Nutrient-limited Growth Research Articles

Impact of critical eddy diffusivity on seasonal bloom dynamics of Phytoplankton in a global set of aquatic environments

The intensity of eddy diffusivity and the spatial average of water velocity at the depths of the water column in oceans and lakes play a fundamental role in phytoplankton production and phytoplankton and zooplankton biomass, and community composition. The critical depth and intensity of turbulent mixing within the water column profoundly affect phytoplankton biomass, which depends on the sinking characteristic of planktonic algal species. We propose an Nutrient-Phytoplankton-Zooplankton (NPZ) model in 3D space with light and nutrient-limited growth in a micro-scale ecological study. To incorporate micro-scale observation of phytoplankton intermittency in bloom mechanism in stationary as well as oceanic turbulent flows, a moment closure method has been applied in this study. Experimental observations imply that an increase in turbulence is sometimes ecologically advantageous for non-motile planktonic algae. How do we ensure whether there will be a bloom cycle or whether there can be any bloom at all when the existing phytoplankton group is buoyant, heavier, motile, or non-motile? To address these questions, we have explored the effects of critical depth, the intensity of eddy diffusivity, spatial average of water velocity, on the concentration as well as horizontal and vertical distribution of phytoplankton and zooplankton biomass using a mathematical model and moment closure technique. We quantify a critical threshold value of eddy diffusivity and the spatial average of water velocity and observe the corresponding changes in the phytoplankton bloom dynamics. Our results highlight the importance of eddy diffusivity and the spatial average of water velocity on seasonal bloom dynamics and also mimic different real-life bloom scenarios in Mikawa Bay (Japan), Tokyo Bay (Japan), Arakawa River (Japan), the Baltic Sea, the North Atlantic Ocean, Gulf Alaska, the North Arabian Sea, the Cantabrian Sea, Lake Nieuwe Meer (Netherlands) and several shallower lakes.

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere

BackgroundPlant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed.ResultsWe analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network.ConclusionsThe results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria.B5pQk-pebCjYS-vjJfR65XVideo

Biofilm formation is correlated with low nutrient and simulated microgravity conditions in a Burkholderia isolate from the ISS water processor assembly

The International Space Station (ISS) Water Processor Assembly (WPA) experiences intermittent dormancy in the WPA wastewater tank during water recycling events which promotes biofilm formation within the system. In this work we aimed to gain a deeper understanding of the impact of nutrient limitation on bacterial growth and biofilm formation under microgravity in support of biofilm mitigation efforts in exploration water recovery systems. A representative species of bacteria that is commonly cultured from the ISS WPA was cultured in an WPA influent water ersatz formulation tailored for microbiological studies. An isolate of Burkholderia contaminans was cultured under a simulated microgravity (SμG) treatment in a vertically rotating high-aspect rotating vessel (HARV) to create the low shear modeled microgravity (LSMMG) environment on a rotating wall vessel (RWV), with a rotating control (R) in the horizontal plane at the predetermined optimal rotation per minute (rpm) speed of 20. Over the course of the growth curve, the bacterial culture in ersatz media was harvested for bacterial counts, and transcriptomic and nutrient content analyses. The cultures under SμG treatment showed a transcriptomic signature indicative of nutrient stress and biofilm formation as compared to the R control treatment. Further analysis of the WPA ersatz over the course of the growth curve suggests that the essential nutrients of the media were consumed faster in the early stages of growth for the SμG treatment and thus approached a nutrient limited growth condition earlier than in the R control culture. The observed limited nutrient response may serve as one element to explain a moderate enhancement of adherent biofilm formation in the SμG treatment after 24 h. While nutrients levels can be modulated, one implication of this investigation is that biofilm mitigation in the ISS environment could benefit from methods such as mixing or the maintenance of minimum flow within a dormant water system in order to force convection and offset the response of microbes to the secondary effects of microgravity.

Neisseria meningitidis Sibling Small Regulatory RNAs Connect Metabolism with Colonization by Controlling Propionate Use.

Neisseria meningitidis (meningococcus) colonizes the human nasopharynx, primarily as a commensal, but sporadically causing septicemia and meningitis. During colonization and invasion, it encounters different niches with specific nutrient compositions. Small noncoding RNAs (sRNAs) are used to fine-tune expression of genes, allowing adaptation to their physiological differences. We have previously characterized sRNAs (Neisseria metabolic switch regulators [NmsRs]) controlling switches between cataplerotic and anaplerotic metabolism. Here, we extend the NmsR regulon by studying methylcitrate lyase (PrpF) and propionate kinase (AckA-1) involved in the methylcitrate cycle and serine hydroxymethyltransferase (GlyA) and 3-hydroxyacid dehydrogenase (MmsB) involved in protein degradation. These proteins were previously shown to be dysregulated in a ΔnmsRs strain. Levels of transcription of target genes and NmsRs were assessed by reverse transcriptase quantitative PCR (RT-qPCR). We also used a novel gene reporter system in which the 5' untranslated region (5' UTR) of the target gene is fused to mcherry to study NmsRs-target gene interaction in the meningococcus. Under nutrient-rich conditions, NmsRs downregulate expression of PrpF and AckA-1 by direct interaction with the 5' UTR of their mRNA. Overexpression of NmsRs impaired growth under nutrient-limiting growth conditions with pyruvate and propionic acid as the only carbon sources. Our data strongly suggest that NmsRs downregulate propionate metabolism by lowering methylcitrate enzyme activity under nutrient-rich conditions. Under nutrient-poor conditions, NmsRs are downregulated, increasing propionate metabolism, resulting in higher tricarboxylic acid (TCA) activities. IMPORTANCE Neisseria meningitidis colonizes the human nasopharynx, forming a reservoir for the sporadic occurrence of epidemic invasive meningococcal disease like septicemia and meningitis. Propionic acid generated by other bacteria that coinhabit the human nasopharynx can be utilized by meningococci for replication in this environment. Here, we showed that sibling small RNAs, designated NmsRs, riboregulate propionic acid utilization by meningococci and, thus, colonization. Under conditions mimicking the nasopharyngeal environment, NmsRs are downregulated. This leads to the conversion of propionic acid to pyruvate and succinate, resulting in higher tricarboxylic acid cycle activity, allowing colonization of the nasopharynx. NmsRs link metabolic state with colonization, which is a crucial step on the trajectory to invasive meningococcal disease.

Cultivation of Desmodesmus multivariabilis for the Treatment of Cosmetic Wastewater

The discharge of cosmetic wastewater into the wastewater treatment systems has become an environmental concern due to high concentrations of nutrients. The current study explored the phytoremediation potential of Desmodesmus multivariabilis, under mixotrophic growth, to remove total organic carbon (TOC), sulfur (TS), nitrogen (TN), and phosphorus (TP) from cosmetic wastewater (CWW). The CWW was prepared using samples supplied by a local cosmetic production company (two dyes, two hair relaxers, as well as two shampoos and conditioners). The bioremediation potential of D. multivariabilis was tested under four different conditions: raw CWW with 0% CO2 in the aeration stream (i.e., atmospheric air); pre-treated CWW with 0% CO2, 2.5% CO2, and 5% CO2. Control experiments were run in parallel. Under mixotrophic growth, the microalga performed best at 5% CO2 in the pre-treated CWW where TOC, TN, TP, and TS removal of >88%, >98%, >95%, and >90% were measured, respectively. The corresponding biomass (dry weight) was >203 mg/L. Relaxers promoted growth most prominently; however, it was observed that there was significant nutrient removal even in the absence of growth in all experiments. The growth followed Liebig’s Law, displaying three distinct phases (CO2 concentration, CO2 mass transfer, and nutrient limited growth). The results demonstrated the potential for the successful bioremediation of cosmetic wastewater by D. multivariabilis.

Sequestration of a dual function DNA-binding protein by Vibrio cholerae CRP

Although the mechanism by which the cyclic AMP receptor protein (CRP) regulates global gene transcription has been intensively studied for decades, new discoveries remain to be made. Here, we report that, during rapid growth, CRP associates with both the well-conserved, dual-function DNA-binding protein peptidase A (PepA) and the cell membrane. These interactions are not present under nutrient-limited growth conditions, due to post-translational modification of three lysines on a single face of CRP. Although coincident DNA binding is rare, dissociation from CRP results in increased PepA occupancy at many chromosomal binding sites and differential regulation of hundreds of genes, including several encoding cyclic dinucleotide phosphodiesterases. We show that PepA represses biofilm formation and activates motility/chemotaxis. We propose a model in which membrane-bound CRP interferes with PepA DNA binding. Under nutrient limitation, PepA is released. Together, CRP and free PepA activate a transcriptional response that impels the bacterium to seek a more hospitable environment. This work uncovers a function for CRP in the sequestration of a regulatory protein. More broadly, it describes a paradigm of bacterial transcriptome modulation through metabolically regulated association of transcription factors with the cell membrane.

Morphological instability and roughening of growing 3D bacterial colonies.

How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size-eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an "active fluid" whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies-as well as other forms of growing active matter, such as tumors and engineered living materials-in 3D environments.

Incorporating parameter variability into Monod models of nutrient-limited growth of non-diazotrophic and diazotrophic cyanobacteria.

Models are widely used tools in aquatic science to understand the mechanism of phytoplankton growth and anticipate the occurrence of harmful algal blooms. However, model parameterization remains challenging and issues that may introduce prediction uncertainty exist. Many models use the Monod equation to predict cyanobacteria growth rate based on ambient nutrient concentrations. The half-saturation concentrations in the Monod equation varies greatly among different studies and depends on environmental conditions. In this study, we estimated the growth rate due to nutrient limitations for two cyanobacteria species (Microcystis aeruginosa and Dolichospermum flos-aquae) using a modified Monod model which allows the half-saturation concentration to vary according to initial nitrogen (N) conditions. The model is calibrated against observations from laboratory experiment where cyanobacteria growth and ambient nutrient concentrations were measured simultaneously, which is rarely done in the literature. Our results show this modified model produce better predictions on growth rate and biomass, indicating many commonly used mechanistic models may need improvement regarding phytoplankton growth representation. Furthermore, our study quantifies the flexibility in cyanobacteria growth parameter across a wide range of environmental N in eutrophic lakes thus provides important information for large-scale modelling applications.

The importance of turbulent ocean–sea ice nutrient exchanges for simulation of ice algal biomass and production with CICE6.1 and Icepack 1.2

Abstract. Different sea ice models apply unique approaches in the computation of nutrient diffusion between the ocean and the ice bottom, which are generally decoupled from the calculation of turbulent heat flux. A simple molecular diffusion formulation is often used. We argue that nutrient transfer from the ocean to sea ice should be as consistent as possible with heat transfer, since all of these fluxes respond to varying forcing in a similar fashion. We hypothesize that biogeochemical models that do not consider such turbulent nutrient exchanges between the ocean and the sea ice, despite considering brine drainage and bulk exchanges through ice freezing and melting, may underestimate bottom-ice algal production. The Los Alamos Sea Ice Model (CICE + Icepack) was used to test this hypothesis by comparing simulations without and with diffusion of nutrients across the sea ice bottom that are dependent on velocity shear, implemented in a way that is consistent with turbulent heat exchanges. Simulation results support the hypothesis, showing a significant enhancement of ice algal production and biomass when nutrient limitation was relieved by bottom-ice turbulent exchange. Our results emphasize the potentially critical role of turbulent exchanges to sea ice algal blooms and thus the importance of properly representing them in biogeochemical models. The relevance of this becomes even more apparent considering ongoing trends in the Arctic Ocean, with a predictable shift from light-limited to nutrient-limited growth of ice algae earlier in the spring, as the sea ice becomes more fractured and thinner with a larger fraction of young ice with thin snow cover.

Modeling of Continuous PHA Production by a Hybrid Approach Based on First Principles and Machine Learning

Polyhydroxyalkanoates (PHA) are renewable alternatives to traditional oil-derived polymers. PHA can be produced by different microorganisms in continuous culture under specific media composition, which makes the production process both promising and challenging. In order to achieve large productivities while maintaining high yield and efficiency, the continuous culture needs to be operated in the so-called dual nutrient limitation condition, where both the nitrogen and carbon sources are kept at very low concentrations. Mathematical models can greatly assist both design and operation of the bioprocess, but are challenged by the complexity of the system, in particular by the dual nutrient-limited growth phenomenon, where the cells undergo a metabolic shift that abruptly changes their behavior. Traditional, non-structured mechanistic models based on Monod uptake kinetics can be used to describe the bioreactor operation under specific process conditions. However, in the absence of a model description of the metabolic phenomena inside the cell, the extrapolation to a broader operation domain (e.g., different feeding concentrations and dilution rates) may present mismatches between the predictions and the actual process outcomes. Such detailed models may require almost perfect knowledge of the cell metabolism and omic-level measurements, hampering their development. On the other hand, purely data-driven models that learn correlations from experimental data do not require any prior knowledge of the process and are therefore unbiased and flexible. However, many more data are required for their development and their extrapolation ability is limited to conditions that are similar to the ones used for training. An attractive alternative is the combination of the extrapolation power of first principles knowledge with the flexibility of machine learning methods. This approach results in a hybrid model for the growth and uptake rates that can be used to predict the dynamic operation of the bioreactor. Here we develop a hybrid model to describe the continuous production of PHA by Pseudomonas putida GPo1 culture. After training, the model with experimental data gained under different dilution rates and medium compositions, we demonstrate how the model can describe the process in a wide range of operating conditions, including both single and dual nutrient-limited growth.

Dynamics of N-P-K demand and uptake in cassava

Fertilizers are required to improve productivity of cassava and meet the increasing demand for cassava as food, feed, or raw material for processing industries. Our objective was to develop nutrition indices for N, P, and K to provide quantitative insight in the dynamics of nutrient demand and uptake of cassava. On-farm experiments were conducted at six locations in Nigeria from 2016 to 2018, across the major cassava growing agro-ecologies of West Africa. Nitrogen, P, and K were applied at different rates. Uptake of nutrients was measured in leaves, stems, and storage roots at 4, 8, and 12 or 14 months after planting (MAP) and used to construct NPK dilution curves and nutrition indices. About 67, 61, and 52% of total N, P, and K were taken up at 4 MAP, with a maximum uptake rate of 0.21, 0.03, and 0.12 g/m2/d for N, P, and K, respectively. Nutrient concentrations in stems and storage roots declined gradually, in contrast to concentrations in the leaves that fluctuated within narrow ranges. Dilution curves and nutrition indices for N, P, and K were established for the first time in cassava. Dilution curves of N, P, and K in the crop for the highest NPK application treatment were described as Nc = 82DM−0.61, Pc = 7.4DM−0.54, and Kc = 43DM−0.54, when total biomass was between 5 and 57 t/ha dry matter (DM). The nutrition indices were linearly related to relative crop biomass. Insight into the nutrient uptake and dilution patterns during the growth cycle can help to understand the temporal nutrient demands of cassava and identify sustainable management practices. Initial ample supply of N and P and moderate K, with extra K top-dress during the second growth phase, will benefit cassava growth and yield. Furthermore, such information provides a basis to develop a dynamic model to simulate nutrient-limited growth of cassava.

A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii.

Industry screens of large chemical libraries traditionally have relied on rich media to ensure rapid bacterial growth in high-throughput testing. We used eukaryotic, nutrient-limited growth media in a compound screen that unmasked a previously unknown hyper-activity of the old antibiotic, rifabutin (RBT), against highly resistant Acinetobacter baumannii. In nutrient-limited, but not rich media, RBT was 200-fold more potent than rifampin (RIF). RBT was also substantially more effective in vivo. The mechanism of enhanced efficacy was a Trojan horse-like import of RBT but not RIF through FhuE, only in nutrient-limited conditions. These results are of fundamental importance to efforts to discover antibacterial agents.

Development of Biopolyesters (PHA) as Part of the Swiss Priority Program in Biotechnology.

The Swiss Priority Program in Biotechnology of the Swiss National Science Foundation that lasted between 1992 and 2001 had a boosting effect on many biotech disciplines and on the developments of polyhydroxyalkanoates (PHAs) in Switzerland in particular. The funding organization led by Prof. Oreste Ghisalba enabled a better understanding of the PHA biosynthesis and the development, as well as the implementation of novel bioprocesses (e.g. two-phase fermentations, multiple nutrient limited growth conditions, multi-stage chemostats, and product formation in different host organisms). However, production of PHA in Switzerland appeared to be impossible for cost reasons due to the strong competition from cheaper, petrol-based plastics. The recent reports on environmental issues with non-degradable plastics has triggered a general change in the perception of biodegradable plastics, giving them an added value and thus justifying a higher price. Ongoing research focuses on the sustainable production of PHAs using carbon waste streams, synthesis gas or even CO₂.

The Adaptive Morphology of Bacillus subtilis Biofilms: A Defense Mechanism against Bacterial Starvation

Biofilms are commonly defined as accumulations of microbes, embedded in a self-secreted, polysaccharide-rich extra-cellular matrix. This study aimed to characterize specific morphological changes that occur in Bacillus subtilis biofilms under nutrient-limiting growth conditions. Under varying levels of nutrient depletion, colony-type biofilms were found to exhibit different rates of spatial expansion and green fluorescent protein production. Specifically, colony-type biofilms grown on media with decreased lysogeny broth content exhibited increased spatial expansion and more stable GFP production over the entire growth period. By modeling the surface morphology of colony-type biofilms using confocal and multiphoton microscopy, we analyzed the appearance of distinctive folds or “wrinkles” that form as a result of lysogeny broth content reduction in the solid agar growth media. When subjected to varying nutritional conditions, the channel-like folds were shown to alter their morphology; growth on nutrient-depleted media was found to trigger the formation of large and straight wrinkles connecting the colony core to its periphery. To test a possible functional role of the formed channels, a fluorescent analogue of glucose was used to demonstrate preferential native uptake of the molecules into the channels’ interiors which supports their possible role in the transport of molecules throughout biofilm structures.

Fed-Batch Cultivations of Rhodospirillum rubrum Under Multiple Nutrient-Limited Growth Conditions on Syngas as a Novel Option to Produce Poly(3-Hydroxybutyrate) (PHB).

Syngas from gasified organic waste materials is a promising feedstock for the biotechnological synthesis of the bioplastic poly([R]-3-hydroxybutyrate) (PHB) with Rhodospirillum rubrum. In a first approach, growth studies were carried out with this strain in gas-tight serum vials. When syngas (40% CO, 40% H2, 10% CO2, and 10% N2 v/v) was diluted with N2 to 60%, a 4-fold higher biomass production was detected compared to samples grown on 100% syngas, thus indicating a growth inhibitory effect. The best performing syngas-mixture was then used for C-, C,N-, and C,P-limited fed-batch fermentations in a bioreactor with continuous syngas and acetate supply. It was found that C,P-limited PHB productivity was 5 times higher than for only C-limited growth and reached a maximal PHB content of 30% w/w. Surprisingly, growth and PHB production stopped when N, as a second nutrient, became growth-limiting. Finally, it was concluded that a minimal supply of 0.2 g CO g−1 biomass h−1 has to be guaranteed in order to cover the cellular maintenance energy.

Tailored biosynthesis of polyhydroxyalkanoates in chemostat cultures.

Polyhydroxyalkanoates (PHAs) are accumulated intracellularly by many bacteria and serve as a carbon and energy storage compound. PHAs are polyesters of high molecular weight and can be isolated by solvent extraction and precipitation in antisolvents. The material properties of PHAs are of great interest due to the inherent biodegradability and excellent biocompatibility. To date, more than 150 different PHA monomers have been described in literature and it has been found that the monomeric unit composition significantly influences the physico-chemical properties of PHAs. The monomer composition may be controlled to some extent by the choice of the PHA production strain but also by the cultivation conditions and the carbon substrate/PHA precursor supply. In previous studies, it has been shown that the most reproducible production method of PHA is the chemostat cultivation of suitable bacteria under multiple nutrient limited growth conditions. This chapter is dedicated to provide step-by step instructions to produce PHAs in a chemostat culture and specifically describes how the composition of PHA copolymers can be tailored during biosynthesis, as well as a set of analytical tools and methods to characterize PHAs.

2H/1H fractionation in microalgal lipids from the North Pacific Ocean: Growth rate and irradiance effects

The hydrogen isotope ratio (2H/1H) of microalgal lipids has become a useful tool for reconstructing hydrologic conditions in the geologic past from marine and lacustrine sediments. Culture studies have shown that, in addition to the 2H/1H ratio of growth water, parameters such as salinity, growth rate, and irradiance, can have a large effect on lipid 2H/1H ratios. But aside from salinity, these effects have not been well studied in the field. In this work, hydrogen isotope fractionation relative to growth water was measured in four algal lipids - C37:3 and C37:2 methyl alkenones, (3β,4α,5α,22E)-4,23-Dimethylergost-22-en-3-ol (dinosterol), and 24-methylcholesta-5,22E-dien-3β-ol (brassicasterol) – in the upper water column of two North Pacific Ocean locations. By comparing lipid 2H/1H variations as a function of depth at tropical Station ALOHA (22°45′N, 158°00′W) and mid-latitude Gyre (41°30′N, 132°00′W in the Transition Zone) it was possible to evaluate the H isotope effects of nutrient limitation and irradiance on natural phytoplankton populations by comparing measured fractionation factors (αlipid) with those derived from laboratory-based empirical relationships. Significant distinctions were observed between the inferred causes of H isotope fractionation in different algal lipids at the two locations. At Station Aloha, 2H/1H fractionation in coccolithophorid-derived alkenones was primarily caused by nutrient-limited growth, while at Gyre it was caused by light limitation. Distinctions were less clear for the two sterols. 2H/1H fractionation in dinosterol was possibly influenced by nutrient-limited growth or light limitation at greater depths at both stations, while 2H/1H fractionation in brassicasterol matched values expected for nutrient-limited growth at both locations. Although systematic trends with depth in αlipid on the order of 10–30‰ were observed for each lipid, inter-day variability was some 3–7‰ depending on the lipid and site, and the magnitude of αlipid changes observed in the field were much less than those expected based on culture studies. This implies that the effects of nutrient and light limitation on natural phytoplankton populations in the ocean may not have a large influence on hydroclimate reconstructions based on 2H/1H ratios of microalgal lipids in marine sediments.

A Wood Biology Agenda to Support Global Vegetation Modelling.

Realistic forecasting of forest responses to climate change critically depends on key advancements in global vegetation modelling. Compared with traditional 'big-leaf' models that simulate forest stands, 'next-generation' vegetation models aim to track carbon-, light-, water-, and nutrient-limited growth of individual trees. Wood biology can play an important role in delivering the required knowledge at tissue-to-individual levels, at minute-to-century scales and for model parameterization and benchmarking. We propose a wood biology research agenda that contributes to filling six knowledge gaps: sink versus source limitation, drivers of intra-annual growth, drought impacts, functional wood traits, dynamic biomass allocation, and nutrient cycling. Executing this agenda will expedite model development and increase the ability of models to forecast global change impact on forest dynamics.

A multiphase multiscale model for nutrient limited tissue growth

A multiphase multiscale model for nutrient limited tissue growth

Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions.

For cells to grow faster they must increase their protein production rate. Microorganisms have traditionally been thought to accomplish this increase by producing more ribosomes to enhance protein synthesis capacity, leading to the linear relationship between ribosome level and growth rate observed under most growth conditions previously examined. Past studies have suggested that this linear relationship represents an optimal resource allocation strategy for each growth rate, independent of any specific nutrient state. Here we investigate protein production strategies in continuous cultures limited for carbon, nitrogen and phosphorus, which differentially impact substrate supply for protein versus nucleic acid metabolism. Unexpectedly, we find that at slow growth rates, Escherichia coli achieves the same protein production rate using three different strategies under the three different nutrient limitations. Under phosphorus (P) limitation, translation is slow due to a particularly low abundance of ribosomes, which are RNA-rich and thus particularly costly for phosphorous-limited cells. Under nitrogen (N) limitation, translation elongation is slowed by processes including ribosome stalling at glutamine codons. Under carbon (C) limitation, translation is slowed by accumulation of inactive ribosomes not bound to messenger RNA. These extra ribosomes enable rapid growth acceleration during nutrient upshift. Thus, bacteria tune ribosome usage across different limiting nutrients to enable balanced nutrient-limited growth while also preparing for future nutrient upshifts.