Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate

Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources. After several growth cycles, cell growth stabilized at the maximum level and exhibited a reproducible growth profile. The specific growth rates measured for benzoate (1.01 ± 0.11 h-1) and citrate (1.11 ± 0.12 h-1) were similar, while a higher yield was observed for benzoate (0.6 and 0.3 g cell mass per g of benzoate and citrate, respectively), reflecting the different degrees of carbon reduction in the two substrates. Comparative proteomic analysis revealed an enrichment of several oxygenases/dehydrogenases in benzoate-grown cells, indicative of the higher carbon reduction of benzoate. Moreover, the upregulation of all 14 proteins implicated in benzoate degradation via the catechol ortho-cleavage pathway was observed, while several stress-response proteins were increased to aid cells to cope with benzoate toxicity. Unexpectedly, citrate posed more challenges than benzoate in the maintenance of pH homeostasis, as indicated by the enhancement of the Na+/H+ antiporter and carbonic anhydrase. The study provides important mechanistic insights into Pseudomonas adaptation to varying carbon sources that are of great relevance to bioremediation efforts

Skew-Laplace and Cell-Size Distribution in Microbial Axenic Cultures: Statistical Assessment and Biological Interpretation

We report a skew-Laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. Cytometry scatters best fit the skew-Laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. Unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-Laplace distribution. Due to its versatile nature, the skew-Laplace distribution approach offers an easy, efficient, and powerful tool for distribution of frequency analysis in tandem with the flow cytometric cell sorting

Uncertainties and recommendations

An assessment of the impacts of changes in climate and UV-B radiation on Arctic terrestrial ecosystems, made within the Arctic Climate Impacts Assessment (ACIA), highlighted the profound implications of projected warming in particular for future ecosystem services, biodiversity and feedbacks to climate. However, although our current understanding of ecological processes and changes driven by climate and UV-B is strong in some geographical areas and in some disciplines, it is weak in others. Even though recently the strength of our predictions has increased dramatically with increased research effort in the Arctic and the introduction of new technologies, our current understanding is still constrained by various uncertainties. The assessment is based on a range of approaches that each have uncertainties, and on data sets that are often far from complete. Uncertainties arise from methodologies and conceptual frameworks, from unpredictable surprises, from lack of validation of models, and from the use of particular scenarios, rather than predictions, of future greenhouse gas emissions and climates. Recommendations to reduce the uncertainties are wide-ranging and relate to all disciplines within the assessment. However, a repeated theme is the critical importance of achieving an adequate spatial and long-term coverage of experiments, observations and monitoring of environmental changes and their impacts throughout the sparsely populated and remote region that is the Arctic

Effects of changes in climate on landscape and regional processes, and feedbacks to the climate system

Biological and physical processes in the Arctic system operate at various temporal and spatial scales to impact large-scale feedbacks and interactions with the earth system. There are four main potential feedback mechanisms between the impacts of climate change on the Arctic and the global climate system: albedo, greenhouse gas emissions or uptake by ecosystems, greenhouse gas emissions from methane hydrates, and increased freshwater fluxes that could affect the thermohaline circulation. All these feedbacks are controlled to some extent by changes in ecosystem distribution and character and particularly by large-scale movement of vegetation zones. Indications from a few, full annual measurements of CO2 fluxes are that currently the source areas exceed sink areas in geographical distribution. The little available information on CH4 sources indicates that emissions at the landscape level are of great importance for the total greenhouse balance of the circumpolar North. Energy and water balances of Arctic landscapes are also important feedback mechanisms in a changing climate. Increasing density and spatial expansion of vegetation will cause a lowering of the albedo and more energy to be absorbed on the ground. This effect is likely to exceed the negative feedback of increased C sequestration in greater primary productivity resulting from the displacements of areas of polar desert by tundra, and areas of tundra by forest. The degradation of permafrost has complex consequences for trace gas dynamics. In areas of discontinuous permafrost, warming, will lead to a complete loss of the permafrost. Depending on local hydrological conditions this may in turn lead to a wetting or drying of the environment with subsequent implications for greenhouse gas fluxes. Overall, the complex interactions between processes contributing to feedbacks, variability over time and space in these processes, and insufficient data have generated considerable uncertainties in estimating the net effects of climate change on terrestrial feedbacks to the climate system. This uncertainty applies to magnitude, and even direction of some of the feedbacks

Responses to projected changes in climate and UV-B at the species level

Environmental manipulation experiments showed that species respond individualistically to each environmental-change variable. The greatest responses of plants were generally to nutrient, particularly nitrogen, addition. Summer warming experiments showed that woody plant responses were dominant and that mosses and lichens became less abundant. Responses to warming were controlled by moisture availability and snow cover. Many invertebrates increased population growth in response to summer warming, as long as desiccation was not induced. CO2 and UV-B enrichment experiments showed that plant and animal responses were small. However, some microorganisms and species of fungi were sensitive to increased UV-B and some intensive mutagenic actions could, perhaps, lead to unexpected epidemic outbreaks. Tundra soil heating, CO 2 enrichment and amendment with mineral nutrients generally accelerated microbial activity. Algae are likely to dominate cyanobacteria in milder climates. Expected increases in winter freeze-thaw cycles leading to ice-crust formation are likely to severely reduce winter survival rate and disrupt the population dynamics of many terrestrial animals. A deeper snow cover is likely to restrict access to winter pastures by reindeer/caribou and their ability to flee from predators while any earlier onset of the snow-free period is likely to stimulate increased plant growth. Initial species responses to climate change might occur at the sub-species level: an Arctic plant or animal species with high genetic/racial diversity has proved an ability to adapt to different environmental conditions in the past and is likely to do so also in the future. Indigenous knowledge, air photographs, satellite images and monitoring show that changes in the distributions of some species are already occurring: Arctic vegetation is becoming more shrubby and more productive, there have been recent changes in the ranges of caribou, and "new" species of insects and birds previously associated with areas south of the treeline have been recorded. In contrast, almost all Arctic breeding bird species are declining and models predict further quite dramatic reductions of the populations of tundra birds due to warming. Species-climate response surface models predict potential future ranges of current Arctic species that are often markedly reduced and displaced northwards in response to warming. In contrast, invertebrates and microorganisms are very likely to quickly expand their ranges northwards into the Arctic

True and Illusory Benefits of Modeling: Comment on “Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid Producing Megasphaera elsdenii. Microorganisms 2020, 8, 539”

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