Undermatching is an emergent property of selection by consequences

A computational theory of selection by consequences [McDowell, J.J, 2004. A computational model of selection by consequences. J. Exp. Anal. Behav. 81, 297-317] was tested by studying the responding of virtual organisms that were animated by the theory on random interval schedules of reinforcement. The theory generated responding by applying principles of selection, reproduction, and mutation to a population of potential behaviors that evolved in response to the selection pressure exerted by reinforcement. The organisms' equilibrium response rates were well described by the modern version of the Herrnstein hyperbola, which includes an exponent on reinforcement rate. Under strong selection pressure this exponent decreased with increasing mutation rate from a value near 1.0 at 1% mutation to an asymptotic value of 0.83 at mutation rates of 10% and greater. This asymptotic value is consistent with values obtained by fitting the equation to data from live organisms responding on single schedules, and with the value of about 0.80 that is expected on the basis of extensive research with live organisms responding on concurrent schedules. These results show that the computational theory is consistent with the modern theory of matching [McDowell, J.J, 2005. On the classic and modern theories of matching. J. Exp. Anal. Behav. 84, 111-127], and that it is a viable candidate for a mathematical dynamics of behavior.     

Essentiality is an emergent property of metabolic network wiring

The topological bases of essentiality in the yeast metabolic network from the perspective of double mutations are the subject of this study. A strong relationship between essentiality and the 'missing alternative' topological property is shown in terms of the presence of multiple genes synthesizing the same enzyme, supplementary enzymes participating in the same metabolic reaction, and availability of other pathways in the graph connecting the separated nodes after the knockouts. We demonstrate that the 'missing alternative' paradigm is sufficient to explain the generation of essentiality for double mutations in which each single deleted element is non-essential.     

Language evolution and an emergent property

Much debate has been stimulated by the recent hypothesis that human language consists of a faculty that is shared with non-human animals (faculty of language in a broad sense; FLB) and a faculty that is specific to human language (faculty of language in a narrow sense; FLN). This hypothesis has encouraged a tendency to emphasize one component of FLN: the cognitive operation of recursion. In consequence, non-syntactical, yet unique, aspects of human language have been neglected. One of these properties consists of vocal learning that enables an abundance of learned syllables. I suggest that FLN is not an independent faculty, but an 'emergent' property, arising from interactions between several other non-syntactical subfaculties of FLB, including vocal learning ability.     

The species concept as an emergent property of population biology

Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications.     

Invasibility as an emergent property of native metapopulation structure

Biological invasions constitute major threats to global biodiversity. Eco‐evolutionary considerations highlight the importance of contemporary evolution in community responses to bioinvasions. However, effects of metapopulation structure on invasion success have been mostly overlooked even though metapopulation structure determines gene flow and is likely to affect evolutionary processes. Here, we investigate a stepping‐stone model with evolving alien native interaction strengths. We demonstrate analytically that the site of invasion can determine the success of an invading consumer because gene flow and demography of a local resource species interact to obstruct local resource adaptation. Our main results are 1) that invasion success is more likely in genetic sink populations of the native species and 2) that invasion is more likely to occur against the migrational flow of native species. These findings suggest that invasibility is best regarded as an emergent property not only of communities but of entire metapopulations. Since migration networks of aliens and natives are often mismatched due to anthropogenic interference, our results indicate how population structure eases the spread of invasives against the migrational flow of natives.     

Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite

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一株MAs (III)脱甲基菌株的分离及功能基因的研究

[目的] 分离并鉴定三价单甲基砷（MAs （III））脱甲基菌株,对MAs （III）脱甲基菌FJ-6中arsI基因进行克隆表达,并对arsI基因表达蛋白进行功能鉴定。[方法] 利用富集培养的方法分离MAs （III）脱甲基菌株,并通过形态学、生理生化特征和16S rDNA基因进化分析进行鉴定;HPLC-ICP-MS鉴定菌株转化MAs （III）的产物为三价砷（As （III））,对菌株FJ-6的基因组进行生物信息学分析,寻找潜在的MAs （III）脱甲基酶编码基因,通过PCR扩增获得arsI全长基因,构建重组质粒pET29a-arsI,转化大肠杆菌BL21（DE3）菌株进行异源表达,通过Ni²⁺-NTA亲和层析柱纯化异源表达的蛋白,以MAs （III）为反应底物,检测MAs （III）脱甲基酶ArsI的酶学特性。通过实时定量PCR观察arsI的表达类型。[结果] Bacillus aryabhattai FJ-6在12 h内能将1 μmol/L MAs （III）完全转化为As （III）。克隆得到MAs （III）脱甲基酶表达基因arsI,构建了pET29a-arsI重组质粒并进行了表达,ArsI蛋白分子量为17.4 kDa。ArsI纯化蛋白具有较高的MAs （III）脱甲基酶的活性;荧光定量PCR实验结果表明arsI受砷诱导表达。[结论] 明确了ArsI蛋白具有MAs （III）脱甲基酶活性。     

The dynamic genetic repertoire of microbial communities

Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity.     

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.     

Mobility as an emergent property of biological organization: Insights from experimental evolution

Anthropologists accept that mobility is a critical dimension of human culture, one that links economy, technology, and social relations. Less often acknowledged is that mobility depends on complex and dynamic interactions between multiple levels of our biological organization, including anatomy, physiology, neurobiology, and genetics. Here, we describe a novel experimental approach to examining the biological foundations of mobility, using mice from a long‐term artificial selection experiment for high levels of voluntary exercise on wheels. In this experiment, mice from selectively bred lines have evolved to run roughly three times as far per day as those from nonselected control lines. We consider three insights gleaned from this experiment as foundational principles for the study of mobility from the perspective of biological evolution. First, an evolutionary change in mobility will necessarily be associated with alterations in biological traits both directly and indirectly connected to mobility. Second, changing mobility will result in trade‐offs and constraints among some of the affected traits. Third, multiple solutions exist to altering mobility, so that various combinations of adjustments to traits linked with mobility can achieve the same overall behavioral outcome. We suggest that anthropological knowledge of variation in human mobility might be improved by greater research attention to its biological dimensions.     

台风利奇马对城市淡水系统中微生物群落和抗生素耐药性基因的影响

【背景】极端天气事件(如台风)带来的强风和降水,会给水生生态系统造成短暂和持久的影响。然而,很少有研究关注台风对水生微生物群落和抗生素耐药性基因(antibiotic resistance genes,ARGs)的影响。【目的】对台风前后城市淡水水域的微生物群落和抗性基因组成进行研究分析,更好地认识极端天气对淡水生态系统的干扰。【方法】在台风前后从4个地点采集了水样,通过宏基因组分析,检测了台风利奇马对温州休闲水域微生物群落和抗性基因的影响。除水生微生物群落和抗性基因外,还分析了每个采样点的物理、化学参数,包括温度、pH、溶解氧、叶绿素a、可溶性活性磷、硝酸盐、亚硝酸盐和铵。【结果】台风登陆后,大多数地点的pH、溶解氧和叶绿素a都有所增加。然而,台风对九山湖的影响要弱于对三垟湿地的影响。台风登陆后,变形菌门、蓝菌门和拟杆菌门的相对丰度增加,而放线菌门的相对丰度下降。在属水平上,栖湖菌的微生物多样性和相对丰度显著增加。在所有的环境因子中,铵是影响微生物群落结构的最重要的环境因子。另外,在所有样本中均检测到35个机会性致病菌类群。台风后,铜绿假单胞菌的相对丰度增加。ARGs显示了空间(采样点间)和时间(台风前后)的变化。冗余分析表明,水总无机氮是影响抗性基因分布的主要环境因子。【结论】这些发现为极端天气(如台风)如何影响淡水系统中的微生物群落和抗性基因提供了新的见解。台风登陆增加了城市淡水系统的公共安全风险,因此,检验检疫方法和手段应该前移,加强对环境健康安全的评价和分析,这将有助于减轻抗生素耐药性和致病菌扩散的风险。     

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched‐leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not ‘picky’ eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non‐endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation.     

Life-history strategies of soil microbial communities in an arid ecosystem

The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.Subject terms: Microbial ecology, Community ecology     

Compost-induced suppression of Pythium damping-off is mediated by fatty-acid-metabolizing seed-colonizing microbial communities

Leaf composts were studied for their suppressive effects on Pythium ultimum sporangium germination, cottonseed colonization, and the severity of Pythium damping-off of cotton. A focus of the work was to assess the role of fatty-acid-metabolizing microbial communities in disease suppression. Suppressiveness was expressed within the first few hours of seed germination as revealed by reduced P. ultimum sporangium germination, reduced seed colonization, and reduced damping-off in transplant experiments. These reductions were not observed when cottonseeds were sown in a conducive leaf compost. Microbial consortia recovered from the surface of cottonseeds during the first few hours of germination in suppressive compost (suppressive consortia) induced significant levels of damping-off suppression, whereas no suppression was induced by microbial consortia recovered from cottonseeds germinated in conducive compost (conducive consortia). Suppressive consortia rapidly metabolized linoleic acid, whereas conducive consortia did not. Furthermore, populations of fatty-acid-metabolizing bacteria and actinobacteria were higher in suppressive consortia than in conducive consortia. Individual bacterial isolates varied in their ability to metabolize linoleic acid and protect seedlings from damping-off. Results indicate that communities of compost-inhabiting microorganisms colonizing cottonseeds within the first few hours after sowing in a Pythium-suppressive compost play a major role in the suppression of P. ultimum sporangium germination, seed colonization, and damping-off. Results further indicate that fatty acid metabolism by these seed-colonizing bacterial consortia can explain the Pythium suppression observed.     

A multifactorial analysis of the combined action of an antibiotic and a low-molecular immunomodulator of microbial origin in experimental plague infection

The combined effect of doxycycline and a low molecular weight immunomodulator of microbial origin was studied in experimental plague infection with mathematical design of the experiment. Synergism of the action of the antibiotic and immunomodulator used in subtherapeutic doses was observed. The action was the most pronounced when the drugs were applied therapeutically. On the basis of the multifactorial analysis the regimens for the use of the antibiotic and immunomodulator were optimized.     

The sum is greater than the parts: exploiting microbial communities to achieve complex functions

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Toward an understanding of microbial communities through analysis of communication networks

Bacteria receive signals from diverse members of their biotic environment. They sense their own species through the process of quorum sensing, which detects the density of bacterial cells and regulates functions such as bioluminescence, virulence, and competence. Bacteria also respond to the presence of other microorganisms and eukaryotic hosts. Most studies of microbial communication focus on signaling between the microbe and one other organism for empirical simplicity and because few experimental systems offer the opportunity to study communication among various types of organisms. But in the real biological world, microorganisms must carry on multiple molecular conversations simultaneously between diverse organisms, thereby constructing communication networks. We propose that biocontrol of plant disease, the process of suppressing disease through application of a microorganism, offers a model for the study of communication among multiple organisms. Successful biocontrol requires the sending and receiving of signals between the biocontrol agent and the pathogen, plant host, and microbial community surrounding the host. We are using Bacillus cereus, a biocontrol agent, and the organisms it must interact with, to dissect a communication network. This system offers an excellent starting point for study because its members are defined and well studied. An understanding of signaling in the B. cereus biocontrol system may provide a model for network communication among organisms that share a habitat and provide a new angle of analysis for understanding the interconnections that define communities. This revised version was published online in August 2006 with corrections to the Cover Date.