulate TAG as well in the new medium as previously demonstrated. Fe and Zn deficiency also induced TAG accumulation as suggested by Nile Red and Bodipy staining. This ionomic approach can be used to efficiently optimize culturing conditions for other algal species to improve growth and assay cell physiology. Sampling of Chlamydomonas CC-1021 (2137) cultivated in TAP medium supplemented with a revised trace element recipe based on ionomic data.

Project description:Interest in exploiting algae as a biofuel source and the role of nutrient deficiency in inducing triacylglyceride (TAG) accumulation in cells necessitates a strategy to efficiently formulate species-specific culture media that can be easily manipulated. Using the reference organism Chlamydomonas reinhardtii, we tested the hypothesis that modeling trace element supplements on the ionomes of cells would result in optimized cell growth. We characterized the ionomes of multiple wild-type Chlamydomonas strains in various culture conditions and developed a revised trace element solution to parallel our measurements. Comparison of cells growing in the revised supplement versus a traditional trace element solution revealed faster growth rates and higher maximum cell densities with the revised recipe. RNA-seq analysis of cultures growing in the traditional versus revised medium suggest that the variation in transcriptomes was smaller than that found between laboratories using the same supplement. Visual observation did not reveal defects in cell motility or mating efficiency. Ni2+-inducible expression from the CYC6 promoter remained a useful tool, albeit with an increased amount of Ni2+ supplementation due to the introduction of an EDTA buffer system in the revised medium. Equilibrium modeling of the revised supplement predicts less metal precipitation in the revised medium. Other advantages include more facile preparation of trace element stock solutions that can readily be adapted for deficiency studies, a reduction in total chemical use, a more consistent batch-to-batch formulation, and long-term stability (up to 5 years). Under the new growth regime, we analyzed cells growing under different macro- and micronutrient-deficiencies. In N and S deficiency, cells accumulate TAG as well in the new medium as previously demonstrated. Fe and Zn deficiency also induced TAG accumulation as suggested by Nile Red and Bodipy staining. This ionomic approach can be used to efficiently optimize culturing conditions for other algal species to improve growth and assay cell physiology.

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Seasonality of Coastal Picophytoplankton Growth, Nutrient Limitation, and Biomass Contribution.

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