Unpredictability of the fitness effects of antimicrobial resistance mutations across environments in Escherichia coli.

The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness effects (i.e., costs) imposed by AMR mutations during growth in the absence of antibiotics. According to this assumption, resistant strains will be outcompeted by susceptible strains that do not pay the cost during the period of restriction. The fitness effects of AMR mutations are generally studied in laboratory reference strains grown in standard growth environments; however, the genetic and environmental context can influence the magnitude and direction of a mutation's fitness effects. In this study, we measure how three sources of variation impact the fitness effects of Escherichia coli AMR mutations: the type of resistance mutation, the genetic background of the host, and the growth environment. We demonstrate that while AMR mutations are generally costly in antibiotic-free environments, their fitness effects vary widely and depend on complex interactions between the mutation, genetic background, and environment. We test the ability of the Rough Mount Fuji fitness landscape model to reproduce the empirical data in simulation. We identify model parameters that reasonably capture the variation in fitness effects due to genetic variation. However, the model fails to accommodate the observed variation when considering multiple growth environments. Overall, this study reveals a wealth of variation in the fitness effects of resistance mutations owing to genetic background and environmental conditions, that will ultimately impact their persistence in natural populations.

STUN: forward-time simulation on TUnable fitNess landscapes in recombining populations.

Motivation: Understanding the population genetics of complex polygenic traits during adaptation is challenging. Results: Here, we implement a forward-in-time population-genetic simulator (STUN) based on Wright-Fisher dynamics. STUN is a flexible and user-friendly software package for simulating the polygenic adaptation of recombining haploid populations using either new mutations or standing genetic variation. STUN assumes that populations adapt to sudden environmental changes by undergoing selection on a new fitness landscape. With pre-implemented fitness landscape models like Rough Mount Fuji, NK, Block, additive, and House-of-Cards, users can explore the effect of different levels of epistasis (ruggedness of the fitness landscape). Custom fitness landscapes and recombination maps can also be defined. STUN empowers both experimentalists and advanced programmers to study the evolution of complex polygenic traits and to dissect the adaptation process. Availability and implementation: STUN is implemented in Rust. Its source code is available at https://github.com/banklab/STUN and archived on Zenodo under doi: 10.5281/zenodo.10246377. The repository includes a link to the software's manual and binary files for Linux, macOS and Windows.

Epistasis decreases with increasing antibiotic pressure but not temperature.

Predicting mutational effects is essential for the control of antibiotic resistance (ABR). Predictions are difficult when there are strong genotype-by-environment (G × E), gene-by-gene (G × G or epistatic) or gene-by-gene-by-environment (G × G × E) interactions. We quantified G × G × E effects in Escherichia coli across environmental gradients. We created intergenic fitness landscapes using gene knock-outs and single-nucleotide ABR mutations previously identified to vary in the extent of G × E effects in our environments of interest. Then, we measured competitive fitness across a complete combinatorial set of temperature and antibiotic dosage gradients. In this way, we assessed the predictability of 15 fitness landscapes across 12 different but related environments. We found G × G interactions and rugged fitness landscapes in the absence of antibiotic, but as antibiotic concentration increased, the fitness effects of ABR genotypes quickly overshadowed those of gene knock-outs, and the landscapes became smoother. Our work reiterates that some single mutants, like those conferring resistance or susceptibility to antibiotics, have consistent effects across genetic backgrounds in stressful environments. Thus, although epistasis may reduce the predictability of evolution in benign environments, evolution may be more predictable in adverse environments. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Rapid adaptation of recombining populations on tunable fitness landscapes.

How does standing genetic variation affect polygenic adaptation in recombining populations? Despite a large body of work in quantitative genetics, epistatic and weak additive fitness effects among simultaneously segregating genetic variants are difficult to capture experimentally or to predict theoretically. In this study, we simulated adaptation on fitness landscapes with tunable ruggedness driven by standing genetic variation in recombining populations. We confirmed that recombination hinders the movement of a population through a rugged fitness landscape. When surveying the effect of epistasis on the fixation of alleles, we found that the combined effects of high ruggedness and high recombination probabilities lead to preferential fixation of alleles that had a high initial frequency. This indicates that positive epistatic alleles escape from being broken down by recombination when they start at high frequency. We further extract direct selection coefficients and pairwise epistasis along the adaptive path. When taking the final fixed genotype as the reference genetic background, we observe that, along the adaptive path, beneficial direct selection appears stronger and pairwise epistasis weaker than in the underlying fitness landscape. Quantitatively, the ratio of epistasis and direct selection is smaller along the adaptive path ( ≈ 1 $$ \approx 1 $$ ) than expected. Thus, adaptation on a rugged fitness landscape may lead to spurious signals of direct selection generated through epistasis. Our study highlights how the interplay of epistasis and recombination constrains the adaptation of a diverse population to a new environment.

Cross-continental importance of CH4 emissions from dry inland-waters.

Despite substantial advances in quantifying greenhouse gas (GHG) emissions from dry inland waters, existing estimates mainly consist of carbon dioxide (CO2) emissions. However, methane (CH4) may also be relevant due to its higher Global Warming Potential (GWP). We report CH4 emissions from dry inland water sediments to i) provide a cross-continental estimate of such emissions for different types of aquatic systems (i.e., lakes, ponds, reservoirs, and streams) and climate zones (i.e., tropical, continental, and temperate); and ii) determine the environmental factors that control these emissions. CH4 emissions from dry inland waters were consistently higher than emissions observed in adjacent uphill soils, across climate zones and in all aquatic systems except for streams. However, the CH4 contribution (normalized to CO2 equivalents; CO2-eq) to the total GHG emissions of dry inland waters was similar for all types of aquatic systems and varied from 10 to 21%. Although we discuss multiple controlling factors, dry inland water CH4 emissions were most strongly related to sediment organic matter content and moisture. Summing CO2 and CH4 emissions revealed a cross-continental average emission of 9.6 ± 17.4 g CO2-eq m-2 d-1 from dry inland waters. We argue that increasing droughts likely expand the worldwide surface area of atmosphere-exposed aquatic sediments, thereby increasing global dry inland water CH4 emissions. Hence, CH4 cannot be ignored if we want to fully understand the carbon (C) cycle of dry sediments.

Precipitation, landscape properties and land use interactively affect water quality of tropical freshwaters.

Globally, conversion of pristine areas to anthropogenic landscapes is one of the main causes of ecosystem service losses. Land uses associated with urbanization and farming can be major sources of pollution to freshwaters promoting artificial inputs of several elements, leading to impaired water quality. However, how the effects of land use on freshwater quality are contingent on properties of the local landscape and climate is still poorly understood. The aim of this study was to evaluate the effects of landscape properties (morphometric measurements of lakes and their catchments), precipitation patterns, and land use properties (extent and proximity of the land use to freshwaters) on water quality of 98 natural lakes and reservoirs in northeast Brazil. Water quality impairment (WQI) was expressed as a composite variable incorporating parameters correlated with eutrophication including nitrogen (N), phosphorus (P) and Chlorophyll-a concentration. Regression tree analysis showed that WQI is mainly related to highly impacted "buffer areas". However, the effects of land use in these adjacent lands were contingent on precipitation variability for 13% of waterbodies and on surface area of the buffer in relation to the volume of waterbody (BA:Vol) for 87% of waterbodies. Overall, effects on WQI originating from the land use in the adjacent portion of the lake were amplified by high precipitation variability for ecosystems with highly impacted buffer areas and by high BA:Vol for ecosystems with less impacted buffer areas, indicating that ecosystems subjected to intense episodic rainfall events (e.g. storms) and higher buffer areas relative to aquatic ecosystem size (i.e. small waterbodies) are more susceptible to impacts of land use. Land use at the catchment scale was important for the largest ecosystems. Thus, our findings point toward the need for considering a holistic approach to managing water quality, which includes watershed management within the context of climate change.

A global trend of caffeine consumption over time and related-environmental impacts.

Caffeine is one of the most consumed substances, and it has been largely detected in aquatic ecosystems. We investigated the trends in caffeine consumption over three decades and its relationships with gross domestic product (GDP) and human development index (HDI) to understand global patterns and to identify potential hotspots of contamination. The total caffeine consumption is increasing mainly due to population growth. Moreover, caffeine consumption per capita is also increasing in some countries, such as Brazil, Italy, and Ethiopia. A high positive correlation between caffeine consumption per capita with HDI and GDP was found for coffee-importing countries in Europe, while a high negative correlation was found for coffee-exporting countries in Africa. The literature review showed that the highest caffeine concentrations coincide with countries that present an increasing caffeine consumption per capita. Also, approximately 35% of the caffeine concentrations reported in the literature were above the predicted no-effect concentration in the environment and, again, overlaps with countries with increasing per capita consumption. Despite the high degradation rate, caffeine consumption tends to increase in a near future, which may also increase the overall amount of caffeine that comes into the environment, possibly exceeding the thresholds of several species described as tolerant to the current environmental concentrations. Therefore, it is essential to prevent caffeine from reaching aquatic ecosystems, implementing sewage treatment systems, and improving their efficiency.

flowDiv: a new pipeline for analyzing flow cytometric diversity.

BACKGROUND: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. RESULTS: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. CONCLUSIONS: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.

Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake.

Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.

Effects of seasonality, trophic state and landscape properties on CO2 saturation in low-latitude lakes and reservoirs.

The role of tropical lakes and reservoirs in the global carbon cycle has received increasing attention in the past decade, but our understanding of its variability is still limited. The metabolism of tropical systems may differ profoundly from temperate systems due to the higher temperatures and wider variations in precipitation. Here, we investigated the spatial and temporal patterns of the variability in the partial pressure of carbon dioxide (pCO2) and its drivers in a set of 102 low-latitude lakes and reservoirs that encompass wide gradients of precipitation, productivity and landscape properties (lake area, perimeter-to-area ratio, catchment size, catchment area-to-lake area ratio, and types of catchment land use). We used multiple regressions and structural equation modeling (SEM) to determine the direct and indirect effects of the main in-lake variables and landscape properties on the water pCO2 variance. We found that these systems were mostly supersaturated with CO2 (92% spatially and 72% seasonally) regardless of their trophic status and landscape properties. The pCO2 values (9-40,020 µatm) were within the range found in tropical ecosystems, and higher (p < 0.005) than pCO2 values recorded from high-latitude ecosystems. Water volume had a negative effect on the trophic state (r = -0.63), which mediated a positive indirect effect on pCO2 (r = 0.4), representing an important negative feedback in the context of climate change-driven reduction in precipitation. Our results demonstrated that precipitation drives the pCO2 seasonal variability, with significantly higher pCO2 during the rainy season (F = 16.67; p < 0.001), due to two potential main mechanisms: (1) phytoplankton dilution and (2) increasing inputs of terrestrial CO2 from the catchment. We conclude that at low latitudes, precipitation is a major climatic driver of pCO2 variability by influencing volume variations and linking lentic ecosystems to their catchments.

Agent-based models of collective intelligence.

Collective or group intelligence is manifested in the fact that a team of cooperating agents can solve problems more efficiently than when those agents work in isolation. Although cooperation is, in general, a successful problem solving strategy, it is not clear whether it merely speeds up the time to find the solution, or whether it alters qualitatively the statistical signature of the search for the solution. Here we review and offer insights on two agent-based models of distributed cooperative problem-solving systems, whose task is to solve a cryptarithmetic puzzle. The first model is the imitative learning search in which the agents exchange information on the quality of their partial solutions to the puzzle and imitate the most successful agent in the group. This scenario predicts a very poor performance in the case imitation is too frequent or the group is too large, a phenomenon akin to Groupthink of social psychology. The second model is the blackboard organization in which agents read and post hints on a public blackboard. This brainstorming scenario performs the best when there is a stringent limit to the amount of information that is exhibited on the board. Both cooperative scenarios produce a substantial speed up of the time to solve the puzzle as compared with the situation where the agents work in isolation. The statistical signature of the search, however, is the same as that of the independent search.

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons.

Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m-1), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 µg L-1). Virus abundance varied from 0.37 × 108 to 117 × 108 virus-like-particle (VLP) mL-1, with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 107 to 56.5 × 107 VLP mL-1 h-1 and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.

A theoretical approach to the size-complexity rule.

The so-called size-complexity rule claims the existence of a positive correlation between organism size and number of cell types. In this spirit, here we address the relationship between organism size and number of potential tasks that can be performed. The modeling relies on the assumption that the states of the cells within the aggregates are such that the maximum fitness is realized, but also relies on the existence of tradeoffs among the distinct functions. For group sizes larger than the number of potential tasks, fitness maximization is attained when all cells in group specialize in a given task. Under this scenario, the number of potential tasks equals the number of cell types. We have found that the morphology and the topology of aggregates, as well as the developmental mode, strongly influence the dynamics of body formation. Particularly, it has been observed that more compact structures, such as sphere-like structures, are more likely to follow the claim of the size-complexity rule, whereas more fragile structures such as linear chains, which are more vulnerable to drastic changes due to division mechanisms, can, in a broad scenario, violate the size-complexity rule.

Redfield Ratios in Inland Waters: Higher Biological Control of C:N:P Ratios in Tropical Semi-arid High Water Residence Time Lakes.

The canonical Redfield C:N:P ratio for algal biomass is often not achieved in inland waters due to higher C and N content and more variability when compared to the oceans. This has been attributed to much lower residence times and higher contributions of the watershed to the total organic matter pool of continental ecosystems. In this study we examined the effect of water residence times in low latitude lakes (in a gradient from humid to a semi-arid region) on seston elemental ratios in different size fractions. We used lake water specific conductivity as a proxy for residence time in a region of Eastern Brazil where there is a strong precipitation gradient. The C:P ratios decreased in the seston and bacterial size-fractions and increased in the dissolved fraction with increasing water retention time, suggesting uptake of N and P from the dissolved pool. Bacterial abundance, production and respiration increased in response to increased residence time and intracellular nutrient availability in agreement with the growth rate hypothesis. Our results reinforce the role of microorganisms in shaping the chemical environment in aquatic systems particularly at long water residence times and highlights the importance of this factor in influencing ecological stoichiometry in all aquatic ecosystems.

Light induced cytotoxicity of nitrofurantoin toward murine melanoma.

The cytotoxicity of nitrofurantoin (NFT) in the dark and after light exposure (UVA irradiation, λ = 385 nm) was evaluated in murine melanoma B16F10 cells. NFT induces both cell proliferation and inhibition of cell viability. The dominance of one or the other effect depends on the drug concentration, incubation time (tinc) and irradiation dose. The uptake of NFT in these cells, as well as its photocytotoxicity, reaches saturation after 24 hours of incubation. The mechanism of cell death in the dark is associated with the enzymatic release of nitric oxide (NO). The increase of NFT cytotoxicity under light irradiation is associated with the increase of NO concentration due to photorelease. NO photorelease by NFT in solution was confirmed by chemiluminescence, while NO formation in cells was confirmed by fluorescence microscopy using DAF-2DA, a specific indicator of NO in living cells. The NFT does not enter nuclei, distributing preferentially in the cell cytoplasm, as shown by fluorescence microscopy.

Acridine orange interaction with DNA: Effect of ionic strength.

BACKGROUND: The study of acridine orange (AO) spectral characteristics and the quenching of its singlet and triplet excited states by TEMPO radical at its binding to DNA in the function of the DNA concentration and in the absence and presence of NaCl is reported. METHODS: The study was performed using steady-state and time resolved optical absorption and florescence, fluorescence correlation spectroscopy and resonant light scattering techniques. RESULTS: The presence of different species in equilibrium: AO monomers and aggregates bound to DNA, has been demonstrated, their relative content depending on the DNA and the AO concentrations. At high DNA concentration the AO monomers are protected against the contact with other molecules, thus reducing the AO excited state quenching. The addition of NaCl reduces the AO binding constant to DNA, thus reducing the AO and DNA aggregation. CONCLUSIONS: The interaction of AO with DNA is a complex process, including aggregation and disaggregation of both components. This modifies the AO excited state characteristics and AO accessibility to other molecules. The salt reduces the DNA effects on the AO excited state characteristics thus attenuating its effects on the AO efficacy in applications. GENERAL SIGNIFICANCE: This study demonstrates that the interaction of photosensitizers with DNA, depending on their relative concentrations, can both decrease and increase the photosensitizer efficacy in applications. The salt is able to attenuate these effects.

Competing metabolic strategies in a multilevel selection model.

The evolutionary mechanisms of energy efficiency have been addressed. One important question is to understand how the optimized usage of energy can be selected in an evolutionary process, especially when the immediate advantage of gathering efficient individuals in an energetic context is not clear. We propose a model of two competing metabolic strategies differing in their resource usage, an efficient strain which converts resource into energy at high efficiency but displays a low rate of resource consumption, and an inefficient strain which consumes resource at a high rate but at low yield. We explore the dynamics in both well-mixed and structured populations. The selection for optimized energy usage is measured by the likelihood that an efficient strain can invade a population of inefficient strains. It is found that the parameter space at which the efficient strain can thrive in structured populations is always broader than observed in well-mixed populations.

Coexistence of competing metabolic pathways in well-mixed populations.

Understanding why strains with different metabolic pathways that compete for a single limiting resource coexist is a challenging issue within a theoretical perspective. Previous investigations rely on mechanisms such as group or spatial structuring to achieve a stable coexistence between competing metabolic strategies. Nevertheless, coexistence has been experimentally reported even in situations where it cannot be attributed to spatial effects [Heredity 100, 471 (2008)HDTYAT0018-067X10.1038/sj.hdy.6801073]. According to that study a toxin expelled by one of the strains can be responsible for the stable maintenance of the two strain types. We propose a resource-based model in which an efficient strain with a slow metabolic rate competes with a second strain type which presents a fast but inefficient metabolism. Moreover, the model assumes that the inefficient strain produces a toxin as a by-product. This toxin affects the growth rate of both strains with different strength. Through an extensive exploration of the parameter space we determine the situations at which the coexistence of the two strains is possible. Interestingly, we observe that the resource influx rate plays a key role in the maintenance of the two strain types. In a scenario of resource scarcity the inefficient is favored, though as the resource influx rate is augmented the coexistence becomes possible and its domain is enlarged.

Potential effects of UV radiation on photosynthetic structures of the bloom-forming cyanobacterium Cylindrospermopsis raciborskii CYRF-01.

Cyanobacteria are aquatic photosynthetic microorganisms. While of enormous ecological importance, they have also been linked to human and animal illnesses around the world as a consequence of toxin production by some species. Cylindrospermopsis raciborskii, a filamentous nitrogen-fixing cyanobacterium, has attracted considerable attention due to its potential toxicity and ecophysiological adaptability. We investigated whether C. raciborskii could be affected by ultraviolet (UV) radiation. Non-axenic cultures of C. raciborskii were exposed to three UV treatments (UVA, UVB, or UVA + UVB) over a 6 h period, during which cell concentration, viability and ultrastructure were analyzed. UVA and UVA + UVB treatments showed significant negative effects on cell concentration (decreases of 56.4 and 64.3%, respectively). This decrease was directly associated with cell death as revealed by a cell viability fluorescent probe. Over 90% of UVA + UVB- and UVA-treated cells died. UVB did not alter cell concentration, but reduced cell viability in almost 50% of organisms. Transmission electron microscopy (TEM) revealed a drastic loss of thylakoids, membranes in which cyanobacteria photosystems are localized, after all treatments. Moreover, other photosynthetic- and metabolic-related structures, such as accessory pigments and polyphosphate granules, were damaged. Quantitative TEM analyses revealed a 95.8% reduction in cell area occupied by thylakoids after UVA treatment, and reduction of 77.6 and 81.3% after UVB and UVA + UVB treatments, respectively. Results demonstrated clear alterations in viability and photosynthetic structures of C. raciborskii induced by various UV radiation fractions. This study facilitates our understanding of the subcellular organization of this cyanobacterium species, identifies specific intracellular targets of UVA and UVB radiation and reinforces the importance of UV radiation as an environmental stressor.