Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

Microbial communities respond quickly to environmental change (1, 2). These responses are typically associated with ecological processes; however, the potential for microbes to evolve and adapt to changes in the environment on ecological timescales remains largely unexplored in natural ecosystems. While evolutionary processes are typically considered over longer timescales, the short generation times, large populations, and high mutation rates indicative of microorganisms may allow for rapid adaptation. Laboratory studies have repeatedly demonstrated rapid evolution of bacterial populations (3) with consequences for organismal physiology (4), yet it remains unclear how these in vitro studies extend to in situ communities (5).Both ecological and evolutionary processes likely contribute simultaneously (6, 7) to the response of a microbiome to changing environmental conditions (8). However, separating these processes for bacteria can be difficult as they occur along a continuum of temporal and genetic scales. In terms of ecological processes, microbiome composition can respond demographically, as selective forces promote the growth and survival of differentially adapted taxa within the bacterial community. Certainly, many studies have observed such shifts in taxonomic composition of 16S ribosomal RNA (rRNA)–defined taxa in response to simulated global changes (9), and these responses are considered an ecological process (e.g., species sorting). Few examples, however, link these responses to trait differences among bacterial taxa (10–13), precluding direct insights into whether these ecological shifts are due to adaptive differentiation among taxa as a result of past evolutionary divergence. Concurrently, the same selective forces can also shift the abundance of conspecific strains and alter the allele frequencies of preexisting genetic variation, which at this genetic scale is defined as an evolutionary process (14). Finally, evolution through de novo mutation can provide a new source of genetic variation that may allow for further adaptation to environmental change.In this study, we aimed to capture this continuum of ecological and evolutionary processes that together produce the response of a microbiome’s diversity to environmental change (Fig. 1A). Studying evolution in microbial communities in situ, however, is challenging. For one, variation in highly conserved marker genes used in many microbiome studies (e.g., 16S rRNA) represents distant evolutionary divergences, and thus these regions are too conserved to detect locally adapted lineages (11, 12, 15), let alone recent evolutionary change within communities (16). To overcome this limitation, studies have leveraged shotgun metagenomic data (17, 18) and genome sequences of co-occurring, closely related strains (19, 20) to characterize evolutionary processes (e.g., recombination and gene flow) structuring the genetic diversity of bacterial lineages. However, these studies are also limited by an inherent challenge in microbiome research: delineating population boundaries, the fundamental unit of evolution. While progress has been made in defining microbial species (21–23), the high genetic heterogeneity within diverse microbial communities, such as soils, convolute the boundaries of the fine-scale patterns of genetic diversity within microbial taxonomic units (12). For instance, metagenome-assembled genomes are often composed of a composite of strains forming a large population of mosaic genomes (24) that may not fully capture the diversity of the local population (25). As such, it remains difficult to study evolutionary rates within microbial communities (however, see refs. 26, 27), and the extent and time scale at which evolutionary processes contribute to both standing and new genetic variation relative to ecological processes.Open in a separate windowFig. 1.Microbial community transplant experiment. (A) Changes in microbial community composition can be due to a continuum of ecological and evolutionary processes. For instance, shifts in standing genetic variation can be attributed to both ecological and evolutionary processes depending on the level of biological resolution, while de novo mutations can be a result from evolutionary adaptation. (B) A schematic of the two parallel transplant experiments at the community and strain level. Inoculated litterbags were transplanted to all sites along an elevation gradient that covaried in temperature and precipitation. Site codes: D=Desert; Sc=Scrubland; G=Grassland; P=Pine-Oak; S=Subalpine.Here, we asked the following question: can we characterize the ecological and evolutionary processes that are contributing concurrently to the response of a soil bacterial community to a changing environment? To answer this question, we utilized a field-based experimental approach to quantify the influence of both ecological and evolutionary processes on one focal soil bacterium in its natural environment, the genus Curtobacterium (28). Specifically, we transplanted the bacterium across an elevation gradient on a common resource (leaf litter) substrate (29) to assess its response to new climates in two parallel experiments over the same 18 mo time period (Fig. 1B). In both experiments, we used microbial cages [nylon mesh bags that allow for nutrient transport (30)] to manipulate microbial composition while restricting microbial migration to eliminate the introduction of new alleles and/or variants from dispersal (31). A reciprocal transplant design allowed for direct testing of microbial adaptation to abiotic conditions (i.e., moisture and temperature) in a natural setting.In the first experiment, we conducted a reciprocal transplant of the entire microbial community (32) and tracked the ecological response of Curtobacterium ecotypes (33). A bacterial ecotype is defined as highly clustered genotypic and phenotypic strains occupying the same ecological niche, somewhat equivalent to a eukaryotic species (34). To test the hypothesis that Curtobacterium ecotypes are locally adapted to their climate conditions, we assessed the convergence of ecotype composition in the transplanted communities to that of control communities (those that remained in their native environment; Fig. 1B). We further hypothesized that the demographic shifts were due to differential adaptation to local climates as a result of trait variation among the ecotypes. Thus, we expected that the climate gradient would select for a strong trait–environment relationship (assessed by community-weighted mean (CWM) trait values) as typically observed in plant communities (35, 36).In parallel, we conducted an in situ evolution experiment by transplanting an isogenic Curtobacterium strain across the same gradient to investigate the potential for rapid evolution on the same timescales. We hypothesized that a variety of genomic mutations would be associated with adaptation to local climate conditions. Therefore, we expected fewer genetic changes when the strain was transplanted to its original environment, the midelevation Grassland site, while the extreme sites of the gradient would impose stronger selective pressures resulting in greater genetic changes. We further expected to observe parallel mutations among replicates within a site, which would be indicative of adaptive events (37). Variation in such mutations across sites would suggest selection differences across the climate gradient. Together, the two experiments capture the simultaneous effects of both ecological and evolutionary processes on the response of a soil bacterium to new climates in the field.     

Antimicrobial resistance of Shigella spp isolated from diarrheal patients between 1989 and 1998 in Vietnam

Shigellosis is an important cause of infectious diarrhea in Vietnam, caused mainly by Shigella flexneri. This study provides for the first time in the international literature, data on the development of antimicrobial resistance in Shigella between 1988 to 1998, including data reported to the National Program for Surveillance of Antimicrobial Resistance (NPSAR). Our studies show that about 80% of the Shigella strains tested were resistant to ampicillin, chloramphenicol, oxytetracycline, trimethoprim and sulfonamides. This combination of drugs was also the most common antibiogram among multiple-resistant S. flexneri (57%). Resistance to tetracyclines, sulfonamides and, in particular trimethoprim (p<0.001), increased during the study period. Our findings indicate that tetracyclines and co-trimoxazole (a combination of a sulfonamide and trimethoprim), which are recommended and commonly used drugs for the treatment of shigellosis in Vietnam, may have limited therapeutic effect. In contrast to neighboring countries, low percentages of resistance were found to nalidixic acid and norfloxacin (3-5%) and no resistance was found to ciprofloxacin, indicating that nalidixic acid with its low cost and safety in children could be recommended for the treatment of shigellosis. The NPSAR provides a useful picture of the levels and development of antimicrobial resistance in Vietnam and should receive continued support for further improvement by increasing the number of provinces covered, the numbers of isolates tested from rural areas, and the communication of results to medical practitioners and others prescribing and/or selling antimicrobials.     

Timescales of developmental toxicity impacting on research and needs for intervention

Much progress has happened in understanding developmental vulnerability to preventable environmental hazards. Along with the improved insight, the perspective has widened, and developmental toxicity now involves latent effects that can result in delayed adverse effects in adults or at old age and additional effects that can be transgenerationally transferred to future generations. Although epidemiology and toxicology to an increasing degree are exploring the adverse effects from developmental exposures in human beings, the improved documentation has resulted in little progress in protection, and few environmental chemicals are currently regulated to protect against developmental toxicity, whether it be neurotoxicity, endocrine disruption or other adverse outcome. The desire to obtain a high degree of certainty and verification of the evidence used for decision‐making must be weighed against the costs and necessary duration of research, as well as the long‐term costs to human health because of delayed protection of vulnerable early‐life stages of human development and, possibly, future generations. Although two‐generation toxicology tests may be useful for initial test purposes, other rapidly emerging tools need to be seriously considered from computational chemistry and metabolomics to CLARITY‐BPA‐type designs, big data and population record linkage approaches that will allow efficient generation of new insight; epigenetic mechanisms may necessitate a set of additional regulatory tests to reveal such effects. As reflected by the Prenatal Programming and Toxicity (PPTOX) VI conference, the current scientific understanding and the timescales involved require an intensified approach to protect against preventable adverse health effects that can harm the next generation and generations to come. While further research is needed, the main emphasis should be on research translation and timely public health intervention to avoid serious, irreversible and perhaps transgenerational harm.     

Perceived risk of osteoporosis: Restricted physical activities?: Qualitative interview study with women in their sixties

OBJECTIVE: To explore elderly women's physical activity in relation to their perception of the risk of osteoporosis. DESIGN: Qualitative study using in-depth interviews. SETTING: Informants were purposely selected from a Danish population-based, age-specific cohort study conducted in the county of Copenhagen with people born in 1936. SUBJECTS: Women in their sixties. RESULTS: Women who perceived a current risk of osteoporosis tended to reduce their physical activity in an attempt to reduce the risk of bone damage. This behaviour was related to the imagined fragility of the bones (the risk inside the body), and the actual situations (the risk outside the body), including places and activities. Knowledge of a reduced bone mass reinforced the women's uncertainty about what their bones could endure. Experiences managing physical activity without injury resulted in reinterpretations of their risk of bone fractures and increased physical activity. CONCLUSIONS: Perceived risk of osteoporosis may lead to decreased physical activity and hence actually increase the risk. When informing individuals about health risk people's images and imaginations of the actual risk have to be acknowledged. When a bone scan is being considered, explicit advice encouraging physical activity - especially the weight-bearing kind - should be stressed.     

Cancer associated thrombosis in everyday practice: perspectives from GARFIELD-VTE

Journal of Thrombosis and Thrombolysis - Venous thromboembolism (VTE) is common in cancer patients and is an important cause of morbidity and mortality. The Global Anticoagulant Registry in the...     

Vitamin D in the General Population of Young Adults with Autism in the Faroe Islands

Vitamin D deficiency has been proposed as a possible risk factor for developing autism spectrum disorder (ASD). 25-Hydroxyvitamin D₃ (25(OH)D₃) levels were examined in a cross-sectional population-based study in the Faroe Islands. The case group consisting of a total population cohort of 40 individuals with ASD (aged 15–24 years) had significantly lower 25(OH)D₃ than their 62 typically-developing siblings and their 77 parents, and also significantly lower than 40 healthy age and gender matched comparisons. There was a trend for males having lower 25(OH)D₃ than females. Effects of age, month/season of birth, IQ, various subcategories of ASD and Autism Diagnostic Observation Schedule score were also investigated, however, no association was found. The very low 25(OH)D₃ in the ASD group suggests some underlying pathogenic mechanism.