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Evolutionary Biology
Intensifying postfire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot
Apr 18, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Slingsby JA, Merow C, Aiello-Lammens M, Allsopp N, Hall S, Kilroy Mollmann H, Turner R, Wilson AM, Silander JA
Intensifying postfire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot
Apr 18, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Prolonged periods of extreme heat or drought in the first year after fire affect the resilience and diversity of fire-dependent ecosystems by inhibiting seed germination or increasing mortality of seedlings and resprouting individuals. This interaction between weather and fire is of growing concern as climate changes, particularly in systems subject to stand-replacing crown fires, such as most Mediterranean-type ecosystems. We examined the longest running set of permanent vegetation plots in the Fynbos of South Africa (44 y), finding a significant decline in the diversity of plots driven by increasingly severe postfire summer weather events (number of consecutive days with high temperatures and no rain) and legacy effects of historical woody alien plant densities 30 y after clearing. Species that resprout after fire and/or have graminoid or herb growth forms were particularly affected by postfire weather, whereas all species were sensitive to invasive plants. Observed differences in the response of functional types to extreme postfire weather could drive major shifts in ecosystem structure and function such as altered fire behavior, hydrology, and carbon storage. An estimated 0.5 °C increase in maximum temperature tolerance of the species sets unique to each survey further suggests selection for species adapted to hotter conditions. Taken together, our results show climate change impacts on biodiversity in the hyperdiverse Cape Floristic Region and demonstrate an important interaction between extreme weather and disturbance by fire that may make flammable ecosystems particularly sensitive to climate change.
Biochemical, Cellular, Physiological and Pathological Consequences of Human loss of N-glycolylneuraminic Acid
Apr 19, 2017   Chembiochem : A European Journal Of Chemical Biology
Okerblom J, Varki A
Biochemical, Cellular, Physiological and Pathological Consequences of Human loss of N-glycolylneuraminic Acid
Apr 19, 2017
Chembiochem : A European Journal Of Chemical Biology
About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation via female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzees. While the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxyl groups at most cell surfaces remains poorly understood, there are multi-scale effects functionally relevant to both sides of the host-pathogen interface. Hominin CMAH loss may also contribute to understanding human evolution, at a time where our ancestors were starting stone tool use, increasing their consumption of meat, and possibly hunting. Comparisons with chimpanzees within ethical and practical limitations have revealed some consequences of human CMAH loss, but more has been learned using a mouse model with a human-like Cmah inactivation. For example, such mice can develop antibodies against Neu5Gc that could affect inflammatory processes like cancer progression in the face of Neu5Gc metabolic incorporation from red meats, display a hyper-reactive immune system, a human-like tendency for delayed wound healing, late onset hearing loss, insulin resistance, susceptibility to muscular dystrophy pathologies, and increased sensitivity to multiple human-adapted pathogens involving sialic acids. Further studies in such mice may provide a model for other human-specific processes and pathologies involving sialic acid biology that have yet to be explored. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Natural hybridization and reproductive isolation between two Primula species
Apr 21, 2017   Journal Of Integrative Plant Biology
Xie Y, Zhu X, Ma Y, Zhao J, Li L, Li Q
Natural hybridization and reproductive isolation between two Primula species
Apr 21, 2017
Journal Of Integrative Plant Biology
Natural hybridization frequently occurs in plants and can facilitate gene flow between species, possibly resulting in species refusion. However, various reproductive barriers block the formation of hybrids and maintain species integrity. Here, we conducted a field survey to examine natural hybridization and reproductive isolation (RI) between sympatric populations of Primula secundiflora and P. poissonii using ten nuclear simple sequence repeat (SSR) loci. Although introgressive hybridization occurred, species boundaries between P. secundiflora and P. poissonii were maintained through nearly complete reproductive isolation. These interfertile species provide an excellent model for studying the RI mechanisms and evolutionary forces that maintain species boundaries. This article is protected by copyright. All rights reserved.
Ancestral legacy effects
Apr 21, 2017   Science (New York, N.Y.)
Purnell BA
Ancestral legacy effects
Apr 21, 2017
Science (New York, N.Y.)
Drivers of salamander extirpation mediated by Batrachochytrium salamandrivorans
Apr 20, 2017   Nature Add nature.com free-link Cancel
Stegen G, Pasmans F, Schmidt BR, Rouffaer LO, Van Praet S, Schaub M, Canessa S, Laudelout A, Kinet T, Adriaensen C, Haesebrouck F, Bert W, Bossuyt F, Martel A
Drivers of salamander extirpation mediated by Batrachochytrium salamandrivorans
Apr 20, 2017
Nature
The recent arrival of Batrachochytrium salamandrivorans in Europe was followed by rapid expansion of its geographical distribution and host range, confirming the unprecedented threat that this chytrid fungus poses to western Palaearctic amphibians. Mitigating this hazard requires a thorough understanding of the pathogen's disease ecology that is driving the extinction process. Here, we monitored infection, disease and host population dynamics in a Belgian fire salamander (Salamandra salamandra) population for two years immediately after the first signs of infection. We show that arrival of this chytrid is associated with rapid population collapse without any sign of recovery, largely due to lack of increased resistance in the surviving salamanders and a demographic shift that prevents compensation for mortality. The pathogen adopts a dual transmission strategy, with environmentally resistant non-motile spores in addition to the motile spores identified in its sister species B. dendrobatidis. The fungus retains its virulence not only in water and soil, but also in anurans and less susceptible urodelan species that function as infection reservoirs. The combined characteristics of the disease ecology suggest that further expansion of this fungus will behave as a 'perfect storm' that is able to rapidly extirpate highly susceptible salamander populations across Europe.
Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes
Apr 20, 2017   Scientific Reports
Wu Y, Wang H, Hadly EA
Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes
Apr 20, 2017
Scientific Reports
Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.
Sequencing of blaIMP-Carrying IncN2 Plasmids, and Comparative Genomics of IncN2 Plasmids Harboring Class 1 Integrons
Apr 20, 2017   Frontiers In Cellular And Infection Microbiology
Jiang X, Yin Z, Yin X, Fang H, Sun Q, Tong Y, Xu Y, Zhang D, Feng J, Chen W, Song Y, Wang J, Chen S, Zhou D
Sequencing of blaIMP-Carrying IncN2 Plasmids, and Comparative Genomics of IncN2 Plasmids Harboring Class 1 Integrons
Apr 20, 2017
Frontiers In Cellular And Infection Microbiology
This work presents the complete nucleotide sequences of p0801-IMP from Klebsiella pneumoniae, p7121-IMP from K. oxytoca, and p17285-IMP from Citrobacter freundii, which are recovered from three different cases of nosocomial infection. These three plasmids represent the first fully sequenced blaIMP-carrying IncN2 plasmids. Further comparative genomics analysis of all the five integron-carrying IncN2 plasmids p0801-IMP, p7121-IMP, p17285-IMP, pJIE137, and p34983-59.134kb indicates that they possess conserved IncN2 backbones with limited genetic variations with respect to gene content and organization. Four class 1 integrons (blaIMP-1-carrying In1223 in p0801-IMP/p7121-IMP, blaIMP-8-carrying In655 in p17285-IMP, In27 in pJIE137, and In1130 in p34983-59.134kb), two insertion sequence-based transposition units (ISEcp1-orfRA1-14 in p17285-IMP, and ISEcp1-blaCTX-M-62-Δorf477-orfRA1-14 in pJIE137), and a novel Tn1696-related transposon Tn6325 carrying In1130 in p34983-59.134kb are indentified in the plasmid accessory regions. In1223 and In655 represent ancestral Tn402-associated integrons, while In27 and In1130 belong to complex class 1 integrons. The relatively small IncN2 backbones are able to integrate different mobile elements which carry various resistance markers, promoting the accumulation and spread of antimicrobial resistance genes among enterobacterial species.
Landscape Population Genomics of Forsythia (Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species
Apr 20, 2017   Frontiers In Plant Science
Yang J, Miao CY, Mao RL, Li Y
Landscape Population Genomics of Forsythia (Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species
Apr 20, 2017
Frontiers In Plant Science
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F. suspensa exist resulting from divergent selection driven by seven environmental variables. A total of 26 outlier loci were identified by both BayeScan and FDIST2, 23 of which were environment-associated loci (EAL). Environmental association analysis revealed that the environmental variables related to the ecological habitats of F. suspensa are associated with high numbers of EAL. Results of EAL characterization in F. suspensa are consistent with the hypothesis that ecological habitats determine the adaptive evolution of this species. Moreover, a model of species adaptation to environmental variables was proposed in this study. The adaptation model was used to further evaluate the adaptation status of F. suspensa to environmental variables. This study will be useful to help us in understanding the adaptive evolution of species in regions lacking strong selection pressure.
Size-Mediated Interaction between a Cushion Species and Other Non-cushion Species at High Elevations of the Hengduan Mountains, SW China
Apr 20, 2017   Frontiers In Plant Science
Yang Y, Chen JG, Schöb C, Sun H
Size-Mediated Interaction between a Cushion Species and Other Non-cushion Species at High Elevations of the Hengduan Mountains, SW China
Apr 20, 2017
Frontiers In Plant Science
Arenaria polytrichoides (Caryophyllaceae) is a common cushion plant occurring at high elevations in the Himalaya-Hengduan Mountains, SW China. It frequently has other non-cushion species growing within its canopy, forming a contrast with the surrounding areas because it creates patches of higher diversity and greater biomass. In this study, we examined the relationship between the cushions and associated non-cushion species along a gradient of cushion size. A total of 200 A. polytrichoides individuals were selected to fit four size classes. Field measurements were carried out to assess canopy structure, functional traits relevant to growth and reproduction, and soil quality below cushions along the size gradient. Furthermore, the size effect of cushions on the richness and abundance of species and biomass production was also examined. All the morphological variables examined exhibited a positive correlation with cushion size, as did the nutrients under cushions. Large and compact cushions were associated with higher soil nutrient contents compared with small and loose cushions. As a result of these biogenic environmental changes, there was a stronger facilitation effect performed by large cushions. Data pertaining to functional traits revealed that large cushions benefit from the enhanced resources within their compact structure and exhibit greater fitness and a higher reproductive output than small cushions. Our data indicated that interactions occur between cushion species and other plants depending on the size of the cushions, probably because of the greater heterogeneity of conditions beneath larger cushions. These findings provide a clear demonstration of the generally overlooked importance of the traits of nurse plants, such as size and age, in terms of their facilitative effects.
The genetic basis of parental care evolution in monogamous mice
Apr 20, 2017   Nature Add nature.com free-link Cancel
Bendesky A, Kwon YM, Lassance JM, Lewarch CL, Yao S, Peterson BK, He MX, Dulac C, Hoekstra HE
The genetic basis of parental care evolution in monogamous mice
Apr 20, 2017
Nature
Parental care is essential for the survival of mammals, yet the mechanisms underlying its evolution remain largely unknown. Here we show that two sister species of mice, Peromyscus polionotus and Peromyscus maniculatus, have large and heritable differences in parental behaviour. Using quantitative genetics, we identify 12 genomic regions that affect parental care, 8 of which have sex-specific effects, suggesting that parental care can evolve independently in males and females. Furthermore, some regions affect parental care broadly, whereas others affect specific behaviours, such as nest building. Of the genes linked to differences in nest-building behaviour, vasopressin is differentially expressed in the hypothalamus of the two species, with increased levels associated with less nest building. Using pharmacology in Peromyscus and chemogenetics in Mus, we show that vasopressin inhibits nest building but not other parental behaviours. Together, our results indicate that variation in an ancient neuropeptide contributes to interspecific differences in parental care.
Individual variation in local interaction rules can explain emergent patterns of spatial organization in wild baboons
Apr 20, 2017   Proceedings. Biological Sciences
Farine DR, Strandburg-Peshkin A, Couzin ID, Berger-Wolf TY, Crofoot MC
Individual variation in local interaction rules can explain emergent patterns of spatial organization in wild baboons
Apr 20, 2017
Proceedings. Biological Sciences
Researchers have long noted that individuals occupy consistent spatial positions within animal groups. However, an individual's position depends not only on its own behaviour, but also on the behaviour of others. Theoretical models of collective motion suggest that global patterns of spatial assortment can arise from individual variation in local interaction rules. However, this prediction remains untested. Using high-resolution GPS tracking of members of a wild baboon troop, we identify consistent inter-individual differences in within-group spatial positioning. We then apply an algorithm that identifies what number of conspecific group members best predicts the future location of each individual (we call this the individual's neighbourhood size) while the troop is moving. We find clear variation in the most predictive neighbourhood size, and this variation relates to individuals' propensity to be found near the centre of their group. Using simulations, we show that having different neighbourhood sizes is a simple candidate mechanism capable of linking variation in local individual interaction rules-in this case how many conspecifics an individual interacts with-to global patterns of spatial organization, consistent with the patterns we observe in wild primates and a range of other organisms. © 2017 The Authors.
Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales)
Apr 20, 2017   BMC Evolutionary Biology
Song J, Cui BK
Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales)
Apr 20, 2017
BMC Evolutionary Biology
The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU). Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area. Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.
Compromised External Validity: Federally Produced Cannabis Does Not Reflect Legal Markets
Apr 19, 2017   Scientific Reports
Vergara D, Bidwell LC, Gaudino R, Torres A, Du G, Ruthenburg TC, deCesare K, Land DP, Hutchison KE, Kane NC
Compromised External Validity: Federally Produced Cannabis Does Not Reflect Legal Markets
Apr 19, 2017
Scientific Reports
As the most widely used illicit drug worldwide, and as a source of numerous under-studied pharmacologically-active compounds, a precise understanding of variability in psychological and physiological effects of Cannabis varieties is essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer of Cannabis for use in US research studies. We sought to compare the chemical profiles of Cannabis varieties that are available to consumers in states that have state-legalized use versus what is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally-produced Cannabis has significantly less variety and lower concentrations of cannabinoids than are observed in state-legal U.S. dispensaries. Most dramatically, NIDA's varieties contain only 27% of the THC levels and as much as 11-23 times the Cannabinol (CBN) content compared to what is available in the state-legal markets. Research restricted to using the current range of federally-produced Cannabis thus may yield limited insights into the chemical, biological and pharmacological properties, and medical potential of material that is available in the state markets. Investigation is urgently needed on the full diversity of Cannabis chemotypes known to be available to the public.
Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
Apr 18, 2017   Molecular Ecology Resources
Singhal S, Grundler M, Colli G, Rabosky DL
Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
Apr 18, 2017
Molecular Ecology Resources
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE, and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci (SqCL) set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically-disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness, and suggest areas for future improvement. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Arabidopsis 14-3-3 epsilon members contribute to polarity of PIN auxin carrier and auxin transport-related development
Apr 19, 2017   ELife
Keicher J, Jaspert N, Weckermann K, Möller C, Throm C, Kintzi A, Oecking C
Arabidopsis 14-3-3 epsilon members contribute to polarity of PIN auxin carrier and auxin transport-related development
Apr 19, 2017
ELife
Eukaryotic 14-3-3 proteins have been implicated in the regulation of diverse biological processes by phosphorylation-dependent protein-protein interactions. The Arabidopsis genome encodes two groups of 14-3-3s, one of which - epsilon - is thought to fulfill conserved cellular functions. Here, we assessed the in vivo role of the ancestral 14-3-3 epsilon group members. Their simultaneous and conditional repression by RNA interference and artificial microRNA in seedlings led to altered distribution patterns of the phytohormone auxin and associated auxin transport-related phenotypes, such as agravitropic growth. Moreover, 14-3-3 epsilon members were required for pronounced polar distribution of PIN-FORMED auxin efflux carriers within the plasma membrane. Defects in defined post-Golgi trafficking processes proved causal for this phenotype and might be due to lack of direct 14-3-3 interactions with factors crucial for membrane trafficking. Taken together, our data demonstrate a fundamental role for the ancient 14-3-3 epsilon group members in regulating PIN polarity and plant development.
Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus
Apr 19, 2017   Frontiers In Microbiology
Novakova E, Woodhams DC, Rodríguez-Ruano SM, Brucker RM, Leff JW, Maharaj A, Amir A, Knight R, Scott J
Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus
Apr 19, 2017
Frontiers In Microbiology
Symbiotic microbial communities augment host phenotype, including defense against pathogen carriage and infection. We sampled the microbial communities in 11 adult mosquito host species from six regions in southern Ontario, Canada over 3 years. Of the factors examined, we found that mosquito species was the largest driver of the microbiota, with remarkable phylosymbiosis between host and microbiota. Seasonal shifts of the microbiome were consistently repeated over the 3-year period, while region had little impact. Both host species and seasonal shifts in microbiota were associated with patterns of West Nile virus (WNV) in these mosquitoes. The highest prevalence of WNV, with a seasonal spike each year in August, was in the Culex pipiens/restuans complex, and high WNV prevalence followed a decrease in relative abundance of Wolbachia in this species. Indeed, mean temperature, but not precipitation, was significantly correlated with Wolbachia abundance. This suggests that at higher temperatures Wolbachia abundance is reduced leading to greater susceptibility to WNV in the subsequent generation of C. pipiens/restuans hosts. Different mosquito genera harbored significantly different bacterial communities, and presence or abundance of Wolbachia was primarily associated with these differences. We identified several operational taxonomic units (OTUs) of Wolbachia that drive overall microbial community differentiation among mosquito taxa, locations and timepoints. Distinct Wolbachia OTUs were consistently found to dominate microbiomes of Cx. pipiens/restuans, and of Coquilletidia perturbans. Seasonal fluctuations of several other microbial taxa included Bacillus cereus, Enterococcus, Methylobacterium, Asaia, Pantoea, Acinetobacter johnsonii, Pseudomonas, and Mycoplasma. This suggests that microbiota may explain some of the variation in vector competence previously attributed to local environmental processes, especially because Wolbachia is known to affect carriage of viral pathogens.
Memory-n strategies of direct reciprocity
Apr 19, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Hilbe C, Martinez-Vaquero LA, Chatterjee K, Nowak MA
Memory-n strategies of direct reciprocity
Apr 19, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.
Natural Resource Landscapes of a Marine Bacterium Reveal Distinct Fitness-Determining Genes Across the Genome
Apr 18, 2017   Environmental Microbiology
Takemura AF, Corzett CH, Hussain F, Arevalo P, Datta M, Yu X, Le Roux F, Polz MF
Natural Resource Landscapes of a Marine Bacterium Reveal Distinct Fitness-Determining Genes Across the Genome
Apr 18, 2017
Environmental Microbiology
Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness tradeoff for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different habitats natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes. This article is protected by copyright. All rights reserved. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.
Decomposing functional trait associations in a Chinese subtropical forest
Apr 18, 2017   PloS One
Li X, Pei K, Kéry M, Niklaus PA, Schmid B
Decomposing functional trait associations in a Chinese subtropical forest
Apr 18, 2017
PloS One
Functional traits, properties of organisms correlated with ecological performance, play a central role in plant community assembly and functioning. To some extents, functional traits vary in concert, reflecting fundamental ecological strategies. While "trait syndromes" characteristic of e.g. fast-growing, early-successional vs. competitive, late-successional species are recognized in principle, less is known about the environmental and genetic factors at the source of trait variation and covariation within plant communities. We studied the three leaf traits leaf half-life (LHL), leaf mass per area (LMA) and nitrogen concentration in green leaves (Ngreen) and the wood trait wood density (WD) in 294 individuals belonging to 45 tree or shrub species in a Chinese subtropical forest from September 2006 to January 2009. Using multilevel ANOVA and decomposition of sums of products, we estimated the amount of trait variation and covariation among species (mainly genetic causes), i.e. plant functional type (deciduous vs. evergreen species), growth form (tree vs. shrub species), family/genus/species differences, and within species (mainly environmental causes), i.e. individual and season. For single traits, the variation between functional types and among species within functional types was large, but only LMA and Ngreen varied significantly among families and thus showed phylogenetic signal. Trait variation among individuals within species was small, but large temporal variation due to seasonal effects was found within individuals. We did not find any trait variation related to soil conditions underneath the measured individuals. For pairs of traits, variation between functional types and among species within functional types was large, reflecting a strong evolutionary coordination of the traits, with LMA, LHL and WD being positively correlated among each other and negatively with Ngreen. This integration of traits was consistent with a putative stem-leaf economics spectrum ranging from deciduous species with thin, high-nitrogen leaves and low-density wood to evergreen species with thick, low-nitrogen leaves and dense wood and was not influenced by phylogenetic history. Trait coordination within species was weak, allowing individual trees to deviate from the interspecific trait coordination and thus respond flexibly to environmental heterogeneity. Our findings suggest that within a single woody plant community variation and covariation in functional traits allows a large number of species to co-exist and cover a broad spectrum of multivariate niche space, which in turn may increase total resource extraction by the community and community functioning.
A distinct cutaneous microbiota pofile in autoimmune bullous disease patients
Apr 18, 2017   Experimental Dermatology
Miodovnik M, Künstner A, Langan EA, Zillikens D, Gläser R, Sprecher E, Baines JF, Schmidt E, Ibrahim SM
A distinct cutaneous microbiota pofile in autoimmune bullous disease patients
Apr 18, 2017
Experimental Dermatology
Bullous Pemphigoid (BP) is the most common autoimmune blistering disease in Europe. As both the incidence of the disease and the relative proportion of the elderly population continue to rise, it represents a significant medical burden. Whereas some progress has been achieved in defining genetic risk factors for autoimmune blistering diseases, no environmental agent has been conclusively identified. Emerging evidence suggests that host immunity may influence the skin microbiota while the latter modulates cutaneous immunity. Nevertheless, the relationship between skin microbial communities and autoimmune bullous disease has yet to be studied in humans. Here, we aim to characterize and compare the skin microbiome of BP patients and healthy, age-matched controls at numerous body sites. Similar to what has been shown in healthy controls, the composition of skin microbiota in BP patients appears to be very divergent and site-specific. Microbial phylum abundances differ between perilesional sites of BP patients and the same anatomic locations of control patients. A distinct cutaneous microbiota profile, which correlates with BP, further strengthens the significance of commensal-host interaction on our immune system. Moreover, these results raise the possibility that the cutaneous microbiome may contribute to the pathogenesis of BP, with important implications for the treatment of this disease. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues
Apr 18, 2017   ELife
Fidler AL, Darris CE, Chetyrkin SV, Pedchenko VK, Boudko SP, Brown KL, Gray Jerome W, Hudson JK, Rokas A, Hudson BG
Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues
Apr 18, 2017
ELife
The role of the cellular microenvironment in enabling metazoan tissue genesis remains obscure. Ctenophora has recently emerged as one of the earliest-branching extant animal phyla, providing a unique opportunity to explore the evolutionary role of the cellular microenvironment in tissue genesis. Here, we characterized the extracellular matrix (ECM), with a focus on collagen IV and its variant, spongin short-chain collagens, of non-bilaterian animal phyla. We identified basement membrane (BM) and collagen IV in Ctenophora, and show that the structural and genomic features of collagen IV are homologous to those of non-bilaterian animal phyla and Bilateria. Yet, ctenophore features are more diverse and distinct, expressing up to twenty genes compared to six in vertebrates. Moreover, collagen IV is absent in unicellular sister-groups. Collectively, we conclude that collagen IV and its variant, spongin, are primordial components of the extracellular microenvironment, and as a component of BM, collagen IV enabled the assembly of a fundamental architectural unit for multicellular tissue genesis.
The phenology of leaf quality and its within-canopy variation are essential for accurate modeling of photosynthesis in tropical evergreen forests
Apr 18, 2017   Global Change Biology
Wu J, Serbin SP, Xu X, Albert LP, Chen M, Meng R, Saleska SR, Rogers A
The phenology of leaf quality and its within-canopy variation are essential for accurate modeling of photosynthesis in tropical evergreen forests
Apr 18, 2017
Global Change Biology
Leaf quantity (i.e. canopy leaf area index, LAI), quality (i.e. per-area photosynthetic capacity), and longevity all influence the photosynthetic seasonality of tropical evergreen forests. However, these components of tropical leaf phenology are poorly represented in most terrestrial biosphere models (TBMs). Here, we explored alternative options for the representation of leaf phenology effects in TBMs that employ the Farquahar, von Caemmerer & Berry (FvCB) representation of CO2 assimilation. We developed a two-fraction leaf (sun and shade), two-layer canopy (upper and lower) photosynthesis model to evaluate different modeling approaches and assessed three components of phenological variations (i.e. leaf quantity, quality, and within-canopy variation in leaf longevity). Our model was driven by the prescribed seasonality of leaf quantity and quality derived from ground based measurements within an Amazonian evergreen forest. Modeled photosynthetic seasonality was not sensitive to leaf quantity, but was highly sensitive to leaf quality and its vertical distribution within the canopy, with markedly more sensitivity to upper canopy leaf quality. This is because light absorption in tropical canopies is near maximal for the entire year, implying that seasonal changes in LAI have little impact on total canopy light absorption; and because leaf quality has a greater effect on photosynthesis of sunlit leaves than light limited, shade leaves and sunlit foliage are more abundant in the upper canopy. Our two-fraction leaf, two-layer canopy model which accounted for all three phenological components was able to simulate photosynthetic seasonality, explaining ~90% of the average seasonal variation in eddy covariance derived CO2 assimilation. This work identifies a parsimonious approach for representing tropical evergreen forest photosynthetic seasonality in TBMs that utilize the FvCB model of CO2 assimilation, and highlights the importance of incorporating more realistic phenological mechanisms in models that seek to improve the projection of future carbon dynamics in tropical evergreen forests. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease
Apr 18, 2017   The New Phytologist
Koskella B, Meaden S, Crowther WJ, Leimu R, Metcalf CJE
A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease
Apr 18, 2017
The New Phytologist
Host susceptibility to pathogens can be shaped by genetic, ecological, and evolutionary factors. The ability to predict the spread of disease therefore requires an integrated understanding of these factors, including effects of pests on pathogen growth and competition between pathogens and commensal microbiota for host resources. We examined interactions between the leaf-mining moth Cameraria ohridella, the bacterial causal agent of bleeding canker disease Pseudomonas syringae pv aesculi, and the bark-associated microbiota of horse chestnut (Aesculus hippocastanum) trees. Through surveys of > 900 trees from 60 sites in the UK, we tested for ecological or life history predictors of leaf miner infestation, bleeding canker, or coinfection. Using culture-independent sequencing, we then compared the bark microbiomes from 46 trees to measure the association between microbiome composition and key ecological variables, including the severity of disease. Both pest and pathogen were found to respond to tree characteristics, but neither explained damage inflicted by the other. However, we found a clear loss of microbial diversity and associated shift in microbiome composition of trees as a function of disease. These results show a link between bark-associated microbiota and tree health that introduces the intriguing possibility that tree microbiota play key roles in the spread of disease. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
The E. coli molecular phenotype under different growth conditions
Apr 18, 2017   Scientific Reports
Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM,   . . . . . .   , Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO
The E. coli molecular phenotype under different growth conditions
Apr 18, 2017
Scientific Reports
Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. Additionally, we provide measurements of doubling times and in-vivo metabolic fluxes through the central carbon metabolism. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling of E. coli gene regulation, transcription, and translation.
Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster
Apr 21, 2017   ELife
Park HB, Perez CE, Barber KW, Rinehart J, Crawford JM
Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster
Apr 21, 2017
ELife
Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis. P. luminescens is a Gammaproteobacterium that undergoes phenotypic variation and can have both pathogenic and mutualistic roles. Through extensive gene deletion, pathway-targeted molecular networking, quantitative proteomic analysis, and NMR, we show that the genetic locus affects the regulation of quorum sensing and secondary metabolic enzymes and encodes new pteridine metabolites functionalized with cis-amide acyl-side chains, termed pepteridine A (1) and B (2). The pepteridines are produced in the pathogenic phenotypic variant and represent the first reported metabolites to be synthesized by a hybrid NRPS-pteridine pathway. These studies expand our view of the combinatorial biosynthetic potential available in bacteria.

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