Fitness In Environments Research Articles

Complete functional analysis of type IV pilus components of a reemergent plant pathogen reveals neofunctionalization of paralog genes.

Type IV pilus (TFP) is a multifunctional bacterial structure involved in twitching motility, adhesion, biofilm formation, as well as natural competence. Here, by site-directed mutagenesis and functional analysis, we determined the phenotype conferred by each of the 38 genes known to be required for TFP biosynthesis and regulation in the reemergent plant pathogenic fastidious prokaryote Xylella fastidiosa. This pathogen infects > 650 plant species and causes devastating diseases worldwide in olives, grapes, blueberries, and almonds, among others. This xylem-limited, insect-transmitted pathogen lives constantly under flow conditions and therefore is highly dependent on TFP for host colonization. In addition, TFP-mediated natural transformation is a process that impacts genomic diversity and environmental fitness. Phenotypic characterization of the mutants showed that ten genes were essential for both movement and natural competence. Interestingly, seven sets of paralogs exist, and mutations showed opposing phenotypes, indicating evolutionary neofunctionalization of subunits within TFP. The minor pilin FimT3 was the only protein exclusively required for natural competence. By combining approaches of molecular microbiology, structural biology, and biochemistry, we determined that the minor pilin FimT3 (but not the other two FimT paralogs) is the DNA receptor in TFP of X. fastidiosa and constitutes an example of neofunctionalization. FimT3 is conserved among X. fastidiosa strains and binds DNA non-specifically via an electropositive surface identified by homolog modeling. This protein surface includes two arginine residues that were exchanged with alanine and shown to be involved in DNA binding. Among plant pathogens, fimT3 was found in ~ 10% of the available genomes of the plant associated Xanthomonadaceae family, which are yet to be assessed for natural competence (besides X. fastidiosa). Overall, we highlight here the complex regulation of TFP in X. fastidiosa, providing a blueprint to understand TFP in other bacteria living under flow conditions.

Review on Good Laboratory Practices

They Are Mainly Intended For Them Laboratories Conducting Studies Have Good Laboratory Practices (GLP) As a result, it can help to preserve a concern for human and environmental fitness and pave the way for a reasonable understanding of scientific challenges. Around this investigation, we have made an effort to investigate the applications of GLP principles in other scientific fields, their acceptability, and potential financial rewards. adherence to regulations. To fulfil the needs of experimental aims, the age of high-quality data, and assay reproducibility, GLP may now be applied to a wide range of scientific domains. Given its importance, it is now accessible in administrative settings, enterprises, and educational institutions all around the world. GLP is a promising strategy for enhancing the reliability and repeatability of examination data, which facilitates universal acceptance. The time has come to summarise and put into practise the GLP vision beyond regulatory inquiries. Presented Era Of Rapidly And Developing Technology And Evidence Based Treatment, Good Laboratory Practice (GLP) Shall Play An A Significant Position In Assuring, Thickness, Trustworthiness, Reproducibility And Quality Of Laboratory Examinations. (1).

Exploring the metabolic basis of growth/defense trade-offs in complex environments with Nicotiana attenuata plants cosilenced in NaMYC2a/b expression.

In response to challenges from herbivores and competitors, plants use fitness-limiting resources to produce (auto)toxic defenses. Jasmonate signaling, mediated by MYC2 transcription factors (TF), is thought to reconfigure metabolism to minimize these formal costs of defense and optimize fitness in complex environments. To study the context-dependence of this metabolic reconfiguration, we cosilenced NaMYC2a/b by RNAi in Nicotiana attenuata and phenotyped plants in the field and increasingly realistic glasshouse setups with competitors and mobile herbivores. NaMYC2a/b had normal phytohormonal responses, and higher growth and fitness in herbivore-reduced environments, but were devastated in high herbivore-load environments in the field due to diminished accumulations of specialized metabolites. In setups with competitors and mobile herbivores, irMYC2a/b plants had lower fitness than empty vector (EV) in single-genotype setups but increased fitness in mixed-genotype setups. Correlational analyses of metabolic, resistance, and growth traits revealed the expected defense/growth associations for most sectors of primary and specialized metabolism. Notable exceptions were some HGL-DTGs and phenolamides that differed between single-genotype and mixed-genotype setups, consistent with expectations of a blurred functional trichotomy of metabolites. MYC2 TFs mediate the reconfiguration of primary and specialized metabolic sectors to allow plants to optimize their fitness in complex environments.

Cyclic di-GMP Modulates a Metabolic Flux for Carbon Utilization in Salmonella enterica Serovar Typhimurium.

Salmonella enterica serovar Typhimurium is an enteric pathogen spreading via the fecal-oral route. Transmission across humans, animals, and environmental reservoirs has forced this pathogen to rapidly respond to changing environments and adapt to new environmental conditions. Cyclic di-GMP (c-di-GMP) is a second messenger that controls the transition between planktonic and sessile lifestyles, in response to environmental cues. Our study reveals the potential of c-di-GMP to alter the carbon metabolic pathways in S. Typhimurium. Cyclic di-GMP overproduction decreased the transcription of genes that encode components of three phosphoenolpyruvate (PEP):carbohydrate phosphotransferase systems (PTSs) allocated for the uptake of glucose (PTSGlc), mannose (PTSMan), and fructose (PTSFru). PTS gene downregulation by c-di-GMP was alleviated in the absence of the three regulators, SgrS, Mlc, and Cra, suggesting their intermediary roles between c-di-GMP and PTS regulation. Moreover, Cra was found to bind to the promoters of ptsG, manX, and fruB. In contrast, c-di-GMP increased the transcription of genes important for gluconeogenesis. However, this effect of c-di-GMP in gluconeogenesis disappeared in the absence of Cra, indicating that Cra is a pivotal regulator that coordinates the carbon flux between PTS-mediated sugar uptake and gluconeogenesis, in response to cellular c-di-GMP concentrations. Since gluconeogenesis supplies precursor sugars required for extracellular polysaccharide production, Salmonella may exploit c-di-GMP as a dual-purpose signal that rewires carbon flux from glycolysis to gluconeogenesis and promotes biofilm formation using the end products of gluconeogenesis. This study sheds light on a new role for c-di-GMP in modulating carbon flux, to coordinate bacterial behavior in response to hostile environments. IMPORTANCE Cyclic di-GMP is a central signaling molecule that determines the transition between motile and nonmotile lifestyles in many bacteria. It stimulates biofilm formation at high concentrations but leads to biofilm dispersal and planktonic status at low concentrations. This study provides new insights into the role of c-di-GMP in programming carbon metabolic pathways. An increase in c-di-GMP downregulated the expression of PTS genes important for sugar uptake, while simultaneously upregulating the transcription of genes important for bacterial gluconeogenesis. The directly opposing effects of c-di-GMP on sugar metabolism were mediated by Cra (catabolite repressor/activator), a dual transcriptional regulator that modulates the direction of carbon flow. Salmonella may potentially harness c-di-GMP to promote its survival and fitness in hostile environments via the coordination of carbon metabolic pathways and the induction of biofilm formation.

C:N:P stoichiometric variations of herbs and its relationships with soil properties and species relative abundance along the Xiaokai River irrigation in the Yellow River Delta, China.

Soil salinity is known to affect plant performance and nutrient stoichiometry by altering their ecophysiology, and thus playing a crucial role in determining plant distribution patterns and nutrient cycles in salinized ecosystems. However, there was little consensus on the effects of salinity stress on plant C, N, and P stoichiometries. Moreover, determining the relationships between species relative species abundance and plant C, N, and P stoichiometries can help to understand the different adaptive strategies between the common and rare species as well as the community assembly process. We determined the plant C, N, P stoichiometries at the community and species levels and the relative abundance of species as well as the corresponding soil properties from five sampling sites along a soil salinity gradient in the Yellow River Delta, China. We found that the C concentration of belowground part increased with soil salinity. Meanwhile, plant community N concentration and C:N ratio tended to decrease with soil salinity, whereas the P concentration, C:P, and N:P ratios exhibited the opposite trends. This indicated that N use efficiency increased, while P use efficiency decreased with soil salinity. Moreover, the decreased N:P ratio indicated that N limitation was gradually aggravated along the soil salinity gradient. The soil C:P ratio and P concentration were the major factors of plant C, N, and P stoichiometries in the early growth stage, whereas the soil pH and P concentration were the major factors of plant C, N, and P stoichiometries in the late growth stage. Compared with that of the rare species, the C:N:P stoichiometry of the most common species was medium. Moreover, the intraspecific variations in the aboveground part N:P ratio and belowground part C concentration showed a significant correlation with species' relative abundance, which indicated that higher intraspecific trait variation might facilitate greater fitness and survival opportunities in environments with high heterogeneity. Our results revealed that the plant community C:N:P stoichiometry and its determining soil properties varied with plant tissues as well as sampling seasons, and emphasized the importance of intraspecific variation in determining the functional response of plant communities to salinity stress.

Tree ecophysiology in the context of climate change

Forest structure and function strongly depend on and concurrently influence environmental conditions. Tree performance is generally governed by its genetics and environment; thus, recent hotspots in this field include tree genotype × environment, phenotype × environment, and functional trait × environment interactions. The editorial, review, and 22 original research articles in this Special Issue, “Tree ecophysiology in the context of climate change”, highlight ecophysiological phenomena (e.g., climate hormesis, seed germination, tree mortality), processes (e.g., tree metabolism, photosynthate allocation, nutrient uptake and transport), indicators (e.g., carbon sequestration, pollutants), measurements (e.g., thermal time methods, soil quality indices, vegetation spectral index, and near-infrared leaf reflectance), and modeling (e.g., climate correlations with tree growth, photosynthetic phenology, hydraulic strategies, OliveCan model) in the context of global climate change. Understanding forest–environment interactions from an ecophysiological perspective as climate changes provides insights into species fitness in suboptimal environments, species competition for limited resources, and phylogenetic divergence or convergence of species, and predicting species distributions.

Modeling the influence of phenotypic plasticity on maize hybrid performance

Phenotypic plasticity, the ability of an individual to alter its phenotype in response to changes in the environment, has been proposed as a target for breeding crop varieties with high environmental fitness. Here, we used phenotypic and genotypic data from multiple maize (Zea mays L.) populations to mathematically model phenotypic plasticity in response to the environment (PPRE) in inbred and hybrid lines. PPRE can be simply described by a linear model in which the two main parameters, intercept a and slope b, reflect two classes of genes responsive to endogenous (class A) and exogenous (class B) signals that coordinate plant development. Together, class A and class B genes contribute to the phenotypic plasticity of an individual in response to the environment. We also made connections between phenotypic plasticity and hybrid performance or general combining ability (GCA) of yield using 30 F1 hybrid populations generated by crossing the same maternal line with 30 paternal lines from different maize heterotic groups. We show that the parameters a and b from two given parental lines must be concordant to reach an ideal GCA of F1 yield. We hypothesize that coordinated regulation of the two classes of genes in the F1 hybrid genome is the basis for high GCA. Based on this theory, we built a series of predictive models to evaluate GCA in silico between parental lines of different heterotic groups.

Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA)

Coastal wetlands are highly efficient ‘blue carbon’ sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments.Graphical Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone.

Zebrafish aversion to infrasound in an open field test.

Aquatic species are capable of detecting infrasound (sub-20 Hz frequencies) which may be a source of anthropogenic pollution and have a detrimental impact on the environmental fitness of fish. Infrasound is generated by infrastructure, producing acoustic frequency peaks that are not discernible by humans. The presence of these frequencies may therefore impact the environmental wellbeing of aquatic laboratory animals, which are often housed in spaces adjacent to facilities producing infrasound. To investigate the potential impact of infrasound, we used wild-type zebrafish (Danio rerio) and exposed them to short periods of infrasound at either 5, 10, 15, or 20 Hz, or 0 Hz as a control group. A motion-tracking software system was used to monitor fish movement in an open field test and arena location, distance moved, and immobility were quantified. There was a significant effect of 15 Hz which caused the fish to spend more time away from the infrasound source. The 20 Hz group also spent significantly less time in the zone closest to the speaker. There were no differences in distance moved or immobility between infrasound and control groups. These findings demonstrate that 15 Hz infrasound has aversive effects on zebrafish, causing them to move away from the sound source. To enhance environmental enrichment and wellbeing of aquatic laboratory animals, sources of infrasound pollution should be investigated and mitigated.

Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species

Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness.

2349. Elucidating the Pathogenesis of Staphylococcus aureus During Hyperglycemic Osteomyelitis

Abstract Background Staphylococcus aureus is a leading cause of antibiotic-resistant bacterial infections and can infect nearly every organ of the human body. One common manifestation of S. aureus disease is invasive bone infection, or osteomyelitis. Osteomyelitis is one of the most difficult to treat infections, often necessitating prolonged antibiotic treatment and surgical interventions. Hyperglycemia, or elevated blood glucose concentration, increases the risk for developing osteomyelitis. We hypothesized that S. aureus adapts specifically to the altered host environment during hyperglycemic osteomyelitis, thereby contributing to the increased infection severity. Methods To model hyperglycemic osteomyelitis, we treated mice with streptozotocin prior to infection with S. aureus in a post-traumatic osteomyelitis model. We analyzed bacterial burdens in homogenized tissues and bone parameters with microcomputed tomography. To identify changes in the spatial molecular architecture of infected, hyperglycemic femurs, we utilized imaging mass spectrometry. Finally, to obtain a comprehensive understanding of S. aureus metabolic and virulence changes and identify genes essential for staphylococcal growth in vivo in hyperglycemic mice, we performed a transposon sequencing experiment. Results We discovered that hyperglycemic mice sustained increased bacterial burdens within infected femurs and greater dissemination to other organs. We also found that hyperglycemic infected mice experienced increased rates of bone destruction and loss of trabecular bone volume, suggesting that hyperglycemia exacerbates infection-associated bone loss. Finally, we identified 71 genes as uniquely essential for S. aureus growth during hyperglycemic infection compared to euglycemic infection. Conclusion Hyperglycemia results in increased osteomyelitis infection severity. Multiple S. aureus genes involved in metabolism with roles in bacterial fitness in acidic environments were uniquely essential for bacterial fitness during comorbid infection. By identifying genes contributing to S. aureus survival during hyperglycemic osteomyelitis, we have the potential to inform targeted therapeutic development for treatment of exacerbated infections in patients with comorbid hyperglycemia. Disclosures All Authors: No reported disclosures.

Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity.

Protein synthesis is crucial for cell growth and survival yet one of the most energy-consuming cellular processes. How, then, do cells sustain protein synthesis under starvation conditions when energy is limited? To accelerate the translocation of mRNA-tRNAs through the ribosome, bacterial elongation factor G (EF-G) hydrolyzes energy-rich guanosine triphosphate (GTP) for every amino acid incorporated into a protein. Here, we identify an EF-G paralog-EF-G2-that supports translocation without hydrolyzing GTP in the gut commensal bacterium Bacteroides thetaiotaomicron. EF-G2's singular ability to sustain protein synthesis, albeit at slow rates, is crucial for bacterial gut colonization. EF-G2 is ~10-fold more abundant than canonical EF-G1 in bacteria harvested from murine ceca and, unlike EF-G1, specifically accumulates during carbon starvation. Moreover, we uncover a 26-residue region unique to EF-G2 that is essential for protein synthesis, EF-G2 dissociation from the ribosome, and responsible for the absence of GTPase activity. Our findings reveal how cells curb energy consumption while maintaining protein synthesis to advance fitness in nutrient-fluctuating environments.

Hosts, microbiomes, and the evolution of critical windows.

The absence of microbial exposure early in life leaves individuals vulnerable to immune overreaction later in life, manifesting as immunopathology, autoimmunity, or allergies. A key factor is thought to be a "critical window" during which the host's immune system can "learn" tolerance, and beyond which learning is no longer possible. Animal models indicate that many mechanisms have evolved to enable critical windows, and that their time limits are distinct and consistent. Such a variety of mechanisms, and precision in their manifestation suggest the outcome of strong evolutionary selection. To strengthen our understanding of critical windows, we explore their underlying evolutionary ecology using models encompassing demographic and epidemiological transitions, identifying the length of the critical window that would maximize fitness in different environments. We characterize how direct effects of microbes on host mortality, but also indirect effects via microbial ecology, will drive the optimal length of the critical window. We find that indirect effects such as magnitude of transmission, duration of infection, rates of reinfection, vertical transmission, host demography, and seasonality in transmission all have the effect of redistributing the timing and/or likelihood of encounters with microbial taxa across age, and thus increasing or decreasing the optimal length of the critical window. Declining microbial population abundance and diversity are predicted to result in increases in immune dysfunction later in life. We also make predictions for the length of the critical window across different taxa and environments. Overall, our modeling efforts demonstrate how critical windows will be impacted over evolution as a function of both host-microbiome/pathogen interactions and dispersal, raising central questions about potential mismatches between these evolved systems and the current loss of microbial diversity and/or increases in infectious disease.

The structure and assembly of rhizobacterial communities are influenced by poplar genotype.

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3 --N content and 58 genera to NH4 +-N/NO3 --N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3 --N content and fluctuated with increasing NH4 +-N/NO3 --N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions

BackgroundDioecious plants have coevolved with diverse plant microbiomes, which are crucial for the fitness and productivity of their host. Sexual dimorphism in morphology, physiology, or gene expression may relate to different microbial compositions that affect male and female fitness in different environments. However, sex-specific impacts on ecological processes that control the microbiome assembly are not well known. In this study, Populus cathayana males and females were planted in different nitrogen conditions. It was hypothesized that males and females differently affect bacterial and fungal communities in the rhizosphere soil, roots, old leaves, and young leaves. Physiological traits and transcriptome profiles of male and female plants were investigated to reveal potential mechanisms that control the microbiome assembly.ResultsOur results showed strong niche differentiation that shapes microbial communities leading to a rapid loss of diversity along a decreasing pH gradient from the rhizosphere soil to leaves. Sex had different impacts on the microbial assembly in each niche. Especially fungal endophytes showed great differences in the community structure, keystone species, and community complexity between P. cathayana males and females. For example, the fungal co-occurrence network was more complex and the alpha diversity was significantly higher in young female leaves compared to young male leaves. Transcriptome profiles revealed substantial differences in plant-pathogen interactions and physiological traits that clearly demonstrated divergent internal environments for endophytes inhabiting males and females. Starch and pH of young leaves significantly affected the abundance of Proteobacteria, while tannin and pH of roots showed significant effects on the abundance of Chloroflexi, Actinobacteria, and Proteobacteria, and on the bacterial Shannon diversity.ConclusionOur results provided important knowledge for understanding sexual dimorphism that affects microbial assemblies, thus advancing our understanding of plant-microbiome interactions.6fJBNPXyfja-eHSN4N3z_QVideo

The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.

Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation.

Permeability-Engineered Compartmentalization Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems.

In nature, biological compartments such as cells rely on dynamically controlled permeability for matter exchange and complex cellular activities. Likewise, the ability to engineer compartment permeability is crucial for in vitro systems to gain sustainability, robustness, and complexity. However, rendering in vitro compartments such a capability is challenging. Here, a facile strategy is presented to build permeability-configurable compartments, and marked advantages of such compartmentalization are shown in reconstituting sustained synthetic biology systems in vitro. Through microfluidics, the strategy produces micrometer-sized layered microgels whose shell layer serves as a sieving structure for biomolecules and particles. In this configuration, the transport of DNAs, proteins, and bacteriophages across the compartments can be controlled an guided by a physical model. Through permeability engineering, a compartmentalized cell-free protein synthesis system sustains multicycle protein production; ≈100000 compartments are repeatedly used in a five-cycle synthesis, featuring a yield of 2.2mg mL-1 . Further, the engineered bacteria-enclosing compartments possess near-perfect phage resistance and enhanced environmental fitness. In a complex river silt environment, compartmentalized whole-cell biosensors show maintained activity throughout the 32 h pollutant monitoring. It is anticipated that permeability-engineered compartmentalization should pave the way for practical synthetic biology applications such as green bioproduction, environmental sensing, and bacteria-based therapeutics.

Defining, estimating, and understanding the fundamental niches of complex animals in heterogeneous environments

AbstractDuring the past century, the fundamental niche, the complete set of environments that allow an individual, population, or species to persist, has shaped ecological thinking. It is a crucial concept connecting population dynamics, spatial ecology, and evolutionary theory, and a prerequisite for predictive ecological models at a time of rapid environmental change. Yet, its properties have eluded quantification, particularly for mobile, cognitively complex organisms. These difficulties are mainly a result of the separation between niche theory and field data, and the dichotomy between environmental and geographical spaces. Here, I combine recent mathematical and statistical results linking habitats to population growth, to achieve a quantitative and intuitive understanding of the fundamental niches of animals. I trace the development of niche ideas from the early steps of ecology to their use in modern statistical and conservation practice. I examine how animal mobility and behavior may blur the division between geographical and environmental space. I discuss how the central models of population and spatial ecology lead to a concise mathematical equation for the fundamental niche of animals and demonstrate how fitness parameters can be understood and directly estimated by fitting this model simultaneously to data on population growth and spatial distributions. I first illustrate these concepts theoretically for territorial species. I then fit the fundamental niche model to a data set of house sparrow colonies to quantify how a species of selective animals can increase their fitness in heterogeneous environments. This work confirms ideas that had been anticipated in the historical niche literature. Specifically, within traditionally defined environmental spaces, habitat heterogeneity and behavioral plasticity make the fundamental niche more complex and malleable than was historically envisaged. However, once examined in higher‐dimensional environmental spaces, accounting for spatial heterogeneity, the niche is more predictable than recently suspected. This re‐evaluation quantifies how organisms might buffer themselves from change by bending the boundaries of viable environmental space and offers a framework for designing optimal habitat interventions to protect biodiversity or obstruct invasive species. It therefore promotes the fundamental niche as a key concept for understanding animal responses to changing environments and a central tool for environmental management.

Variation in shape and consistency of selection between populations of the threatened Hihi (Notiomystis cincta).

The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a "lag load"). In endangered species, often characterized by small population size, the lack of genetic diversity is expected to limit the response to this constant need to adjust to fluctuating selection, increasing the fitness burden and thus the risk of extinction. Here, we use long-term monitoring data to assess whether the type of selection for a key fitness trait (i.e., lay date) differs between two reintroduced populations of a threatened passerine bird, the hihi (Notiomystis cincta). We apply recent statistical developments to test for the presence or absence of fluctuation in selection in both the Tiritiri Mātangi Island and the Kārori sanctuary populations. Our results support the presence of stabilizing selection in Tiritiri Mātangi with a potential moving optimum for lay date. In Kārori our results favour a regime of directional selection. Although the shape of selection may differ, for both populations an earlier lay date generally increases fitness in both environments. Further, the moving optimum models of lay date on Tiritiri Mātangi, suggesting that selection varies between years, imply a substantial lag load in addition to the fitness burden caused by the population laying too late. Our results highlight the importance of characterizing the form and temporal variation of selection for each population to predict the effects of environmental change and to inform management.

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts.

ABSTRACTPopulation genetic diversity of Plasmodium falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The prevalence of genetically distinct haplotypes at these loci, while well characterized in humans, has not been thoroughly compared between human and mosquito hosts. We assessed parasite haplotype prevalence, diversity, and evenness using human and mosquito P. falciparum infections collected from the same households during a 14-month longitudinal cohort study using amplicon deep sequencing of two antigenic gene fragments (ama1 and csp). To a prior set of infected humans (n = 1,175/2,813; 86.2% sequencing success) and mosquito abdomens (n = 199/1,448; 95.5% sequencing success), we added sequences from infected mosquito heads (n = 134/1,448; 98.5% sequencing success). The overall and sample-level parasite populations were more diverse in mosquitoes than in humans. Additionally, haplotype prevalences were more even in the P. falciparum human population than in the mosquito population, consistent with balancing selection occurring at these loci in humans. In contrast, we observed that infections in humans were more likely to harbor a dominant haplotype than infections in mosquitoes, potentially due to removal of unfit strains by the human immune system. Finally, within a given mosquito, there was little overlap in genetic composition of abdomen and head infections, suggesting that infections may be cleared from the abdomen during a mosquito’s lifespan. Taken together, our observations provide evidence for the mosquito vector acting as a reservoir of sequence diversity in malaria parasite populations.