高盐环境可培养细菌噬菌体的研究进展

病毒广泛存在于各类环境中并担负着重要的生态功能,其中包括高盐环境。对高盐环境病毒的研究已成为极端环境微生物研究领域的新热点,目前已被报道的100多株盐病毒中,90多株感染古菌,仅有14株感染细菌。本文综述了目前已知的14株高盐环境细菌噬菌体的形态特征、盐度响应及基因组学的研究进展,并分析了高盐噬菌体的形态多样性、生存策略以及包含在基因组中的进化和起源信息,分析结果表明:高盐噬菌体以有尾噬菌体为主;它们具有广盐性(Euryhaline)的特征,盐度极大地影响其吸附和增殖;它们与非高盐环境噬菌体可能具有共同的起源。高盐噬菌体虽然历经近30年的研究历程,但仅有14株被分离与培养,所以其分离纯化是今后重要工作之一,且结合免培养技术揭示高盐噬菌体的多样性与生态功能是其研究的发展方向。     

Embryos of non-native anoles are robust to urban thermal environments

The transformation of natural habitats into urban landscapes dramatically alters thermal environments, which in turn, can impact local biota. Ectothermic organisms that are oviparous are particularly sensitive to these altered environments because their embryos cannot behaviorally thermoregulate and the surrounding environment determines the temperature experienced during development. We studied the effects of urban and forested thermal environments on embryo development and hatchling phenotypes in two non-native lizards (Anolis sagrei and A. cristatellus) in metropolitan Miami, Florida. To determine if embryos from urban and forested sites are adapted to their respective thermal environments, we incubated eggs from each site using temperatures that simulate likely nest conditions in both urban and forested environments. For both species, urban thermal environments accelerated embryonic development, but had no impact on egg survival or any of the phenotypic traits that were measured (e.g., body size, running performance, and locomotor behavior). Our results provide no evidence that embryos from urban and forested sites are adapted to their respective thermal environments. Instead, the lack of any major effects suggest that embryos of both species are physiologically robust with respect to novel environments, which could have facilitated their success in establishing in non-native ranges and in human-modified landscapes.     

Fungal pollution of indoor environments and its management

Indoor environments play important roles in human health. The health hazards posed by polluted indoor environments include allergy, infections and toxicity. Life style changes have resulted in a shift from open air environments to air tight, energy efficient, environments, in which people spend a substantial portion of their time. Most indoor air pollution comes from the hazardous non biological agents and biological agents. Fungi are ubiquitous in distribution and are a serious threat to public health in indoor environments. In this communication, we have reviewed the current status on biotic indoor air pollution, role of fungi as biological contaminants and their impact on human health.     

不同生态环境对蒲公英超氧物歧化酶（SOD）的影响

选择干生,湿生,阳生,阴生四种生境中生长的蒲公英Taraxacum mongolicum Hand.-Mazz分根,叶,花分别测定了SOD活性和比活性,并比较了同工酶谱的变化情况,结果表明不同生境未能改变SOD的同工酶条带数,但对其活性大小有影响,这种影响尤其表现在根上,湿生和阴生根的SOD活性明显高于干生和阳生根的SOD活性,显示出蒲公英的不同器官适应不同的环境效应。     

The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics

We model the evolution of reaction norms focusing on three aspects: frequency-dependent selection arising from resource competition, maintenance and production costs of phenotypic plasticity, and three characteristics of environmental heterogeneity (frequency of environments, their intrinsic carrying capacity and the sensitivity to phenotypic maladaptation in these environments). We show that (i) reaction norms evolve so as to trade adaptation for acquiring resources against cost avoidance; (ii) maintenance costs cause reaction norms to better adapt to frequent rather than to infrequent environments, whereas production costs do not; and (iii) evolved reaction norms confer better adaptation to environments with low rather than with high intrinsic carrying capacity. The two previous findings contradict earlier theoretical results and originate from two previously unexplored features that are included in our model. First, production costs of phenotypic plasticity are only incurred when a given phenotype is actually produced. Therefore, they are proportional to the frequency of environments, and these frequencies thus affect the selection pressure to avoid costs just as much as the selection pressure to improve adaptation. This prevents the frequency of environments from affecting the evolving reaction norm. Secondly, our model describes the evolution of plasticity for a phenotype determining an individual's capability to acquire resources, and thus its realized carrying capacity. When individuals are distributed randomly across environments, they cannot avoid experiencing environments with intrinsically low carrying capacity. As selection pressures arising from the need to improve adaptation are stronger under such extreme conditions than under mild ones, better adaptation to environments with low rather than with high intrinsic carrying capacity results.     

Importance of adaptation and genotype × environment interactions in tropical beef breeding systems

This paper examines the relative importance of productive and adaptive traits in beef breeding systems based on Bos taurus and tropically adapted breeds across temperate and (sub)tropical environments. In the (sub)tropics, differences that exist between breeds in temperate environments are masked by the effects of environmental stressors. Hence in tropical environments, breeds are best categorised into breed types to compare their performance across environments. Because of the presence of environmental stressors, there are more sources of genetic variation in tropical breeding programmes. It is therefore necessary to examine the genetic basis of productive and adaptive traits for breeding programmes in those environments. This paper reviews the heritabilities and genetic relationships between economically important productive and adaptive traits relevant to (sub)tropical breeding programmes. It is concluded that it is possible to simultaneously genetically improve productive and adaptive traits in tropically adapted breeds of beef cattle grazed in tropical environments without serious detrimental consequences for either adaptation or production. However, breed-specific parameters are required for genetic evaluations. The paper also reviews the magnitude of genotype × environment (G × E) interactions impacting on production and adaptation of cattle, where 'genotype' is defined as breed (within a crossbreeding system), sire within breed (in a within-breed selection programme) or associations between economically important traits and single nucleotide polymorphisms (SNPs - within a marker-assisted selection programme). It is concluded that re-ranking of breeds across environments is best managed by the use of the breed type(s) best suited to the particular production environment. Re-ranking of sires across environments is apparent in poorly adapted breed types across extreme tropical and temperate environments or where breeding animals are selected in a temperate environment for use in the (sub)tropics. However, G × E interactions are unlikely to be of major importance in tropically adapted beef cattle grazed in either temperate or (sub)tropical environments, although sex × environment interactions may provide new opportunities for differentially selecting to simultaneously improve steer performance in benign environments and female performance in harsher environments. Early evidence suggests that re-ranking of SNPs occurs across temperate and tropical environments, although their magnitude is still to be confirmed in well-designed experiments. The major limitation to genetic improvement of beef cattle over the next decade is likely to be a deficiency of large numbers of accurately recorded phenotypes for most productive and adaptive traits and, in particular, for difficult-to-measure adaptive traits such as resistance to disease and environmental stressors.     

Mercury (micro)biogeochemistry in polar environments

The contamination of polar regions with mercury that is transported as inorganic mercury from lower latitudes has resulted in the accumulation of methylmercury in the food chain of polar environments, risking the health of humans and wildlife. This problem is likely to be particularly severe in coastal marine environments where active cycling occurs. Little is currently known about how mercury is methylated in polar environments. Relating observations on mercury deposition and transport through polar regions to knowledge of the microbiology of cold environments and considering the principles of mercury transformations as have been elucidated in temperate aquatic environments, we propose that in polar regions (1) variable pathways for mercury methylation may exist, (2) mercury bioavailability to microbial transformations may be enhanced, and (3) microbial niches within sea ice are sites where active microorganisms are localized in proximity to high concentrations of mercury. Thus, microbial transformations, and consequently mercury biogeochemistry, in the Arctic and Antarctic are both unique and common to these processes in lower latitudes, and understanding their dynamics is needed for the management of mercury-contaminated polar environments.     

Neurofunctional Correlates of Environmental Cognition: An fMRI Study with Images from Episodic Memory

This study capitalizes on individual episodic memories to investigate the question, how dif-ferent environments affect us on a neural level. Instead of using predefined environmental stimuli, this study relied on individual representations of beauty and pleasure. Drawing upon episodic memories we conducted two experiments. Healthy subjects imagined pleasant and non-pleasant environments, as well as beautiful and non-beautiful environments while neural activity was measured by using functional Magnetic Resonance Imaging. Although subjects found the different conditions equally simple to visualize, our results revealed more distribut-ed brain activations for non-pleasant and non-beautiful environments than for pleasant and beautiful environments. The additional regions activated in non-pleasant (left lateral prefrontal cortex) and non-beautiful environments (supplementary motor area, anterior cortical midline structures) are involved in self-regulation and top-down cognitive control. Taken together, the results show that perceptual experiences and emotional evaluations of environments within a positive and a negative frame of reference are based on distinct patterns of neural activity. We interpret the data in terms of a different cognitive and processing load placed by exposure to different environments. The results hint at the efficiency of subject-generated representations as stimulus material.     

Alternative partitioning of the genotype-by-environment interaction

Summary Alternative methods for partitioning the genotype-by-environment interaction, for an arbitrary number of genotypes or environments, were examined. Partitioning of the interaction is important in order to determine the nature of the interaction. Two methods of partitioning were examined; both separated the interaction into two types: (1) due to heterogeneous variances or (2) due to imperfect correlations. Method 1 was based on heterogeneity among environments in the scaling of differences among genotypes. Method 2 was based on heterogeneity among genotypes in the scaling of differences among environments. Any remaining interaction arises from deviations from the perfect positive correlation of genotypic rankings among environments (Method 1) or of environmental rankings among genotypes (Method 2). Method 1 is more appropriate for random genotypes that are to be tested in either fixed or random environments. With Method 1, the interactions that arise mainly from heterogeneity of genotypic scaling among environments are generally unimportant. However, if environments are fixed and interactions are mainly due to imperfect correlations of rankings, specialized lines may be indicated for each environment. Method 2 is more useful in evaluating fixed genotypes for sensitivity to random environments. A partitioning of the interaction into that due to the type of interaction within each genotype was shown to be useful in that situation.Journal Paper No. 123737 of the Purdue University Agricultural Experiment Station     

Genetic correlations and their dependence on environmental similarity—Insights from livestock data

Genetic correlations for a trait across environments are predicted to decrease as environments diverge. However, estimates of genetic correlations from natural populations are typically defined across a limited environmental range and prone to very large standard errors, making it difficult to test this prediction. We address the importance of environmental distance on genetic correlations by employing data from domestic cattle in which abundant and accurate estimates are available from a wide range of environments. Three production traits related to milk yield show a clear decrease in genetic correlations with increasing environmental divergence. This pattern was also evident for growth traits and other yield traits but not for traits related to reproduction, morphology, physiology, or disease. We suspect that this reflects weaker selection on these latter trait classes compared to production traits, or alternatively the effects of selection are constrained by unfavorable genetic correlations between traits. The results support the notion that traits that historically have been under strong directional selection in a small range of frequently encountered environments will evolve high genetic correlations across these environments, while exposure to uncommon (and dissimilar) environments lead to a reranking of gene effects and a decrease in genetic correlations across environments.     

Phenotypic Correlation of Juvenile Growth Rate between Different Consecutive foraging Environments in a Salmonid fish: A Field Experiment

Many organisms occupy considerably different environments during individual's lifespan. We are interested in how the phenotypic characteristics that are favourable in the earlier environment predict fitness in the later environment. High predictability of fitness between the two consecutive environments suggests that the either the same traits are favored in both environments, or that the favourable traits are genetically correlated. In this study, we ask how similarity of consecutive foraging environments affects the phenotypic correlation of juvenile brown trout growth rate. More specifically, we used a genetically narrow stock of hatchery-bred fish to contrast individual growth rates between high and low density hatchery environments, and thereafter between hatchery and natural lake environment. As expected, growth rate was highly dependent on the environment, and the fish showed considerable phenotypic plasticity. Furthermore, we found a strong positive correlation in growth rate between similar foraging environments, for example, between high and low density hatchery stocks, and between hatchery and a lake with small fish as main prey. However, hatchery growth did not predict growth rate in lakes where fish had to forage on bottom-dwelling invertebrates. Our results suggest that when the consecutive environments differed dramatically with respect to traits that fish use for foraging, relative performance of individual fish changed, earlier performance not being an accurate predictor of performance in the new environment. In this case, fitness of the fish was determined by an environment-specific set of traits that were not the same between the two consecutive environments. The result indicates that assessment of individual performance may be highly environment specific in trout. This revised version was published online in July 2006 with corrections to the Cover Date.     

Adaptation: "a critique of some current evolutionary thought"

In his classic Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought (1966), George Williams showed definitively that our understanding of adaptation, a central concept of evolutionary theory, must be gene-centered. The purpose of adaptations is to further the replication of genes. Genes are machines for turning out more genes; and adaptations are the means by which genes pluck resources from the world to promote this self-replication. Thus adaptations transform potential resources from part of the indifferent world-at-large into tailor-made environments, environments brimming with resources for organisms' distinctive adaptive needs. Systematically dif ferent adaptive problems therefore give rise to different environments; and so different species, for example, have different environments. Thus a gene-centered analysis of adaptations implies a gene-centered theory of environments. Without genes to specify what constitutes an environment, environments would not exist. Rather than being separate from biology, an autonomous, independent force, environments are themselves the products of biology. So a gene-centered view, far from depreciating the environment, furnishes a rich and precise understanding of its importance.     

Landscape classification and strategic assessment for conservation: an analysis of native cover loss in far south-east Australia

If two forest types are poorly related, their conservation status will have limited mutual relevance. Conversely, if two forest types are highly related, their conservation status will have substantial mutual relevance. The interpretation of measured conditions within any landscape class will be sensitive to conditions in other landscape classes in a region according to the strength of relations, or affinity, between them. This paper investigates the importance of recognising and accounting for relations between landscape classes in the context of assessing the conservation status of natural environments and in determining priorities for conservation. A typology of relations between landscape classes is presented and the concept of the 'relational profile' is introduced. The investigation is based on an analysis of native cover loss in environments identified in far south-east Australia. Environmental heterogeneity is defined in terms of climatic attributes which describe meso-scaled thermal and water resources distributions. Environment classes and relations between classes are defined and expressed using agglomerative clustering techniques. A comparison is made of two environments in the region that retain small proportions of extant natural cover, showing that very different conditions exist in the other environments to which they respectively relate. The study demonstrates that conclusions about the conservation status of environments and the identification of opportunities for environmental protection may depend on conditions in related environments and the strength of relations between these environments. The implications of the analysis for strategic assessment in conservation are discussed.     

Euryhalinity of Palaeozoic articulate brachiopods

OMonotypic and very low diversity virgianid shell beds from the Upper Ordovician to Lower Silurian dolomites of North Greenland were formed in marginal marine quiet-water hypersaline environments. In the light of this evidence the salinity tolerances of other Palaeozoic articulate brachiopods is evaluated. There are only a small number of species apparently invading hypersaline or brackish environments, but it is significant considering that previously all articulate brachiopods were thought to be fully marine. Two types of occurrence are noted, those species specifically related to marginally marine environments, disappearing with the introduction of fully marine faunas, and the majority of species which extend their normal marine range into marginal conditions. No brachiopod species appears to have invaded very hypersaline or truly brackish conditions. No single group of articulate brachiopods specifically specialised in colonising marginal marine environments, apart from possibly the virgianid pentamerids. Palaeozoic, Upper Ordovician, Lower Silurian, Brachiopoda. Pentamerida, Virgianidae, Greenland, palaeoecology. hypersaline environments, brackish environments .     

Spreading Speeds in Slowly Oscillating Environments

In this paper, we derive exact asymptotic estimates of the spreading speeds of solutions of some reaction-diffusion models in periodic environments with very large periods. Contrarily to the other limiting case of rapidly oscillating environments, there was previously no explicit formula in the case of slowly oscillating environments. The knowledge of these two extremes permits to quantify the effect of environmental fragmentation on the spreading speeds. On the one hand, our analytical estimates and numerical simulations reveal speeds which are higher than expected for Shigesada–Kawasaki–Teramoto models with Fisher-KPP reaction terms in slowly oscillating environments. On the other hand, spreading speeds in very slowly oscillating environments are proved to be 0 in the case of models with strong Allee effects; such an unfavorable effect of aggregation is merely seen in reaction-diffusion models.     

All eggs are not equal: the maternal environment affects progeny reproduction and developmental fate in Caenorhabditis elegans

Background

Maternal effects on progeny traits are common and these can profoundly alter progeny life history. Maternal effects can be adaptive, representing attempts to appropriately match offspring phenotype to the expected environment and are often mediated via trade-offs between progeny number and quality. Here we have investigated the effect of maternal food availability on progeny life history in the free-living nematode Caenorhabditis elegans.

Methodology/Principal Findings

The maternal environment affects both reproductive traits and progeny development. Comparisons of the progeny of worms from high and low maternal food environments indicates that low maternal food availability reduces progeny reproduction in good environments, increases progeny reproduction in poor environments and decreases the likelihood that progeny will develop as dauer larvae. These analyses also indicate that the effects on progeny are not a simple consequence of changes in maternal body size, but are associated with an increase in the size of eggs produced by worms at low maternal food availabilities.

Conclusions/Significance

These results indicate that the maternal environment affects both progeny reproduction and development in C. elegans and therefore that all progeny are not equal. The observed effects are consistent with changes to egg provisioning, which are beneficial in harsh environments, and of changes to progeny development, which are beneficial in harsh environments and detrimental in benign environments. These changes in progeny life history suggest that mothers in poor quality environments may be producing larger eggs that are better suited to poor conditions.     

DOES ENVIRONMENTAL ROBUSTNESS PLAY A ROLE IN FLUCTUATING ENVIRONMENTS?

Fluctuating environments are expected to select for individuals that have highest geometric fitness over the experienced environments. This leads to the prediction that genetically determined environmental robustness in fitness, and average fitness across environments should be positively genetically correlated to fitness in fluctuating environments. Because quantitative genetic experiments resolving these predictions are missing, we used a full‐sib, half‐sib breeding design to estimate genetic variance for egg‐to‐adult viability in Drosophila melanogaster exposed to two constant or fluctuating temperatures that were above the species’ optimum temperature, during development. Viability in two constant environments (25°C or 30°C) was used to estimate breeding values for environmental robustness of viability (i.e., reaction norm slope) and overall viability (reaction norm elevation). These breeding values were regressed against breeding values of viability at two different fluctuating temperatures (with a mean of 25°C or 30°C). Our results based on genetic correlations show that average egg‐to‐adult viability across different constant thermal environments, and not the environmental robustness, was the most important factor for explaining the fitness in fluctuating thermal environments. Our results suggest that the role of environmental robustness in adapting to fluctuating environments might be smaller than anticipated.     

Occurrence of hopanoid lipids in anaerobic Geobacter species

Geobacter metallireducens and G. sulfurreducens have been classified as strictly anaerobic bacteria which grow and thrive in subsurface and sediment environments. Hopanoids are pentacyclic triterpenoid lipids and are important for bacterial membrane stability and functioning. Hopanoids predominantly occur in aerobically growing bacteria of oxic environments. They rarely have been found in facultatively anaerobic bacteria and, to date, not at all in strict anaerobes. Our research shows that anaerobically grown G. metallireducens and G. sulfurreducens bacteria contain a range of hopanoid lipids, such as diploptene (i.e. hop-22(29)-ene) and hop-21-ene, and more complex, elongated hopanoids. In geological formations, diagenetic derivatives of hopanoids are widely used as biomarkers and are recognized as molecular fossils of bacterial origin. To date, these biomarkers have largely been interpreted as those derived from ancient oxic environments. Our findings presented here suggest that this interpretation needs to be re-evaluated. In addition to the origin in oxic environments, 'geohopanoids' may originate from ancient anaerobic environments as well.     

Variation in the strength of inbreeding depression across environments: Effects of stress and density dependence

In what types of environments should we expect to find strong inbreeding depression? Previous studies indicate that inbreeding depression, δ, is positively correlated with the stressfulness of the environment in which it is measured. However, it remains unclear why stress, per se, should increase δ. To our knowledge, only “competitive stress” has a logical connection to δ. Through competition for resources, better quality (outbred) individuals make the environment worse for lower quality (inbred) individuals, accentuating the differences between them. For this reason, we expect inbreeding depression to be stronger in environments where the fitness of individuals is more sensitive to the presence of conspecifics (i.e., where fitness is more density dependent). Indeed, some studies suggest a role for competition within environments, but this idea has not been tested in the context of understanding variation in δ across environments. Using Drosophila melanogaster, we estimated δ for viability in 22 different environments. These environments were simultaneously characterized for (1) stressfulness and (2) density dependence. Although stress and density dependence are moderately correlated with each other, inbreeding depression is much more strongly correlated with density dependence. These results suggest that mean selection across the genome is stronger in environments where competition is intense, rather than in environments that are stressful for other reasons.     

Conformational sampling of peptides in cellular environments

Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over alpha-helical conformations at the dipeptide level at and below dielectric constants of 5-10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at epsilon = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response.