Science.gov

Sample records for bacterioplankton genomes inferred

  1. A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters

    PubMed Central

    Grzymski, Joseph J; Riesenfeld, Christian S; Williams, Timothy J; Dussaq, Alex M; Ducklow, Hugh; Erickson, Matthew; Cavicchioli, Ricardo; Murray, Alison E

    2012-01-01

    Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean' mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content. PMID:22534611

  2. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton.

    PubMed

    Labonté, Jessica M; Swan, Brandon K; Poulos, Bonnie; Luo, Haiwei; Koren, Sergey; Hallam, Steven J; Sullivan, Matthew B; Woyke, Tanja; Wommack, K Eric; Stepanauskas, Ramunas

    2015-11-01

    Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus-host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus-host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage-host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. Our study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host-virus interactions in complex microbial communities. PMID:25848873

  3. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

    PubMed Central

    Labonté, Jessica M; Swan, Brandon K; Poulos, Bonnie; Luo, Haiwei; Koren, Sergey; Hallam, Steven J; Sullivan, Matthew B; Woyke, Tanja; Eric Wommack, K; Stepanauskas, Ramunas

    2015-01-01

    Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. Our study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities. PMID:25848873

  4. Inferring ancestry from population genomic data and its applications

    PubMed Central

    Padhukasahasram, Badri

    2014-01-01

    Ancestry inference is a frequently encountered problem and has many applications such as forensic analyses, genetic association studies, and personal genomics. The main goal of ancestry inference is to identify an individual’s population of origin based on our knowledge of natural populations. Because both self-reported ancestry in humans or the sampling location of an organism can be inaccurate for this purpose, the use of genetic markers can facilitate accurate and reliable inference of an individual’s ancestral origins. At a higher level, there are two different paradigms in ancestry inference: global ancestry inference which tries to compute the genome-wide average of the population contributions and local ancestry inference which tries to identify the regional ancestry of a genomic segment. In this mini review, I describe the numerous approaches that are currently available for both kinds of ancestry inference from population genomic datasets. I first describe the general ideas underlying such inference methods and their relationship to one another. Then, I describe practical applications in which inference of ancestry has proven useful. Lastly, I discuss challenges and directions for future research work in this area. PMID:25071832

  5. Inferring parental genomic ancestries using pooled semi-Markov processes

    PubMed Central

    Zou, James Y.; Halperin, Eran; Burchard, Esteban; Sankararaman, Sriram

    2015-01-01

    Motivation: A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns. Results: We model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents’ genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning. Contact: jazo@microsoft.com PMID:26072482

  6. Inferring Correlation Networks from Genomic Survey Data

    PubMed Central

    Friedman, Jonathan; Alm, Eric J.

    2012-01-01

    High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate the complex inner workings of natural microbial communities - be they from the world's oceans or the human gut. A key step in exploring such data is the identification of dependencies between members of these communities, which is commonly achieved by correlation analysis. However, it has been known since the days of Karl Pearson that the analysis of the type of data generated by such techniques (referred to as compositional data) can produce unreliable results since the observed data take the form of relative fractions of genes or species, rather than their absolute abundances. Using simulated and real data from the Human Microbiome Project, we show that such compositional effects can be widespread and severe: in some real data sets many of the correlations among taxa can be artifactual, and true correlations may even appear with opposite sign. Additionally, we show that community diversity is the key factor that modulates the acuteness of such compositional effects, and develop a new approach, called SparCC (available at https://bitbucket.org/yonatanf/sparcc), which is capable of estimating correlation values from compositional data. To illustrate a potential application of SparCC, we infer a rich ecological network connecting hundreds of interacting species across 18 sites on the human body. Using the SparCC network as a reference, we estimated that the standard approach yields 3 spurious species-species interactions for each true interaction and misses 60% of the true interactions in the human microbiome data, and, as predicted, most of the erroneous links are found in the samples with the lowest diversity. PMID:23028285

  7. Inferring correlation networks from genomic survey data.

    PubMed

    Friedman, Jonathan; Alm, Eric J

    2012-01-01

    High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate the complex inner workings of natural microbial communities - be they from the world's oceans or the human gut. A key step in exploring such data is the identification of dependencies between members of these communities, which is commonly achieved by correlation analysis. However, it has been known since the days of Karl Pearson that the analysis of the type of data generated by such techniques (referred to as compositional data) can produce unreliable results since the observed data take the form of relative fractions of genes or species, rather than their absolute abundances. Using simulated and real data from the Human Microbiome Project, we show that such compositional effects can be widespread and severe: in some real data sets many of the correlations among taxa can be artifactual, and true correlations may even appear with opposite sign. Additionally, we show that community diversity is the key factor that modulates the acuteness of such compositional effects, and develop a new approach, called SparCC (available at https://bitbucket.org/yonatanf/sparcc), which is capable of estimating correlation values from compositional data. To illustrate a potential application of SparCC, we infer a rich ecological network connecting hundreds of interacting species across 18 sites on the human body. Using the SparCC network as a reference, we estimated that the standard approach yields 3 spurious species-species interactions for each true interaction and misses 60% of the true interactions in the human microbiome data, and, as predicted, most of the erroneous links are found in the samples with the lowest diversity. PMID:23028285

  8. Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny

    PubMed Central

    Herniou, Elisabeth A.; Luque, Teresa; Chen, Xinwen; Vlak, Just M.; Winstanley, Doreen; Cory, Jennifer S.; O'Reilly, David R.

    2001-01-01

    Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses. PMID:11483757

  9. Robust Demographic Inference from Genomic and SNP Data

    PubMed Central

    Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu

    2013-01-01

    We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets. PMID:24204310

  10. Ancestral genome inference using a genetic algorithm approach.

    PubMed

    Gao, Nan; Yang, Ning; Tang, Jijun

    2013-01-01

    Recent advancement of technologies has now made it routine to obtain and compare gene orders within genomes. Rearrangements of gene orders by operations such as reversal and transposition are rare events that enable researchers to reconstruct deep evolutionary histories. An important application of genome rearrangement analysis is to infer gene orders of ancestral genomes, which is valuable for identifying patterns of evolution and for modeling the evolutionary processes. Among various available methods, parsimony-based methods (including GRAPPA and MGR) are the most widely used. Since the core algorithms of these methods are solvers for the so called median problem, providing efficient and accurate median solver has attracted lots of attention in this field. The "double-cut-and-join" (DCJ) model uses the single DCJ operation to account for all genome rearrangement events. Because mathematically it is much simpler than handling events directly, parsimony methods using DCJ median solvers has better speed and accuracy. However, the DCJ median problem is NP-hard and although several exact algorithms are available, they all have great difficulties when given genomes are distant. In this paper, we present a new algorithm that combines genetic algorithm (GA) with genomic sorting to produce a new method which can solve the DCJ median problem in limited time and space, especially in large and distant datasets. Our experimental results show that this new GA-based method can find optimal or near optimal results for problems ranging from easy to very difficult. Compared to existing parsimony methods which may severely underestimate the true number of evolutionary events, the sorting-based approach can infer ancestral genomes which are much closer to their true ancestors. The code is available at http://phylo.cse.sc.edu. PMID:23658708

  11. Genome-Wide Inference of Ancestral Recombination Graphs

    PubMed Central

    Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the “ancestral recombination graph” (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of chromosomes conditional on an ARG of chromosomes, an operation we call “threading.” Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  12. Genome-wide inference of ancestral recombination graphs.

    PubMed

    Rasmussen, Matthew D; Hubisz, Melissa J; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  13. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    PubMed

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-01

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago. PMID:23040495

  14. Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation

    PubMed Central

    Kidd, Jeffrey M.; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D.; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F.; Peckham, Heather E.; Omberg, Larsson; Bormann Chung, Christina A.; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G.; Russell, Archie; Reynolds, Andy; Clark, Andrew G.; Reese, Martin G.; Lincoln, Stephen E.; Butte, Atul J.; De La Vega, Francisco M.; Bustamante, Carlos D.

    2012-01-01

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas—70% of the European ancestry in today’s African Americans dates back to European gene flow happening only 7–8 generations ago. PMID:23040495

  15. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

    PubMed

    Baker, Brett J; Saw, Jimmy H; Lind, Anders E; Lazar, Cassandre Sara; Hinrichs, Kai-Uwe; Teske, Andreas P; Ettema, Thijs J G

    2016-01-01

    The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere. PMID:27572167

  16. Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank

    PubMed Central

    Amaral, Gilda Rose S.; Silva, Bruno Sergio de O.; Santos, Eidy O.; Dias, Graciela M.; Lopes, Rubens M.; Edwards, Robert A.; Thompson, Cristiane C.

    2012-01-01

    Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number of coding sequences (CDS) is 6,359, as determined according to the Rapid Annotation using Subsystem Technology (RAST) server. The number of ribosomal genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A contains genes related to virulence and fitness, including a complete proteorhodopsin cluster, complete type II and III secretion systems, incomplete type I, IV, and VI secretion systems, a hemolysin, and CTXΦ. PMID:22535939

  17. Genome sequence of the bacterioplanktonic, mixotrophic Vibrio campbellii strain PEL22A, isolated in the Abrolhos Bank.

    PubMed

    Amaral, Gilda Rose S; Silva, Bruno Sergio de O; Santos, Eidy O; Dias, Graciela M; Lopes, Rubens M; Edwards, Robert A; Thompson, Cristiane C; Thompson, Fabiano L

    2012-05-01

    Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number of coding sequences (CDS) is 6,359, as determined according to the Rapid Annotation using Subsystem Technology (RAST) server. The number of ribosomal genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A contains genes related to virulence and fitness, including a complete proteorhodopsin cluster, complete type II and III secretion systems, incomplete type I, IV, and VI secretion systems, a hemolysin, and CTXΦ. PMID:22535939

  18. Inferring the Dynamics of Effective Population Size Using Autosomal Genomes.

    PubMed

    Hou, Zheng; Luo, Yin; Wang, Zhisheng; Zheng, Hong-Xiang; Wang, Yi; Zhou, Hang; Wu, Leqin; Jin, Li

    2016-01-01

    Next-generation sequencing technology has provided a great opportunity for inferring human demographic history by investigating changes in the effective population size (Ne). In this report, we introduce a strategy for estimating Ne dynamics, allowing the exploration of large multi-locus SNP datasets. We applied this strategy to the Phase 1 Han Chinese samples from the 1000 Genomes Project. The Han Chinese population has undergone a continuous expansion since 25,000 years ago, at first slowly from about 7,300 to 9,800 (at the end of the last glacial maximum about 15,000 YBP), then more quickly to about 46,000 (at the beginning of the Neolithic about 8,000 YBP), and then even more quickly to reach a population size of about 140,000 (recently). PMID:26832887

  19. Inferring the Dynamics of Effective Population Size Using Autosomal Genomes

    PubMed Central

    Hou, Zheng; Luo, Yin; Wang, Zhisheng; Zheng, Hong-Xiang; Wang, Yi; Zhou, Hang; Wu, Leqin; Jin, Li

    2016-01-01

    Next-generation sequencing technology has provided a great opportunity for inferring human demographic history by investigating changes in the effective population size (Ne). In this report, we introduce a strategy for estimating Ne dynamics, allowing the exploration of large multi-locus SNP datasets. We applied this strategy to the Phase 1 Han Chinese samples from the 1000 Genomes Project. The Han Chinese population has undergone a continuous expansion since 25,000 years ago, at first slowly from about 7,300 to 9,800 (at the end of the last glacial maximum about 15,000 YBP), then more quickly to about 46,000 (at the beginning of the Neolithic about 8,000 YBP), and then even more quickly to reach a population size of about 140,000 (recently). PMID:26832887

  20. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions.

    PubMed

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  1. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

    PubMed Central

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  2. Catchment-scale biogeography of riverine bacterioplankton.

    PubMed

    Read, Daniel S; Gweon, Hyun S; Bowes, Michael J; Newbold, Lindsay K; Field, Dawn; Bailey, Mark J; Griffiths, Robert I

    2015-02-01

    Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river. PMID:25238398

  3. Catchment-scale biogeography of riverine bacterioplankton

    PubMed Central

    Read, Daniel S; Gweon, Hyun S; Bowes, Michael J; Newbold, Lindsay K; Field, Dawn; Bailey, Mark J; Griffiths, Robert I

    2015-01-01

    Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river. PMID:25238398

  4. Genetic Variation Between Two Cucumber Genotypes Inferred from Genome-wide Microsatellite Polymorphism Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability at microsatellite loci has been used widely to infer the extent of genetic diversity among related plant taxa. However, typically, only the most polymorphic loci in the genome were analyzed that may result in a biased, and generally overestimated picture of genome-wide microsatellite div...

  5. Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

    PubMed Central

    MacLeod, Iona M.; Larkin, Denis M.; Lewin, Harris A.; Hayes, Ben J.; Goddard, Mike E.

    2013-01-01

    Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant challenges to fully utilize such large data sets and to ensure that sequencing errors do not introduce bias into the inferred demography. Using whole-genome sequence data from two Holstein cattle, we demonstrate a new method to correct for bias caused by hidden errors and then infer stepwise changes in ancestral demography up to present. There was a strong upward bias in estimates of recent effective population size (Ne) if the correction method was not applied to the data, both for our method and the Li and Durbin (Inference of human population history from individual whole-genome sequences. Nature 475:493–496) pairwise sequentially Markovian coalescent method. To infer demography, we use an analytical predictor of multiloci linkage disequilibrium (LD) based on a simple coalescent model that allows for changes in Ne. The LD statistic summarizes the distribution of runs of homozygosity for any given demography. We infer a best fit demography as one that predicts a match with the observed distribution of runs of homozygosity in the corrected sequence data. We use multiloci LD because it potentially holds more information about ancestral demography than pairwise LD. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago, possibly related to the divergence of African and European Bos taurus cattle. This is followed by a further reduction coinciding with the period of cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. Our approach can be applied to whole-genome sequence from any diploid species and can be scaled up to use sequence from multiple individuals. PMID:23842528

  6. Using Genetic Distance to Infer the Accuracy of Genomic Prediction.

    PubMed

    Scutari, Marco; Mackay, Ian; Balding, David

    2016-09-01

    The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which implicitly assumes that new individuals (whose phenotypes we would like to predict) originate from the same population the genomic prediction model is trained on. In this paper we propose an approach based on clustering and resampling to investigate the effect of increasing genetic distance between training and target populations when predicting quantitative traits. This is important for plant and animal genetics, where genomic selection programs rely on the precision of predictions in future rounds of breeding. Therefore, estimating how quickly predictive accuracy decays is important in deciding which training population to use and how often the model has to be recalibrated. We find that the correlation between true and predicted values decays approximately linearly with respect to either FST or mean kinship between the training and the target populations. We illustrate this relationship using simulations and a collection of data sets from mice, wheat and human genetics. PMID:27589268

  7. A Cooperative Co-Evolutionary Genetic Algorithm for Tree Scoring and Ancestral Genome Inference.

    PubMed

    Gao, Nan; Zhang, Yan; Feng, Bing; Tang, Jijun

    2015-01-01

    Recent advances of technology have made it easy to obtain and compare whole genomes. Rearrangements of genomes through operations such as reversals and transpositions are rare events that enable researchers to reconstruct deep evolutionary history among species. Some of the popular methods need to search a large tree space for the best scored tree, thus it is desirable to have a fast and accurate method that can score a given tree efficiently. During the tree scoring procedure, the genomic structures of internal tree nodes are also provided, which provide important information for inferring ancestral genomes and for modeling the evolutionary processes. However, computing tree scores and ancestral genomes are very difficult and a lot of researchers have to rely on heuristic methods which have various disadvantages. In this paper, we describe the first genetic algorithm for tree scoring and ancestor inference, which uses a fitness function considering co-evolution, adopts different initial seeding methods to initialize the first population pool, and utilizes a sorting-based approach to realize evolution. Our extensive experiments show that compared with other existing algorithms, this new method is more accurate and can infer ancestral genomes that are much closer to the true ancestors. PMID:26671797

  8. Inferring gene transcriptional modulatory relations: a genetical genomics approach

    SciTech Connect

    Li, Hongqiang; Lu, Lu; Manly, Kenneth; Chesler, Elissa J; Bao, Lei; Wang, Jintao; Zhou, Mi; Williams, Robert; Cui, Yan

    2005-01-01

    Bayesian network modeling is a promising approach to define and evaluate gene expression circuits in diverse tissues and cell types under different experimental conditions. The power and practicality of this approach can be improved by restricting the number of potential interactions among genes and by defining causal relations before evaluating posterior probabilities for billions of networks. A newly developed genetical genomics method that combines transcriptome profiling with complex trait analysis now provides strong constraints on network architecture. This method detects those chromosomal intervals responsible for differences in mRNA expression using quantitative trait locus (QTL) mapping. We have developed an efficient Bayesian approach that exploits the genetical genomics method to focus computational effort on the most plausible gene modulatory networks. We exploit a dense marker map for a genetic reference population (GRP) that consists of 32 BXD strains of mice made by intercrossing two progenitor strains- C57BL/6J and DBA/2J. These progenitors differ at 1.3 million known single nucleotide polymorphisms (SNPs), all of which can be exploited to estimate the probability that a gene contains functional polymorphisms that segregate within the GRP. We constructed 66 candidate networks that include all the candidate modulator genes located in the 209 statistically significant trans-acting QTL regions. SNPs that distinguish between the two progenitor strains were used to further winnow the list of candidate modulators. Bayesian network was then used to identify the genetic modulatory relations that best explain the microarray data.

  9. EMu: probabilistic inference of mutational processes and their localization in the cancer genome

    PubMed Central

    2013-01-01

    The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific opportunity for different mutation types according to sequence composition. Applying EMu to breast cancer data, we derive detailed maps of the activity of each process, both genome-wide and within specific local regions of the genome. Our work provides new opportunities to study the mutational processes underlying cancer development. EMu is available at http://www.sanger.ac.uk/resources/software/emu/. PMID:23628380

  10. The History of Slavs Inferred from Complete Mitochondrial Genome Sequences

    PubMed Central

    Mielnik-Sikorska, Marta; Daca, Patrycja; Malyarchuk, Boris; Derenko, Miroslava; Skonieczna, Katarzyna; Perkova, Maria; Dobosz, Tadeusz; Grzybowski, Tomasz

    2013-01-01

    To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ∼4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1). PMID:23342138

  11. Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

    PubMed Central

    Didelot, Xavier; Lawson, Daniel; Darling, Aaron; Falush, Daniel

    2010-01-01

    Bacteria and archaea reproduce clonally, but sporadically import DNA into their chromosomes from other organisms. In many of these events, the imported DNA replaces an homologous segment in the recipient genome. Here we present a new method to reconstruct the history of recombination events that affected a given sample of bacterial genomes. We introduce a mathematical model that represents both the donor and the recipient of each DNA import as an ancestor of the genomes in the sample. The model represents a simplification of the previously described coalescent with gene conversion. We implement a Monte Carlo Markov chain algorithm to perform inference under this model from sequence data alignments and show that inference is feasible for whole-genome alignments through parallelization. Using simulated data, we demonstrate accurate and reliable identification of individual recombination events and global recombination rate parameters. We applied our approach to an alignment of 13 whole genomes from the Bacillus cereus group. We find, as expected from laboratory experiments, that the recombination rate is higher between closely related organisms and also that the genome contains several broad regions of elevated levels of recombination. Application of the method to the genomic data sets that are becoming available should reveal the evolutionary history and private lives of populations of bacteria and archaea. The methods described in this article have been implemented in a computer software package, ClonalOrigin, which is freely available from http://code.google.com/p/clonalorigin/. PMID:20923983

  12. A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

    PubMed Central

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

  13. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

    SciTech Connect

    Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

    2014-09-29

    Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.

  14. Systems Biology and Ecology of Streamlined Bacterioplankton

    NASA Astrophysics Data System (ADS)

    Giovannoni, S. J.

    2014-12-01

    The salient feature of streamlined cells is their small genome size, but "streamlining" refers more generally to selection that favors minimization of cell size and complexity. The essence of streamlining theory is that selection is most efficient in organisms that have large effective population sizes, and, in nutrient-limited systems, favors cell architecture that minimizes resources required for replication. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function, raising the questions, what genome features are expendable, and how do cells become highly successful with a minimal genomic repertoire? One consequence of reductive evolution in streamlined organisms is atypical patterns of prototrophy, for example the recent discovery of a requirement for the thiamin precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine in some plankton taxa. Examples such as this fit within the framework of the Black Queen Hypothesis, which describes genome reduction that results in reliance on community goods and increased community connectivity. Other examples of genome reduction include losses of regulatory functions, or replacement with simpler regulatory systems, and increased metabolic integration. In one such case, in the order Pelagibacterales, the PII system for regulating responses to N limitation has been replaced with a simpler system composed of fewer genes. Both the absence of common regulatory systems and atypical patterns of prototrophy have been linked to difficulty in culturing Pelagibacterales, lending credibility to the idea that streamlining might broadly explain the phenomenon of the uncultured microbial majority. The success of streamlined osmotrophic bacterioplankton suggests that they successfully compete for labile organic matter and capture a large share of this resource, but an alternative theory postulates they are not good resource competitors and instead prosper by avoiding predation. The answers to these

  15. Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data.

    PubMed

    O'Brien, John D; Iqbal, Zamin; Wendler, Jason; Amenga-Etego, Lucas

    2016-06-01

    We present a rigorous statistical model that infers the structure of P. falciparum mixtures-including the number of strains present, their proportion within the samples, and the amount of unexplained mixture-using whole genome sequence (WGS) data. Applied to simulation data, artificial laboratory mixtures, and field samples, the model provides reasonable inference with as few as 10 reads or 50 SNPs and works efficiently even with much larger data sets. Source code and example data for the model are provided in an open source fashion. We discuss the possible uses of this model as a window into within-host selection for clinical and epidemiological studies. PMID:27362949

  16. Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data

    PubMed Central

    O’Brien, John D.; Amenga-Etego, Lucas

    2016-01-01

    We present a rigorous statistical model that infers the structure of P. falciparum mixtures—including the number of strains present, their proportion within the samples, and the amount of unexplained mixture—using whole genome sequence (WGS) data. Applied to simulation data, artificial laboratory mixtures, and field samples, the model provides reasonable inference with as few as 10 reads or 50 SNPs and works efficiently even with much larger data sets. Source code and example data for the model are provided in an open source fashion. We discuss the possible uses of this model as a window into within-host selection for clinical and epidemiological studies. PMID:27362949

  17. Inferring Genome-Wide Recombination Landscapes from Advanced Intercross Lines: Application to Yeast Crosses

    PubMed Central

    Illingworth, Christopher J. R.; Parts, Leopold; Bergström, Anders; Liti, Gianni; Mustonen, Ville

    2013-01-01

    Accurate estimates of recombination rates are of great importance for understanding evolution. In an experimental genetic cross, recombination breaks apart and rejoins genetic material, such that the genomes of the resulting isolates are comprised of distinct blocks of differing parental origin. We here describe a method exploiting this fact to infer genome-wide recombination profiles from sequenced isolates from an advanced intercross line (AIL). We verified the accuracy of the method against simulated data. Next, we sequenced 192 isolates from a twelve-generation cross between West African and North American yeast Saccharomyces cerevisiae strains and inferred the underlying recombination landscape at a fine genomic resolution (mean segregating site distance 0.22 kb). Comparison was made with landscapes inferred for a similar cross between four yeast strains, and with a previous single-generation, intra-strain cross (Mancera et al., Nature 2008). Moderate congruence was identified between landscapes (correlation 0.58–0.77 at 5 kb resolution), albeit with variance between mean genome-wide recombination rates. The multiple generations of mating undergone in the AILs gave more precise inference of recombination rates than could be achieved from a single-generation cross, in particular in identifying recombination cold-spots. The recombination landscapes we describe have particular utility; both AILs are part of a resource to study complex yeast traits (see e.g. Parts et al., Genome Res 2011). Our results will enable future applications of this resource to take better account of local linkage structure heterogeneities. Our method has general applicability to other crossing experiments, including a variety of experimental designs. PMID:23658715

  18. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

    PubMed Central

    Pickrell, Joseph K.; Pritchard, Jonathan K.

    2012-01-01

    Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and “ancient” Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com. PMID:23166502

  19. Improved genome inference in the MHC using a population reference graph

    PubMed Central

    Dilthey, Alexander; Cox, Charles; Iqbal, Zamin; Nelson, Matthew R.; McVean, Gil

    2015-01-01

    While much is known about human genetic variation, such information is typically ignored in assembling novel genomes. Instead, reads are mapped to a single reference, which can lead to poor characterization of regions of high sequence or structural diversity. We introduce a population reference graph, which combines multiple reference sequences and catalogues of variation. The genomes of novel samples are reconstructed as paths through the graph using an efficient hidden Markov model, allowing for recombination between different haplotypes and additional variants. By applying the method to the 4.5Mb extended MHC region on human chromosome 6, combining eight assembled haplotypes, sequences of known classical HLA alleles and 87,640 SNP variants from the 1000 Genomes Project, we demonstrate, using simulations, SNP genotyping, short-read and long-read data, how the method improves the accuracy of genome inference and reveals regions where the current set of reference sequences is substantially incomplete. PMID:25915597

  20. How to Infer Relative Fitness from a Sample of Genomic Sequences

    PubMed Central

    Dayarian, Adel; Shraiman, Boris I.

    2014-01-01

    Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman’s coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright–Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1–0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks. PMID:24770330

  1. How to infer relative fitness from a sample of genomic sequences.

    PubMed

    Dayarian, Adel; Shraiman, Boris I

    2014-07-01

    Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman's coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright-Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1-0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks. PMID:24770330

  2. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences

    PubMed Central

    Li, Hu; Shao, Renfu; Song, Nan; Song, Fan; Jiang, Pei; Li, Zhihong; Cai, Wanzhi

    2015-01-01

    Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera. PMID:25704094

  3. Inference of gorilla demographic and selective history from whole-genome sequence data.

    PubMed

    McManus, Kimberly F; Kelley, Joanna L; Song, Shiya; Veeramah, Krishna R; Woerner, August E; Stevison, Laurie S; Ryder, Oliver A; Ape Genome Project, Great; Kidd, Jeffrey M; Wall, Jeffrey D; Bustamante, Carlos D; Hammer, Michael F

    2015-03-01

    Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection. PMID:25534031

  4. Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data

    PubMed Central

    McManus, Kimberly F.; Kelley, Joanna L.; Song, Shiya; Veeramah, Krishna R.; Woerner, August E.; Stevison, Laurie S.; Ryder, Oliver A.; Ape Genome Project, Great; Kidd, Jeffrey M.; Wall, Jeffrey D.; Bustamante, Carlos D.; Hammer, Michael F.

    2015-01-01

    Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection. PMID:25534031

  5. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  6. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

    PubMed Central

    Didelot, Xavier; Wilson, Daniel J.

    2015-01-01

    Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/. PMID:25675341

  7. How do divergent ecological strategies emerge among marine bacterioplankton lineages?

    PubMed

    Luo, Haiwei; Moran, Mary Ann

    2015-09-01

    Heterotrophic bacteria in pelagic marine environments are frequently categorized into two canonical ecological groups: patch-associated and free-living. This framework provides a conceptual basis for understanding bacterial utilization of oceanic organic matter. Some patch-associated bacteria are ecologically linked with eukaryotic phytoplankton, and this observation fits with predicted coincidence of their genome expansion with marine phytoplankton diversification. By contrast, free-living bacteria in today's oceans typically live singly with streamlined metabolic and regulatory functions that allow them to grow in nutrient-poor seawater. Recent analyses of marine Alphaproteobacteria suggest that some free-living bacterioplankton lineages evolved from patch-associated ancestors up to several hundred million years ago. While evolutionary analyses agree with the hypothesis that natural selection has maintained these distinct ecological strategies and genomic traits in present-day populations, they do not rule out a major role for genetic drift in driving ancient ecological switches. These two evolutionary forces may have acted on ocean bacteria at different geological time scales and under different geochemical constraints, with possible implications for future adaptations to a changing ocean. New evolutionary models and genomic data are leading to a more comprehensive understanding of marine bacterioplankton evolutionary history. PMID:26051014

  8. Extensive error in the number of genes inferred from draft genome assemblies.

    PubMed

    Denton, James F; Lugo-Martinez, Jose; Tucker, Abraham E; Schrider, Daniel R; Warren, Wesley C; Hahn, Matthew W

    2014-12-01

    Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process. PMID:25474019

  9. Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles

    PubMed Central

    Subramanian, Ayshwarya; Shackney, Stanley; Schwartz, Russell

    2013-01-01

    Computational cancer phylogenetics seeks to enumerate the temporal sequences of aberrations in tumor evolution, thereby delineating the evolution of possible tumor progression pathways, molecular subtypes and mechanisms of action. We previously developed a pipeline for constructing phylogenies describing evolution between major recurring cell types computationally inferred from whole-genome tumor profiles. The accuracy and detail of the phylogenies, however, depends on the identification of accurate, high-resolution molecular markers of progression, i.e., reproducible regions of aberration that robustly differentiate different subtypes and stages of progression. Here we present a novel hidden Markov model (HMM) scheme for the problem of inferring such phylogenetically significant markers through joint segmentation and calling of multi-sample tumor data. Our method classifies sets of genome-wide DNA copy number measurements into a partitioning of samples into normal (diploid) or amplified at each probe. It differs from other similar HMM methods in its design specifically for the needs of tumor phylogenetics, by seeking to identify robust markers of progression conserved across a set of copy number profiles. We show an analysis of our method in comparison to other methods on both synthetic and real tumor data, which confirms its effectiveness for tumor phylogeny inference and suggests avenues for future advances. PMID:24407301

  10. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

    DOE PAGESBeta

    Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

    2014-09-29

    Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

  11. Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.

    PubMed

    Bunnefeld, Lynsey; Frantz, Laurent A F; Lohse, Konrad

    2015-11-01

    The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks--extreme population size changes of short duration--not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin's pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations. PMID:26341659

  12. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    PubMed Central

    Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

    2010-01-01

    RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov. PMID:20542910

  13. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    SciTech Connect

    Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

    2010-05-26

    RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

  14. Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus.

    PubMed

    Jarvis, Matthew C; Lam, Ham Ching; Zhang, Yan; Wang, Leyi; Hesse, Richard A; Hause, Ben M; Vlasova, Anastasia; Wang, Qiuhong; Zhang, Jianqiang; Nelson, Martha I; Murtaugh, Michael P; Marthaler, Douglas

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV. PMID:26611651

  15. Inferring Where and When Replication Initiates from Genome-Wide Replication Timing Data

    NASA Astrophysics Data System (ADS)

    Baker, A.; Audit, B.; Yang, S. C.-H.; Bechhoefer, J.; Arneodo, A.

    2012-06-01

    Based on an analogy between DNA replication and one dimensional nucleation-and-growth processes, various attempts to infer the local initiation rate I(x,t) of DNA replication origins from replication timing data have been developed in the framework of phase transition kinetics theories. These works have all used curve-fit strategies to estimate I(x,t) from genome-wide replication timing data. Here, we show how to invert analytically the Kolmogorov-Johnson-Mehl-Avrami model and extract I(x,t) directly. Tests on both simulated and experimental budding-yeast data confirm the location and firing-time distribution of replication origins.

  16. Inferring human population size and separation history from multiple genome sequences

    PubMed Central

    Schiffels, Stephan; Durbin, Richard

    2014-01-01

    The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe. PMID:24952747

  17. Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation

    SciTech Connect

    Denef, Vincent; Verberkmoes, Nathan C; Shah, Manesh B; Abraham, Paul E; Lefsrud, Mark G; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2009-01-01

    Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics-inferred genome typing (PIGT) was used to determine the genomic make-up of Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a four-year period. We observed six distinct genotypes that are recombinants comprised of segments from two parental genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were overrepresented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly underrepresented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system.

  18. Boolean Models of Genomic Regulatory Networks: Reduction Mappings, Inference, and External Control

    PubMed Central

    Ivanov, Ivan

    2009-01-01

    Computational modeling of genomic regulation has become an important focus of systems biology and genomic signal processing for the past several years. It holds the promise to uncover both the structure and dynamical properties of the complex gene, protein or metabolic networks responsible for the cell functioning in various contexts and regimes. This, in turn, will lead to the development of optimal intervention strategies for prevention and control of disease. At the same time, constructing such computational models faces several challenges. High complexity is one of the major impediments for the practical applications of the models. Thus, reducing the size/complexity of a model becomes a critical issue in problems such as model selection, construction of tractable subnetwork models, and control of its dynamical behavior. We focus on the reduction problem in the context of two specific models of genomic regulation: Boolean networks with perturbation (BNP) and probabilistic Boolean networks (PBN). We also compare and draw a parallel between the reduction problem and two other important problems of computational modeling of genomic networks: the problem of network inference and the problem of designing external control policies for intervention/altering the dynamics of the model. PMID:20190953

  19. Joint modeling of RNase footprint sequencing profiles for genome-wide inference of RNA structure.

    PubMed

    Zou, Chenchen; Ouyang, Zhengqing

    2015-10-30

    Recent studies have revealed significant roles of RNA structure in almost every step of RNA processing, including transcription, splicing, transport and translation. RNase footprint sequencing (RNase-seq) has emerged to dissect RNA structures at the genome scale. However, it remains challenging to analyze RNase-seq data because of the issues of signal sparsity, variability and correlations among various RNases. We present a probabilistic framework, joint Poisson-gamma mixture (JPGM), for integrative modeling of multiple RNase-seq profiles. Combining JPGM with hidden Markov model allows genome-wide inference of RNA structures. We apply the joint modeling approach for inferring base pairing states on simulated data sets and RNase-seq profiles of the double-strand specific RNase V1 and single-strand specific RNase S1 in yeast. We demonstrate that joint analysis of V1 and S1 profiles outputs interpretable RNA structure states, while approaches that analyze each profile separately do not. The joint modeling approach predicts the structure states of all nucleotides in 3196 transcripts of yeast without compromising accuracy, while the simple thresholding approach misses 43% of the nucleotides. Furthermore, the posterior probabilities outputted by our model are able to resolve the structural ambiguity of ≈300 000 nucleotides with overlapping V1 and S1 cleavage sites. Our model also generates RNA accessibilities, which are associated with three-dimensional conformations. PMID:26400167

  20. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

    PubMed Central

    2014-01-01

    Background Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade

  1. Inferring causal genomic alterations in breast cancer using gene expression data

    PubMed Central

    2011-01-01

    Background One of the primary objectives in cancer research is to identify causal genomic alterations, such as somatic copy number variation (CNV) and somatic mutations, during tumor development. Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of these studies. Results We developed a framework for identifying recurrent regions of CNV and distinguishing the cancer driver genes from the passenger genes in the regions. By inferring CNV regions across many datasets we were able to identify 109 recurrent amplified/deleted CNV regions. Many of these regions are enriched for genes involved in many important processes associated with tumorigenesis and cancer progression. Genes in these recurrent CNV regions were then examined in the context of gene regulatory networks to prioritize putative cancer driver genes. The cancer driver genes uncovered by the framework include not only well-known oncogenes but also a number of novel cancer susceptibility genes validated via siRNA experiments. Conclusions To our knowledge, this is the first effort to systematically identify and validate drivers for expression based CNV regions in breast cancer. The framework where the wavelet analysis of copy number alteration based on expression coupled with the gene regulatory network analysis, provides a blueprint for leveraging genomic data to identify key regulatory components and gene targets. This integrative approach can be applied to many other large-scale gene expression studies and other novel types of cancer data such as next-generation sequencing based expression (RNA-Seq) as well as CNV data. PMID:21806811

  2. Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations.

    PubMed

    Shi, Hongbo; Zhang, Guangde; Zhou, Meng; Cheng, Liang; Yang, Haixiu; Wang, Jing; Sun, Jie; Wang, Zhenzhen

    2016-01-01

    MicroRNAs (miRNAs) play an important role in the development and progression of human diseases. The identification of disease-associated miRNAs will be helpful for understanding the molecular mechanisms of diseases at the post-transcriptional level. Based on different types of genomic data sources, computational methods for miRNA-disease association prediction have been proposed. However, individual source of genomic data tends to be incomplete and noisy; therefore, the integration of various types of genomic data for inferring reliable miRNA-disease associations is urgently needed. In this study, we present a computational framework, CHNmiRD, for identifying miRNA-disease associations by integrating multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. The performance of CHNmiRD was evaluated by experimentally verified miRNA-disease associations, which achieved an area under the ROC curve (AUC) of 0.834 for 5-fold cross-validation. In particular, CHNmiRD displayed excellent performance for diseases without any known related miRNAs. The results of case studies for three human diseases (glioblastoma, myocardial infarction and type 1 diabetes) showed that all of the top 10 ranked miRNAs having no known associations with these three diseases in existing miRNA-disease databases were directly or indirectly confirmed by our latest literature mining. All these results demonstrated the reliability and efficiency of CHNmiRD, and it is anticipated that CHNmiRD will serve as a powerful bioinformatics method for mining novel disease-related miRNAs and providing a new perspective into molecular mechanisms underlying human diseases at the post-transcriptional level. CHNmiRD is freely available at http://www.bio-bigdata.com/CHNmiRD. PMID:26849207

  3. Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing.

    PubMed

    Kopf, Anna; Kostadinov, Ivaylo; Wichels, Antje; Quast, Christian; Glöckner, Frank Oliver

    2015-02-01

    Marine metatranscriptome data was generated as part of a study investigating the bacterioplankton communities towards the end of a diatom-dominated spring phytoplankton bloom. This genomic resource article reports a metatranscriptomic dataset from amidst the winter time prior to the occurrence of the spring diatom bloom. Up to 58% of all sequences could be assigned to predicted genes. Taxonomic analysis based on expressed 16S ribosomal RNA genes identified Alphaproteobacteria and Gammaproteobacteria as the most active community members. PMID:25479944

  4. Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data

    PubMed Central

    He, Yungang; Wang, Wei R.; Xu, Shuhua; Jin, Li; SNP Consortium, Pan-Asia

    2012-01-01

    The genetic origins of Japanese populations have been controversial. Upper Paleolithic Japanese, i.e. Jomon, developed independently in Japanese islands for more than 10,000 years until the isolation was ended with the influxes of continental immigrants about 2,000 years ago. However, the knowledge of origin of Jomon and its contribution to the genetic pool of contemporary Japanese is still limited, albeit the extensive studies using mtDNA and Y chromosomes. In this report, we aimed to infer the origin of Jomon and to estimate its contribution to Japanese by fitting an admixture model with missing data from Jomon to a genome-wide data from 94 worldwide populations. Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin. PMID:22482036

  5. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data.

    PubMed

    Cahill, James A; Soares, André E R; Green, Richard E; Shapiro, Beth

    2016-07-19

    Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325835

  6. Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

    PubMed Central

    Burleigh, J. Gordon; Bansal, Mukul S.; Eulenstein, Oliver; Hartmann, Stefanie; Wehe, André; Vision, Todd J.

    2011-01-01

    Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life. PMID:21186249

  7. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

    PubMed Central

    Riaz, Tiayyba; Shehzad, Wasim; Viari, Alain; Pompanon, François; Taberlet, Pierre; Coissac, Eric

    2011-01-01

    Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers. PMID:21930509

  8. Inferring Quantitative Trait Pathways Associated with Bull Fertility from a Genome-Wide Association Study

    PubMed Central

    Peñagaricano, Francisco; Weigel, Kent A.; Rosa, Guilherme J. M.; Khatib, Hasan

    2013-01-01

    Whole-genome association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. As such, the objective of this study was to perform a pathway-based association analysis in Holstein dairy cattle in order to identify relevant pathways involved in bull fertility. The results of a single-marker association analysis, using 1,755 bulls with sire conception rate data and genotypes for 38,650 single nucleotide polymorphisms (SNPs), were used in this study. A total of 16,819 annotated genes, including 2,767 significantly associated with bull fertility, were used to interrogate a total of 662 Gene Ontology (GO) terms and 248 InterPro (IP) entries using a test of proportions based on the cumulative hypergeometric distribution. After multiple-testing correction, 20 GO categories and one IP entry showed significant overrepresentation of genes statistically associated with bull fertility. Several of these functional categories such as small GTPases mediated signal transduction, neurogenesis, calcium ion binding, and cytoskeleton are known to be involved in biological processes closely related to male fertility. These results could provide insight into the genetic architecture of this complex trait in dairy cattle. In addition, this study shows that quantitative trait pathways inferred from single-marker analyses could enhance our interpretations of the results of genome-wide association studies. PMID:23335935

  9. Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data.

    PubMed

    Stuglik, Michał T; Babik, Wiesław

    2016-07-01

    The role of gene flow in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of gene flow between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical gene flow between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical gene flow. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging genes for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence gene flow resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific gene flow. This study demonstrates the complexity of long-term gene flow between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago. PMID:27386093

  10. Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

    PubMed Central

    Yang, Ya; Smith, Stephen A.

    2014-01-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  11. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

    PubMed

    Yang, Ya; Smith, Stephen A

    2014-11-01

    Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction. PMID:25158799

  12. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a prio...

  13. Covariance Between Genotypic Effects and its Use for Genomic Inference in Half-Sib Families

    PubMed Central

    Wittenburg, Dörte; Teuscher, Friedrich; Klosa, Jan; Reinsch, Norbert

    2016-01-01

    In livestock, current statistical approaches utilize extensive molecular data, e.g., single nucleotide polymorphisms (SNPs), to improve the genetic evaluation of individuals. The number of model parameters increases with the number of SNPs, so the multicollinearity between covariates can affect the results obtained using whole genome regression methods. In this study, dependencies between SNPs due to linkage and linkage disequilibrium among the chromosome segments were explicitly considered in methods used to estimate the effects of SNPs. The population structure affects the extent of such dependencies, so the covariance among SNP genotypes was derived for half-sib families, which are typical in livestock populations. Conditional on the SNP haplotypes of the common parent (sire), the theoretical covariance was determined using the haplotype frequencies of the population from which the individual parent (dam) was derived. The resulting covariance matrix was included in a statistical model for a trait of interest, and this covariance matrix was then used to specify prior assumptions for SNP effects in a Bayesian framework. The approach was applied to one family in simulated scenarios (few and many quantitative trait loci) and using semireal data obtained from dairy cattle to identify genome segments that affect performance traits, as well as to investigate the impact on predictive ability. Compared with a method that does not explicitly consider any of the relationship among predictor variables, the accuracy of genetic value prediction was improved by 10–22%. The results show that the inclusion of dependence is particularly important for genomic inference based on small sample sizes. PMID:27402363

  14. Spatiotemporal pattern of bacterioplankton in Donghu Lake

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang; Yan, Qingyun; Yu, Yuhe; Dai, Lili

    2014-05-01

    Bacterioplankton play key roles in the biogeochemical cycle and in organic contaminant degradation. The species richness and abundance of bacterial subgroups are generally distinct from each other, and this is attributed to their different functions in aquatic ecosystems. The spatiotemporal variations of eight phylogenetic subgroups (Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomycetes, alpha-, beta-, and gamma-Proteobacteria) derived from Donghu Lake were investigated using PCR-DGGE fingerprinting, to explore their responses to environmental factors. Results indicate that Actinobacteria and beta-Proteobacteria were the two largest bacterial subgroups detected. These two groups and Bacteroidetes showed clear seasonal patterns in composition of the operational taxonomic unit. Results also suggest that the bacterioplankton subgroups in Donghu Lake were significantly correlated with different environmental factors. In brief, the total nitrogen was one of the major factors regulating all the bacterioplankton except for Actinobacteria. However, total phosphorus, another important eutrophication factor, contributed to the two largest bacterial groups (Actinobacteria and beta-Proteobacteria), as well as to the Cyanobacteria and Firmicutes. Therefore, the responses of bacterioplankton subgroups to environmental factors were different, and this should be attributed to the differences in the functions of different groups.

  15. Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome.

    PubMed

    Platt, Daniel E; Utro, Filippo; Parida, Laxmi

    2014-06-01

    Accessible biotechnology is enabling the cataloging of genetic variants in individuals in populations at unprecedented scales. The use of phylogeny of the individuals within populations allows a model-based approach to studying these variations, which is important in understanding relationships between and across populations. For the somatic genome, however, the phylogeny must take recombinations (and other genetic mixing events) into account. Hence the resulting topology is more complex than a tree. Unlike a tree topology, it is not as apparent which events are visible from the extant samples. An earlier work presented a mathematical model (called the minimal descriptor) for teasing apart the inherent visible information from that which any specific algorithm might see. We use this framework to study the effect of sampling sizes on the overall inferred genetic history. In this paper, we seek to understand the extent, characteristics (in terms of recent versus ancient genetic events) and reliability of what was resolvable within field samples drawn from modern populations. We observed that most of the visible ancient events are recoverable from relatively small sample sizes. However, without identification of this relatively small minority of ancient genetic events, most of the signal will appear to reflect modern events and admixtures. We also found that the more ancient events are likely to be reproduced with higher fidelity between multiple samplings, and that the identified older events are less likely to yield false positive discrimination between populations. We conclude that a recombinant phylogenetic reconstruction is necessary to identify which markers are most likely to discriminate ancient events, and to discriminate between populations with lower risk of false positives. Secondly, on a broader note, this study also provides a general methodology for a critical assessment of the inferred common genetic history of populations (say, in plant cultivars or

  16. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton.

    PubMed

    Milici, Mathias; Deng, Zhi-Luo; Tomasch, Jürgen; Decelle, Johan; Wos-Oxley, Melissa L; Wang, Hui; Jáuregui, Ruy; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H; Wurst, Mascha; Pieper, Dietmar H; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S-47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone. PMID:27199970

  17. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

    PubMed Central

    Milici, Mathias; Deng, Zhi-Luo; Tomasch, Jürgen; Decelle, Johan; Wos-Oxley, Melissa L.; Wang, Hui; Jáuregui, Ruy; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H.; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone. PMID:27199970

  18. Comparative Analysis of Mitochondrial Genomes in Diplura (Hexapoda, Arthropoda): Taxon Sampling Is Crucial for Phylogenetic Inferences

    PubMed Central

    Chen, Wan-Jun; Koch, Markus; Mallatt, Jon M.; Luan, Yun-Xia

    2014-01-01

    Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference. PMID:24391151

  19. An application of collaborative targeted maximum likelihood estimation in causal inference and genomics.

    PubMed

    Gruber, Susan; van der Laan, Mark J

    2010-01-01

    A concrete example of the collaborative double-robust targeted likelihood estimator (C-TMLE) introduced in a companion article in this issue is presented, and applied to the estimation of causal effects and variable importance parameters in genomic data. The focus is on non-parametric estimation in a point treatment data structure. Simulations illustrate the performance of C-TMLE relative to current competitors such as the augmented inverse probability of treatment weighted estimator that relies on an external non-collaborative estimator of the treatment mechanism, and inefficient estimation procedures including propensity score matching and standard inverse probability of treatment weighting. C-TMLE is also applied to the estimation of the covariate-adjusted marginal effect of individual HIV mutations on resistance to the anti-retroviral drug lopinavir. The influence curve of the C-TMLE is used to establish asymptotically valid statistical inference. The list of mutations found to have a statistically significant association with resistance is in excellent agreement with mutation scores provided by the Stanford HIVdb mutation scores database. PMID:21731530

  20. An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics

    PubMed Central

    Gruber, Susan; van der Laan, Mark J.

    2010-01-01

    A concrete example of the collaborative double-robust targeted likelihood estimator (C-TMLE) introduced in a companion article in this issue is presented, and applied to the estimation of causal effects and variable importance parameters in genomic data. The focus is on non-parametric estimation in a point treatment data structure. Simulations illustrate the performance of C-TMLE relative to current competitors such as the augmented inverse probability of treatment weighted estimator that relies on an external non-collaborative estimator of the treatment mechanism, and inefficient estimation procedures including propensity score matching and standard inverse probability of treatment weighting. C-TMLE is also applied to the estimation of the covariate-adjusted marginal effect of individual HIV mutations on resistance to the anti-retroviral drug lopinavir. The influence curve of the C-TMLE is used to establish asymptotically valid statistical inference. The list of mutations found to have a statistically significant association with resistance is in excellent agreement with mutation scores provided by the Stanford HIVdb mutation scores database. PMID:21731530

  1. Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data

    PubMed Central

    Bhaskar, Anand; Wang, Y.X. Rachel; Song, Yun S.

    2015-01-01

    With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. PMID:25564017

  2. Genome Size Variation and Species Relationships in Hieracium Sub-genus Pilosella (Asteraceae) as Inferred by Flow Cytometry

    PubMed Central

    Suda, Jan; Krahulcová, Anna; Trávníček, Pavel; Rosenbaumová, Radka; Peckert, Tomáš; Krahulec, František

    2007-01-01

    Background and Aims Hieracium sub-genus Pilosella (hawkweeds) is a taxonomically complicated group of vascular plants, the structure of which is substantially influenced by frequent interspecific hybridization and polyploidization. Two kinds of species, ‘basic’ and ‘intermediate’ (i.e. hybridogenous), are usually recognized. In this study, genome size variation was investigated in a representative set of Central European hawkweeds in order to assess the value of such a data set for species delineation and inference of evolutionary relationships. Methods Holoploid and monoploid genome sizes (C- and Cx-values) were determined using propidium iodide flow cytometry for 376 homogeneously cultivated individuals of Hieracium sub-genus Pilosella, including 24 species (271 individuals), five recent natural hybrids (seven individuals) and experimental F1 hybrids from four parental combinations (98 individuals). Chromosome counts were available for more than half of the plant accessions. Base composition (proportion of AT/GC bases) was cytometrically estimated in 73 individuals. Key Results Seven different ploidy levels (2x–8x) were detected, with intraspecific ploidy polymorphism (up to four different cytotypes) occurring in 11 wild species. Mean 2C-values varied approx. 4·3-fold from 3·53 pg in diploid H. hoppeanum to 15·30 pg in octoploid H. brachiatum. 1Cx-values ranged from 1·72 pg in H. pilosella to 2·16 pg in H. echioides (1·26-fold). The DNA content of (high) polyploids was usually proportional to the DNA values of their diploid/low polyploid counterparts, indicating lack of processes altering genome size (i.e. genome down-sizing). Most species showed constant nuclear DNA amounts, exceptions being three hybridogenous taxa, in which introgressive hybridization was suggested as a presumable trigger for genome size variation. Monoploid genome sizes of hybridogenous species were always between the corresponding values of their putative parents. In addition

  3. Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence▿†

    PubMed Central

    Ravcheev, Dmitry A.; Best, Aaron A.; Tintle, Nathan; DeJongh, Matthew; Osterman, Andrei L.; Novichkov, Pavel S.; Rodionov, Dmitry A.

    2011-01-01

    Transcriptional regulatory networks are fine-tuned systems that help microorganisms respond to changes in the environment and cell physiological state. We applied the comparative genomics approach implemented in the RegPredict Web server combined with SEED subsystem analysis and available information on known regulatory interactions for regulatory network reconstruction for the human pathogen Staphylococcus aureus and six related species from the family Staphylococcaceae. The resulting reference set of 46 transcription factor regulons contains more than 1,900 binding sites and 2,800 target genes involved in the central metabolism of carbohydrates, amino acids, and fatty acids; respiration; the stress response; metal homeostasis; drug and metal resistance; and virulence. The inferred regulatory network in S. aureus includes ∼320 regulatory interactions between 46 transcription factors and ∼550 candidate target genes comprising 20% of its genome. We predicted ∼170 novel interactions and 24 novel regulons for the control of the central metabolic pathways in S. aureus. The reconstructed regulons are largely variable in the Staphylococcaceae: only 20% of S. aureus regulatory interactions are conserved across all studied genomes. We used a large-scale gene expression data set for S. aureus to assess relationships between the inferred regulons and gene expression patterns. The predicted reference set of regulons is captured within the Staphylococcus collection in the RegPrecise database (http://regprecise.lbl.gov). PMID:21531804

  4. Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

    PubMed Central

    Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I.; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

    2013-01-01

    Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to

  5. Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain.

    PubMed

    Schrider, Daniel R; Kern, Andrew D

    2015-12-01

    The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods. PMID:26590212

  6. Reference set of regulons in Desulfovibrionales inferred by comparative genomics approach

    SciTech Connect

    Kazakov, A.E.; Rodionov, D.A.; Price, M.N.; Arkin, A.P.; Dubchak, I.; Novichkov, P.S.

    2010-11-15

    in this study, we carried out large-scale comparative genomics analysis of regulatory interactions in Desulfovibrio vulgaris and 12 related genomes from Desulfovibrionales order using our recently developed web server RegPredict (http://regpredict.lbl.gov). An overall reference collection of 26 Desulfovibrionales regulogs can be accessed through RegPrecise database (http://regpredict.lbl.gov).

  7. Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

    PubMed Central

    Schrider, Daniel R.; Kern, Andrew D.

    2015-01-01

    The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods. PMID:26590212

  8. BACTERIOPLANKTON DYNAMICS IN A SUBTROPICAL ESTUARY: EVIDENCE FOR SUBSTRATE LIMITATION

    EPA Science Inventory

    Bacterioplankton abundance and metabolic characteristics were measured along a transect in Pensacola Bay, Florida, USA, to examine the factors that control microbial water column processes in this subtropical estuary. The microbial measures included 3 H-L-leucine incorporation, e...

  9. Oceanic fronts: transition zones for bacterioplankton community composition.

    PubMed

    Baltar, Federico; Currie, Kim; Stuck, Esther; Roosa, Stéphanie; Morales, Sergio E

    2016-02-01

    Oceanic fronts are widespread mesoscale features that exist in the boundary between different water masses. Despite the recognized importance of bacterioplankton (including bacteria and archaea) on the marine biogeochemical cycles and the ubiquitousness of fronts, the effect of frontal zones on the distribution of bacterioplankton community remains unknown. Using 16S rRNA gene sequencing coupled with a high spatial resolution analysis of the physical properties of the water masses, we demonstrate strong shifts in bacterioplankton community composition (BCC) across the subtropical frontal zone off New Zealand. The transition between water masses resulted in a clear modification of the dominant taxa and a significant increase in community dissimilarity. Our results, linking physical oceanography and marine molecular ecology, support the strong role of oceanic frontal zones in delimiting the distribution of bacterioplankton in the ocean. PMID:26636656

  10. PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants

    PubMed Central

    Chen, Charles; DeClerck, Genevieve; Tian, Feng; Spooner, William; McCouch, Susan; Buckler, Edward

    2012-01-01

    PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize – a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information. PMID:23144785

  11. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences.

    PubMed

    Yuan, Ming-Long; Zhang, Qi-Lin; Zhang, Li; Guo, Zhong-Long; Liu, Yong-Jian; Shen, Yu-Ying; Shao, Renfu

    2016-11-01

    The Coleoptera (beetles) exhibits tremendous morphological, ecological, and behavioral diversity. To better understand the phylogenetics and evolution of beetles, we sequenced three complete mitogenomes from two families (Cleridae and Meloidae), which share conserved mitogenomic features with other completely sequenced beetles. We assessed the influence of six datasets and three inference methods on topology and nodal support within the Coleoptera. We found that both Bayesian inference and maximum likelihood with homogeneous-site models were greatly affected by nucleotide compositional heterogeneity, while the heterogeneous-site mixture model in PhyloBayes could provide better phylogenetic signals for the Coleoptera. The amino acid dataset generated more reliable tree topology at the higher taxonomic levels (i.e. suborders and series), where the inclusion of rRNA genes and the third positions of protein-coding genes improved phylogenetic inference at the superfamily level, especially under a heterogeneous-site model. We recovered the suborder relationships as (Archostemata+Adephaga)+(Myxophaga+Polyphaga). The series relationships within Polyphaga were recovered as (Scirtiformia+(Elateriformia+((Bostrichiformia+Scarabaeiformia+Staphyliniformia)+Cucujiformia))). All superfamilies within Cucujiformia were recovered as monophyletic. We obtained a cucujiform phylogeny of (Cleroidea+(Coccinelloidea+((Lymexyloidea+Tenebrionoidea)+(Cucujoidea+(Chrysomeloidea+Curculionoidea))))). This study showed that although tree topologies were sensitive to data types and inference methods, mitogenomic data could provide useful information for resolving the Coleoptera phylogeny at various taxonomic levels by using suitable datasets and heterogeneous-site models. PMID:27497607

  12. Distribution and Evolution of Repeated Sequences in Genomes of Triatominae (Hemiptera-Reduviidae) Inferred from Genomic In Situ Hybridization

    PubMed Central

    Pita, Sebastian; Panzera, Francisco; Sánchez, Antonio; Panzera, Yanina; Palomeque, Teresa; Lorite, Pedro

    2014-01-01

    The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily. PMID:25478792

  13. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

    PubMed Central

    Krause, David J.; Whitaker, Rachel J.

    2015-01-01

    Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms. PMID:26316424

  14. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.

    PubMed

    Keller, Andreas; Graefen, Angela; Ball, Markus; Matzas, Mark; Boisguerin, Valesca; Maixner, Frank; Leidinger, Petra; Backes, Christina; Khairat, Rabab; Forster, Michael; Stade, Björn; Franke, Andre; Mayer, Jens; Spangler, Jessica; McLaughlin, Stephen; Shah, Minita; Lee, Clarence; Harkins, Timothy T; Sartori, Alexander; Moreno-Estrada, Andres; Henn, Brenna; Sikora, Martin; Semino, Ornella; Chiaroni, Jacques; Rootsi, Siiri; Myres, Natalie M; Cabrera, Vicente M; Underhill, Peter A; Bustamante, Carlos D; Vigl, Eduard Egarter; Samadelli, Marco; Cipollini, Giovanna; Haas, Jan; Katus, Hugo; O'Connor, Brian D; Carlson, Marc R J; Meder, Benjamin; Blin, Nikolaus; Meese, Eckart; Pusch, Carsten M; Zink, Albert

    2012-01-01

    The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis. PMID:22426219

  15. Interspecific Chromosome Substitution Lines as Genetic Resources for Improvement, Trait Analyses and Genomic Inference

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three of the research areas likely to very significantly impact genetic improvement of cotton are interspecific introgression, genetic dissection of complex traits and sequencing of [AD] genomes. Interspecific introgression is expected to increase genetic diversity of breeding germplasm, creating op...

  16. Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae.

    PubMed

    Low, Chen-Fei; Bunawan, Hamidun

    2016-09-01

    In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset. PMID:27617282

  17. Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions

    PubMed Central

    Tucci, Serena; de Manuel, Marc; Ghirotto, Silvia; Benazzo, Andrea; Prado-Martinez, Javier; Lorente-Galdos, Belen; Nam, Kiwoong; Dabad, Marc; Hernandez-Rodriguez, Jessica; Comas, David; Navarro, Arcadi; Schierup, Mikkel H.; Andres, Aida M.; Barbujani, Guido; Hvilsom, Christina; Marques-Bonet, Tomas

    2016-01-01

    The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81–1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41–0.78] with further internal separations at 0.32 Mya [0.22–0.43] and 0.16 Mya [0.17–0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics. PMID:27345955

  18. Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

    PubMed

    Lobon, Irene; Tucci, Serena; de Manuel, Marc; Ghirotto, Silvia; Benazzo, Andrea; Prado-Martinez, Javier; Lorente-Galdos, Belen; Nam, Kiwoong; Dabad, Marc; Hernandez-Rodriguez, Jessica; Comas, David; Navarro, Arcadi; Schierup, Mikkel H; Andres, Aida M; Barbujani, Guido; Hvilsom, Christina; Marques-Bonet, Tomas

    2016-01-01

    The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics. PMID:27345955

  19. Adaptation, Ecology, and Evolution of the Halophilic Stromatolite Archaeon Halococcus hamelinensis Inferred through Genome Analyses

    PubMed Central

    Gudhka, Reema K.; Neilan, Brett A.; Burns, Brendan P.

    2015-01-01

    Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer. PMID:25709556

  20. Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.

    PubMed

    Gudhka, Reema K; Neilan, Brett A; Burns, Brendan P

    2015-01-01

    Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer. PMID:25709556

  1. Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae).

    PubMed

    Do, Hoang Dang Khoa; Kim, Jung Sung; Kim, Joo-Hwan

    2013-11-10

    The sequence of the chloroplast genome, which is inherited maternally, contains useful information for many scientific fields such as plant systematics, biogeography and biotechnology because its characteristics are highly conserved among species. There is an increase in chloroplast genomes of angiosperms that have been sequenced in recent years. In this study, the nucleotide sequence of the chloroplast genome (cpDNA) of Veratrum patulum Loes. (Melanthiaceae, Liliales) was analyzed completely. The circular double-stranded DNA of 153,699 bp consists of two inverted repeat (IR) regions of 26,360 bp each, a large single copy of 83,372 bp, and a small single copy of 17,607 bp. This plastome contains 81 protein-coding genes, 30 distinct tRNA and four genes of rRNA. In addition, there are six hypothetical coding regions (ycf1, ycf2, ycf3, ycf4, ycf15 and ycf68) and two open reading frames (ORF42 and ORF56), which are also found in the chloroplast genomes of the other species. The gene orders and gene contents of the V. patulum plastid genome are similar to that of Smilax china, Lilium longiflorum and Alstroemeria aurea, members of the Smilacaceae, Liliaceae and Alstroemeriaceae (Liliales), respectively. However, the loss rps16 exon 2 in V. patulum results in the difference in the large single copy regions in comparison with other species. The base substitution rate is quite similar among genes of these species. Additionally, the base substitution rate of inverted repeat region was smaller than that of single copy regions in all observed species of Liliales. The IR regions were expanded to trnH_GUG in V. patulum, a part of rps19 in L. longiflorum and A. aurea, and whole sequence of rps19 in S. china. Furthermore, the IGS lengths of rbcL-accD-psaI region were variable among Liliales species, suggesting that this region might be a hotspot of indel events and the informative site for phylogenetic studies in Liliales. In general, the whole chloroplast genome of V. patulum, a

  2. Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies.

    PubMed

    Sharakhov, Igor V; Artemov, Gleb N; Sharakhova, Maria V

    2016-04-01

    Polymorphic inversions in mosquitoes are distributed nonrandomly among chromosomes and are associated with ecological, behavioral, and physiological adaptations related to pathogen transmission. Despite their significance, the patterns and mechanism of genome rearrangements are not well understood. Recent sequencing and physical mapping of the genomes for 16 Anopheles mosquito species provided an opportunity to study chromosome evolution at the highest resolution. New studies revealed that fixed rearrangement accumulated [Formula: see text]3 times faster on the X chromosome than on autosomes. The highest densities of transposable elements (TEs) and satellites of different sizes have also been found on the X chromosome, suggesting a mechanism for the inversion generation. The high rate of X chromosome rearrangements is in sharp contrast with the paucity of polymorphic inversions on the X in the majority of anopheline species. This paper highlights the advances in understanding chromosome evolution in malaria vectors and discusses possible future directions in studying mechanisms and biological roles of genome rearrangements. PMID:27021248

  3. Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order

    PubMed Central

    Bancroft, Ian; Fraser, Fiona; Morgan, Colin; Trick, Martin

    2015-01-01

    This data article includes SNP scoring across lines of the Brassica napus TNDH population based on Illumina sequencing of mRNA, expanded to 75 lines. The 21, 323 mapped markers defined 887 recombination bins, representing an updated genetic linkage map for the species. Based on this new map, 5 genome sequence scaffolds were split and the order and orientation of scaffolds updated to establish a new pseudomolecule specification. The order of unigenes and SNP array probes within these pseudomolecules was determined. Unigenes were assessed for sequence similarity to the A and C genomes. The 57, 246 that mapped to both enabled the collinearity of the A and C genomes to be illustrated graphically. Although the great majority was in collinear positions, some were not. Analyses of 60 such instances are presented, suggesting that the breakdown in collinearity was largely due to either the absence of the homoeologue on one genome (resulting in sequence match to a paralogue) or multiple similar sequences being present. The mRNAseq datasets for the TNDH lines are available from the SRA repository (ERA283648); the remaining datasets are supplied with this article. PMID:26217717

  4. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

    PubMed

    Qiu, Yu-Qing; Tian, Xue; Zhang, Shihua

    2015-01-01

    Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes. PMID:26451823

  5. Interspecific chromosome substitution lines as genetic resources for improvement, trait analysis and genomic inference

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic base that cotton breeders commonly use to improve Upland cultivars is very narrow. The AD-genome species G. barbadense, G. tomentosum, and G. mustelinum are part of the primary germplasm pool, too, and constitute genetic reservoirs of genes for resistance to abiotic stress, pests and pa...

  6. Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome.

    PubMed

    Barghi, Neda; Concepcion, Gisela P; Olivera, Baldomero M; Lluisma, Arturo O

    2016-02-01

    The evolvability of venom components (in particular, the gene-encoded peptide toxins) in venomous species serves as an adaptive strategy allowing them to target new prey types or respond to changes in the prey field. The structure, organization, and expression of the venom peptide genes may provide insights into the molecular mechanisms that drive the evolution of such genes. Conus is a particularly interesting group given the high chemical diversity of their venom peptides, and the rapid evolution of the conopeptide-encoding genes. Conus genomes, however, are large and characterized by a high proportion of repetitive sequences. As a result, the structure and organization of conopeptide genes have remained poorly known. In this study, a survey of the genome of Conus tribblei was undertaken to address this gap. A partial assembly of C. tribblei genome was generated; the assembly, though consisting of a large number of fragments, accounted for 2160.5 Mb of sequence. A large number of repetitive genomic elements consisting of 642.6 Mb of retrotransposable elements, simple repeats, and novel interspersed repeats were observed. We characterized the structural organization and distribution of conotoxin genes in the genome. A significant number of conopeptide genes (estimated to be between 148 and 193) belonging to different superfamilies with complete or nearly complete exon regions were observed, ~60 % of which were expressed. The unexpressed conopeptide genes represent hidden but significant conotoxin diversity. The conotoxin genes also differed in the frequency and length of the introns. The interruption of exons by long introns in the conopeptide genes and the presence of repeats in the introns may indicate the importance of introns in facilitating recombination, evolution and diversification of conotoxins. These findings advance our understanding of the structural framework that promotes the gene-level molecular evolution of venom peptides. PMID:26423067

  7. Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

    PubMed Central

    Ruiz-Herrera, Aurora; Robinson, Terence J

    2007-01-01

    Background Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all

  8. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)

    PubMed Central

    Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

    2016-01-01

    Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus. PMID:27336696

  9. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    PubMed

    Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

    2016-03-01

    Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

  10. Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.

    PubMed

    Nobu, Masaru K; Dodsworth, Jeremy A; Murugapiran, Senthil K; Rinke, Christian; Gies, Esther A; Webster, Gordon; Schwientek, Patrick; Kille, Peter; Parkes, R John; Sass, Henrik; Jørgensen, Bo B; Weightman, Andrew J; Liu, Wen-Tso; Hallam, Steven J; Tsiamis, George; Woyke, Tanja; Hedlund, Brian P

    2016-02-01

    The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate. PMID:26090992

  11. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

    PubMed Central

    Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

    2016-01-01

    Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

  12. Simple Math is Enough: Two Examples of Inferring Functional Associations from Genomic Data

    NASA Technical Reports Server (NTRS)

    Liang, Shoudan

    2003-01-01

    Non-random features in the genomic data are usually biologically meaningful. The key is to choose the feature well. Having a p-value based score prioritizes the findings. If two proteins share a unusually large number of common interaction partners, they tend to be involved in the same biological process. We used this finding to predict the functions of 81 un-annotated proteins in yeast.

  13. Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

    PubMed

    Renz, Adina J; Meyer, Axel; Kuraku, Shigehiro

    2013-01-01

    Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon. PMID:23825540

  14. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

    PubMed Central

    Hodgson, Jason A.; Burrell, Andrew S.; Sterner, Kirstin N.; Raaum, Ryan L.; Disotell, Todd R.

    2014-01-01

    The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56 Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74 Ma. This result supports a short fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled. PMID:24583291

  15. Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels.

    PubMed

    Li, T; Wang, J; Su, W; Nie, W; Yang, F

    2006-01-01

    Cross-species chromosome painting has made a great contribution to our understanding of the evolution of karyotypes and genome organizations of mammals. Several recent papers of comparative painting between tree and flying squirrels have shed some light on the evolution of the family Sciuridae and the order Rodentia. In the present study we have extended the comparative painting to the Himalayan marmot (Marmotahimalayana) and the African ground squirrel (Xerus cf. erythropus), i.e. representative species from another important squirrel group--the ground squirrels--, and have established genome-wide comparative chromosome maps between human, eastern gray squirrel, and these two ground squirrels. The results show that 1) the squirrels so far studied all have conserved karyotypes that resemble the ancestral karyotype of the order Rodentia; 2) the African ground squirrels could have retained the ancestral karyotype of the family Sciuridae. Furthermore, we have mapped the evolutionary rearrangements onto a molecular-based consensus phylogenetic tree of the family Sciuridae. PMID:16484783

  16. Inferring Properties of Ancient Cyanobacteria from Biogeochemical Activity and Genomes of Siderophilic Cyanobacteria

    NASA Technical Reports Server (NTRS)

    McKay, David S.; Brown, I. I.; Tringe, S. G.; Thomas-Keprta, K. E.; Bryant, D. A.; Sarkisova, S. S.; Malley, K.; Sosa, O.; Klatt, C. G.; McKay, D. S.

    2010-01-01

    Interrelationships between life and the planetary system could have simultaneously left landmarks in genomes of microbes and physicochemical signatures in the lithosphere. Verifying the links between genomic features in living organisms and the mineralized signatures generated by these organisms will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models [1] for insights into ancient life since organisms may have originated on Earth and probably Mars in association with hydrothermal activity [2,3]. IDHS also seem to be appropriate models for studying certain biogeochemical processes that could have taken place in the late Archean and,-or early Paleoproterozoic eras [4, 5]. It has been suggested that inorganic polyphosphate (PPi), in chains of tens to hundreds of phosphate residues linked by high-energy bonds, is environmentally ubiquitous and abundant [6]. Cyanobacteria (CB) react to increased heavy metal concentrations and UV by enhanced generation of PPi bodies (PPB) [7], which are believed to be signatures of life [8]. However, the role of PPi in oxygenic prokaryotes for the suppression of oxidative stress induced by high Fe is poorly studied. Here we present preliminary results of a new mechanism of Fe mineralization in oxygenic prokaryotes, the effect of Fe on the generation of PPi bodies in CB, as well as preliminary analysis of the diversity and phylogeny of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

  17. King penguin demography since the last glaciation inferred from genome-wide data

    PubMed Central

    Trucchi, Emiliano; Gratton, Paolo; Whittington, Jason D.; Cristofari, Robin; Le Maho, Yvon; Stenseth, Nils Chr; Le Bohec, Céline

    2014-01-01

    How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition. PMID:24920481

  18. Evolutionary landscape of amphibians emerging from ancient freshwater fish inferred from complete mitochondrial genomes.

    PubMed

    Wang, Xiao-Tong; Zhang, Yan-Feng; Wu, Qian; Zhang, Hao

    2012-05-01

    It is very interesting that the only extant marine amphibian is the marine frog, Fejervarya cancrivora. This study investigated the reasons for this apparent rarity by conducting a phylogenetic tree analysis of the complete mitochondrial genomes from 14 amphibians, 67 freshwater fishes, four migratory fishes, 35 saltwater fishes, and one hemichordate. The results showed that amphibians, living fossil fishes, and the common ancestors of modern fishes are phylogenetically separated. In general, amphibians, living fossil fishes, saltwater fishes, and freshwater fishes are clustered in different clades. This suggests that the ancestor of living amphibians arose from a type of primordial freshwater fish, rather than the coelacanth, lungfish, or modern saltwater fish. Modern freshwater fish and modern saltwater fish were probably separated from a common ancestor by a single event, caused by crustal movement. PMID:22503684

  19. Stream Hydrological Fragmentation Drives Bacterioplankton Community Composition

    PubMed Central

    Fazi, Stefano; Vázquez, Eusebi; Casamayor, Emilio O.; Amalfitano, Stefano; Butturini, Andrea

    2013-01-01

    In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition. PMID:23741302

  20. Conflicting genomic signals affect phylogenetic inference in four species of North American pines.

    PubMed

    Koralewski, Tomasz E; Mateos, Mariana; Krutovsky, Konstantin V

    2016-01-01

    Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata-taeda, genes linked to plant defence supported the clade echinata-elliottii and genes linked to water management properties supported the clade echinata-palustris The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations. PMID:27060161

  1. Conflicting genomic signals affect phylogenetic inference in four species of North American pines

    PubMed Central

    Koralewski, Tomasz E.; Mateos, Mariana; Krutovsky, Konstantin V.

    2016-01-01

    Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata–taeda, genes linked to plant defence supported the clade echinata–elliottii and genes linked to water management properties supported the clade echinata–palustris. The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations. PMID

  2. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding

    PubMed Central

    Gilad, Yoav; Pritchard, Jonathan K.; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede. PMID:26406244

  3. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.

    PubMed

    Raj, Anil; Shim, Heejung; Gilad, Yoav; Pritchard, Jonathan K; Stephens, Matthew

    2015-01-01

    Understanding global gene regulation depends critically on accurate annotation of regulatory elements that are functional in a given cell type. CENTIPEDE, a powerful, probabilistic framework for identifying transcription factor binding sites from tissue-specific DNase I cleavage patterns and genomic sequence content, leverages the hypersensitivity of factor-bound chromatin and the information in the DNase I spatial cleavage profile characteristic of each DNA binding protein to accurately infer functional factor binding sites. However, the model for the spatial profile in this framework fails to account for the substantial variation in the DNase I cleavage profiles across different binding sites. Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available. In this work, we introduce new methods, based on multi-scale models for inhomogeneous Poisson processes, to account for such variation in DNase I cleavage patterns both within and across binding sites. These models account for the spatial structure in the heterogeneity in DNase I cleavage patterns for each factor. Using DNase-seq measurements assayed in a lymphoblastoid cell line, we demonstrate the improved performance of this model for several transcription factors by comparing against the Chip-seq peaks for those factors. Finally, we explore the effects of DNase I sequence bias on inference of factor binding using a simple extension to our framework that allows for a more flexible background model. The proposed model can also be easily applied to paired-end ATAC-seq and DNase-seq data. msCentipede, a Python implementation of our algorithm, is available at http://rajanil.github.io/msCentipede. PMID:26406244

  4. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

    SciTech Connect

    Mueller, Rachel Lockridge; Macey, J. Robert; Jaekel, Martin; Wake, David B.; Boore, Jeffrey L.

    2004-08-01

    The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent, molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, ML, and MP phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (PP > 0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three out of four major groups is rejected. Reanalysis of current hypotheses in light of these new evolutionary relationships suggests that (1) a larval life history stage re-evolved from a direct-developing ancestor multiple times, (2) there is no phylogenetic support for the ''Out of Appalachia'' hypothesis of plethodontid origins, and (3) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these novel scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.

  5. Origins of the Moken Sea Gypsies inferred from mitochondrial hypervariable region and whole genome sequences.

    PubMed

    Dancause, Kelsey Needham; Chan, Chim W; Arunotai, Narumon Hinshiranan; Lum, J Koji

    2009-02-01

    The origins of the Moken 'Sea Gypsies,' a group of traditionally boat-dwelling nomadic foragers, remain speculative despite previous examinations from linguistic, sociocultural and genetic perspectives. We explored Moken origin(s) and affinities by comparing whole mitochondrial genome and hypervariable segment I sequences from 12 Moken individuals, sampled from four islands of the Mergui Archipelago, to other mainland Asian, Island Southeast Asian (ISEA) and Oceanic populations. These analyses revealed a major (11/12) and a minor (1/12) haplotype in the population, indicating low mitochondrial diversity likely resulting from historically low population sizes, isolation and consequent genetic drift. Phylogenetic analyses revealed close relationships between the major lineage (MKN1) and ISEA, mainland Asian and aboriginal Malay populations, and of the minor lineage (MKN2) to populations from ISEA. MKN1 belongs to a recently defined subclade of the ancient yet localized M21 haplogroup. MKN2 is not closely related to any previously sampled lineages, but has been tentatively assigned to the basal M46 haplogroup that possibly originated among the original inhabitants of ISEA. Our analyses suggest that MKN1 originated within coastal mainland SEA and dispersed into ISEA and rapidly into the Mergui Archipelago within the past few thousand years as a result of climate change induced population pressure. PMID:19158811

  6. Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.

    PubMed

    Vanet, A; Marsan, L; Labigne, A; Sagot, M F

    2000-03-24

    Helicobacter pylori is adapted to life in a unique niche, the gastric epithelium of primates. Its promoters may therefore be different from those of other bacteria. Here, we determine motifs possibly involved in the recognition of such promoter sequences by the RNA polymerase using a new motif identification method. An important feature of this method is that the motifs are sought with the least possible assumptions about what they may look like. The method starts by considering the whole genome of H. pylori and attempts to infer directly from it a description for a family of promoters. Thus, this approach differs from searching for such promoters with a previously established description. The two algorithms are based on the idea of inferring motifs by flexibly comparing words in the sequences with an external object, instead of between themselves. The first algorithm infers single motifs, the second a combination of two motifs separated from one another by strictly defined, sterically constrained distances. Besides independently finding motifs known to be present in other bacteria, such as the Shine-Dalgarno sequence and the TATA-box, this approach suggests the existence in H. pylori of a new, combined motif, TTAAGC, followed optimally 21 bp downstream by TATAAT. Between these two motifs, there is in some cases another, TTTTAA or, less frequently, a repetition of TTAAGC separated optimally from the TATA-box by 12 bp. The combined motif TTAAGCx(21+/-2)TATAAT is present with no errors immediately upstream from the only two copies of the ribosomal 23 S-5 S RNA genes in H. pylori, and with one error upstream from the only two copies of the ribosomal 16 S RNA genes. The operons of both ribosomal RNA molecules are strongly expressed, representing an encouraging sign of the pertinence of the motifs found by the algorithms. In 25 cases out of a possible 30, the combined motif is found with no more than three substitutions immediately upstream from ribosomal proteins, or

  7. Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters

    PubMed Central

    Timme, Ruth E.; Pettengill, James B.; Allard, Marc W.; Strain, Errol; Barrangou, Rodolphe; Wehnes, Chris; Van Kessel, JoAnn S.; Karns, Jeffrey S.; Musser, Steven M.; Brown, Eric W.

    2013-01-01

    The enteric pathogen Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles—some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large-scale S. enterica subsp. enterica phylogeny inferred from a new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (102 were newly sequenced) reveals two major lineages, each with many strongly supported sublineages. One of these lineages is the S. Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and CRISPR loci reveal different evolutionary patterns than that of the phylogeny, suggesting that a horizontal gene transfer or possibly a shared environmental acquisition might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms. PMID:24158624

  8. Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses.

    PubMed

    Siering, P L; Ghiorse, W C

    1996-01-01

    Phase-contrast light microscopy revealed that only one of eight cultivated strains belonging to the Sphaerotilus-Leptothrix group of sheathed bacteria actually produced a sheath in standard growth media. Two Sphaerotilus natans strains produced branched cells, but other morphological characteristics that were used to identify these bacteria were consistent with previously published descriptions. Genomic fingerprints, which were obtained by performing PCR amplification with primers corresponding to enterobacterial repetitive intergenic consensus sequences, were useful for distinguishing between the genera Sphaerotilus and Leptothrix, as well as among individual strains. The complete 16S ribosomal DNA (rDNA) sequences of two strains of "Leptothrix discophora" (strains SP-6 and SS-1) were determined. In addition, partial sequences (approximately 300 nucleotides) of one strain of Leptothrix cholodnii (strain LMG 7171), an unidentified Leptothrix strain (strain NC-1), and four strains of Sphaerotilus natans (strains ATCC 13338T [T = type strain], ATCC 15291, ATCC 29329, and ATCC 29330) were determined. We found that two of the S. natans strains (ATCC 15291 and ATCC 13338T), which differed in morphology and in their genomic fingerprints, had identical sequences in the 300-nucleotide region sequenced. Both parsimony and distance matrix methods were used to infer the evolutionary relationships of the eight strains in a comparison of the 16S rDNA sequences of these organisms with 16S rDNA sequences obtained from ribosomal sequence databases. All of the strains clustered in the Rubrivivax subdivision of the beta subclass of the Proteobacteria, which confirmed previously published conclusions concerning selected individual strains. Additional analyses revealed that all of the S. natans strains clustered in one closely related group, while the Leptothrix strains clustered in two separate lineages that were approximately equidistant from the S. natans cluster. This finding

  9. Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling

    PubMed Central

    Benavides, Julio A; Cross, Paul C; Luikart, Gordon; Creel, Scott

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced. PMID:25469159

  10. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling.

    PubMed

    Lindh, Markus V; Sjöstedt, Johanna; Andersson, Anders F; Baltar, Federico; Hugerth, Luisa W; Lundin, Daniel; Muthusamy, Saraladevi; Legrand, Catherine; Pinhassi, Jarone

    2015-07-01

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure. PMID:25403576

  11. The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches

    PubMed Central

    Wemheuer, Bernd; Wemheuer, Franziska; Hollensteiner, Jacqueline; Meyer, Frauke-Dorothee; Voget, Sonja; Daniel, Rolf

    2015-01-01

    Phytoplankton blooms exhibit a severe impact on bacterioplankton communities as they change nutrient availabilities and other environmental factors. In the current study, the response of a bacterioplankton community to a Phaeocystis globosa spring bloom was investigated in the southern North Sea. For this purpose, water samples were taken inside and reference samples outside of an algal spring bloom. Structural changes of the bacterioplankton community were assessed by amplicon-based analysis of 16S rRNA genes and transcripts generated from environmental DNA and RNA, respectively. Several marine groups responded to bloom presence. The abundance of the Roseobacter RCA cluster and the SAR92 clade significantly increased in bloom presence in the total and active fraction of the bacterial community. Functional changes were investigated by direct sequencing of environmental DNA and mRNA. The corresponding datasets comprised more than 500 million sequences across all samples. Metatranscriptomic data sets were mapped on representative genomes of abundant marine groups present in the samples and on assembled metagenomic and metatranscriptomic datasets. Differences in gene expression profiles between non-bloom and bloom samples were recorded. The genome-wide gene expression level of Planktomarina temperata, an abundant member of the Roseobacter RCA cluster, was higher inside the bloom. Genes that were differently expressed included transposases, which showed increased expression levels inside the bloom. This might contribute to the adaptation of this organism toward environmental stresses through genome reorganization. In addition, several genes affiliated to the SAR92 clade were significantly upregulated inside the bloom including genes encoding for proteins involved in isoleucine and leucine incorporation. Obtained results provide novel insights into compositional and functional variations of marine bacterioplankton communities as response to a phytoplankton bloom. PMID

  12. Genome at Juncture of Early Human Migration: A Systematic Analysis of Two Whole Genomes and Thirteen Exomes from Kuwaiti Population Subgroup of Inferred Saudi Arabian Tribe Ancestry

    PubMed Central

    Alsmadi, Osama; Hebbar, Prashantha; Antony, Dinu; Behbehani, Kazem; Thanaraj, Thangavel Alphonse

    2014-01-01

    Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are ‘novel’. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10−16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3′ UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian

  13. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

    PubMed Central

    Martinez-Garcia, Manuel; Swan, Brandon K; Poulton, Nicole J; Gomez, Monica Lluesma; Masland, Dashiell; Sieracki, Michael E; Stepanauskas, Ramunas

    2012-01-01

    Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10–23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments

  14. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.

    PubMed

    Martinez-Garcia, Manuel; Swan, Brandon K; Poulton, Nicole J; Gomez, Monica Lluesma; Masland, Dashiell; Sieracki, Michael E; Stepanauskas, Ramunas

    2012-01-01

    Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments

  15. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis.

    PubMed

    Imoto, Junichi M; Saitoh, Kenji; Sasaki, Takeshi; Yonezawa, Takahiro; Adachi, Jun; Kartavtsev, Yuri P; Miya, Masaki; Nishida, Mutsumi; Hanzawa, Naoto

    2013-02-10

    The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily. Phylogenetic analysis suggests that the Far Eastern phoxinin species comprised the monophyletic clades Tribolodon, Pseudaspius, Oreoleuciscus and Far Eastern Phoxinus. The Far Eastern phoxinin clade was independent of other Leuciscinae lineages and was closer to North American phoxinins than European leuciscins. All of our analysis also suggested that leuciscins and phoxinins each constituted monophyletic groups. Divergence time estimation suggested that Leuciscinae species diverged from outgroups such as Tincinae to be 83.3 million years ago (Mya) in the Late Cretaceous and leuciscin and phoxinin shared a common ancestor 70.7 Mya. Radiation of Leuciscinae lineages occurred during the Late Cretaceous to Paleocene. This period also witnessed the radiation of tetrapods. Reconstruction of ancestral areas indicates Leuciscinae species originated within Europe. Leuciscin species evolved in Europe and the ancestor of phoxinin was distributed in North America. The Far Eastern phoxinins would have dispersed from North America to Far East across the Beringia land bridge. The present study suggests important roles for the continental rearrangements during the

  16. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

    PubMed Central

    2012-01-01

    Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13

  17. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

    PubMed Central

    2013-01-01

    Background A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. Results The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. Conclusions Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. Reviewers This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia PMID:23607440

  18. Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary

    PubMed Central

    Laas, Peeter; Simm, Jaak; Lips, Inga; Lips, Urmas; Kisand, Veljo; Metsis, Madis

    2015-01-01

    This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilities to utilize different electron receptors and donors (including trace metal and single carbon compounds). On the other hand, temporal shifts in the bacterioplankton community composition at the surface layer were mainly connected to the seasonal succession of phytoplankton and the inflow of freshwater species. We also conclude that many relatively abundant populations are indigenous and well-established in the area. PMID:25860812

  19. Functional characterization of somatic mutations in cancer using network-based inference of protein activity | Office of Cancer Genomics

    Cancer.gov

    Identifying the multiple dysregulated oncoproteins that contribute to tumorigenesis in a given patient is crucial for developing personalized treatment plans. However, accurate inference of aberrant protein activity in biological samples is still challenging as genetic alterations are only partially predictive and direct measurements of protein activity are generally not feasible.

  20. Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships

    PubMed Central

    Brewer, Michael S.; Swafford, Lynn; Spruill, Chad L.; Bond, Jason E.

    2013-01-01

    Background Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. Results The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. Conclusions The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the

  1. Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

    PubMed Central

    Rappé, Michael S.

    2013-01-01

    In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

  2. Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

    USGS Publications Warehouse

    Urbach, Ena; Vergin, Kevin L.; Morse, Ariel

    2001-01-01

    The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (<=16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

  3. Bacterioplankton carbon cycling along the Subtropical Frontal Zone off New Zealand

    NASA Astrophysics Data System (ADS)

    Baltar, Federico; Stuck, Esther; Morales, Sergio; Currie, Kim

    2015-06-01

    Marine heterotrophic bacterioplankton (Bacteria and Archaea) play a central role in ocean carbon cycling. As such, identifying the factors controlling these microbial populations is crucial to fully understanding carbon fluxes. We studied bacterioplankton activities along a transect crossing three water masses (i.e., Subtropical waters [STW], Sub-Antarctic waters [SAW] and neritic waters [NW]) with contrasting nutrient regimes across the Subtropical Frontal Zone. In contrast to bacterioplankton production and community respiration, bacterioplankton respiration increased in the offshore SAW, causing a seaward increase in the contribution of bacteria to community respiration (from 7% to 100%). Cell-specific bacterioplankton respiration also increased in SAW, but cell-specific production did not, suggesting that prokaryotic cells in SAW were investing more energy towards respiration than growth. This was reflected in a 5-fold decline in bacterioplankton growth efficiency (BGE) towards SAW. One way to explain this decrease in BGE could be due to the observed reduction in phytoplankton biomass (and presumably organic matter concentration) towards SAW. However, this would not explain why bacterioplankton respiration was highest in SAW, where phytoplankton biomass was lowest. Another factor affecting BGE could be the iron limitation characteristic of high-nutrient low-chlorophyll (HNLC) regions like SAW. Our field-study based evidences would agree with previous laboratory experiments in which iron stress provoked a decrease in BGE of marine bacterial isolates. Our results suggest that there is a strong gradient in bacterioplankton carbon cycling rates along the Subtropical Frontal Zone, mainly due to the HNLC conditions of SAW. We suggest that Fe-induced reduction of BGE in HNLC regions like SAW could be relevant in marine carbon cycling, inducing bacterioplankton to act as a link or a sink of organic carbon by impacting on the quantity of organic carbon they incorporate

  4. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

    PubMed Central

    Stinear, Timothy P.; Seemann, Torsten; Pidot, Sacha; Frigui, Wafa; Reysset, Gilles; Garnier, Thierry; Meurice, Guillaume; Simon, David; Bouchier, Christiane; Ma, Laurence; Tichit, Magali; Porter, Jessica L.; Ryan, Janine; Johnson, Paul D.R.; Davies, John K.; Jenkin, Grant A.; Small, Pamela L.C.; Jones, Louis M.; Tekaia, Fredj; Laval, Françoise; Daffé, Mamadou; Parkhill, Julian; Cole, Stewart T.

    2007-01-01

    Mycobacterium ulcerans is found in aquatic ecosystems and causes Buruli ulcer in humans, a neglected but devastating necrotic disease of subcutaneous tissue that is rampant throughout West and Central Africa. Here, we report the complete 5.8-Mb genome sequence of M. ulcerans and show that it comprises two circular replicons, a chromosome of 5632 kb and a virulence plasmid of 174 kb. The plasmid is required for production of the polyketide toxin mycolactone, which provokes necrosis. Comparisons with the recently completed 6.6-Mb genome of Mycobacterium marinum revealed >98% nucleotide sequence identity and genome-wide synteny. However, as well as the plasmid, M. ulcerans has accumulated 213 copies of the insertion sequence IS2404, 91 copies of IS2606, 771 pseudogenes, two bacteriophages, and multiple DNA deletions and rearrangements. These data indicate that M. ulcerans has recently evolved via lateral gene transfer and reductive evolution from the generalist, more rapid-growing environmental species M. marinum to become a niche-adapted specialist. Predictions based on genome inspection for the production of modified mycobacterial virulence factors, such as the highly abundant phthiodiolone lipids, were confirmed by structural analyses. Similarly, 11 protein-coding sequences identified as M. ulcerans-specific by comparative genomics were verified as such by PCR screening a diverse collection of 33 strains of M. ulcerans and M. marinum. This work offers significant insight into the biology and evolution of mycobacterial pathogens and is an important component of international efforts to counter Buruli ulcer. PMID:17210928

  5. Prokaryotic genes in eukaryotic genome sequences: when to infer horizontal gene transfer and when to suspect an actual microbe.

    PubMed

    Artamonova, Irena I; Lappi, Tanya; Zudina, Liudmila; Mushegian, Arcady R

    2015-07-01

    Assessment of phylogenetic positions of predicted gene and protein sequences is a routine step in any genome project, useful for validating the species' taxonomic position and for evaluating hypotheses about genome evolution and function. Several recent eukaryotic genome projects have reported multiple gene sequences that were much more similar to homologues in bacteria than to any eukaryotic sequence. In the spirit of the times, horizontal gene transfer from bacteria to eukaryotes has been invoked in some of these cases. Here, we show, using comparative sequence analysis, that some of those bacteria-like genes indeed appear likely to have been horizontally transferred from bacteria to eukaryotes. In other cases, however, the evidence strongly indicates that the eukaryotic DNA sequenced in the genome project contains a sample of non-integrated DNA from the actual bacteria, possibly providing a window into the host microbiome. Recent literature suggests also that common reagents, kits and laboratory equipment may be systematically contaminated with bacterial DNA, which appears to be sampled by metagenome projects non-specifically. We review several bioinformatic criteria that help to distinguish putative horizontal gene transfers from the admixture of genes from autonomously replicating bacteria in their hosts' genome databases or from the reagent contamination. PMID:25919787

  6. The new physician as unwitting quantum mechanic: is adapting Dirac's inference system best practice for personalized medicine, genomics, and proteomics?

    PubMed

    Robson, Barry

    2007-08-01

    What is the Best Practice for automated inference in Medical Decision Support for personalized medicine? A known system already exists as Dirac's inference system from quantum mechanics (QM) using bra-kets and bras where A and B are states, events, or measurements representing, say, clinical and biomedical rules. Dirac's system should theoretically be the universal best practice for all inference, though QM is notorious as sometimes leading to bizarre conclusions that appear not to be applicable to the macroscopic world of everyday world human experience and medical practice. It is here argued that this apparent difficulty vanishes if QM is assigned one new multiplication function @, which conserves conditionality appropriately, making QM applicable to classical inference including a quantitative form of the predicate calculus. An alternative interpretation with the same consequences is if every i = radical-1 in Dirac's QM is replaced by h, an entity distinct from 1 and i and arguably a hidden root of 1 such that h2 = 1. With that exception, this paper is thus primarily a review of the application of Dirac's system, by application of linear algebra in the complex domain to help manipulate information about associations and ontology in complicated data. Any combined bra-ket can be shown to be composed only of the sum of QM-like bra and ket weights c(), times an exponential function of Fano's mutual information measure I(A; B) about the association between A and B, that is, an association rule from data mining. With the weights and Fano measure re-expressed as expectations on finite data using Riemann's Incomplete (i.e., Generalized) Zeta Functions, actual counts of observations for real world sparse data can be readily utilized. Finally, the paper compares identical character, distinguishability of states events or measurements, correlation, mutual information, and orthogonal character, important issues in data mining

  7. Horizontal Variation of Bacterioplankton in the Baltic Sea

    PubMed Central

    Heinänen, Anne; Kuparinen, Jorma

    1991-01-01

    Variations in the thymidine incorporation rate, bacterial abundance, and mean cell volumes in the surface water (0.5 m) of the Baltic Sea in spring and summer were compared in studies with different spatial scales (570 nautical miles [nmi] [ca. 1056 km], 220 nmi [ca. 407 km], 24 nmi [ca. 44 km], 12 nmi [ca. 22 km], and 200 m). The objective of the comparison was to investigate whether a single sample taken at one sampling point is representative enough for researchers to make generalizations about a larger water area. Bacterioplankton variation was connected more to seasonal characteristics than to the spatial scale of sampling. Variation was greater and more random in spring than in summer. The state variables (bacterial abundance and mean cell volume) varied less than the rate variable (thymidine incorporation). The results suggest that the sampling design for bacterioplankton studies in northern temperate seas should be planned primarily according to the season and that more stress should be put on rate variable measurements than on those of state variables. PMID:16348580

  8. Phylogeny and genetic history of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870) inferred from complete mitochondrial genomes.

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Denisova, Galina

    2013-05-01

    We assessed phylogeny of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), the most northern ectothermic, terrestrial vertebrate in Eurasia, by sequence analysis of complete mitochondrial genomes in 26 specimens from different localities (China, Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka, Ural, European part of Russia). In addition, a complete mitochondrial genome of the Schrenck salamander, Salamandrella schrenckii, was determined for the first time. Bayesian phylogenetic analysis of the entire mtDNA genomes of S. keyserlingii demonstrates that two haplotype clades, AB and C, radiated about 1.4 million years ago (Mya). Bayesian skyline plots of population size change through time show an expansion around 250 thousand years ago (kya) and then a decline around the Last Glacial Maximum (25 kya) with subsequent restoration of population size. Climatic changes during the Quaternary period have dramatically affected the population genetic structure of the Siberian salamanders. In addition, complete mtDNA sequence analysis allowed us to recognize that the vast area of Northern Eurasia was colonized only by the Siberian salamander clade C1b during the last 150 kya. Meanwhile, we were unable to find evidence of molecular adaptation in this clade by analyzing the whole mitochondrial genomes of the Siberian salamanders. PMID:23415986

  9. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.

    PubMed

    Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis

    2016-01-01

    Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal

  10. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

    PubMed Central

    Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis

    2016-01-01

    Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal

  11. BACTERIOPLANKTON DYNAMICS IN NORTHERN SAN FRANCISCO BAY: ROLE OF PARTICLE ASSOCIATION AND SEASONAL FRESHWATER FLOW

    EPA Science Inventory

    Bacterioplankton abundance and metabolic characteristics were observed in northern San Francisco Bay, California, during spring and summer 1996 at three sites: Central Bay, Suisun Bay, and the Sacramento River. These sites spanned a salinity gradient from marine to freshwater, an...

  12. UTILIZATION OF DISSOLVED NITROGEN BY HETEROTROPHIC BACTERIOPLANKTON: A COMPARISON OF THREE ECOSYSTEMS

    EPA Science Inventory

    The contributions of different organic and inorganic nitrogen and organic carbon sources to heterotrophic bacterioplankton in batch cultures of oceanic, estuarine, and eutrophic riverine environments were compared. he importance of the studied compounds was surprisingly similar a...

  13. Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations

    PubMed Central

    Yawata, Yutaka; Cordero, Otto X.; Menolascina, Filippo; Hehemann, Jan-Hendrik; Polz, Martin F.; Stocker, Roman

    2014-01-01

    Although competition–dispersal tradeoffs are commonly invoked to explain species coexistence for animals and plants in spatially structured environments, such mechanisms for coexistence remain unknown for microorganisms. Here we show that two recently speciated marine bacterioplankton populations pursue different behavioral strategies to exploit nutrient particles in adaptation to the landscape of ephemeral nutrient patches characteristic of ocean water. These differences are mediated primarily by differential colonization of and dispersal among particles. Whereas one population is specialized to colonize particles by attaching and growing biofilms, the other is specialized to disperse among particles by rapidly detecting and swimming toward new particles, implying that it can better exploit short-lived patches. Because the two populations are very similar in their genomic composition, metabolic abilities, chemotactic sensitivity, and swimming speed, this fine-scale behavioral adaptation may have been responsible for the onset of the ecological differentiation between them. These results demonstrate that the principles of spatial ecology, traditionally applied at macroscales, can be extended to the ocean’s microscale to understand how the rich spatiotemporal structure of the resource landscape contributes to the fine-scale ecological differentiation and species coexistence among marine bacteria. PMID:24706766

  14. Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset

    PubMed Central

    Guo, Jie; Wu, Xiaomei; Zhang, Da-Yong; Lin, Kui

    2008-01-01

    High-throughput studies of protein interactions may have produced, experimentally and computationally, the most comprehensive protein–protein interaction datasets in the completely sequenced genomes. It provides us an opportunity on a proteome scale, to discover the underlying protein interaction patterns. Here, we propose an approach to discovering motif pairs at interaction sites (often 3–8 residues) that are essential for understanding protein functions and helpful for the rational design of protein engineering and folding experiments. A gold standard positive (interacting) dataset and a gold standard negative (non-interacting) dataset were mined to infer the interacting motif pairs that are significantly overrepresented in the positive dataset compared to the negative dataset. Four negative datasets assembled by different strategies were evaluated and the one with the best performance was used as the gold standard negatives for further analysis. Meanwhile, to assess the efficiency of our method in detecting potential interacting motif pairs, other approaches developed previously were compared, and we found that our method achieved the highest prediction accuracy. In addition, many uncharacterized motif pairs of interest were found to be functional with experimental evidence in other species. This investigation demonstrates the important effects of a high-quality negative dataset on the performance of such statistical inference. PMID:18281313

  15. Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters

    PubMed Central

    2010-01-01

    Background The vertebrate globin genes encoding the α- and β-subunits of the tetrameric hemoglobins are clustered at two unlinked loci. The highly conserved linear order of the genes flanking the hemoglobins provides a strong anchor for inferring common ancestry of the globin clusters. In fish, the number of α-β-linked globin genes varies considerably between different sublineages and seems to be related to prevailing physico-chemical conditions. Draft sequences of the Atlantic cod genome enabled us to determine the genomic organization of the globin repertoire in this marine species that copes with fluctuating environments of the temperate and Arctic regions. Results The Atlantic cod genome was shown to contain 14 globin genes, including nine hemoglobin genes organized in two unlinked clusters designated β5-α1-β1-α4 and β3-β4-α2-α3-β2. The diverged cod hemoglobin genes displayed different expression levels in adult fish, and tetrameric hemoglobins with or without a Root effect were predicted. The novel finding of maternally inherited hemoglobin mRNAs is consistent with a potential role played by fish hemoglobins in the non-specific immune response. In silico analysis of the six teleost genomes available showed that the two α-β globin clusters are flanked by paralogs of five duplicated genes, in agreement with the proposed teleost-specific duplication of the ancestral vertebrate globin cluster. Screening the genome of extant urochordate and cephalochordate species for conserved globin-flanking genes revealed linkage of RHBDF1, MPG and ARHGAP17 to globin genes in the tunicate Ciona intestinalis, while these genes together with LCMT are closely positioned in amphioxus (Branchiostoma floridae), but seem to be unlinked to the multiple globin genes identified in this species. Conclusion The plasticity of Atlantic cod to variable environmental conditions probably involves the expression of multiple globins with potentially different properties. The

  16. Phytoplankton Communities Exhibit a Stronger Response to Environmental Changes than Bacterioplankton in Three Subtropical Reservoirs.

    PubMed

    Liu, Lemian; Yang, Jun; Lv, Hong; Yu, Xiaoqing; Wilkinson, David M; Yang, Jun

    2015-09-15

    The simultaneous analysis of multiple components of ecosystems is crucial for comprehensive studies of environmental changes in aquatic ecosystems, but such studies are rare. In this study, we analyzed simultaneously the bacterioplankton and phytoplankton communities in three Chinese subtropical reservoirs and compared the response of these two components to seasonal environmental changes. Time-lag analysis indicated that the temporal community dynamics of both bacterioplankton and phytoplankton showed significant directional changes, and variance partitioning suggested that the major reason was the gradual improvement of reservoir water quality from middle eutrophic to oligo-mesotrophic levels during the course of our study. In addition, we found a higher level of temporal stability or stochasticity in the bacterioplankton community than in the phytoplankton community. Potential explanations are that traits associated with bacteria, such as high abundance, widespread dispersal, potential for rapid growth rates, and rapid evolutionary adaptation, may underlie the different stability or stochasticity of bacterioplankton and phytoplankton communities to the environmental changes. In addition, the indirect response of bacterioplankton to nitrogen and phosphorus may result in the fact that environmental deterministic selection was stronger for the phytoplankton than for the bacterioplankton communities. PMID:26287966

  17. The phylogenetic position of the roughskin skate Dipturus trachyderma (Krefft & Stehmann, 1975) (Rajiformes, Rajidae) inferred from the mitochondrial genome.

    PubMed

    Vargas-Caro, Carolina; Bustamante, Carlos; Lamilla, Julio; Bennett, Michael B; Ovenden, Jennifer R

    2016-07-01

    The complete mitochondrial genome of the roughskin skate Dipturus trachyderma is described from 1 455 724 sequences obtained using Illumina NGS technology. Total length of the mitogenome was 16 909 base pairs, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Phylogenetic analysis based on mtDNA revealed low genetic divergence among longnose skates, in particular, those dwelling the continental shelf and slope off the coasts of Chile and Argentina. PMID:26122334

  18. Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Stinear, Timothy P; Holt, Kathryn E; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P

    2014-02-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change. PMID:24482534

  19. Adaptive Change Inferred from Genomic Population Analysis of the ST93 Epidemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Stinear, Timothy P.; Holt, Kathryn E.; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L.; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P.

    2014-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change. PMID:24482534

  20. Structure, expression profile and phylogenetic inference of chalcone isomerase-like genes from the narrow-leafed lupin (Lupinus angustifolius L.) genome

    PubMed Central

    Przysiecka, Łucja; Książkiewicz, Michał; Wolko, Bogdan; Naganowska, Barbara

    2015-01-01

    Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI), a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL), and fatty acid-binding (FAP) proteins. Here, two Lupinus angustifolius (narrow-leafed lupin) CHILs, LangCHIL1 and LangCHIL2, were identified and characterized using DNA fingerprinting, cytogenetic and linkage mapping, sequencing and expression profiling. Clones carrying CHIL sequences were assembled into two contigs. Full gene sequences were obtained from these contigs, and mapped in two L. angustifolius linkage groups by gene-specific markers. Bacterial artificial chromosome fluorescence in situ hybridization approach confirmed the localization of two LangCHIL genes in distinct chromosomes. The expression profiles of both LangCHIL isoforms were very similar. The highest level of transcription was in the roots of the third week of plant growth; thereafter, expression declined. The expression of both LangCHIL genes in leaves and stems was similar and low. Comparative mapping to reference legume genome sequences revealed strong syntenic links; however, LangCHIL2 contig had a much more conserved structure than LangCHIL1. LangCHIL2 is assumed to be an ancestor gene, whereas LangCHIL1 probably appeared as a result of duplication. As both copies are transcriptionally active, questions arise concerning their hypothetical functional divergence. Screening of the narrow-leafed lupin genome and transcriptome with CHI-fold protein sequences, followed by Bayesian inference of phylogeny and cross-genera synteny survey, identified representatives of all but one (CHI1) main subfamilies. They are as follows: two copies of CHI2, FAPa2 and CHIL, and single copies of FAPb and FAPa1. Duplicated genes are remnants of whole genome duplication which is assumed to have occurred after the divergence of Lupinus, Arachis, and Glycine

  1. Complete genome and molecular epidemiological data infer the maintenance of rabies among kudu (Tragelaphus strepsiceros) in Namibia.

    PubMed

    Scott, Terence P; Fischer, Melina; Khaiseb, Siegfried; Freuling, Conrad; Höper, Dirk; Hoffmann, Bernd; Markotter, Wanda; Müller, Thomas; Nel, Louis H

    2013-01-01

    Rabies in kudu is unique to Namibia and two major peaks in the epizootic have occurred since it was first noted in 1977. Due to the large numbers of kudu that were affected, it was suspected that horizontal transmission of rabies occurs among kudu and that rabies was being maintained independently within the Namibian kudu population - separate from canid cycles, despite geographic overlap. In this study, it was our aim to show, through phylogenetic analyses, that rabies was being maintained independently within the Namibian kudu population. We also tested, through complete genome sequencing of four rabies virus isolates from jackal and kudu, whether specific mutations occurred in the virus genome due to host adaptation. We found the separate grouping of all rabies isolates from kudu to those of any other canid species in Namibia, suggesting that rabies was being maintained independently in kudu. Additionally, we noted several mutations unique to isolates from kudu, suggesting that these mutations may be due to the adaptation of rabies to a new host. In conclusion, we show clear evidence that rabies is being maintained independently in the Namibian kudu population - a unique phenomenon with ecological and economic impacts. PMID:23527015

  2. Haplo-block structure of Southern African village chicken populations inferred using genome-wide SNP data.

    PubMed

    Khanyile, K S; Dzomba, E F; Muchadeyi, F C

    2015-01-01

    This study investigated the haplo-block structure, haplotype sharing, and diversity in extensively raised chicken populations of Southern Africa. Two hundred ninety village chickens from Malawi (N = 30), South Africa (N = 132), and Zimbabwe (N = 128) were included in the study, from which 649, 2104, and 2442 haplo-blocks were observed, respectively. The majority of haplo-blocks were smaller than 25 kb in size and only five blocks were more than 2000 kb in size. The low chromosomal coverage of haplo-blocks observed across the genome suggests that multiple recombination events fragmented the ancestral haplo-blocks into smaller sizes. Haplo-block sharing was observed between populations with 2325 haplo-blocks common between Zimbabwe and Malawi and 2689 between South Africa and Zimbabwe. Haplotype sharing allows transferability of genomic tools between these extensively raised chicken populations of Southern Africa. The unique haplo-blocks could have originated from isolated evolution taking place in specific agro-ecological zones. Quantitative trait loci analysis revealed that genes related to body composition were spanned by these haplo-blocks. Body composition traits are important for village chicken populations, which have to harness poor quality feed obtained from the environment to meet their maintenance and production needs. PMID:26505376

  3. Complete Genome and Molecular Epidemiological Data Infer the Maintenance of Rabies among Kudu (Tragelaphus strepsiceros) in Namibia

    PubMed Central

    Scott, Terence P.; Fischer, Melina; Khaiseb, Siegfried; Freuling, Conrad; Höper, Dirk; Hoffmann, Bernd; Markotter, Wanda; Müller, Thomas; Nel, Louis H.

    2013-01-01

    Rabies in kudu is unique to Namibia and two major peaks in the epizootic have occurred since it was first noted in 1977. Due to the large numbers of kudu that were affected, it was suspected that horizontal transmission of rabies occurs among kudu and that rabies was being maintained independently within the Namibian kudu population – separate from canid cycles, despite geographic overlap. In this study, it was our aim to show, through phylogenetic analyses, that rabies was being maintained independently within the Namibian kudu population. We also tested, through complete genome sequencing of four rabies virus isolates from jackal and kudu, whether specific mutations occurred in the virus genome due to host adaptation. We found the separate grouping of all rabies isolates from kudu to those of any other canid species in Namibia, suggesting that rabies was being maintained independently in kudu. Additionally, we noted several mutations unique to isolates from kudu, suggesting that these mutations may be due to the adaptation of rabies to a new host. In conclusion, we show clear evidence that rabies is being maintained independently in the Namibian kudu population – a unique phenomenon with ecological and economic impacts. PMID:23527015

  4. Bacterioplankton growth and production at the Louisiana hydrocarbon seeps

    NASA Astrophysics Data System (ADS)

    Larock, P. A.; Hyun, J.-H.; Bennison, B. W.

    1994-06-01

    The growth rate and potential production of bacterioplankton in cold hydrocarbon seeps located along the Louisiana coast were determined using a pulse-labeling technique. Surprisingly, community doubling times are on the order of 1.1 h, which compares to laboratory-grown cultures. We also found that there are differences in growth rates on relatively small geographic scales, suggesting the influence of site-specific geological features (e.g., gas hydrate mounds). Proceeding downslope to deeper waters, methane-oxidizing bacteria appeared to play a more significant role in community productivity. These preliminary experiments indicated, quite unexpectedly, that water column microbes are growing at a more rapid rate than in any other marine system so far studied and that methane may serve as a primary nutrient (carbon) source in these seep-associated microbial assemblages.

  5. The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome.

    PubMed

    Bustamante, Carlos; Barría, Claudio; Vargas-Caro, Carolina; Ovenden, Jennifer R; Bennett, Michael B

    2016-09-01

    The giant devil ray, Mobula mobular, is a member of one of the most distinct groups of cartilaginous fishes, the Mobulidae (manta and devil rays), and is the only mobulid assessed as Endangered due its restricted distribution, high bycatch mortality and suspected population decline. The complete mitochondrial genome is 18 913 base pairs in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison with the partial mitogenome of M. japanica suggests a sister-cryptic species complex and two different taxonomic units. However, the limited divergence within the species (>99.9% genetic identity) may be the result of a geographically and numerically restricted population of M. mobular within the Mediterranean Sea. PMID:26260171

  6. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    PubMed

    Singchat, Worapong; Hitakomate, Ekarat; Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  7. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization

    PubMed Central

    Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  8. Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.

    PubMed

    Vieira, Leila do Nascimento; Dos Anjos, Karina Goulart; Faoro, Helisson; Fraga, Hugo Pacheco de Freitas; Greco, Thiago Machado; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Rogalski, Marcelo; de Souza, Robson Francisco; Guerra, Miguel Pedro

    2016-05-01

    The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe. PMID:26643654

  9. First all-in-one diagnostic tool for DNA intelligence: genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip.

    PubMed

    Keating, Brendan; Bansal, Aruna T; Walsh, Susan; Millman, Jonathan; Newman, Jonathan; Kidd, Kenneth; Budowle, Bruce; Eisenberg, Arthur; Donfack, Joseph; Gasparini, Paolo; Budimlija, Zoran; Henders, Anjali K; Chandrupatla, Hareesh; Duffy, David L; Gordon, Scott D; Hysi, Pirro; Liu, Fan; Medland, Sarah E; Rubin, Laurence; Martin, Nicholas G; Spector, Timothy D; Kayser, Manfred

    2013-05-01

    When a forensic DNA sample cannot be associated directly with a previously genotyped reference sample by standard short tandem repeat profiling, the investigation required for identifying perpetrators, victims, or missing persons can be both costly and time consuming. Here, we describe the outcome of a collaborative study using the Identitas Version 1 (v1) Forensic Chip, the first commercially available all-in-one tool dedicated to the concept of developing intelligence leads based on DNA. The chip allows parallel interrogation of 201,173 genome-wide autosomal, X-chromosomal, Y-chromosomal, and mitochondrial single nucleotide polymorphisms for inference of biogeographic ancestry, appearance, relatedness, and sex. The first assessment of the chip's performance was carried out on 3,196 blinded DNA samples of varying quantities and qualities, covering a wide range of biogeographic origin and eye/hair coloration as well as variation in relatedness and sex. Overall, 95 % of the samples (N = 3,034) passed quality checks with an overall genotype call rate >90 % on variable numbers of available recorded trait information. Predictions of sex, direct match, and first to third degree relatedness were highly accurate. Chip-based predictions of biparental continental ancestry were on average ~94 % correct (further support provided by separately inferred patrilineal and matrilineal ancestry). Predictions of eye color were 85 % correct for brown and 70 % correct for blue eyes, and predictions of hair color were 72 % for brown, 63 % for blond, 58 % for black, and 48 % for red hair. From the 5 % of samples (N = 162) with <90 % call rate, 56 % yielded correct continental ancestry predictions while 7 % yielded sufficient genotypes to allow hair and eye color prediction. Our results demonstrate that the Identitas v1 Forensic Chip holds great promise for a wide range of applications including criminal investigations, missing person investigations, and for national security

  10. Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus.

    PubMed

    Shafer, Aaron B A; Gattepaille, Lucie M; Stewart, Robert E A; Wolf, Jochen B W

    2015-01-01

    Approximate Bayesian computation (ABC) is a powerful tool for model-based inference of demographic histories from large genetic data sets. For most organisms, its implementation has been hampered by the lack of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap genome-scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent-based ABC approach where GBS data were modelled with either a population mutation parameter (θ) or a fixed site (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50 000 loci, a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1000 loci for migration and split time in simple population divergence models. In more complex models, posterior distributions were wide and almost reverted to the uninformative prior even with 50 000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite-likelihood method. Bottleneck scenarios proved particularly difficult, and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor-allele-frequency filters - usual practice for GBS data - negatively affected nearly all estimates. With this in mind, we used a combination of FS and θ approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a high Arctic bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC-coalescence framework and proposes a best-practice approach. PMID:25482153

  11. Southeast Asian origins of five Hill Tribe populations and correlation of genetic to linguistic relationships inferred with genome-wide SNP data.

    PubMed

    Listman, J B; Malison, R T; Sanichwankul, K; Ittiwut, C; Mutirangura, A; Gelernter, J

    2011-02-01

    In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have nonmutually intelligible languages. To test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2,445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results ofrecent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages. PMID:20979205

  12. Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China.

    PubMed

    Wang, Yongming; Yang, Jun; Liu, Lemian; Yu, Zheng

    2015-07-01

    Bacterioplankton are important components of freshwater ecosystems and play essential roles in ecological functions and processes; however, little is known about their geographical distribution and the factors influencing their ecology, especially in stream ecosystems. To examine how geographical and environmental factors affect the composition of bacterioplankton communities, we used denaturing gradient gel electrophoresis and clone sequencing to survey bacterioplankton communities in 31 samples of streamwater from seven nature reserves in Fujian province, southeast China. Our results revealed that dominant bacterioplankton communities exhibited a distinct geographical pattern. Further, we provided evidence for distance decay relationships in bacterioplankton community similarity and found similar community gradients in response to elevation and latitude. Both redundancy analyses and Mantel tests showed that bacterioplankton community composition was significantly correlated with both environmental (electrical conductivity, total phosphorus, and PO4-P) and geographical factors (latitude, longitude, and elevation). Variance partitioning further showed that the joint effect of geographical and environmental factors explained the largest proportion of the variation in distribution of bacterioplankton communities (13.6 %), followed by purely geographical factors (11.2 %), and purely environmental factors (0.6 %). The Betaproteobacteria were the most common taxa in the streams, followed by Firmicutes and Gammaproteobacteria. Therefore, our results suggest that the biogeographical patterns of stream bacterioplankton communities across the Fujian nature reserves are more influenced by geographical factors than by local physicochemical properties. PMID:25787217

  13. GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans

    PubMed Central

    Lao, Oscar; Liu, Fan; Wollstein, Andreas; Kayser, Manfred

    2014-01-01

    Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations. Here we introduce a new algorithm for transforming a genetic distance matrix that reduces the within-population variation considerably. Extensive computer simulations revealed that the transformed matrix captured the genetic population differentiation better than the original one which was based on the T1 statistic. In an empirical genomic data set comprising 2,457 individuals from 23 different European subpopulations, the proportion of individuals that were determined as a genetic neighbour to another individual from the same sampling location increased from 25% with the original matrix to 52% with the transformed matrix. Similarly, the percentage of genetic variation explained between populations by means of Analysis of Molecular Variance (AMOVA) increased from 1.62% to 7.98%. Furthermore, the first two dimensions of a classical multidimensional scaling (MDS) using the transformed matrix explained 15% of the variance, compared to 0.7% obtained with the original matrix. Application of MDS with Mclust, SPA with Mclust, and GemTools algorithms to the same dataset also showed that the transformed matrix gave a better association of the genetic clusters with the sampling locations, and particularly so when it was used in the AMOVA framework with a genetic algorithm. Overall, the new matrix transformation introduced here substantially reduces the within population genetic differentiation, and can be broadly applied to methods such as AMOVA to enhance their sensitivity to reveal population substructure. We herewith provide a publically available (http://www.erasmusmc.nl/fmb/resources/GAGA) model-free method for improved genetic population substructure detection that can be applied to human as well as any other species data in future studies relevant to

  14. High Temporal but Low Spatial Heterogeneity of Bacterioplankton in the Chesapeake Bay▿ †

    PubMed Central

    Kan, Jinjun; Suzuki, Marcelino T.; Wang, Kui; Evans, Sarah E.; Chen, Feng

    2007-01-01

    Compared to freshwater and the open ocean, less is known about bacterioplankton community structure and spatiotemporal dynamics in estuaries, particularly those with long residence times. The Chesapeake Bay is the largest estuary in the United States, but despite its ecological and economic significance, little is known about its microbial community composition. A rapid screening approach, ITS (internal transcribed spacer)-LH (length heterogeneity)-PCR, was used to screen six rRNA operon (16S rRNA-ITS-23S rRNA) clone libraries constructed from bacterioplankton collected in three distinct regions of the Chesapeake Bay over two seasons. The natural length variation of the 16S-23S rRNA gene ITS region, as well as the presence and location of tRNA-alanine coding regions within the ITS, was determined for 576 clones. Clones representing unique ITS-LH-PCR sizes were sequenced and identified. Dramatic shifts in bacterial composition (changes within subgroups or clades) were observed for the Alphaproteobacteria (Roseobacter clade, SAR11), Cyanobacteria (Synechococcus), and Actinobacteria, suggesting strong seasonal variation within these taxonomic groups. Despite large gradients in salinity and phytoplankton parameters, a remarkably homogeneous bacterioplankton community was observed in the bay in each season. Stronger seasonal, rather than spatial, variation of the bacterioplankton population was also supported by denaturing gradient gel electrophoresis and LH-PCR analyses, indicating that environmental parameters with stronger seasonal, rather than regional, dynamics, such as temperature, might determine bacterioplankton community composition in the Chesapeake Bay. PMID:17827310

  15. The effect of water exchange on bacterioplankton depletion and inorganic nutrient dynamics in coral reef cavities

    NASA Astrophysics Data System (ADS)

    van Duyl, F. C.; Scheffers, S. R.; Thomas, F. I. M.; Driscoll, M.

    2006-03-01

    We studied the effect of water exchange on the depletion (or accumulation) of bacterioplankton, dissolved organic matter and inorganic nutrients in small open framework cavities (50-70 l) at 15 m depth on the coral reef along Curaçao, Netherlands Antilles. The bacterioplankton removal rate in cavities increased with increasing water exchange rates up to a threshold of 0.0045 s-1, reaching values of 50-100 mg C m-2 total interior cavity surface area (CSA) per day. Beyond the threshold, bacterioplankton removal dropped. The cryptic community is apparently adapted to the average water exchange in these cavities (0.0041 s-1). Dissolved inorganic nitrogen (DIN), nitrate + nitrite (NO x ) in particular, accumulated in cavity water and the accumulation decreased with increasing water exchange. Net NO x effluxes exceeded net DIN effluxes from cavities (average efflux rate of 1.9 mmol NO x vs. 0.8 mmol DIN m-2 interior CSA per day). The difference is ascribed to net ammonium losses (NH4) in cavities at reef concentrations >0.025 μM NH4, possibly due to enhanced nitrification. Dissolved inorganic phosphate accumulated in cavities, but was not related to water exchange. The cryptic biota in cavities depend on water exchange for optimization of consumption of bacterioplankton and removal of inorganic nitrogen. Coral cavities are an evident sink of bacterioplankton and a source of NO x and PO{4/3-}.

  16. Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy.

    PubMed

    Xiong, Jinbo; Xiong, Shangling; Qian, Peng; Zhang, Demin; Liu, Lian; Fei, Yuejun

    2016-12-01

    Elevated seawater temperature has altered the coupling between coastal primary production and heterotrophic bacterioplankton respiration. This shift, in turn, could influence the feedback of ocean ecosystem to climate warming. However, little is known about how natural bacterioplankton community responds to increasing seawater temperature. To investigate warming effects on the bacterioplankton community, we collected water samples from temperature gradients (ranged from 15.0 to 18.6 °C) created by a thermal flume of a coal power plant. The results showed that increasing temperatures significantly stimulated bacterial abundance, grazing rate, and altered bacterioplankton community compositions (BCCs). The spatial distribution of bacterioplankton community followed a distance similarity decay relationship, with a turnover of 0.005. A variance partitioning analysis showed that temperature directly constrained 2.01 % variation in BCCs, while temperature-induced changes in water geochemical and grazing rate indirectly accounted for 4.03 and 12.8 % of the community variance, respectively. Furthermore, the relative abundances of 24 bacterial families were linearly increased or decreased (P < 0.05 in all cases) with increasing temperatures. Notably, the change pattern for a given bacterial family was in concert with its known functions. In addition, community functional redundancy consistently decreased along the temperature gradient. This study demonstrates that elevated temperature, combined with substrate supply and trophic interactions, dramatically alters BCCs, concomitant with decreases in functional redundancy. The responses of sensitive assemblages are temperature dependent, which could indicate temperature departures. PMID:27620732

  17. Ecological Inference

    NASA Astrophysics Data System (ADS)

    King, Gary; Rosen, Ori; Tanner, Martin A.

    2004-09-01

    This collection of essays brings together a diverse group of scholars to survey the latest strategies for solving ecological inference problems in various fields. The last half-decade has witnessed an explosion of research in ecological inference--the process of trying to infer individual behavior from aggregate data. Although uncertainties and information lost in aggregation make ecological inference one of the most problematic types of research to rely on, these inferences are required in many academic fields, as well as by legislatures and the Courts in redistricting, by business in marketing research, and by governments in policy analysis.

  18. Spatiotemporal distribution of bacterioplankton and bacteriobenthos in the Amur Liman and adjacent sea areas

    NASA Astrophysics Data System (ADS)

    Karetnikova, E. A.; Garetova, L. A.

    2015-09-01

    Data on the abundance and the ecological-trophic structure of bacterioplankton and bacteriobenthos communities in the Amur Liman and adjacent waters collected in June 2007 have been compared to the relevant data of 2006. Interyear changes of bacterioplankton abundance have been found to depend on the intensity of the Amur River runoff. Correlation analysis has revealed a negative dependence of the abundance of bacterioplankton, bacteriobenthos, and their ecological-trophic groups on water salinity, as well as direct relations between these biotic components and organic matter in water and bottom sediments. The microbiological indicators of water quality ranked the studied waters as classes III-IV in 2006 and as classes II-III in 2007. The high total abundance of bacteriobenthos (109-1010 cells/g) is a result of the functioning of a marginal filter rather than the direct pollution of the liman.

  19. Richness and Diversity of Bacterioplankton Species along an Estuarine Gradient in Moreton Bay, Australia

    PubMed Central

    Hewson, Ian; Fuhrman, Jed A.

    2004-01-01

    Bacterioplankton community diversity was investigated in the subtropical Brisbane River-Moreton Bay estuary, Australia (27°25′S, 153°5′E). Bacterial communities were studied using automated rRNA intergenic spacer analysis (ARISA), which amplifies 16S-23S ribosomal DNA internally transcribed spacer regions from mixed-community DNA and detects the separated products on a fragment analyzer. Samples were collected from eight sites throughout the estuary and east to the East Australian Current (Coral Sea). Bacterioplankton communities had the highest operational taxonomic unit (OTU) richness, as measured by ARISA at eastern bay stations (S [total richness] = 84 to 85 OTU) and the lowest richness in the Coral Sea (S = 39 to 59 OTU). Richness correlated positively with bacterial abundance; however, there were no strong correlations between diversity and salinity, NO3− and PO43− concentrations, or chlorophyll a concentration. Bacterioplankton communities at the riverine stations were different from communities in the bay or Coral Sea. The main differences in OTU richness between stations were in taxa that each represented 0.1% (the detection limit) to 0.5% of the total amplified DNA, i.e., the “tail” of the distribution. We found that some bacterioplankton taxa are specific to distinct environments while others have a ubiquitous distribution from river to sea. Bacterioplankton richness and diversity patterns in the estuary are potentially a consequence of greater niche availability, mixing of local and adjacent environment communities, or intermediate disturbance. Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters. PMID:15184140

  20. Energetic differences between bacterioplankton trophic groups and coral reef resistance.

    PubMed

    McDole Somera, Tracey; Bailey, Barbara; Barott, Katie; Grasis, Juris; Hatay, Mark; Hilton, Brett J; Hisakawa, Nao; Nosrat, Bahador; Nulton, James; Silveira, Cynthia B; Sullivan, Chris; Brainard, Russell E; Rohwer, Forest

    2016-04-27

    Coral reefs are among the most productive and diverse marine ecosystems on the Earth. They are also particularly sensitive to changing energetic requirements by different trophic levels. Microbialization specifically refers to the increase in the energetic metabolic demands of microbes relative to macrobes and is significantly correlated with increasing human influence on coral reefs. In this study, metabolic theory of ecology is used to quantify the relative contributions of two broad bacterioplankton groups, autotrophs and heterotrophs, to energy flux on 27 Pacific coral reef ecosystems experiencing human impact to varying degrees. The effective activation energy required for photosynthesis is lower than the average energy of activation for the biochemical reactions of the Krebs cycle, and changes in the proportional abundance of these two groups can greatly affect rates of energy and materials cycling. We show that reef-water communities with a higher proportional abundance of microbial autotrophs expend more metabolic energy per gram of microbial biomass. Increased energy and materials flux through fast energy channels (i.e. water-column associated microbial autotrophs) may dampen the detrimental effects of increased heterotrophic loads (e.g. coral disease) on coral reef systems experiencing anthropogenic disturbance. PMID:27097927

  1. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

    PubMed

    Szabo, Gitta; Preheim, Sarah P; Kauffman, Kathryn M; David, Lawrence A; Shapiro, Jesse; Alm, Eric J; Polz, Martin F

    2013-03-01

    How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across years. We compare Vibrionaceae lifestyles in the bacterioplankton (combinations of free-living, particle, or zooplankton associations) measured using the same sampling scheme in 2006 and 2009 to assess whether the same groups show the same environmental association year after year. This reveals complex dynamics with populations falling primarily into two categories: (i) nearly equally represented in each of the two samplings and (ii) highly skewed, often to an extent that they appear exclusive to one or the other sampling times. Importantly, populations recovered at the same abundance in both samplings occupied highly similar habitats suggesting predictable and robust environmental association while skewed abundances of some populations may be triggered by shifts in ecological conditions. The latter is supported by difference in the composition of large eukaryotic plankton between years, with samples in 2006 being dominated by copepods, and those in 2009 by diatoms. Overall, the comparison supports highly predictable population-habitat linkage but highlights the fact that complex, and often unmeasured, environmental dynamics in habitat occurrence may have strong effects on population dynamics. PMID:23178668

  2. pH influences the importance of niche-related and neutral processes in lacustrine bacterioplankton assembly.

    PubMed

    Ren, Lijuan; Jeppesen, Erik; He, Dan; Wang, Jianjun; Liboriussen, Lone; Xing, Peng; Wu, Qinglong L

    2015-05-01

    pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity. PMID:25724952

  3. Phylogenetic Composition of Bacterioplankton Assemblages from the Arctic Ocean

    PubMed Central

    Bano, Nasreen; Hollibaugh, James T.

    2002-01-01

    We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: α (36%)-, γ (32%)-, δ (14%)-, and ɛ (1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to α-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to γ-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria

  4. Bacterioplankton: a sink for carbon in a coastal marine plankton community

    SciTech Connect

    Ducklow, H.W.; Purdie, D.A.; Williams, P.J.LeB.; Davis, J.M.

    1986-05-16

    Recent determinations of high production rates (up to 30% of primary production in surface waters) implicate free-living marine bacterioplankton as a link in a microbial loop that supplements phytoplankton as food for herbivores. An enclosed water column of 300 cubic meters was used to test the microbial loop hypothesis by following the fate of carbon-14-labeled bacterioplankton for over 50 days. Only 2% of the label initially fixed from carbon-14-labeled glucose by bacteria was present in larger organisms after 13 days, at which time about 20% of the total label added remained in the particulate fraction. Most of the label appeared to pass directly from particles smaller than 1 micrometer (heterotrophic bacterioplankton and some bacteriovores) to respired labeled carbon dioxide or to regenerated dissolved organic carbon-14. Secondary (and, by implication, primary) production by organisms smaller than 1 micrometer may not be an important food source in marine food chains. Bacterioplankton can be a sink for carbon in planktonic food webs and may serve principally as agents of nutrient regeneration rather than as food.

  5. In situ interactions between photosynthetic picoeukaryotes and bacterioplankton in the Atlantic Ocean: evidence for mixotrophy.

    PubMed

    Hartmann, Manuela; Zubkov, Mikhail V; Scanlan, Dave J; Lepère, Cécile

    2013-12-01

    Heterotrophic bacterioplankton, cyanobacteria and phototrophic picoeukaryotes (< 5 μm in size) numerically dominate planktonic oceanic communities. While feeding on bacterioplankton is often attributed to aplastidic protists, recent evidence suggests that phototrophic picoeukaryotes could be important bacterivores. Here, we present direct visual evidence from the surface mixed layer of the Atlantic Ocean that bacterioplankton are internalized by phototrophic picoeukaryotes. In situ interactions of phototrophic picoeukaryotes and bacterioplankton (specifically Prochlorococcus cyanobacteria and the SAR11 clade) were investigated using a combination of flow cytometric cell sorting and dual tyramide signal amplification fluorescence in situ hybridization. Using this method, we observed plastidic Prymnesiophyceae and Chrysophyceae cells containing Prochlorococcus, and to a lesser extent SAR11 cells. These microscopic observations of in situ microbial trophic interactions demonstrate the frequency and likely selectivity of phototrophic picoeukaryote bacterivory in the surface mixed layer of both the North and South Atlantic subtropical gyres and adjacent equatorial region, broadening our views on the ecological role of the smallest oceanic plastidic protists. PMID:24249292

  6. Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean.

    PubMed

    Jamieson, Rachel E; Rogers, Alex D; Billett, David S M; Smale, Dan A; Pearce, David A

    2012-05-01

    Spatial patchiness in marine surface bacterioplankton populations was investigated in the Southern Ocean, where the Antarctic Circumpolar Current meets the islands of the Scotia Arc and is subjected to terrestrial input, upwelling of nutrients and seasonal phytoplankton blooms. Total bacterioplankton population density, group-specific taxonomic distribution and six of eight dominant members of the bacterioplankton community were found to be consistent across 18 nearshore sites at eight locations around the Scotia Arc. Results from seven independent 16S rRNA gene clone libraries (1223 sequences in total) and fluorescent in situ hybridization suggested that microbial assemblages were predominantly homogeneous between Scotia Arc sites, where the Alphaproteobacteria, Gammaproteobacteria and the Cytophaga-Flavobacterium-Bacteroidetes cluster were the dominant bacterial groups. Of the 1223 useable sequences generated, 1087 (89%) shared ≥ 97% similarity with marine microorganisms and 331 (27%) matched published sequences previously detected in permanently cold Arctic and Antarctic marine environments. Taken together, results suggest that the dominant bacterioplankton groups are consistent between locations, but significant differences may be detected across the rare biodiversity. PMID:22273466

  7. Annual dynamics of North Sea bacterioplankton: seasonal variability superimposes short-term variation.

    PubMed

    Lucas, Judith; Wichels, Antje; Teeling, Hanno; Chafee, Meghan; Scharfe, Mirco; Gerdts, Gunnar

    2015-09-01

    The dynamics of coastal marine microbial communities are driven by seasonally changing abiotic and biotic factors as well as by rapidly occurring short-term changes such as river fresh water influxes or phytoplankton blooms. We examined the variability of the free-living bacterioplankton at Helgoland Roads (German Bight, North Sea) over a period of one year with high temporal and taxonomic resolution to reveal variation patterns and main influencing factors. 16S rRNA gene tag sequencing of the bacterioplankton community hints at annual recurrence and resilience of few main taxa belonging to Alphaproteobacteria, Betaproteobacteria, Flavobacteriia, Acidimicrobiia and Thermoplasmata. Multiple regression analyses with various environmental factors revealed changes in water current patterns and resulting phytoplankton blooms as the main driving factors for short-term variation and temperature as the overlying factor for seasonal variation. Comparison of bacterioplankton successions during spring and summer phytoplankton blooms revealed the same dominating Flavobacteriia operational taxonomic units (OTUs) but shifts in Roseobacter related OTUs (Alphaproteobacteria) and SAR92 clade members (Gammaproteobacteria). Network analysis suggests that during spring and summer phytoplankton blooms temperature-dependent guilds are formed. In conclusion, our data imply that short-term bacterioplankton successions in response to phytoplankton blooms are indirectly affected by temperature, which is a major niche-defining factor in the German Bight. PMID:26298013

  8. Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities.

    PubMed

    Bouvier, Thierry; Venail, Patrick; Pommier, Thomas; Bouvier, Corinne; Barbera, Claire; Mouquet, Nicolas

    2012-01-01

    The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations. PMID:22701572

  9. Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks.

    PubMed

    Niño-García, Juan Pablo; Ruiz-González, Clara; Del Giorgio, Paul A

    2016-07-01

    Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum. PMID:26849312

  10. BACTERIOPLANKTON DYNAMICS IN PENSACOLA BAY, FL, USA: ROLE OF PHYTOPLANKTON AND DETRIAL CARBON SOURCES

    EPA Science Inventory

    Bacterioplankton Dynamics in Pensacola Bay, FL, USA: Role of Phytoplankton and Detrital Carbon Sources (Abstract). To be presented at the16th Biennial Conference of the Estuarine Research Foundation, ERF 2001: An Estuarine Odyssey, 4-8 November 2001, St. Pete Beach, FL. 1 p. (ER...

  11. An ecological assessment of factors determining bacterioplankton dynamics in Tsimlyanskaya reservoir

    SciTech Connect

    Katretskii, Y.A.

    1984-07-01

    In this paper the author establishes that the abundance of bacterioplankton in Tsimlyanskaya reservoir is affected by such ecological factors as temperature, quality of organic solutes as well as intrapopulation factors. He concludes that factors dependent on density (consumption by zooplankton, sorption of suspensions) are the main regulators of the volume of bacterial population in the reservoir plankton.

  12. Effects of nutrients on specific growth rate of bacterioplankton in oligotrophic lake water cultures

    SciTech Connect

    Coveney, M.F.; Wetzel, R.G. )

    1992-01-01

    The effects of organic and inorganic nutrient additions on the specific growth rates of bacterioplankton in oligotrophic lake water cultures were investigated. Lake water was first passed through 0.8-{mu}m-pore-size filters (prescreening) to remove bacterivores and to minimize confounding effects of algae. Specific growth rates were calculated from changes in both bacterial cell numbers and biovolumes over 36 h. Gross specific growth rates in unmanipulated control samples were estimated through separate measurements of grazing losses by use of penicillin. The addition of mixed organic substrates alone to prescreened water did not significantly increase bacterioplankton specific growth rates. The addition of inorganic phosphorus alone significantly increased one or both specific growth rates in three of four experiments, and one experiment showed a secondary stimulation by organic substrates. The stimulatory effects of phosphorus addition were greatest concurrently with the highest alkaline phosphatase activity in the lake water. Because bacteria have been shown to dominate inorganic phosphorus uptake in other P-deficient systems, the demonstration that phosphorus, rather than organic carbon, can limit bacterioplankton growth suggests direct competition between phytoplankton and bacterioplankton for inorganic phosphorus.

  13. INFLUENCE OF LIGHT ON BACTERIOPLANKTON PRODUCTION AND RESPIRATION IN A SUBTROPICAL CORAL REEF

    EPA Science Inventory

    The influence of sunlight on bacterioplankton production (14C-leucine (Leu) and 3H-thymidine (TdR) incorporation; changes in cell abundances) and O2 consumption was investigated in a shallow subtropical coral reef located near Key Largo, Florida. Quartz (light) and opaque (dark) ...

  14. Entropic Inference

    NASA Astrophysics Data System (ADS)

    Caticha, Ariel

    2011-03-01

    In this tutorial we review the essential arguments behing entropic inference. We focus on the epistemological notion of information and its relation to the Bayesian beliefs of rational agents. The problem of updating from a prior to a posterior probability distribution is tackled through an eliminative induction process that singles out the logarithmic relative entropy as the unique tool for inference. The resulting method of Maximum relative Entropy (ME), includes as special cases both MaxEnt and Bayes' rule, and therefore unifies the two themes of these workshops—the Maximum Entropy and the Bayesian methods—into a single general inference scheme.

  15. Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages

    PubMed Central

    Nelson, Craig E; Goldberg, Stuart J; Wegley Kelly, Linda; Haas, Andreas F; Smith, Jennifer E; Rohwer, Forest; Carlson, Craig A

    2013-01-01

    Increasing algal cover on tropical reefs worldwide may be maintained through feedbacks whereby algae outcompete coral by altering microbial activity. We hypothesized that algae and coral release compositionally distinct exudates that differentially alter bacterioplankton growth and community structure. We collected exudates from the dominant hermatypic coral holobiont Porites spp. and three dominant macroalgae (one each Ochrophyta, Rhodophyta and Chlorophyta) from reefs of Mo'orea, French Polynesia. We characterized exudates by measuring dissolved organic carbon (DOC) and fractional dissolved combined neutral sugars (DCNSs) and subsequently tracked bacterioplankton responses to each exudate over 48 h, assessing cellular growth, DOC/DCNS utilization and changes in taxonomic composition (via 16S rRNA amplicon pyrosequencing). Fleshy macroalgal exudates were enriched in the DCNS components fucose (Ochrophyta) and galactose (Rhodophyta); coral and calcareous algal exudates were enriched in total DCNS but in the same component proportions as ambient seawater. Rates of bacterioplankton growth and DOC utilization were significantly higher in algal exudate treatments than in coral exudate and control incubations with each community selectively removing different DCNS components. Coral exudates engendered the smallest shift in overall bacterioplankton community structure, maintained high diversity and enriched taxa from Alphaproteobacteria lineages containing cultured representatives with relatively few virulence factors (VFs) (Hyphomonadaceae and Erythrobacteraceae). In contrast, macroalgal exudates selected for less diverse communities heavily enriched in copiotrophic Gammaproteobacteria lineages containing cultured pathogens with increased VFs (Vibrionaceae and Pseudoalteromonadaceae). Our results demonstrate that algal exudates are enriched in DCNS components, foster rapid growth of bacterioplankton and select for bacterial populations with more potential VFs than

  16. Response of Bacterioplankton Communities to Cadmium Exposure in Coastal Water Microcosms with High Temporal Variability

    PubMed Central

    Wang, Kai; Xiong, Jinbo; Chen, Xinxin; Zheng, Jialai; Hu, Changju; Yang, Yina; Zhu, Jianlin

    2014-01-01

    Multiple anthropogenic disturbances to bacterial diversity have been investigated in coastal ecosystems, in which temporal variability in the bacterioplankton community has been considered a ubiquitous process. However, far less is known about the temporal dynamics of a bacterioplankton community responding to pollution disturbances such as toxic metals. We used coastal water microcosms perturbed with 0, 10, 100, and 1,000 μg liter−1 of cadmium (Cd) for 2 weeks to investigate temporal variability, Cd-induced patterns, and their interaction in the coastal bacterioplankton community and to reveal whether the bacterial community structure would reflect the Cd gradient in a temporally varying system. Our results showed that the bacterioplankton community structure shifted along the Cd gradient consistently after a 4-day incubation, although it exhibited some resistance to Cd at low concentration (10 μg liter−1). A process akin to an arms race between temporal variability and Cd exposure was observed, and the temporal variability overwhelmed Cd-induced patterns in the bacterial community. The temporal succession of the bacterial community was correlated with pH, dissolved oxygen, NO3−-N, NO2−-N, PO43−-P, dissolved organic carbon, and chlorophyll a, and each of these parameters contributed more to community variance than Cd did. However, elevated Cd levels did decrease the temporal turnover rate of community. Furthermore, key taxa, affiliated to the families Flavobacteriaceae, Rhodobacteraceae, Erythrobacteraceae, Piscirickettsiaceae, and Alteromonadaceae, showed a high frequency of being associated with Cd levels during 2 weeks. This study provides direct evidence that specific Cd-induced patterns in bacterioplankton communities exist in highly varying manipulated coastal systems. Future investigations on an ecosystem scale across longer temporal scales are needed to validate the observed pattern. PMID:25326310

  17. Perceptual inference.

    PubMed

    Aggelopoulos, Nikolaos C

    2015-08-01

    Perceptual inference refers to the ability to infer sensory stimuli from predictions that result from internal neural representations built through prior experience. Methods of Bayesian statistical inference and decision theory model cognition adequately by using error sensing either in guiding action or in "generative" models that predict the sensory information. In this framework, perception can be seen as a process qualitatively distinct from sensation, a process of information evaluation using previously acquired and stored representations (memories) that is guided by sensory feedback. The stored representations can be utilised as internal models of sensory stimuli enabling long term associations, for example in operant conditioning. Evidence for perceptual inference is contributed by such phenomena as the cortical co-localisation of object perception with object memory, the response invariance in the responses of some neurons to variations in the stimulus, as well as from situations in which perception can be dissociated from sensation. In the context of perceptual inference, sensory areas of the cerebral cortex that have been facilitated by a priming signal may be regarded as comparators in a closed feedback loop, similar to the better known motor reflexes in the sensorimotor system. The adult cerebral cortex can be regarded as similar to a servomechanism, in using sensory feedback to correct internal models, producing predictions of the outside world on the basis of past experience. PMID:25976632

  18. Bacterioplankton responses to iron enrichment during the SAGE experiment

    NASA Astrophysics Data System (ADS)

    Kuparinen, J.; Hall, J.; Ellwood, M.; Safi, K.; Peloquin, J.; Katz, D.

    2011-03-01

    We studied the microbial food web in the upper 100 m of the water column in iron-limited sub-Antarctic HNLC waters south-east of New Zealand in the SAGE experiment in 2004, with focus on bacterioplankton. Samples were collected daily from inside and outside the iron enriched patch. Short term enrichment experiments were conducted on board in 4 L polycarbonate bottles with water outside the iron enriched patch to study single and combined effects of micronutrient additions on microbial food web. Low bacterial growth was recorded in the study area with community turnover times of 50 h or more during the study period. Measurements of bacterial standing stocks and production rates in the study show minor responses to the large scale iron enrichment, with increase in rates and stocks after the first enrichment and at the end of the study period after the third iron enrichment when solar radiation increased and wind mixing decreased. The average daily bacterial production rates were 31.5 and 33.7 mgCm -2 d -1 for the OUT and IN stations, respectively; thus overall there was not a significant difference between the control and the iron-enriched patch. In the bottle experiments bacterial thymidine incorporation showed responses to single iron and silicic acid enrichments and a major growth response to the combined iron and sucrose enrichments. Phytoplankton chlorophyll- a showed clear stimulation by single additions of iron and silicic acid and silicic acid enhanced the iron impact. Cobalt additions had no effect on bacteria growth and a negative effect on phytoplankton growth. Low bacterial in situ growth rates and the enrichment experiments suggest that bacteria are co-limited by iron and carbon, and that bacterial iron uptake is dependent on carbon supply by the food web. With the high iron quota (μmol Fe mol C -1) bacteria may scavenge considerable amounts of the excess iron, and thus influence the relative importance of the microbial food web as a carbon sink.

  19. Use of 16S Ribosomal DNA for Delineation of Marine Bacterioplankton Species

    PubMed Central

    Hagström, Åke; Pommier, Thomas; Rohwer, Forest; Simu, Karin; Stolte, Willem; Svensson, Dominika; Zweifel, Ulla Li

    2002-01-01

    All of the marine bacterioplankton-derived 16S ribosomal DNA sequences previously deposited in GenBank were reanalyzed to determine the number of bacterial species in the oceanic surface waters. These sequences have been entered into the database since 1990. The rate of new additions reached a peak in 1999 and subsequently leveled off, suggesting that much of the marine microbial species richness has been sampled. When the GenBank sequences were dereplicated by using 97% similarity as a cutoff, 1,117 unique ribotypes were found. Of the unique sequences, 609 came from uncultured environmental clones and 508 came from cultured bacteria. We conclude that the apparent bacterioplankton species richness is relatively low. PMID:12089052

  20. Impact of solar radiation on bacterioplankton in Laguna Vilama, a hypersaline Andean lake (4650 m)

    NASA Astrophysics Data System (ADS)

    FaríAs, MaríA. Eugenia; FernáNdez-Zenoff, Verónica; Flores, Regina; OrdóñEz, Omar; EstéVez, Cristina

    2009-06-01

    Laguna Vilama is a hypersaline Lake located at 4660 m altitude in the northwest of Argentina high up in the Andean Puna. The impact of ultraviolet (UV) radiation on bacterioplankton was studied by collecting samples at different times of the day. Molecular analysis (DGGE) showed that the bacterioplankton community is characterized by Gamma-proteobacteria (Halomonas sp., Marinobacter sp.), Alpha-proteobacteria (Roseobacter sp.), HGC (Agrococcus jenensis and an uncultured bacterium), and CFB (uncultured Bacteroidetes). During the day, minor modifications in bacterial diversity such as intensification of Bacteroidetes' signal and an emergence of Gamma-proteobacteria (Marinobacter flavimaris) were observed after solar exposure. DNA damage, measured as an accumulation of Cyclobutane Pyrimidine Dimers (CPDs), in bacterioplankton and naked DNA increased from 100 CPDs MB-1 at 1200 local time (LT) to 300 CPDs MB-1 at 1600 LT, and from 80 CPDs MB-1 at 1200 LT to 640 CPDs MB-1 at 1600 LT, respectively. In addition, pure cultures of Pseudomonas sp. V1 and Brachybacterium sp. V5, two bacteria previously isolated from this environment, were exposed simultaneously with the community, and viability of both strains diminished after solar exposure. No CPD accumulation was observed in either of the exposed cultures, but an increase in mutagenesis was detected in V5. Of both strains only Brachybacterium sp. V5 showed CPD accumulation in naked DNA. These results suggest that the bacterioplankton community is well adapted to this highly solar irradiated environment showing little accumulation of CPDs and few changes in the community composition. They also demonstrate that these microorganisms contain efficient mechanisms against UV damage.

  1. Magnitude and regulation of bacterioplankton respiratory quotient across freshwater environmental gradients.

    PubMed

    Berggren, Martin; Lapierre, Jean-François; del Giorgio, Paul A

    2012-05-01

    Bacterioplankton respiration (BR) may represent the largest single sink of organic carbon in the biosphere and constitutes an important driver of atmospheric carbon dioxide (CO(2)) emissions from freshwaters. Complete understanding of BR is precluded by the fact that most studies need to assume a respiratory quotient (RQ; mole of CO(2) produced per mole of O(2) consumed) to calculate rates of BR. Many studies have, without clear support, assumed a fixed RQ around 1. Here we present 72 direct measurements of bacterioplankton RQ that we carried out in epilimnetic samples of 52 freshwater sites in Québec (Canada), using O(2) and CO(2) optic sensors. The RQs tended to converge around 1.2, but showed large variability (s.d.=0.45) and significant correlations with major gradients of ecosystem-level, substrate-level and bacterial community-level characteristics. Experiments with natural bacterioplankton using different single substrates suggested that RQ is intimately linked to the elemental composition of the respired compounds. RQs were on average low in net autotrophic systems, where bacteria likely were utilizing mainly reduced substrates, whereas we found evidence that the dominance of highly oxidized substrates, for example, organic acids formed by photo-chemical processes, led to high RQ in the more heterotrophic systems. Further, we suggest that BR contributes to a substantially larger share of freshwater CO(2) emissions than presently believed based on the assumption that RQ is ∼1. Our study demonstrates that bacterioplankton RQ is not only a practical aspect of BR determination, but also a major ecosystem state variable that provides unique information about aquatic ecosystem functioning. PMID:22094347

  2. Covariance of bacterioplankton composition and environmental variables in a temperate delta system

    USGS Publications Warehouse

    Stepanauskas, R.; Moran, M.A.; Bergamaschi, B.A.; Hollibaugh, J.T.

    2003-01-01

    We examined seasonal and spatial variation in bacterioplankton composition in the Sacramento-San Joaquin River Delta (CA) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Cloned 16S rRNA genes from this system were used for putative identification of taxa dominating the T-RFLP profiles. Both cloning and T-RFLP analysis indicated that Actinobacteria, Verrucomicrobia, Cytophaga-Flavobacterium and Proteobacteria were the most abundant bacterioplankton groups in the Delta. Despite the broad variety of sampled habitats (deep water channels, lakes, marshes, agricultural drains, freshwater and brackish areas), and the spatial and temporal differences in hydrology, temperature and water chemistry among the sampling campaigns, T-RFLP electropherograms from all samples were similar, indicating that the same bacterioplankton phylotypes dominated in the various habitats of the Delta throughout the year. However, principal component analysis (PCA) and partial least-squares regression (PLS) of T-RFLP profiles revealed consistent grouping of samples on a seasonal, but not a spatial, basis. ??-Proteobacteria related to Ralstonia, Actinobacteria related to Microthrix, and ??-Proteobacteria identical to the environmental Clone LD12 had the highest relative abundance in summer/fall T-RFLP profiles and were associated with low river flow, high pH, and a number of optical and chemical characteristics of dissolved organic carbon (DOC) indicative of an increased proportion of phytoplankton-produced organic material as opposed to allochthonous, terrestrially derived organic material. On the other hand, Geobacter-related ??-Proteobacteria showed a relative increase in abundance in T-RFLP analysis during winter/spring, and probably were washed out from watershed soils or sediment. Various phylotypes associated with the same phylogenetic division, based on tentative identification of T-RFLP fragments, exhibited diverse seasonal patterns, suggesting that ecological

  3. Magnitude and regulation of bacterioplankton respiratory quotient across freshwater environmental gradients

    PubMed Central

    Berggren, Martin; Lapierre, Jean-François; del Giorgio, Paul A

    2012-01-01

    Bacterioplankton respiration (BR) may represent the largest single sink of organic carbon in the biosphere and constitutes an important driver of atmospheric carbon dioxide (CO2) emissions from freshwaters. Complete understanding of BR is precluded by the fact that most studies need to assume a respiratory quotient (RQ; mole of CO2 produced per mole of O2 consumed) to calculate rates of BR. Many studies have, without clear support, assumed a fixed RQ around 1. Here we present 72 direct measurements of bacterioplankton RQ that we carried out in epilimnetic samples of 52 freshwater sites in Québec (Canada), using O2 and CO2 optic sensors. The RQs tended to converge around 1.2, but showed large variability (s.d.=0.45) and significant correlations with major gradients of ecosystem-level, substrate-level and bacterial community-level characteristics. Experiments with natural bacterioplankton using different single substrates suggested that RQ is intimately linked to the elemental composition of the respired compounds. RQs were on average low in net autotrophic systems, where bacteria likely were utilizing mainly reduced substrates, whereas we found evidence that the dominance of highly oxidized substrates, for example, organic acids formed by photo-chemical processes, led to high RQ in the more heterotrophic systems. Further, we suggest that BR contributes to a substantially larger share of freshwater CO2 emissions than presently believed based on the assumption that RQ is ∼1. Our study demonstrates that bacterioplankton RQ is not only a practical aspect of BR determination, but also a major ecosystem state variable that provides unique information about aquatic ecosystem functioning. PMID:22094347

  4. Spatially uniform but temporally variable bacterioplankton in a semi-enclosed coastal area.

    PubMed

    Meziti, Alexandra; Kormas, Konstantinos A; Moustaka-Gouni, Maria; Karayanni, Hera

    2015-07-01

    Studies focusing on the temporal and spatial dynamics of bacterioplankton communities within littoral areas undergoing direct influences from the coast are quite limited. In addition, they are more complicated to resolve compared to communities in the open ocean. In order to elucidate the effects of spatial vs. temporal variability on bacterial communities in a highly land-influenced semi-enclosed gulf, surface bacterioplankton communities from five coastal sites in Igoumenitsa Gulf (Ionian Sea, Greece) were analyzed over a nine-month period using 16S rDNA 454-pyrosequencing. Temporal differences were more pronounced than spatial ones, with lower diversity indices observed during the summer months. During winter and early spring, bacterial communities were dominated by SAR11 representatives, while this pattern changed in May when they were abruptly replaced by members of Flavobacteriales, Pseudomonadales, and Alteromonadales. Additionally, correlation analysis showed high negative correlations between the presence of SAR11 OTUs in relation to temperature and sunlight that might have driven, directly or indirectly, the disappearance of these OTUs in the summer months. The dominance of SAR11 during the winter months further supported the global distribution of the clade, not only in the open-sea, but also in coastal systems. This study revealed that specific bacteria exhibited distinct succession patterns in an anthropogenic-impacted coastal system. The major bacterioplankton component was represented by commonly found marine bacteria exhibiting seasonal dynamics, while freshwater and terrestrial-related phylotypes were absent. PMID:25976032

  5. Identification of polyamine-responsive bacterioplankton taxa in South Atlantic Bight.

    PubMed

    Lu, Xinxin; Sun, Shulei; Hollibaugh, James T; Mou, Xiaozhen

    2015-12-01

    Putrescine and spermidine are short-chained aliphatic polyamines (PAs) that are ubiquitously distributed in seawater. These compounds may be important sources of dissolved organic carbon and nitrogen for marine bacterioplankton. Here, we used pyrotag sequencing to quantify the response of bacterioplankton to putrescine and spermidine amendments in microcosms established using surface waters collected at various stations in the South Atlantic Bight in October 2011. Our analysis showed that PA-responsive bacterioplankton consisted of bacterial taxa that are typically dominant in marine systems. Rhodobacteraceae (Alphaproteobacteria) was the taxon most responsive to PA additions at the nearshore site. Gammaproteobacteria of the families Piscirickettsiaceae; Vibrionaceae; and Vibrionaceae and Pseudoalteromonadaceae, were the dominant PA-responsive taxa in samples from the river-influenced coastal station, offshore station and open ocean station, respectively. The spatial variability of PA-responsive taxa may be attributed to differences in composition of the initial bacterial community and variations of in situ physiochemical conditions among sites. Our results also provided the first empirical evidence that Gammaproteobacteria might play an important role in PA transformation in marine systems. PMID:26109269

  6. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda.

    PubMed

    Parsons, Rachel J; Nelson, Craig E; Carlson, Craig A; Denman, Carmen C; Andersson, Andreas J; Kledzik, Andrew L; Vergin, Kevin L; McNally, Sean P; Treusch, Alexander H; Giovannoni, Stephen J

    2015-10-01

    Understanding bacterioplankton community dynamics in coastal hypoxic environments is relevant to global biogeochemistry because coastal hypoxia is increasing worldwide. The temporal dynamics of bacterioplankton communities were analysed throughout the illuminated water column of Devil's Hole, Bermuda during the 6-week annual transition from a strongly stratified water column with suboxic and high-pCO2 bottom waters to a fully mixed and ventilated state during 2008. A suite of culture-independent methods provided a quantitative spatiotemporal characterization of bacterioplankton community changes, including both direct counts and rRNA gene sequencing. During stratification, the surface waters were dominated by the SAR11 clade of Alphaproteobacteria and the cyanobacterium Synechococcus. In the suboxic bottom waters, cells from the order Chlorobiales prevailed, with gene sequences indicating members of the genera Chlorobium and Prosthecochloris--anoxygenic photoautotrophs that utilize sulfide as a source of electrons for photosynthesis. Transitional zones of hypoxia also exhibited elevated levels of methane- and sulfur-oxidizing bacteria relative to the overlying waters. The abundance of both Thaumarcheota and Euryarcheota were elevated in the suboxic bottom waters (> 10(9) cells l(-1)). Following convective mixing, the entire water column returned to a community typical of oxygenated waters, with Euryarcheota only averaging 5% of cells, and Chlorobiales and Thaumarcheota absent. PMID:24589037

  7. Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton.

    PubMed

    Nelson, Craig E; Carlson, Craig A

    2012-06-01

    Bacterioplankton are the primary trophic conduit for dissolved organic carbon (DOC) and linking community structure with DOC utilization is central to understanding global carbon cycling. We coupled stable isotope probing (SIP) with 16S rRNA pyrosequencing in dark seawater culture experiments on euphotic and mesopelagic communities from the Sargasso Sea. Parallel cultures were amended with equimolar quantities of four DO(13) C substrates to simultaneously evaluate community utilization and population-specific incorporation. Of the substrates tested - two cyanobacterial products (exudates or lysates from a culture of Synechococcus) and two defined monosaccharides (glucose or gluconic acid) - the cyanobacterial exudates were incorporated by the greatest diversity of oligotrophic bacterioplankton populations in surface waters, including taxa from > 10 major subclades within the Flavobacteria, Actinobacteria, Verrucomicrobia and Proteobacteria (including SAR11). In contrast, the monosaccharide glucose was not incorporated by any taxa belonging to extant oligotrophic oceanic clades. Conversely, proteobacterial copiotrophs, which were rare in the ambient water (< 0.1% of sequences), grew rapidly on all DOC amendments at both depths, but with different substrate preferences among lineages. We present a new analytical framework for using SIP to detect DOC incorporation across diverse oligotrophic bacterioplankton and discuss implications for the ecology of bacterial-DOC interactions among populations of diverging trophic strategies. PMID:22507662

  8. Alkaline phosphatases in microbialites and bacterioplankton from Alchichica soda lake, Mexico.

    PubMed

    Valdespino-Castillo, Patricia M; Alcántara-Hernández, Rocio J; Alcocer, Javier; Merino-Ibarra, Martín; Macek, Miroslav; Falcón, Luisa I

    2014-11-01

    Dissolved organic phosphorus utilization by different members of natural communities has been closely linked to microbial alkaline phosphatases whose affiliation and diversity is largely unknown. Here we assessed genetic diversity of bacterial alkaline phosphatases phoX and phoD, using highly diverse microbial consortia (microbialites and bacterioplankton) as study models. These microbial consortia are found in an oligo-mesotrophic soda lake with a particular geochemistry, exhibiting a low calcium concentration and a high Mg : Ca ratio relative to seawater. In spite of the relative low calcium concentration in the studied system, our results highlight the diversity of calcium-based metallophosphatases phoX and phoD-like in heterotrophic bacteria of microbialites and bacterioplankton, where phoX was the most abundant alkaline phosphatase found. phoX and phoD-like phylotypes were more numerous in microbialites than in bacterioplankton. A larger potential community for DOP utilization in microbialites was consistent with the TN : TP ratio, suggesting P limitation within these assemblages. A cross-system comparison indicated that diversity of phoX in Lake Alchichica was similar to that of other aquatic systems with a naturally contrasting ionic composition and trophic state, although no phylotypes were shared among systems. PMID:25112496

  9. Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean.

    PubMed

    Yu, Zheng; Yang, Jun; Liu, Lemian; Zhang, Wenjing; Amalfitano, Stefano

    2015-01-01

    The Southern Ocean is among the least explored marine environments on Earth, and still little is known about regional and vertical variability in the diversity of Antarctic marine prokaryotes. In this study, the bacterioplankton community in both epipelagic and mesopelagic waters was assessed at two adjacent stations by high-throughput sequencing and quantitative PCR. Water temperature was significantly higher in the superficial photic zone, while higher salinity and dissolved oxygen were recorded in the deeper water layers. The highest abundance of the bacterioplankton was found at a depth of 75 m, corresponding to the deep chlorophyll maximum layer. Both Alphaproteobacteria and Gammaproteobacteria were the most abundant taxa throughout the water column, while more sequences affiliated to Cyanobacteria and unclassified bacteria were identified from surface and the deepest waters, respectively. Temperature was the most significant environmental variable affecting the bacterial community structure. The bacterial community composition displayed significant differences at the epipelagic layers between two stations, whereas those in the mesopelagic waters were more similar to each other. Our results indicated that the epipelagic bacterioplankton might be dominated by short-term environmental variable conditions, whereas the mesopelagic communities appeared to be structured by longer water-mass residence time and relative stable environmental factors. PMID:26256889

  10. In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

    PubMed Central

    Salcher, Michaela M; Posch, Thomas; Pernthaler, Jakob

    2013-01-01

    The substrate partitioning of sympatric populations of freshwater bacterioplankton was studied via microautoradiography and fluorescence in situ hybridization. Fourteen radiolabeled tracers were used to assess microbial acquisition spectra of low-molecular-weight (LMW) organic compounds. The most abundant group, ac1 Actinobacteria, were highly active in leucine, thymidine and glucose assimilation, whereas Alphaproteobacteria from the LD12 lineage (the freshwater sister clade of SAR11) only weakly incorporated these tracers, but exhibited a distinct preference for glutamine and glutamate. Different Bacteroidetes showed contrasting uptake patterns: Flavobacteriales did not incorporate significant amounts of any LMW compound, and Cyclobacteriaceae were clearly specialized on leucine, glucose and arginine. Betaproteobacteria represented the most active and versatile bacterioplankton fraction and >90% of them could be assigned to eight species- to genus-like populations with contrasting substrate specialization. Limnohabitans sp. were the most abundant and active Betaproteobacteria, incorporating almost all tracers. While three closely related betaproteobacterial populations substantially differed in their uptake spectra, two more distantly related lineages had very similar preferences, and one population did not incorporate any tracer. The dominant phototrophic microorganism, the filamentous cyanobacterium Planktothrix rubescens, assimilated several substrates, whereas other (pico)cyanobacteria had no heterotrophic activity. The variable extent of specialization by the studied bacterial taxa on subsets of LMW compounds contrasts theoretical considerations about non-selective microbial substrate assimilation at oligotrophic conditions. This physiological niche separation might be one explanation for the coexistence of freshwater bacterioplankton species in a seemingly uniform environment. PMID:23235289

  11. Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland.

    PubMed

    Quiroga, María Victoria; Valverde, Angel; Mataloni, Gabriela; Cowan, Don

    2015-06-01

    Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems. PMID:25727763

  12. Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean

    PubMed Central

    Yu, Zheng; Yang, Jun; Liu, Lemian; Zhang, Wenjing; Amalfitano, Stefano

    2015-01-01

    The Southern Ocean is among the least explored marine environments on Earth, and still little is known about regional and vertical variability in the diversity of Antarctic marine prokaryotes. In this study, the bacterioplankton community in both epipelagic and mesopelagic waters was assessed at two adjacent stations by high-throughput sequencing and quantitative PCR. Water temperature was significantly higher in the superficial photic zone, while higher salinity and dissolved oxygen were recorded in the deeper water layers. The highest abundance of the bacterioplankton was found at a depth of 75 m, corresponding to the deep chlorophyll maximum layer. Both Alphaproteobacteria and Gammaproteobacteria were the most abundant taxa throughout the water column, while more sequences affiliated to Cyanobacteria and unclassified bacteria were identified from surface and the deepest waters, respectively. Temperature was the most significant environmental variable affecting the bacterial community structure. The bacterial community composition displayed significant differences at the epipelagic layers between two stations, whereas those in the mesopelagic waters were more similar to each other. Our results indicated that the epipelagic bacterioplankton might be dominated by short-term environmental variable conditions, whereas the mesopelagic communities appeared to be structured by longer water-mass residence time and relative stable environmental factors. PMID:26256889

  13. Seasonal succession and UV sensitivity of marine bacterioplankton at an Antarctic coastal site.

    PubMed

    Piquet, Anouk M-T; Bolhuis, Henk; Davidson, Andrew T; Buma, Anita G J

    2010-07-01

    Despite extensive microbial biodiversity studies around the globe, studies focusing on diversity and community composition of Bacteria in Antarctic coastal regions are still scarce. Here, we studied the diversity and development of bacterioplankton communities from Prydz Bay (Eastern Antarctic) during spring and early summer 2002-2003. Additionally, we investigated the possible shaping effects of solar UV radiation (UV-R: 280-400 nm) on bacterioplankton communities incubated for 13-14 days in 650-L minicosm tanks. Ribosomal DNA sequence analysis of the natural bacterioplankton communities revealed an initial springtime community composed of three evenly abundant bacterial classes: Cytophaga-Flavobacteria-Bacteroidetes (CFB), Gammaproteobacteria and Alphaproteobacteria. At the end of spring, a shift occurred toward a CFB-dominated community, most likely a response to the onset of a springtime phytoplankton bloom. The tail end of Prydz Bay clone library diversity revealed sequences related to Deltaproteobacteria, Verrucomicrobiales, Planctomycetes, Gemmatimonadetes and an unclassified bacterium (ANT4E12). Minicosm experiments showed that incubation time was the principal determinant of bacterial community composition and that UV-R treatment significantly changed the composition in only two of the four experiments. Thus, the successional maturity of the microbial community in our minicosm studies appears to be a greater determinant of bacterial community composition rather than the nonprofound and subtle effects of UV-R. PMID:20455939

  14. Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation

    PubMed Central

    2013-01-01

    Background The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart. Results The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in

  15. Effects of temperature and nutrients on changes in genetic diversity of bacterioplankton communities in a semi-closed bay, South Korea.

    PubMed

    Kim, Hyun Jung; Jung, Seung Won; Lim, Dhong-Il; Jang, Min-Chul; Lee, Taek-Kyun; Shin, Kyoungsoon; Ki, Jang-Seu

    2016-05-15

    Bacterioplankton communities in a semi-closed bay (Jangmok Bay, South Korea) were analysed using a 16S rDNA multiplex 454 pyrosequencing approach. Diversity and operational taxonomic units of bacterioplankton communities in the Jangmok Bay are highest in cold water seasons and lowest in warm water ones. During cold seasons, α-proteobacteria respond rapidly to pulses of the concentration of inorganic nutrients, while γ-proteobacteria during warm water seasons are the most active type of bacterioplankton resent in the prevailing conditions, which include high dissolved organic carbon, chemical oxygen demand and primary production. Cyanobacteria, a minor group constituting 4.58% of the total bacterioplankton, are more abundant at low temperature. Flavobacteria are more abundant in nutrient-rich conditions and the abundance of this group also demonstrated a delayed decline following summer phytoplankton blooms. The pronounced seasonal oscillations in phosphorus concentration and temperature exert strong selection pressure on bacterioplankton communities. PMID:27001714

  16. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

    PubMed Central

    2012-01-01

    Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants. PMID:23102090

  17. Physiology and phylogeny of the candidate phylum "Atribacteria" (formerly OP9/JS1) inferred from single-cell genomics and metagenomics

    NASA Astrophysics Data System (ADS)

    Dodsworth, J. A.; Murugapiran, S.; Blainey, P. C.; Nobu, M.; Rinke, C.; Schwientek, P.; Gies, E.; Webster, G.; Kille, P.; Weightman, A.; Liu, W. T.; Hallam, S.; Tsiamis, G.; Swingley, W.; Ross, C.; Tringe, S. G.; Chain, P. S.; Scholz, M. B.; Lo, C. C.; Raymond, J.; Quake, S. R.; Woyke, T.; Hedlund, B. P.

    2014-12-01

    Single-cell sequencing and metagenomics have extended the genomics revolution to yet-uncultivated microorganisms and provided insights into the coding potential of this so-called "microbial dark matter", including microbes belonging candidate phyla with no cultivated representatives. As more datasets emerge, comparison of individual genomes from different lineages and habitats can provide insight into the phylogeny, conserved features, and potential metabolic diversity of candidate phyla. The candidate bacterial phylum OP9 was originally found in Obsidian Pool, Yellowstone National Park, and it has since been detected in geothermal springs, petroleum reservoirs, and engineered thermal environments worldwide. JS1, another uncultivated bacterial lineage affiliated with OP9, is often abundant in marine sediments associated with methane hydrates, hydrocarbon seeps, and on continental margins and shelves, and is found in other non-thermal marine and subsurface environments. The phylogenetic relationship between OP9, JS1, and other Bacteria has not been fully resolved, and to date no axenic cultures from these lineages have been reported. Recently, 31 single amplified genomes (SAGs) from six distinct OP9 and JS1 lineages have been obtained using flow cytometric and microfluidic techniques. These SAGs were used to inform metagenome binning techniques that identified OP9/JS1 sequences in several metagenomes, extending genomic coverage in three of the OP9 and JS1 lineages. Phylogenomic analyses of these SAG and metagenome bin datasets suggest that OP9 and JS1 constitute a single, deeply branching phylum, for which the name "Atribacteria" has recently been proposed. Overall, members of the "Atribacteria" are predicted to be heterotrophic anaerobes without the capacity for respiration, with some lineages potentially specializing in secondary fermentation of organic acids. A set of signature "Atribacteria" genes was tentatively identified, including components of a bacterial

  18. Validity of eucaryote inhibitors for assessing production and grazing mortality of marine bacterioplankton. [Cyclidium sp

    SciTech Connect

    Taylor, G.T.; Pace, M.L.

    1987-01-01

    Application of eucaryote inhibitors to the estimation of production and grazing mortality of bacterioplankton was evaluated. Exposure to a range of concentrations of thiram, cycloheximide, and neutral red (0.4 to 210, 36 to 1777, 4 to 346 ..mu..M, respectively) was 98 to 100% effective at inhibiting growth of a chrysomonad in culture. Exposure to colchicine and griseofulvin (50 to 1000 ..mu..M for both) yielded only 24 to 94 and 53 to 79% inhibition, respectively. Exposures to thiram, neutral red, and griseofulvin were 90 to 100% effective at inhibiting the growth in culture of a ciliate, Cyclidium sp., and the responses to colchicine and cycloheximide were variable (64 to 100 and 0 to 100% inhibition, respectively). Thiram and neutral red inhibited field populations of nanozooplankton more effectively than cycloheximide and colchicine. Direct effects of eucaryote inhibitors on growing cultures of bacterioplankton varied with parameters measured and duration of exposure. After 3-day exposures, specific growth rates and instantaneous heterotrophic potential ((/sup 14/C)glucose uptake) were not consistently affected, but biosynthetic activity (RNA and DNA syntheses) was depressed. The degree of inhibition of isolates and field populations of phytoplankton depended upon type of inhibitor and phytoplankton species. In field experiments, it was possible to calculate rates of bacterioplankton production and grazing mortality for only 16 of 29 inhibitor experiments and for 4 of 10 size fractionation experiments. Because of the inconsistent results obtained in this investigation, the authors strongly recommend exercising caution in the application of inhibitor techniques to ecological problems, especially in phototrophically dominated systems.

  19. Using Cases to Strengthen Inference on the Association between Single Nucleotide Polymorphisms and a Secondary Phenotype in Genome-Wide Association Studies

    PubMed Central

    Li, Huilin; Gail, Mitchell H.; Berndt, Sonja; Chatterjee, Nilanjan

    2010-01-01

    Case-control genome-wide association studies provide a vast amount of genetic information that may be used to investigate secondary phenotypes. We study the situation in which the primary disease is rare and the secondary phenotype and genetic markers are dichotomous. An analysis of the association between a genetic marker and the secondary phenotype based on controls only is valid, whereas standard methods that also use cases result in biased estimates and highly inflated type I error if there is an interaction between the secondary phenotype and the genetic marker on the risk of the primary disease. Here we present an adaptively weighted method that combines the case and control data to study the association, while reducing to the controls only analysis if there is strong evidence of an interaction. The possibility of such an interaction and the misleading results for standard methods, but not for the adaptively weighted or controls only approaches, are illustrated by data from a case-control study of colorectal adenoma, in which the secondary phenotype is smoking. Simulations and asymptotic theory indicate that the adaptively weighted method can reduce the mean square error for estimation with a pre-specified SNP and increase the power to discover a new association in a genome-wide study, compared to an analysis of controls only. Further experience with genome-wide studies is needed to determine when methods that assume no interaction and gain precision and power, thereby can be recommended, and when methods such as the adaptively weighted or controls only approaches are needed to guard against the possibility of non-zero interactions. PMID:20583284

  20. An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

    PubMed Central

    Crow, Karen D.; Smith, Christopher D.; Cheng, Jan-Fang; Wagner, Günter P.; Amemiya, Chris T.

    2012-01-01

    Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates. PMID:22851613

  1. The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondrial genome.

    PubMed

    Nikaido, Masato; Cao, Ying; Okada, Norihiro; Hasegawa, Masami

    2003-02-01

    The complete mitochondrial genome of a lesser hedgehog tenrec Echinops telfairi was determined in this study. It is an endemic African insectivore that is found specifically in Madagascar. The tenrec's back is covered with hedgehog-like spines. Unlike other spiny mammals, such as spiny mice, spiny rats, spiny dormice and porcupines, lesser hedgehog tenrecs look amazingly like true hedgehogs (Erinaceidae). However, they are distinguished morphologically from hedgehogs by the absence of a jugal bone. We determined the complete sequence of the mitochondrial genome of a lesser hedgehog tenrec and analyzed the results phylogenetically to determine the relationships between the tenrec and other insectivores (moles, shrews and hedgehogs), as well as the relationships between the tenrec and endemic African mammals, classified as Afrotheria, that have recently been shown by molecular analysis to be close relatives of the tenrec. Our data confirmed the afrotherian status of the tenrec, and no direct relation was recovered between the tenrec and the hedgehog. Comparing our data with those of others, we found that within-species variations in the mitochondrial DNA of lesser hedgehog tenrecs appear to be the largest recognized to date among mammals, apart from orangutans, which might be interesting from the view point of evolutionary history of tenrecs on Madagascar. PMID:12655143

  2. High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

    PubMed Central

    Schönberg, Anna; Theunert, Christoph; Li, Mingkun; Stoneking, Mark; Nasidze, Ivan

    2011-01-01

    To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40–50 kya, followed by a constant population size, and then another expansion around 15–18 kya for the groups from the Caucasus and Iran. The BSP for Turkey differs the most from the others, with an increase from 35 to 50 kya followed by a prolonged period of constant population size, and no indication of a second period of growth. An approximate Bayesian computation approach was used to estimate divergence times between each pair of populations; the oldest divergence times were between Turkey and the other four groups from the South Caucasus and Iran (∼400–600 generations), while the divergence time of the three Caucasus groups from each other was comparable to their divergence time from Iran (average of ∼360 generations). These results illustrate the value of random sampling of complete mtDNA genome sequences that can be obtained with high-throughput sequencing platforms. PMID:21487439

  3. Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1.

    PubMed

    Rashid, Mahamud-Ur; Almeida, Mathieu; Azman, Andrew S; Lindsay, Brianna R; Sack, David A; Colwell, Rita R; Huq, Anwar; Morris, J Glenn; Alam, Munirul; Stine, O Colin

    2016-06-01

    Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10(-6)) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC. PMID:27190166

  4. The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing

    PubMed Central

    Kuwahara, Tomomi; Ogura, Yositoshi; Oshima, Kenshiro; Kurokawa, Ken; Ooka, Tadasuke; Hirakawa, Hideki; Itoh, Takehiko; Nakayama-Imaohji, Haruyuki; Ichimura, Minoru; Itoh, Kikuji; Ishifune, Chieko; Maekawa, Yoichi; Yasutomo, Koji; Hattori, Masahira; Hayashi, Tetsuya

    2011-01-01

    Numerous microbes inhabit the mammalian intestinal track and strongly impact host physiology; however, our understanding of this ecosystem remains limited owing to the high complexity of the microbial community and the presence of numerous non-culturable microbes. Segmented filamentous bacteria (SFBs), which are clostridia-related Gram-positive bacteria, are among such non-culturable populations and are well known for their unique morphology and tight attachment to intestinal epithelial cells. Recent studies have revealed that SFBs play crucial roles in the post-natal maturation of gut immune function, especially the induction of Th17 lymphocytes. Here, we report the complete genome sequence of mouse SFBs. The genome, which comprises a single circular chromosome of 1 620 005 bp, lacks genes for the biosynthesis of almost all amino acids, vitamins/cofactors and nucleotides, but contains a full set of genes for sporulation/germination and, unexpectedly, for chemotaxis/flagella-based motility. These findings suggest a triphasic lifestyle of the SFB, which comprises two types of vegetative (swimming and epicellular parasitic) phases and a dormant (spore) phase. Furthermore, SFBs encode four types of flagellin, three of which are recognized by Toll-like receptor 5 and could elicit the innate immune response. Our results reveal the non-culturability, lifestyle and immunostimulation mechanisms of SFBs and provide a genetic basis for the future development of the SFB cultivation and gene-manipulation techniques. PMID:21791478

  5. Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1

    PubMed Central

    Rashid, Mahamud-ur; Almeida, Mathieu; Azman, Andrew S.; Lindsay, Brianna R.; Sack, David A.; Colwell, Rita R.; Huq, Anwar; Morris, J. Glenn; Alam, Munirul; Stine, O. Colin

    2016-01-01

    Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10−6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC. PMID:27190166

  6. Stimulated bacterioplankton growth and selection for certain bacterial taxa in the vicinity of the ctenophore Mnemiopsis leidyi

    PubMed Central

    Dinasquet, Julie; Granhag, Lena; Riemann, Lasse

    2012-01-01

    Episodic blooms of voracious gelatinous zooplankton, such as the ctenophore Mnemiopsis leidyi, affect pools of inorganic nutrients and dissolved organic carbon by intensive grazing activities and mucus release. This will potentially influence bacterioplankton activity and community composition, at least at local scales; however, available studies on this are scarce. In the present study we examined effects of M. leidyi on bacterioplankton growth and composition in incubation experiments. Moreover, we examined community composition of bacteria associated with the surface and gut of M. leidyi. High release of ammonium and high bacterial growth was observed in the treatments with M. leidyi relative to controls. Deep 454 pyrosequencing of 16 S rRNA genes showed specific bacterial communities in treatments with M. leidyi as well as specific communities associated with M. leidyi tissue and gut. In particular, members of Flavobacteriaceae were associated with M. leidyi. Our study shows that M. leidyi influences bacterioplankton activity and community composition in the vicinity of the jellyfish. In particular during temporary aggregations of jellyfish, these local zones of high bacterial growth may contribute significantly to the spatial heterogeneity of bacterioplankton activity and community composition in the sea. PMID:22912629

  7. Snowmelt-driven changes in dissolved organic matter and bacterioplankton communities in the Heilongjiang watershed of China.

    PubMed

    Qiu, Linlin; Cui, Hongyang; Wu, Junqiu; Wang, Baijie; Zhao, Yue; Li, Jiming; Jia, Liming; Wei, Zimin

    2016-06-15

    Bacterioplankton plays a significant role in the circulation of materials and ecosystem function in the biosphere. Dissolved organic matter (DOM) from dead plant material and surface soil leaches into water bodies when snow melts. In our study, water samples from nine sampling sites along the Heilongjiang watershed were collected in February and June 2014 during which period snowmelt occurred. The goal of this study was to characterize changes in DOM and bacterioplankton community composition (BCC) associated with snowmelt, the effects of DOM, environmental and geographical factors on the distribution of BCC and interactions of aquatic bacterioplankton populations with different sources of DOM in the Heilongjiang watershed. BCC was measured by denaturing gradient gel electrophoresis (DGGE). DOM was measured by excitation-emission matrix (EEM) fluorescence spectroscopy. Bacterioplankton exhibited a distinct seasonal change in community composition due to snowmelt at all sampling points except for EG. Redundancy analysis (RDA) indicated that BCC was more closely related to DOM (Components 1 and 4, dissolved organic carbon, biochemical oxygen demand and chlorophyll a) and environmental factors (water temperature and nitrate nitrogen) than geographical factors. Furthermore, DOM had a greater impact on BCC than environmental factors (29.80 vs. 15.90% of the variation). Overall, spring snowmelt played an important role in altering the quality and quantity of DOM and BCC in the Heilongjiang watershed. PMID:26974572

  8. A comparative study of genome organization and inferences for the systematics of two large bushcricket genera of the tribe Barbitistini (Orthoptera: Tettigoniidae: Phaneropterinae)

    PubMed Central

    2014-01-01

    Background Poecilimon and Isophya are the largest genera of the tribe Barbitistini and among the most systematically complicated and evolutionarily intriguing groups of Palearctic tettigoniids. We examined the genomic organization of 79 taxa with a stable chromosome number using classical (C–banding, silver and fluorochrome staining) and molecular (fluorescence in situ hybridization with 18S rDNA and (TTAGG) n telomeric probes) cytogenetic techniques. These tools were employed to establish genetic organization and differences or similarities between genera or species within the same genus and determine if cytogenetic markers can be used for identifying some taxonomic groups of species. Results Differences between the karyotypes of the studied genera include some general changes in the morphology of the X chromosome in Isophya (in contrast to Poecilimon). The number of major rDNA clusters per haploid genome divided Poecilimon into two main almost equal groups (with either one or two clusters), while two rDNA clusters predominated in Isophya. In both genera, rDNA loci were preferentially located in the paracentromeric region of the autosomes and rarely in the sex chromosomes. Our results demonstrate a coincidence between the location of rDNA loci and active NORs and GC-rich heterochromatin regions. The C/DAPI/CMA3 bands observed in most Poecilimon chromosomes suggest the presence of more families of repetitive DNA sequences as compared to the heterochromatin patterns in Isophya. Conclusions The results show both differences and similarities in genome organization among species of the same genus and between genera. Previous views on the systematics and phylogenetic grouping of certain lineages are discussed in light of the present cytogenetic results. In some cases, variation of chromosome markers was observed to correspond with variation in other evolutionary traits, which is related to the processes of ongoing speciation and hybridization in zones of secondary

  9. Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site.

    PubMed

    Baltar, Federico; Palovaara, Joakim; Vila-Costa, Maria; Salazar, Guillem; Calvo, Eva; Pelejero, Carles; Marrasé, Cèlia; Gasol, Josep M; Pinhassi, Jarone

    2015-06-01

    Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow. PMID:26032602

  10. Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters

    PubMed Central

    Farnelid, Hanna M.; Turk-Kubo, Kendra A.; Zehr, Jonathan P.

    2016-01-01

    Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions. PMID:27148165

  11. Impact of warming on phyto-bacterioplankton coupling and bacterial community composition in experimental mesocosms.

    PubMed

    von Scheibner, Markus; Dörge, Petra; Biermann, Antje; Sommer, Ulrich; Hoppe, Hans-Georg; Jürgens, Klaus

    2014-03-01

    Global warming is assumed to alter the trophic interactions and carbon flow patterns of aquatic food webs. The impact of temperature on phyto-bacterioplankton coupling and bacterial community composition (BCC) was the focus of the present study, in which an indoor mesocosm experiment with natural plankton communities from the western Baltic Sea was conducted. A 6 °C increase in water temperature resulted, as predicted, in tighter coupling between the diatom-dominated phytoplankton and heterotrophic bacteria, accompanied by a strong increase in carbon flow into bacterioplankton during the phytoplankton bloom phase. Suppressed bacterial development at cold in situ temperatures probably reflected lowered bacterial production and grazing by protists, as the latter were less affected by low temperatures. BCC was strongly influenced by the phytoplankton bloom stage and to a lesser extent by temperature. Under both temperature regimes, Gammaproteobacteria clearly dominated during the phytoplankton peak, with Glaciecola sp. as the single most abundant taxon. However, warming induced the appearance of additional bacterial taxa belonging to Betaproteobacteria and Bacteroidetes. Our results show that warming during an early phytoplankton bloom causes a shift towards a more heterotrophic system, with the appearance of new bacterial taxa suggesting a potential for utilization of a broader substrate spectrum. PMID:23869806

  12. Influence of macrophyte decomposition on growth rate and community structure of okefenokee swamp bacterioplankton.

    PubMed

    Murray, R E; Hodson, R E

    1986-02-01

    Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released from senescent Nymphaea leaves caused a transient reduction in the abundance and activity of water column bacterioplankton, followed by a period of intense bacterial growth. Rates of [H]thymidine incorporation and turnover of dissolved d-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h [H]thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of the bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers. PMID:16346986

  13. Bacterioplankton and bacteriobenthos of the Amur estuary and the adjacent areas in the Summer of 2006

    NASA Astrophysics Data System (ADS)

    Karetnikova, E. A.; Garetova, L. A.

    2009-06-01

    This work presents the results of the study of the plankton and benthic microbiocenoses of the Amur estuary. It is shown that the distribution of the total abundance and indicator groups of the bacteriobenthos are characterized by stronger heterogeneity compared with the bacterioplankton and that it depends on the Amur river drainage and the bottom type. The river drainage helps by increasing the overall bacterioplankton abundance in the near-mouth part of the estuary. Microorganisms utilizing low concentrations of OM play a major role in the processes of the OM utilization in the water and bottom sediments. Saprophytic bacteria play a significant role in the OM utilization only in the water at certain sampling sites in the Tatarskiy Strait and Sakhalin Bay and in the bottom sediments taken in the mouth part of the estuary. Some parts of the estuary subject to organic contamination are found according to the microbiological characteristics. It is shown that the fluctuation of the salinity leads to a change of the share of bacteria with different food demands in the microbial community.

  14. Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2

    NASA Astrophysics Data System (ADS)

    Bunse, Carina; Lundin, Daniel; Karlsson, Christofer M. G.; Akram, Neelam; Vila-Costa, Maria; Palovaara, Joakim; Svensson, Lovisa; Holmfeldt, Karin; González, José M.; Calvo, Eva; Pelejero, Carles; Marrasé, Cèlia; Dopson, Mark; Gasol, Josep M.; Pinhassi, Jarone

    2016-05-01

    Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l-1) however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l-1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

  15. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    PubMed

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems. PMID:23637924

  16. Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance

    PubMed Central

    Sjöstedt, Johanna; Koch-Schmidt, Per; Pontarp, Mikael; Canbäck, Björn; Tunlid, Anders; Lundberg, Per; Hagström, Åke

    2012-01-01

    A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml−1) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes. PMID:22194288

  17. Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River

    PubMed Central

    Ma, Lili; Mao, Guannan; Liu, Jie; Gao, Guanghai; Zou, Changliang; Bartlam, Mark G.; Wang, Yingying

    2016-01-01

    To date, few aquatic microbial ecology studies have discussed the variability of the microbial community in exorheic river ecosystems on both the spatial and seasonal scales. In this study, we examined the spatio-temporal variation of bacterioplankton community composition in an anthropogenically influenced exorheic river, the Haihe River in Tianjin, China, using pyrosequencing analysis of 16S rRNA genes. It was verified by one-way ANOVA that the spatial variability of the bacterioplankton community composition over the whole river was stronger than the seasonal variation. Salinity was a major factor leading to spatial differentiation of the microbial community structure into riverine and estuarial parts. A high temperature influence on the seasonal bacterial community variation was only apparent within certain kinds of environments (e.g., the riverine part). Bacterial community richness and diversity both exhibited significant spatial changes, and their seasonal variations were completely different in the two environments studied here. Furthermore, riverine bacterial community assemblages were subdivided into urban and rural groups due to changes in the nutritional state of the river. In addition, the nutrient-loving group including Limnohabitans, Hydrogenophaga, and Polynucleobacter were abundant in the urbanized Haihe River, indicating the environmental factors in these anthropogenic waterbodies heavily influence the core freshwater community composition. PMID:26973627

  18. Influence of macrophyte decomposition on growth rate and community structure of Okefenokee Swamp bacterioplankton

    SciTech Connect

    Murray, R.E.; Hodson, R.E.

    1986-02-01

    Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released bacterioplankton, followed by a period of intense bacterial growth. Rates of (/sup 3/H)thymidine incorporation and turnover of dissolved D-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h (/sup 3/H)thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of the bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers.

  19. Impact of photochemical processing of DOC on the bacterioplankton respiratory quotient in aquatic ecosystems

    NASA Astrophysics Data System (ADS)

    Allesson, Lina; Ström, Lena; Berggren, Martin

    2016-07-01

    Many studies assume a respiratory quotient (RQ = molar ratio of CO2 produced to O2 consumed) close to 1 when calculating bacterioplankton respiration. However, evidence suggests that RQ depends on the chemical composition of the respired substrate pool that may be altered by photochemical production of oxygen-rich substrates, resulting in elevated RQs. Here we conducted a novel study of the impact of photochemical processing of dissolved organic carbon (DOC) on RQ. We monitored the bacterial RQ in bioassays of both ultraviolet light irradiated and nonirradiated humic lake water, using optic gas-pressure sensors. In the experimentally irradiated samples the average RQ value was significantly higher (3.4-3.5 [±0.4 standard error (SE)]) than that in the dark controls (1.3 [±0.1 SE]). Our results show that the RQ is systematically higher than 1 when the bacterial metabolism in large part is based on photoproducts. By assuming an RQ of 1, bacterioplankton respiration in freshwater ecosystems may be greatly underestimated.

  20. Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level

    PubMed Central

    Lucas, Judith; Koester, Irina; Wichels, Antje; Niggemann, Jutta; Dittmar, Thorsten; Callies, Ulrich; Wiltshire, Karen H.; Gerdts, Gunnar

    2016-01-01

    Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation. PMID:27014241

  1. Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance

    PubMed Central

    Xiong, Jinbo; Chen, Heping; Hu, Changju; Ye, Xiansen; Kong, Dingjiang; Zhang, Demin

    2015-01-01

    Understanding the underlying mechanisms that shape the temporal dynamics of a microbial community has important implications for predicting the trajectory of an ecosystem’s response to anthropogenic disturbances. Here, we evaluated the seasonal dynamics of bacterioplankton community composition (BCC) following more than three decades of mariculture disturbance in Xiangshan Bay. Clear seasonal succession and site (fish farm and control site) separation of the BCC were observed, which were primarily shaped by temperature, dissolved oxygen and sampling time. However, the sensitive bacterial families consistently changed in relative abundance in response to mariculture disturbance, regardless of the season. Temporal changes in the BCC followed the time-decay for similarity relationship at both sites. Notably, mariculture disturbance significantly (P < 0.001) flattened the temporal turnover but intensified bacterial species-to-species interactions. The decrease in bacterial temporal turnover under long-term mariculture disturbance was coupled with a consistent increase in the percentage of deterministic processes that constrained bacterial assembly based on a null model analysis. The results demonstrate that the BCC is sensitive to mariculture disturbance; however, a bacterioplankton community could adapt to a long-term disturbance via attenuating temporal turnover and intensifying species-species interactions. These findings expand our current understanding of microbial assembly in response to long-term anthropogenic disturbances. PMID:26471739

  2. Metagenomic Identification of Bacterioplankton Taxa and Pathways Involved in Microcystin Degradation in Lake Erie

    PubMed Central

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems. PMID:23637924

  3. Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level.

    PubMed

    Lucas, Judith; Koester, Irina; Wichels, Antje; Niggemann, Jutta; Dittmar, Thorsten; Callies, Ulrich; Wiltshire, Karen H; Gerdts, Gunnar

    2016-01-01

    Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation. PMID:27014241

  4. Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf

    NASA Astrophysics Data System (ADS)

    Alongi, Daniel M.; Patten, Nicole L.; McKinnon, David; Köstner, Nicole; Bourne, David G.; Brinkman, Richard

    2015-02-01

    Bacterioplankton and phytoplankton dynamics, pelagic respiration, virioplankton abundance, and the diversity of pelagic diazotrophs and other bacteria were examined in relation to water-column nutrients and vertical mixing across the southern Great Barrier Reef (GBR) shelf where sharp inshore to offshore gradients in water chemistry and hydrology prevail. A principal component analysis (PCA) revealed station groups clustered geographically, suggesting across-shelf differences in plankton function and structure driven by changes in mixing intensity, sediment resuspension, and the relative contributions of terrestrial, reef and oceanic nutrients. At most stations and sampling periods, microbial abundance and activities peaked both inshore and at channels between outer shelf reefs of the Pompey Reef complex. PCA also revealed that virioplankton numbers and biomass correlated with bacterioplankton numbers and production, and that bacterial growth and respiration correlated with net primary production, suggesting close virus-bacteria-phytoplankton interactions; all plankton groups correlated with particulate C, N, and P. Strong vertical mixing facilitates tight coupling of pelagic and benthic shelf processes as, on average, 37% and 56% of N and P demands of phytoplankton are derived from benthic nutrient regeneration and resuspension. These across-shelf planktonic trends mirror those of the benthic microbial community.

  5. Bacterioplankton Community Shifts in an Arctic Lake Correlate with Seasonal Changes in Organic Matter Source

    PubMed Central

    Crump, Byron C.; Kling, George W.; Bahr, Michele; Hobbie, John E.

    2003-01-01

    Seasonal shifts in bacterioplankton community composition in Toolik Lake, a tundra lake on the North Slope of Alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (DOM). A shift in community composition, measured by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes, occurred at 4°C in near-surface waters beneath seasonal ice and snow cover in spring. This shift was associated with an annual peak in bacterial productivity ([14C]leucine incorporation) driven by the large influx of labile terrestrial DOM associated with snow meltwater. A second shift occurred after the flux of terrestrial DOM had ended in early summer as ice left the lake and as the phytoplankton community developed. Bacterioplankton communities were composed of persistent populations present throughout the year and transient populations that appeared and disappeared. Most of the transient populations could be divided into those that were advected into the lake with terrestrial DOM in spring and those that grew up from low concentrations during the development of the phytoplankton community in early summer. Sequencing of DNA in DGGE bands demonstrated that most bands represented single ribotypes and that matching bands from different samples represented identical ribotypes. Bacteria were identified as members of globally distributed freshwater phylogenetic clusters within the α- and β-Proteobacteria, the Cytophaga-Flavobacteria-Bacteroides group, and the Actinobacteria. PMID:12676708

  6. Distribution patterns of bacterioplankton in the oligotrophic south-eastern Mediterranean Sea.

    PubMed

    Keuter, Sabine; Rahav, Eyal; Herut, Barak; Rinkevich, Baruch

    2015-08-01

    The spatial variability in the composition of bacterioplankton communities from the Levantine basin off the Israeli coast (south-eastern Mediterranean Sea) was studied using water samples from nine stations down to 1880 m depth. An nMDS (non-metric multidimensional scaling) ordination plot of ARISA (automated rRNA intergenic spacer analyses) fingerprints performed on 39 water samples revealed three groups of communities based on depth (epi, meso and bathypelagial waters), while the stations' geographical location did not seem to have an effect on the distribution of bacterioplankton assemblages. Interestingly, communities from the two deep pelagic zones were further grouped depending on the three prevailing water masses in the Levantine basin, and depth, salinity, temperature and silicic acid were significantly related to the variations of the bacterial community compositions. Cloning of internal transcribed spacer (ITS) sequences of dominant ARISA peaks showed that abundant bacteria in all depths were ubiquitous uncultured Alpha- and Gammaproteobacteria. The results further indicate that distinct microbial community profiles in the Levantine basin are associated with prevailing water masses that have formed due to different physico-chemical parameters and thus might act as physical barriers rather than physiological discriminators, as has been suggested in studies from other ocean regions. PMID:26109135

  7. The bioinvasion of Guam: inferring geographic origin, pace, pattern and process of an invasive lizard (Carlia) in the Pacific using multi-locus genomic data

    USGS Publications Warehouse

    Austin, C.C.; Rittmeyer, E.N.; Oliver, L.A.; Andermann, J.O.; Zug, G.R.; Rodda, G.H.; Jackson, N.D.

    2011-01-01

    Invasive species often have dramatic negative effects that lead to the deterioration and loss of biodiversity frequently coupled with the burden of expensive biocontrol programs and subversion of socioeconomic stability. The fauna and flora of oceanic islands are particularly susceptible to invasive species and the increase of global movements of humans and their products since WW II has caused numerous anthropogenic translocations and increased the ills of human-mediated invasions. We use a multi-locus genomic dataset to identify geographic origin, pace, pattern and historical process of an invasive scincid lizard (Carlia) that has been inadvertently introduced to Guam, the Northern Marianas, and Palau. This lizard is of major importance as its introduction is thought to have assisted in the establishment of the invasive brown treesnake (Boiga irregularis) on Guam by providing a food resource. Our findings demonstrate multiple waves of introductions that appear to be concordant with movements of Allied and Imperial Japanese forces in the Pacific during World War II.

  8. Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae.

    PubMed

    Man, Zhang; Yishu, Wang; Peng, Yan; Xiaobing, Wu

    2011-07-01

    We report complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae, whose gene orders match those of other crocodilians. Phylogenetic analyses based on the sequences of 12 mitochondrial protein-coding genes support monophyly of two crocodilian taxonomic families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma). Our results are consistent with monophyly of all crocodilian genera. Within Alligatoridae, genus Alligator is the sister taxon of a clade comprising Caiman and Paleosuchus. Within Crocodylidae, the basal phylogenetic split separates a clade comprising Gavialis and Tomistoma from a clade comprising Crocodylus, Mecistops, and Osteolaemus. Mecistops and Osteolaemus form the sister taxon to Crocodylus. Within Crocodylus, we sampled five Indopacific species, whose phylogenetic ordering is ((C. mindorensis, C. novaeguineae), (C. porosus, (C. siamensis, C. palustris))). The African species C. niloticus and New World species C. acutus form the sister taxon to the Indopacific species, although our sampling lacks three other New World species and an Australian species of Crocodylus. PMID:21463698

  9. Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

    PubMed

    Nakagome, Shigeki; Sato, Takehiro; Ishida, Hajime; Hanihara, Tsunehiko; Yamaguchi, Tetsutaro; Kimura, Ryosuke; Mano, Shuhei; Oota, Hiroki

    2015-06-01

    Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history. PMID:25758010

  10. Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed.

    PubMed

    Grossart, Hans-Peter

    2010-12-01

    In recent years, microbial ecology has developed from a peripheral discipline into a central field of microbiology. This change in state and perception is mainly driven by a rapid development of methods applied in the manifold fields related to microbial ecology. In biogeochemistry, for example, the use of high-resolution techniques such as FT-ICR-MS (Fourier transform ion cyclotron mass spectroscopy) has uncovered an enormous diversity and complexity of natural organic matter produced or degraded microbially either in dissolved or particulate forms. On the other hand, the introduction of high-throughput sequencing methods, such as 454 pyrosequencing, in combination with advances in bioinformatics allows for studying the bacterial diversity in natural samples circumventing cultivation dependent approaches. These new molecular tools enable in depth studies on single-cell genomes, distinct populations or even metacommunities. In combination with metatranscriptome and proteome studies it is for the first time possible to simultaneously unravel the structure and function of complex communities in situ. These technique-derived findings have, on the one hand, dramatically increased our knowledge on the vast diversity and complexity of bacterial habitats and, on the other hand, on phylogentic diversity and physiological responses of natural bacterial communities to their environment. However, until now microbial ecology is lacking an ecologically relevant species definition and useful tools for the identification of ecologically coherent taxa. Studies on intra- and interspecies interactions even with higher organisms demonstrate that bacteria can rapidly adapt to temporal and spatial changes in their environment. Aquatic bacteria have optimized and dramatically expanded their living space by efficient exploitation of organic matter point sources such as particles/aggregates and higher organisms. Although it is evident that particles/aggregates and organisms such as

  11. Deep Learning for Population Genetic Inference

    PubMed Central

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  12. Deep Learning for Population Genetic Inference.

    PubMed

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  13. Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China.

    PubMed

    Li, Jiancheng; Chen, Cheng; Lu, Jun; Lei, Anping; Hu, Zhangli

    2016-01-01

    The bacterioplankton community composition's (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao'an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria. PMID:27322295

  14. Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

    PubMed Central

    Li, Jiancheng; Chen, Cheng; Lu, Jun; Lei, Anping; Hu, Zhangli

    2016-01-01

    The bacterioplankton community composition’s (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao’an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria. PMID:27322295

  15. Marine bacterioplankton diversity and community composition in an antarctic coastal environment.

    PubMed

    Lo Giudice, Angelina; Caruso, Consolazione; Mangano, Santina; Bruni, Vivia; De Domenico, Maria; Michaud, Luigi

    2012-01-01

    The bacterial community inhabiting the water column at Terra Nova Bay (Ross Sea, Antarctica) was examined by the fluorescent in situ hybridization (FISH) technique and the genotypic and phenotypic characterization of 606 bacterial isolates. Overall, the FISH analysis revealed a bacterioplankton composition that was typical of Antarctic marine environments with the Cytophaga/Flavobacter (CF) group of Bacteroidetes that was equally dominant with the Actinobacteria and Gammaproteobacteria. As sampling was performed during the decay of sea-ice, it is plausible to assume the origin of Bacteroidetes from the sea-ice compartment where they probably thrive in high concentration of DOM which is efficiently remineralized to inorganic nutrients. This finding was supported by the isolation of Gelidibacter, Polaribacter, and Psychroflexus members (generally well represented in Antarctic sea-ice) which showed the ability to hydrolyze macromolecules, probably through the production of extracellular enzymes. A consistently pronounced abundance of the Gammaproteobacteria (67.8%) was also detected within the cultivable fraction. Altogether, the genera Psychromonas and Pseudoalteromonas accounted for 65.4% of total isolates and were ubiquitous, thus suggesting that they may play a key role within the analyzed bacterioplankton community. In particular, Pseudoalteromonas isolates possessed nitrate reductase and were able to hydrolyze substrates for protease, esterase, and β-galactosidase, thus indicating their involvement in the carbon and nitrogen cycling. Finally, the obtained results highlight the ability of the Actinobacteria to survive and proliferate in the Terra Nova Bay seawater as they generally showed a wide range of salt tolerance and appeared to be particularly competitive with strictly marine bacteria by better utilizing supplied carbon sources. PMID:21748267

  16. Quantification of carbon and phosphorus co-limitation in bacterioplankton: new insights on an old topic.

    PubMed

    Dorado-García, Irene; Medina-Sánchez, Juan Manuel; Herrera, Guillermo; Cabrerizo, Marco J; Carrillo, Presentación

    2014-01-01

    Because the nature of the main resource that limits bacterioplankton (e.g. organic carbon [C] or phosphorus [P]) has biogeochemical implications concerning organic C accumulation in freshwater ecosystems, empirical knowledge is needed concerning how bacteria respond to these two resources, available alone or together. We performed field experiments of resource manipulation (2×2 factorial design, with the addition of C, P, or both combined) in two Mediterranean freshwater ecosystems with contrasting trophic states (oligotrophy vs. eutrophy) and trophic natures (autotrophy vs. heterotrophy, measured as gross primary production:respiration ratio). Overall, the two resources synergistically co-limited bacterioplankton, i.e. the magnitude of the response of bacterial production and abundance to the two resources combined was higher than the additive response in both ecosystems. However, bacteria also responded positively to single P and C additions in the eutrophic ecosystem, but not to single C in the oligotrophic one, consistent with the value of the ratio between bacterial C demand and algal C supply. Accordingly, the trophic nature rather than the trophic state of the ecosystems proves to be a key feature determining the expected types of resource co-limitation of bacteria, as summarized in a proposed theoretical framework. The actual types of co-limitation shifted over time and partially deviated (a lesser degree of synergism) from the theoretical expectations, particularly in the eutrophic ecosystem. These deviations may be explained by extrinsic ecological forces to physiological limitations of bacteria, such as predation, whose role in our experiments is supported by the relationship between the dynamics of bacteria and bacterivores tested by SEMs (structural equation models). Our study, in line with the increasingly recognized role of freshwater ecosystems in the global C cycle, suggests that further attention should be focussed on the biotic interactions that

  17. Quantification of Carbon and Phosphorus Co-Limitation in Bacterioplankton: New Insights on an Old Topic

    PubMed Central

    Dorado-García, Irene; Medina-Sánchez, Juan Manuel; Herrera, Guillermo; Cabrerizo, Marco J.; Carrillo, Presentación

    2014-01-01

    Because the nature of the main resource that limits bacterioplankton (e.g. organic carbon [C] or phosphorus [P]) has biogeochemical implications concerning organic C accumulation in freshwater ecosystems, empirical knowledge is needed concerning how bacteria respond to these two resources, available alone or together. We performed field experiments of resource manipulation (2×2 factorial design, with the addition of C, P, or both combined) in two Mediterranean freshwater ecosystems with contrasting trophic states (oligotrophy vs. eutrophy) and trophic natures (autotrophy vs. heterotrophy, measured as gross primary production:respiration ratio). Overall, the two resources synergistically co-limited bacterioplankton, i.e. the magnitude of the response of bacterial production and abundance to the two resources combined was higher than the additive response in both ecosystems. However, bacteria also responded positively to single P and C additions in the eutrophic ecosystem, but not to single C in the oligotrophic one, consistent with the value of the ratio between bacterial C demand and algal C supply. Accordingly, the trophic nature rather than the trophic state of the ecosystems proves to be a key feature determining the expected types of resource co-limitation of bacteria, as summarized in a proposed theoretical framework. The actual types of co-limitation shifted over time and partially deviated (a lesser degree of synergism) from the theoretical expectations, particularly in the eutrophic ecosystem. These deviations may be explained by extrinsic ecological forces to physiological limitations of bacteria, such as predation, whose role in our experiments is supported by the relationship between the dynamics of bacteria and bacterivores tested by SEMs (structural equation models). Our study, in line with the increasingly recognized role of freshwater ecosystems in the global C cycle, suggests that further attention should be focussed on the biotic interactions that

  18. Transient changes in bacterioplankton communities induced by the submarine volcanic eruption of El Hierro (Canary Islands).

    PubMed

    Ferrera, Isabel; Arístegui, Javier; González, José M; Montero, María F; Fraile-Nuez, Eugenio; Gasol, Josep M

    2015-01-01

    The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1-V3 regions for Bacteria and V3-V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70-200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed. PMID

  19. Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands)

    PubMed Central

    Ferrera, Isabel; Arístegui, Javier; González, José M.; Montero, María F.; Fraile-Nuez, Eugenio; Gasol, Josep M.

    2015-01-01

    The submarine volcanic eruption occurring near El Hierro (Canary Islands) in October 2011 provided a unique opportunity to determine the effects of such events on the microbial populations of the surrounding waters. The birth of a new underwater volcano produced a large plume of vent material detectable from space that led to abrupt changes in the physical-chemical properties of the water column. We combined flow cytometry and 454-pyrosequencing of 16S rRNA gene amplicons (V1–V3 regions for Bacteria and V3–V5 for Archaea) to monitor the area around the volcano through the eruptive and post-eruptive phases (November 2011 to April 2012). Flow cytometric analyses revealed higher abundance and relative activity (expressed as a percentage of high-nucleic acid content cells) of heterotrophic prokaryotes during the eruptive process as compared to post-eruptive stages. Changes observed in populations detectable by flow cytometry were more evident at depths closer to the volcano (~70–200 m), coinciding also with oxygen depletion. Alpha-diversity analyses revealed that species richness (Chao1 index) decreased during the eruptive phase; however, no dramatic changes in community composition were observed. The most abundant taxa during the eruptive phase were similar to those in the post-eruptive stages and to those typically prevalent in oceanic bacterioplankton communities (i.e. the alphaproteobacterial SAR11 group, the Flavobacteriia class of the Bacteroidetes and certain groups of Gammaproteobacteria). Yet, although at low abundance, we also detected the presence of taxa not typically found in bacterioplankton communities such as the Epsilonproteobacteria and members of the candidate division ZB3, particularly during the eruptive stage. These groups are often associated with deep-sea hydrothermal vents or sulfur-rich springs. Both cytometric and sequence analyses showed that once the eruption ceased, evidences of the volcano-induced changes were no longer observed

  20. Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring bloom in the Baltic Sea.

    PubMed

    Lindh, Markus V; Riemann, Lasse; Baltar, Federico; Romero-Oliva, Claudia; Salomon, Paulo S; Granéli, Edna; Pinhassi, Jarone

    2013-04-01

    Despite the paramount importance of bacteria for biogeochemical cycling of carbon and nutrients, little is known about the potential effects of climate change on these key organisms. The consequences of the projected climate change on bacterioplankton community dynamics were investigated in a Baltic Sea spring phytoplankton bloom mesocosm experiment by increasing temperature with 3°C and decreasing pH by approximately 0.4 units via CO₂ addition in a factorial design. Temperature was the major driver of differences in community composition during the experiment, as shown by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA gene fragments. Several bacterial phylotypes belonging to Betaproteobacteria were predominant at 3°C but were replaced by members of the Bacteriodetes in the 6°C mesocosms. Acidification alone had a limited impact on phylogenetic composition, but when combined with increased temperature, resulted in the proliferation of specific microbial phylotypes. Our results suggest that although temperature is an important driver in structuring bacterioplankton composition, evaluation of the combined effects of temperature and acidification is necessary to fully understand consequences of climate change for marine bacterioplankton, their implications for future spring bloom dynamics, and their role in ecosystem functioning. PMID:23584969

  1. The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

    PubMed Central

    Kasalický, Vojtěch; Jezbera, Jan; Hahn, Martin W.; Šimek, Karel

    2013-01-01

    Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology. PMID:23505469

  2. Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations.

    PubMed

    Mou, Xiaozhen; Moran, Mary Ann; Stepanauskas, Ramunas; González, José M; Hodson, Robert E

    2005-03-01

    Marine bacterioplankton transform dimethylsulfoniopropionate (DMSP) into the biogeochemically important and climatically active gas dimethylsulfide. In order to identify specific bacterial taxa mediating DMSP processing in a natural marine ecosystem, we amended water samples from a southeastern U.S. salt marsh with 20 microM DMSP and tracked community shifts with flow cytometry (FCM) coupled to 16S rRNA gene analyses. In two out of four seasons studied, DMSP amendments induced the formation of distinct bacterioplankton populations with elevated nucleic acid (NA) content within 24 h, indicative of cells actively utilizing DMSP. The 16S rRNA genes of the cells with and without elevated NA content were analyzed following cell sorting and PCR amplification with sequencing and terminal restriction fragment length polymorphism approaches. Compared to cells in the control FCM populations, bacteria with elevated NA content in the presence of DMSP were relatively enriched in taxa related to Loktanella, Oceanicola, and Sulfitobacter (Roseobacter lineage, alpha-Proteobacteria); Caulobacter (alpha-Proteobacteria); and Brachymonas and Xenophilus (beta-Proteobacteria) in the May-02 sample and to Ketogulonicigenium (Roseobacter lineage, alpha-Proteobacteria) and novel gamma-Proteobacteria in the Sept-02 sample. Our study suggests that diverse bacterioplankton participate in the metabolism of DMSP in coastal marine systems and that their relative importance varies temporally. PMID:15746343

  3. Response of bacterioplankton community structure to an artificial gradient of pCO2 in the Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Zhang, R.; Xia, X.; Lau, S. C. K.; Motegi, C.; Weinbauer, M. G.; Jiao, N.

    2013-06-01

    In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA) was performed in Kings Bay (Kongsfjorden), Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs) in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

  4. Flow-Cytometric Cell Sorting and Subsequent Molecular Analyses for Culture-Independent Identification of Bacterioplankton Involved in Dimethylsulfoniopropionate Transformations

    PubMed Central

    Mou, Xiaozhen; Moran, Mary Ann; Stepanauskas, Ramunas; González, José M.; Hodson, Robert E.

    2005-01-01

    Marine bacterioplankton transform dimethylsulfoniopropionate (DMSP) into the biogeochemically important and climatically active gas dimethylsulfide. In order to identify specific bacterial taxa mediating DMSP processing in a natural marine ecosystem, we amended water samples from a southeastern U.S. salt marsh with 20 μM DMSP and tracked community shifts with flow cytometry (FCM) coupled to 16S rRNA gene analyses. In two out of four seasons studied, DMSP amendments induced the formation of distinct bacterioplankton populations with elevated nucleic acid (NA) content within 24 h, indicative of cells actively utilizing DMSP. The 16S rRNA genes of the cells with and without elevated NA content were analyzed following cell sorting and PCR amplification with sequencing and terminal restriction fragment length polymorphism approaches. Compared to cells in the control FCM populations, bacteria with elevated NA content in the presence of DMSP were relatively enriched in taxa related to Loktanella, Oceanicola, and Sulfitobacter (Roseobacter lineage, α-Proteobacteria); Caulobacter (α-Proteobacteria); and Brachymonas and Xenophilus (β-Proteobacteria) in the May-02 sample and to Ketogulonicigenium (Roseobacter lineage, α-Proteobacteria) and novel γ-Proteobacteria in the Sept-02 sample. Our study suggests that diverse bacterioplankton participate in the metabolism of DMSP in coastal marine systems and that their relative importance varies temporally. PMID:15746343

  5. Bacterioplankton in antarctic ocean waters during late austral winter: abundance, frequency of dividing cells, and estimates of production.

    PubMed

    Hanson, R B; Shafer, D; Ryan, T; Pope, D H; Lowery, H K

    1983-05-01

    Bacterioplankton productivity in Antarctic waters of the eastern South Pacific Ocean and Drake Passage was estimated by direct counts and frequency of dividing cells (FDC). Total bacterioplankton assemblages were enumerated by epifluorescent microscopy. The experimentally determined relationship between in situ FDC and the potential instantaneous growth rate constant (mu) is best described by the regression equation ln mu = 0.081 FDC - 3.73. In the eastern South Pacific Ocean, bacterioplankton abundance (2 x 10 to 3.5 x 10 cells per ml) and FDC (11%) were highest at the Polar Front (Antarctic Convergence). North of the Subantarctic Front, abundance and FDC were between 1 x 10 to 2 x 10 cells per ml and 3 to 5%, respectively, and were vertically homogeneous to a depth of 600 m. In Drake Passage, abundance (10 x 10 cells per ml) and FDC (16%) were highest in waters south of the Polar Front and near the sea ice. Subantarctic waters in Drake Passage contained 4 x 10 cells per ml with 4 to 5% FDC. Instantaneous growth rate constants ranged between 0.029 and 0.088 h. Using estimates of potential mu and measured standing stocks, we estimated productivity to range from 0.62 mug of C per liter . day in the eastern South Pacific Ocean to 17.1 mug of C per liter . day in the Drake Passage near the sea ice. PMID:16346297

  6. Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients

    PubMed Central

    Liu, Jiwen; Fu, Bingbing; Yang, Hongmei; Zhao, Meixun; He, Biyan; Zhang, Xiao-Hua

    2015-01-01

    The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments. PMID:25713564

  7. Inference or Observation?

    ERIC Educational Resources Information Center

    Finson, Kevin D.

    2010-01-01

    Learning about what inferences are, and what a good inference is, will help students become more scientifically literate and better understand the nature of science in inquiry. Students in K-4 should be able to give explanations about what they investigate (NSTA 1997) and that includes doing so through inferring. This article provides some tips…

  8. Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America.

    PubMed

    Souffreau, Caroline; Van der Gucht, Katleen; van Gremberghe, Ineke; Kosten, Sarian; Lacerot, Gissell; Lobão, Lúcia Meirelles; de Moraes Huszar, Vera Lúcia; Roland, Fabio; Jeppesen, Erik; Vyverman, Wim; De Meester, Luc

    2015-07-01

    Metacommunity studies on lake bacterioplankton indicate the importance of environmental factors in structuring communities. Yet most of these studies cover relatively small spatial scales. We assessed the relative importance of environmental and spatial factors in shaping bacterioplankton communities across a > 6000 km latitudinal range, studying 48 shallow lowland lakes in the tropical, tropicali (isothermal subzone of the tropics) and tundra climate regions of South America using denaturing gradient gel electrophoresis. Bacterioplankton community composition (BCC) differed significantly across regions. Although a large fraction of the variation in BCC remained unexplained, the results supported a consistent significant contribution of local environmental variables and to a lesser extent spatial variables, irrespective of spatial scale. Upon correction for space, mainly biotic environmental factors significantly explained the variation in BCC. The abundance of pelagic cladocerans remained particularly significant, suggesting grazer effects on bacterioplankton communities in the studied lakes. These results confirm that bacterioplankton communities are predominantly structured by environmental factors, even over a large-scale latitudinal gradient (6026 km), and stress the importance of including biotic variables in studies that aim to understand patterns in BCC. PMID:25471233

  9. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China.

    PubMed

    Fan, Zhou; Han, Rui-Ming; Ma, Jie; Wang, Guo-Xiang

    2016-07-01

    nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors. PMID:27048324

  10. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  11. Inferring genetic networks from microarray data.

    SciTech Connect

    May, Elebeoba Eni; Davidson, George S.; Martin, Shawn Bryan; Werner-Washburne, Margaret C.; Faulon, Jean-Loup Michel

    2004-06-01

    In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are: (1) inferring the network; (2) estimating the stability of the inferred network; and (3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns. The inference of genetic networks from genome-wide experimental data is an important biological problem which has received much attention. Approaches to this problem have typically included application of clustering algorithms [6]; the use of Boolean networks [12, 1, 10]; the use of Bayesian networks [8, 11]; and the use of continuous models [21, 14, 19]. Overviews of the problem and general approaches to network inference can be found in [4, 3]. Our approach to network inference is similar to earlier methods in that we use both clustering and Boolean network inference. However, we have attempted to extend the process to better serve the end-user, the biologist. In particular, we have incorporated a system to assess the reliability of our network, and we have developed tools which allow interactive visualization of the proposed network.

  12. Physical limits of inference

    NASA Astrophysics Data System (ADS)

    Wolpert, David H.

    2008-07-01

    We show that physical devices that perform observation, prediction, or recollection share an underlying mathematical structure. We call devices with that structure “inference devices”. We present a set of existence and impossibility results concerning inference devices. These results hold independent of the precise physical laws governing our universe. In a limited sense, the impossibility results establish that Laplace was wrong to claim that even in a classical, non-chaotic universe the future can be unerringly predicted, given sufficient knowledge of the present. Alternatively, these impossibility results can be viewed as a non-quantum-mechanical “uncertainty principle”. The mathematics of inference devices has close connections to the mathematics of Turing Machines (TMs). In particular, the impossibility results for inference devices are similar to the Halting theorem for TMs. Furthermore, one can define an analog of Universal TMs (UTMs) for inference devices. We call those analogs “strong inference devices”. We use strong inference devices to define the “inference complexity” of an inference task, which is the analog of the Kolmogorov complexity of computing a string. A task-independent bound is derived on how much the inference complexity of an inference task can differ for two different inference devices. This is analogous to the “encoding” bound governing how much the Kolmogorov complexity of a string can differ between two UTMs used to compute that string. However no universe can contain more than one strong inference device. So whereas the Kolmogorov complexity of a string is arbitrary up to specification of the UTM, there is no such arbitrariness in the inference complexity of an inference task. We informally discuss the philosophical implications of these results, e.g., for whether the universe “is” a computer. We also derive some graph-theoretic properties governing any set of multiple inference devices. We also present an

  13. The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China.

    PubMed

    Liu, Lemian; Yang, Jun; Yu, Zheng; Wilkinson, David M

    2015-09-01

    Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance-decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance-decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems. PMID:25748371

  14. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes.

    PubMed

    Cleary, Daniel F R; Becking, Leontine E; Polónia, Ana R M; Freitas, Rossana M; Gomes, Newton C M

    2016-05-01

    In the present study, we compared communities of bacteria in two jellyfish species (the 'golden' jellyfishMastigiascf.papuaand the box jellyfishTripedaliacf.cystophora) and water in three marine lakes located in the Berau region of northeastern Borneo, Indonesia. Jellyfish-associated bacterial communities were compositionally distinct and less diverse than bacterioplankton communities. Alphaproteobacteria, Gammaproteobacteria, Synechococcophycidae and Flavobacteriia were the most abundant classes in water. Jellyfish-associated bacterial communities were dominated by OTUs assigned to the Gammaproteobacteria (family Endozoicimonaceae), Mollicutes, Spirochaetes and Alphaproteobacteria (orders Kiloniellales and Rhodobacterales). Mollicutes were mainly restricted toMastigiaswhereas Spirochaetes and the order Kiloniellales were most abundant inTripedaliahosts. The most abundant OTU overall in jellyfish hosts was assigned to the family Endozoicimonaceae and was highly similar to organisms in Genbank obtained from various hosts including an octocoral, bivalve and fish species. Other abundant OTUs included an OTU assigned to the order Entomoplasmatales and mainly found inMastigiashosts and OTUs assigned to the Spirochaetes and order Kiloniellales and mainly found inTripedaliahosts. The low sequence similarity of the Entomoplasmatales OTU to sequences in Genbank suggests that it may be a novel lineage inhabitingMastigiasand possibly restricted to marine lakes. PMID:27004797

  15. Diversity of bacterioplankton in the surface seawaters of Drake Passage near the Chinese Antarctic station.

    PubMed

    Xing, Mengxin; Li, Zhao; Wang, Wei; Sun, Mi

    2015-07-01

    The determination of relative abundances and distribution of different bacterial groups is a critical step toward understanding the functions of various bacteria and its surrounding environment. Few studies focus on the taxonomic composition and functional diversity of microbial communities in Drake Passage. In this study, marine bacterioplankton communities from surface seawaters at five locations in Drake Passage were examined by 16S rRNA gene sequence analyses. The results indicated that psychrophilic bacteria were the most abundant group in Drake Passage, and mainly made up of Bacillus, Aeromonas, Psychrobacter, Pseudomonas and Halomonas. Diversity analysis showed that surface seawater communities had no significant correlation with latitudinal gradient. Additionally, a clear difference among five surface seawater communities was evident, with 1.8% OTUs (only two) belonged to Bacillus consistent across five locations and 71% OTUs (80) existed in only one location. However, the few cosmopolitans had the largest population sizes. Our results support the hypothesis that the dominant bacterial groups appear to be analogous between geographical sites, but significant differences may be detected among rare bacterial groups. The microbial diversity of surface seawaters would be liable to be affected by environmental factors. PMID:26184094

  16. Away from darkness: a review on the effects of solar radiation on heterotrophic bacterioplankton activity

    PubMed Central

    Ruiz-González, Clara; Simó, Rafel; Sommaruga, Ruben; Gasol, Josep M.

    2013-01-01

    Heterotrophic bacterioplankton are main consumers of dissolved organic matter (OM) in aquatic ecosystems, including the sunlit upper layers of the ocean and freshwater bodies. Their well-known sensitivity to ultraviolet radiation (UVR), together with some recently discovered mechanisms bacteria have evolved to benefit from photosynthetically available radiation (PAR), suggest that natural sunlight plays a relevant, yet difficult to predict role in modulating bacterial biogeochemical functions in aquatic ecosystems. Three decades of experimental work assessing the effects of sunlight on natural bacterial heterotrophic activity reveal responses ranging from high stimulation to total inhibition. In this review, we compile the existing studies on the topic and discuss the potential causes underlying these contrasting results, with special emphasis on the largely overlooked influences of the community composition and the previous light exposure conditions, as well as the different temporal and spatial scales at which exposure to solar radiation fluctuates. These intricate sunlight-bacteria interactions have implications for our understanding of carbon fluxes in aquatic systems, yet further research is necessary before we can accurately evaluate or predict the consequences of increasing surface UVR levels associated with global change. PMID:23734148

  17. Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China.

    PubMed

    Liu, Zhenghui; Huang, Shaobin; Sun, Guoping; Xu, Zhencheng; Xu, Meiying

    2012-04-01

    Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems. PMID:22133045

  18. Large-scale distribution and production of bacterioplankton in the Adriatic Sea

    NASA Astrophysics Data System (ADS)

    Gallina, Alessandra A.; Celussi, Mauro; Del Negro, Paola

    2011-08-01

    Two oceanographic cruises encompassing the whole Adriatic Sea were carried out during February and October 2008. Selected stations were sampled at several depths to determine total prokaryotes and picocyanobacteria abundance using epifluorescence microscopy, and to estimate prokaryotic carbon production by 3H-leucine incorporation. Biological data were related to physical parameters including temperature, salinity and fluorescence, and an attempt to associate bacterial dynamics to water mass characteristics was performed. In both seasons prokaryotic distribution and production showed a decreasing latitudinal gradient likely dependent on riverine inputs highlighted by a strong negative correlation with salinity ( P < 0.001). A vertical gradient with higher cell numbers at the surface and lower values at the bottom layer was also always detected. In the southern basin in February, however, picocyanobacteria were retrieved also in deep waters, probably linked to higher nutrient loads carried by the Levantine Intermediate Waters and/or the deep water ventilation known to occur in this area. From an oceanographic point of view, we sampled within four different water types, but no relationship between these water types and bacterioplankton abundances was found. The present work contributes to the acquisition of a more holistic overview of prokaryotic distribution and production in the Adriatic Sea, both on a spatial and temporal scale.

  19. Longitudinal and depth variation of bacterioplankton productivity and related factors in a temperate estuary

    NASA Astrophysics Data System (ADS)

    Peierls, Benjamin L.; Paerl, Hans W.

    2011-11-01

    Bacterioplankton productivity (BP) spatial variation was investigated in relation to potential resources, including primary productivity and dissolved organic matter, in the micro-tidal Neuse River-Pamlico Sound estuarine system, North Carolina, USA. Estuarine BP was predicted to correlate with the trophic gradient, decreasing along the salinity gradient in parallel with the decrease in organic matter and primary productivity. This prediction was tested over four years at spatial scales ranging from kilometers to meters along the riverine axis and with depth. The general pattern of BP across the salinity gradient was unimodal and matched the phytoplankton patterns in peak location and variability. Peak locations varied with discharge, especially in 2003 when above average discharge moved peaks downstream. Spatial coherence of BP with other variables was much less at short time scales. The effect of temperature, nutrients, and phytoplankton on BP varied by location, especially fresh versus brackish stations, although only temperature explained more than 20% of the BP variation. Depth variation of BP was as great as longitudinal variation and bottom samples were often higher than surface. BP was strongly correlated with particulate organic carbon at the pycnocline and bottom, highlighting the importance of particulate matter as a resource. Station-averaged BP and phytoplankton data corresponded well with two published meta-analyses, although the offset of the freshwater station suggested longitudinal differences in community composition or resource availability.

  20. Linking the patterns of change in composition and function in bacterioplankton successions along environmental gradients.

    PubMed

    Comte, Jérôme; del Giorgio, Paul A

    2010-05-01

    The connections that exist between the composition of bacterial communities and their functional attributes are still a matter of intense debate, despite over a decade of intense studies. Here we explored three different facets of the links that may exist between bacterioplankton compositional and functional successions that occurred along the water flow path in a complex watershed in southern Quebec. We analyzed the correlation between composition and function in terms of their absolute patterns, and in terms of their rates of change relative to transit time in environmental transitions, and relative to shifts in resources along the same transitions. Our results showed that the absolute patterns in bacterial community composition (BCC, using DGGE [denaturing gradient gel electrophoresis] profiles) and functional capacities (FC, using BIOLOG profiles) were not correlated, but that the rates of change in BCC and FC along the transitions were strongly correlated to each other. Further, we observed that the strength and shape of the relationship between the changes in BCC and FC varied relative to the type and intensity of gradient considered. Collectively, these results showed that BCC and FC are strongly related but in a very dynamic manner, such that their absolute patterns do not appear to be connected. This in turn suggests a high level of functional redundancy that occurs both within the existing community and in the meta-community from which phylotypes are selected to occupy the new niches that are created along the transitions. PMID:20503878

  1. Tips and tricks for high quality MAR-FISH preparations: focus on bacterioplankton analysis.

    PubMed

    Alonso, Cecilia

    2012-12-01

    The combination of microautoradiography and fluorescence in situ hybridization (MAR-FISH) is a powerful technique for tracking the incorporation of radiolabelled compounds by specific bacterial populations at a single cell resolution. It has been widely applied in aquatic microbial ecology as a tool to unveil key ecophysiological features, shedding light on relevant ecological issues such as bacterial biomass production, the role of different bacterioplankton groups in the global carbon and sulphur cycle, and, at the same time, providing insights into the life styles and niche differentiation of cosmopolitan members of the aquatic microbial communities. Despite its great potential, its application has remained restricted to a few laboratories around the world, in part due to its reputation as a "difficult technique". Therefore, the objective of this minireview is to highlight the impact of MAR-FISH application on aquatic microbial ecology, and also to provide basic concepts, as well as practical tips, for processing MAR-FISH preparations, thus aiming to contribute to a more widespread application of this powerful method. PMID:22502862

  2. Gene-network inference by message passing

    NASA Astrophysics Data System (ADS)

    Braunstein, A.; Pagnani, A.; Weigt, M.; Zecchina, R.

    2008-01-01

    The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.

  3. Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns

    PubMed Central

    Millar, Justin J.; Payne, Jason T.; Ochs, Clifford A.

    2014-01-01

    The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with Cyanobacteria were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like Alphaproteobacteria. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages. PMID:25217018

  4. Inference in `poor` languages

    SciTech Connect

    Petrov, S.

    1996-10-01

    Languages with a solvable implication problem but without complete and consistent systems of inference rules (`poor` languages) are considered. The problem of existence of finite complete and consistent inference rule system for a ``poor`` language is stated independently of the language or rules syntax. Several properties of the problem arc proved. An application of results to the language of join dependencies is given.

  5. A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters.

    PubMed

    Williams, Timothy J; Long, Emilie; Evans, Flavia; Demaere, Mathew Z; Lauro, Federico M; Raftery, Mark J; Ducklow, Hugh; Grzymski, Joseph J; Murray, Alison E; Cavicchioli, Ricardo

    2012-10-01

    A metaproteomic survey of surface coastal waters near Palmer Station on the Antarctic Peninsula, West Antarctica, was performed, revealing marked differences in the functional capacity of summer and winter communities of bacterioplankton. Proteins from Flavobacteria were more abundant in the summer metaproteome, whereas winter was characterized by proteins from ammonia-oxidizing Marine Group I Crenarchaeota. Proteins prevalent in both seasons were from SAR11 and Rhodobacterales clades of Alphaproteobacteria, as well as many lineages of Gammaproteobacteria. The metaproteome data were used to elucidate the main metabolic and energy generation pathways and transport processes occurring at the microbial level in each season. In summer, autotrophic carbon assimilation appears to be driven by oxygenic photoautotrophy, consistent with high light availability and intensity. In contrast, during the dark polar winter, the metaproteome supported the occurrence of chemolithoautotrophy via the 3-hydroxypropionate/4-hydroxybutyrate cycle and the reverse tricarboxylic acid cycle of ammonia-oxidizing archaea and nitrite-oxidizing bacteria, respectively. Proteins involved in nitrification were also detected in the metaproteome. Taurine appears to be an important source of carbon and nitrogen for heterotrophs (especially SAR11), with transporters and enzymes for taurine uptake and degradation abundant in the metaproteome. Divergent heterotrophic strategies for Alphaproteobacteria and Flavobacteria were indicated by the metaproteome data, with Alphaproteobacteria capturing (by high-affinity transport) and processing labile solutes, and Flavobacteria expressing outer membrane receptors for particle adhesion to facilitate the exploitation of non-labile substrates. TonB-dependent receptors from Gammaproteobacteria and Flavobacteria (particularly in summer) were abundant, indicating that scavenging of substrates was likely an important strategy for these clades of Southern Ocean bacteria

  6. Temporal and Vertical Distributions of Bacterioplankton at the Gray's Reef National Marine Sanctuary

    PubMed Central

    Lu, Xinxin; Sun, Shulei; Zhang, Yu-Qin; Hollibaugh, James T.

    2014-01-01

    Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll a. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the Roseobacter clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans. PMID:25416764

  7. Temporal and vertical distributions of bacterioplankton at the Gray's Reef National Marine Sanctuary.

    PubMed

    Lu, Xinxin; Sun, Shulei; Zhang, Yu-Qin; Hollibaugh, James T; Mou, Xiaozhen

    2015-02-01

    Large spatial scales and long-term shifts of bacterial community composition (BCC) in the open ocean can often be reliably predicted based on the dynamics of physical-chemical variables. The power of abiotic factors in shaping BCC on shorter time scales in shallow estuarine mixing zones is less clear. We examined the diurnal variation in BCC at different water depths in the spring and fall of 2011 at a station in the Gray's Reef National Marine Sanctuary (GRNMS). This site is located in the transition zone between the estuarine plume and continental shelf waters of the South Atlantic Bight. A total of 234,516 pyrotag sequences of bacterial 16S rRNA genes were recovered; they were taxonomically affiliated with >200 families of 23 bacterial phyla. Nonmetric multidimensional scaling analysis revealed significant differences in BCC between spring and fall samples, likely due to seasonality in the concentrations of dissolved organic carbon and nitrate plus nitrite. Within each diurnal sampling, BCC differed significantly by depth only in the spring and differed significantly between day and night only in the fall. The former variation largely tracked changes in light availability, while the latter was most correlated with concentrations of polyamines and chlorophyll a. Our results suggest that at the GRNMS, a coastal mixing zone, diurnal variation in BCC is attributable to the mixing of local and imported bacterioplankton rather than to bacterial growth in response to environmental changes. Our results also indicate that, like members of the Roseobacter clade, SAR11 bacteria may play an important role in processing dissolved organic material in coastal oceans. PMID:25416764

  8. Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship

    PubMed Central

    Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L.; Decelle, Johan; Jáuregui, Ruy; Wang, Hui; Deng, Zhi-Luo; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H.; Wurst, Mascha; Pieper, Dietmar H.; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    In order to determine the influence of geographical distance, depth, and Longhurstian province on bacterial community composition and compare it with the composition of photosynthetic micro-eukaryote communities, 382 samples from a depth-resolved latitudinal transect (51°S–47°N) from the epipelagic zone of the Atlantic ocean were analyzed by Illumina amplicon sequencing. In the upper 100 m of the ocean, community similarity decreased toward the equator for 6000 km, but subsequently increased again, reaching similarity values of 40–60% for samples that were separated by ~12,000 km, resulting in a U-shaped distance-decay curve. We conclude that adaptation to local conditions can override the linear distance-decay relationship in the upper epipelagial of the Atlantic Ocean which is apparently not restrained by barriers to dispersal, since the same taxa were shared between the most distant communities. The six Longhurstian provinces covered by the transect were comprised of distinct microbial communities; ~30% of variation in community composition could be explained by province. Bacterial communities belonging to the deeper layer of the epipelagic zone (140–200 m) lacked a distance-decay relationship altogether and showed little provincialism. Interestingly, those biogeographical patterns were consistently found for bacteria from three different size fractions of the plankton with different taxonomic composition, indicating conserved underlying mechanisms. Analysis of the chloroplast 16S rRNA gene sequences revealed that phytoplankton composition was strongly correlated with both free-living and particle associated bacterial community composition (R between 0.51 and 0.62, p < 0.002). The data show that biogeographical patterns commonly found in macroecology do not hold for marine bacterioplankton, most likely because dispersal and evolution occur at drastically different rates in bacteria. PMID:27199923

  9. Virio- and Bacterioplankton Microscale Distributions at the Sediment-Water Interface

    PubMed Central

    Dann, Lisa M.; Mitchell, James G.; Speck, Peter G.; Newton, Kelly; Jeffries, Thomas; Paterson, James

    2014-01-01

    The marine sediment-water interface is an important location for microbially controlled nutrient and gas exchange processes. While microbial distributions on the sediment side of the interface are well established in many locations, the distributions of microbes on the water side of the interface are less well known. Here, we measured that distribution for marine virio- and bacterioplankton with a new two-dimensional technique. Our results revealed higher heterogeneity in sediment-water interface biomass distributions than previously reported with a greater than 45– and 2500-fold change cm−1 found within bacterial and viral subpopulations compared to previous maxima of 1.5- and 1.4-fold cm−1 in bacteria and viruses in the same environments. The 45-fold and 2500-fold changes were due to patches of elevated and patches of reduced viral and bacterial abundance. The bacterial and viral hotspots were found over single and multiple sample points and the two groups often coincided whilst the coldspots only occurred over single sample points and the bacterial and viral abundances showed no correlation. The total mean abundances of viruses strongly correlated with bacteria (r = 0.90, p<0.0001, n = 12) for all three microplates (n = 1350). Spatial autocorrelation analysis via Moran’s I and Geary’s C revealed non-random distributions in bacterial subpopulations and random distributions in viral subpopulations. The variable distributions of viral and bacterial abundance over centimetre-scale distances suggest that competition and the likelihood of viral infection are higher in the small volumes important for individual cell encounters than bulk measurements indicate. We conclude that large scale measurements are not an accurate measurement of the conditions under which microbial dynamics exist. The high variability we report indicates that few microbes experience the ‘average’ concentrations that are frequently measured. PMID:25057797

  10. Depth profiles of bacterioplankton assemblages and their activities in the Ross Sea

    NASA Astrophysics Data System (ADS)

    Celussi, Mauro; Cataletto, Bruno; Fonda Umani, Serena; Del Negro, Paola

    2009-12-01

    The identification of bacterial community structure has led, since the beginning of the 1990s, to the idea that bacterioplankton populations are stratified in the water column and that diverse lineages with mostly unknown phenotypes dominate marine microbial communities. The diversity of depth-related assemblages is also reflected in their patterns of activities, as bacteria affiliated to different groups can express different activities in a given ecosystem. We analysed bacterial assemblages (DGGE fingerprinting) and their activities (prokaryotic carbon production, protease, phosphatase, chitinase, beta-glucosidase and lipase activities) in two areas in the Ross Sea, differing mainly in their productivity regime: two stations are located in the Terra Nova Bay polynya area (highly productive during summer) and two close to Cape Adare (low phytoplankton biomass and activity). At every station a pronounced stratification of bacterial assemblages was identified, highlighting epipelagic communities differing substantially from the mesopelagic and the bathypelagic communities. Multivariate analysis suggested that pressure and indirectly light-affected variables (i.e. oxygen and fluorescence) had a great effect on the bacterial communities outcompeting the possible influences of temperature and dissolved organic carbon concentration. Generally activities decreased with depth even though a signal of the Circumpolar Deep Water (CDW) at one of the northern stations corresponded to an increase in some of the degradative activities, generating some 'hot spots' in the profile. We also found that similar assemblages express similar metabolic requirements reflected in analogous patterns of activity (similar degradative potential and leucine uptake rate). Furthermore, the presence of eukaryotic chloroplasts' 16S rDNA in deep samples highlighted how in some cases the dense surface-water formation (in this case High Salinity Shelf Water—HSSW) and downwelling can affect, at least

  11. Bacterioplankton Biogeography of the Atlantic Ocean: A Case Study of the Distance-Decay Relationship.

    PubMed

    Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L; Decelle, Johan; Jáuregui, Ruy; Wang, Hui; Deng, Zhi-Luo; Plumeier, Iris; Giebel, Helge-Ansgar; Badewien, Thomas H; Wurst, Mascha; Pieper, Dietmar H; Simon, Meinhard; Wagner-Döbler, Irene

    2016-01-01

    In order to determine the influence of geographical distance, depth, and Longhurstian province on bacterial community composition and compare it with the composition of photosynthetic micro-eukaryote communities, 382 samples from a depth-resolved latitudinal transect (51°S-47°N) from the epipelagic zone of the Atlantic ocean were analyzed by Illumina amplicon sequencing. In the upper 100 m of the ocean, community similarity decreased toward the equator for 6000 km, but subsequently increased again, reaching similarity values of 40-60% for samples that were separated by ~12,000 km, resulting in a U-shaped distance-decay curve. We conclude that adaptation to local conditions can override the linear distance-decay relationship in the upper epipelagial of the Atlantic Ocean which is apparently not restrained by barriers to dispersal, since the same taxa were shared between the most distant communities. The six Longhurstian provinces covered by the transect were comprised of distinct microbial communities; ~30% of variation in community composition could be explained by province. Bacterial communities belonging to the deeper layer of the epipelagic zone (140-200 m) lacked a distance-decay relationship altogether and showed little provincialism. Interestingly, those biogeographical patterns were consistently found for bacteria from three different size fractions of the plankton with different taxonomic composition, indicating conserved underlying mechanisms. Analysis of the chloroplast 16S rRNA gene sequences revealed that phytoplankton composition was strongly correlated with both free-living and particle associated bacterial community composition (R between 0.51 and 0.62, p < 0.002). The data show that biogeographical patterns commonly found in macroecology do not hold for marine bacterioplankton, most likely because dispersal and evolution occur at drastically different rates in bacteria. PMID:27199923

  12. Bacterioplankton features and its relations with doc characteristics and other limnological variables in Paraná river floodplain environments (PR/MS-Brazil)

    PubMed Central

    Teixeira, Mariana Carolina; Santana, Natália Fernanda; de Azevedo, Júlio César Rodrigues; Pagioro, Thomaz Aurélio

    2011-01-01

    Since the introduction of the Microbial Loop concept, many studies aimed to explain the role of bacterioplankton and dissolved organic carbon (DOC) in aquatic ecosystems. Paraná River floodplain system is a very complex environment where these subjects were little explored. The aim of this work was to characterize bacterial community in terms of density, biomass and biovolume in some water bodies of this floodplain and to verify its temporal variation and its relation with some limnological variables, including some indicators of DOC quality, obtained through Ultraviolet-visible (UV-VIS) and fluorescence spectroscopic analysis. Bacterial density, biomass and biovolume are similar to those from other freshwater environments and both density and biomass were higher in the period with less rain. The limnological and spectroscopic features that showed any relation with bacterioplankton were the concentrations of N-NH4 and P-PO4, water transparency, and some indicators of DOC quality and origin. The analysis of these relations showed a possible competition between bacterioplankton and phytoplankton for inorganic nutrients and that the DOC used by bacterioplankton is labile and probably from aquatic macrophytes. PMID:24031705

  13. DUAL STAINING OF NATURAL BACTERIOPLANKTON WITH 4,6-DIAMINDO-2-PHENYLINDOLE AND FLUORESCENT OLIGONUCLEOTIDE PROBES TARGETING KINGDOM-LEVEL 16S RRNA SEQUENCES

    EPA Science Inventory

    A method for quantifying eubacterial cell densities in dilute communities of small bacterioplankton is presented. ells in water samples were stained with 4',6-diamidino-2-phenylindole (DAPI), transferred to gelatin-coated slides, and hybridized with rhodamine-labeled oligonucleot...

  14. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy.

    PubMed

    Nelson, Craig E; Carlson, Craig A; Ewart, Courtney S; Halewood, Elisa R

    2014-03-01

    Eddies are mesoscale oceanographic features (∼ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth-resolved distributions of bacterial populations across an anticyclonic mode-water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment-based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom-inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans. PMID:24589288

  15. Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

    USGS Publications Warehouse

    Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

    2007-01-01

    The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

  16. Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea)

    PubMed Central

    Laas, Peeter; Šatova, Elina; Lips, Inga; Lips, Urmas; Simm, Jaak; Kisand, Veljo; Metsis, Madis

    2016-01-01

    Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its ‘arm’ into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems. PMID:27213812

  17. Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea).

    PubMed

    Laas, Peeter; Šatova, Elina; Lips, Inga; Lips, Urmas; Simm, Jaak; Kisand, Veljo; Metsis, Madis

    2016-01-01

    Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its 'arm' into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems. PMID:27213812

  18. Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.

    PubMed

    Lindh, Markus V; Lefébure, Robert; Degerman, Rickard; Lundin, Daniel; Andersson, Agneta; Pinhassi, Jarone

    2015-06-01

    Predicted increases in runoff of terrestrial dissolved organic matter (DOM) and sea surface temperatures implicate substantial changes in energy fluxes of coastal marine ecosystems. Despite marine bacteria being critical drivers of marine carbon cycling, knowledge of compositional responses within bacterioplankton communities to such disturbances is strongly limited. Using 16S rRNA gene pyrosequencing, we examined bacterioplankton population dynamics in Baltic Sea mesocosms with treatments combining terrestrial DOM enrichment and increased temperature. Among the 200 most abundant taxa, 62 % either increased or decreased in relative abundance under changed environmental conditions. For example, SAR11 and SAR86 populations proliferated in combined increased terrestrial DOM/temperature mesocosms, while the hgcI and CL500-29 clades (Actinobacteria) decreased in the same mesocosms. Bacteroidetes increased in both control mesocosms and in the combined increased terrestrial DOM/temperature mesocosms. These results indicate considerable and differential responses among distinct bacterial populations to combined climate change effects, emphasizing the potential of such effects to induce shifts in ecosystem function and carbon cycling in the future Baltic Sea. PMID:26022323

  19. Response of bacterioplankton community structure to an artificial gradient of pCO2 in the Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Zhang, R.; Xia, X.; Lau, S. C. K.; Motegi, C.; Weinbauer, M. G.; Jiao, N.

    2012-08-01

    The influences of ocean acidification on bacterial diversity were investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples collected from the largest CO2 manipulation mesocosm study that had been performed thus far. Terminal restriction fragment length polymorphism analysis of the PCR amplicons of the 16S rRNA genes revealed that bacterial diversity, species richness and community structure varied with the time of incubation but not the degree of ocean acidification. The phylogenetic composition of the major bacterial assemblage after a 30-day incubation under various pCO2 concentrations did not show clear effects of pCO2 levels. However, the maximum apparent diversity and species richness which occurred during incubation differed in the high and low pCO2 treatments, in which different bacterial community structure harbored. In addition, total alkalinity was one of the contributing factors for the temporal variations in bacterial community structure observed during incubation. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment. Our study suggested that ocean acidification affected the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem.

  20. Consequences of contaminant mixture on the dynamics and functional diversity of bacterioplankton in a southwestern Mediterranean coastal ecosystem.

    PubMed

    Pringault, Olivier; Lafabrie, Céline; Avezac, Murielle; Bancon-Montigny, Chrystelle; Carre, Claire; Chalghaf, Mohamed; Delpoux, Sophie; Duvivier, Adrien; Elbaz-Poulichet, Françoise; Gonzalez, Catherine; Got, Patrice; Leboulanger, Christophe; Spinelli, Sylvie; Hlaili, Asma Sakka; Bouvy, Marc

    2016-02-01

    Contamination of coastal environments is often due to a complex mixture of pollutants, sometimes in trace levels, that may have significant effects on diversity and function of organisms. The aim of this study was to evaluate the short-term dynamics of bacterioplankton exposed to natural and artificial mixtures of contaminants. Bacterial communities from a southwestern Mediterranean ecosystem, lagoon and the bay (offshore) of Bizerte were exposed to i) elutriate from resuspension of contaminated sediment, and ii) an artificial mixture of metals and herbicides mimicking the contamination observed during sediment resuspension. Elutriate incubation as well as artificial spiking induced strong enrichments in nutrients (up to 18 times), metals (up to six times) and herbicides (up to 20 times) relative to the in situ concentrations in the offshore station, whereas the increases in contaminants were less marked in the lagoon station. In the offshore waters, the artificial mixture of pollutants provoked a strong inhibition of bacterial abundance, production and respiration and significant modifications of the potential functional diversity of bacterioplankton with a strong decrease of the carbohydrate utilization. In contrast, incubation with elutriate resulted in a stimulation of bacterial activities and abundances, suggesting that the toxic effects of pollutants were modified by the increase in nutrient and DOM concentrations due to the sediment resuspension. The effects of elutriate and the artificial mixture of pollutants on bacterial dynamics and the functional diversity were less marked in the lagoon waters, than in offshore waters, suggesting a relative tolerance of lagoon bacteria against contaminants. PMID:26451655

  1. Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships

    PubMed Central

    Logue, Jürg Brendan; Langenheder, Silke; Andersson, Anders F; Bertilsson, Stefan; Drakare, Stina; Lanzén, Anders; Lindström, Eva S

    2012-01-01

    A central goal in ecology is to grasp the mechanisms that underlie and maintain biodiversity and patterns in its spatial distribution can provide clues about those mechanisms. Here, we investigated what might determine the bacterioplankton richness (BR) in lakes by means of 454 pyrosequencing of the 16S rRNA gene. We further provide a BR estimate based upon a sampling depth and accuracy, which, to our knowledge, are unsurpassed for freshwater bacterioplankton communities. Our examination of 22 669 sequences per lake showed that freshwater BR in fourteen nutrient-poor lakes was positively influenced by nutrient availability. Our study is, thus, consistent with the finding that the supply of available nutrients is a major driver of species richness; a pattern that may well be universally valid to the world of both micro- and macro-organisms. We, furthermore, observed that BR increased with elevated landscape position, most likely as a consequence of differences in nutrient availability. Finally, BR decreased with increasing lake and catchment area that is negative species–area relationships (SARs) were recorded; a finding that re-opens the debate about whether positive SARs can indeed be found in the microbial world and whether positive SARs can in fact be pronounced as one of the few ‘laws' in ecology. PMID:22170419

  2. Molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern Gulf of Mexico.

    PubMed

    Olapade, Ola A

    2010-10-01

    Bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern Gulf of Mexico (GOM) using 16S rRNA gene libraries and fluorescence in situ hybridization approaches. The majority of the sequences (30%-60%) were similar to the 16S rRNA gene sequences of unknown bacteria; however, the operational taxonomic units from members of the Cyanobacteria, Proteobacteria, and Bacteroidetes were also present at the 3 GOM sites. Overall, sequence diversity was more similar between the Gulf sites of Carrabelle and Ochlockonee than between either of the Gulf sites and Apalachicola Bay. Fluorescence in situ hybridization analyses revealed the quantitative predominance of members of the Alphaproteobacteria subclass and the Cytophaga-Flavobacterium cluster within the bacterioplankton assemblages. In general, the study further reveals the presence of many bacterial taxa that have been previously found to be dominant in coastal marine environments. Differences observed in the representation of the various bacterial phylogenetic groups among the GOM coastal sites could be partly attributed to dynamic variations in several site-specific conditions, including intermittent tidal events, nutrient availability, and anthropogenic influences. PMID:20962909

  3. The green macroalga Dictyosphaeria ocellata influences the structure of the bacterioplankton community through differential effects on individual bacterial phylotypes.

    PubMed

    Sneed, Jennifer M; Pohnert, Georg

    2011-02-01

    Marine macroalgae are subjected to large numbers of bacteria in their environment. These bacteria have the potential to affect the health and ecology of algae in a variety of ways and can be both beneficial and harmful to the algae. Therefore, algae have likely evolved mechanisms to differentially regulate the growth of bacterial species. In this study, we examined the effects of the green alga Dictyosphaeria ocellata on the bacterioplankton community in field enclosure experiments and on individual, naturally co-occurring bacterial strains in laboratory co-culture experiments. In field experiments, we compared the bacterioplankton communities of enclosures with and without D. ocellata using denaturing gradient gel electrophoresis and found that the alga significantly changed the bacterial community composition. Seven bacterial phylotypes were eliminated in the presence of the alga and five were found exclusively with the alga. We also examined the effects of algal-treated water on the development of the bacterial community within enclosures and found no change in the community composition. Laboratory co-culture experiments revealed that D. ocellata and D. ocellata extracts affect the growth of individual bacterial strains in a species-specific manner and that the mechanisms responsible for these effects also differed by bacterial species. PMID:21155850

  4. Bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH).

    PubMed

    Pearce, D A

    2003-07-01

    The bacterioplankton community structure in Moss Lake, a maritime Antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on Signy Island in the South Orkney Islands. Bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (DAPI) stained cells, PCR amplification of 16S rRNA gene fragments, denaturing gradient gel electrophoresis (DGGE) and in situ hybridization with group-specific, fluorescently labeled oligonucleotide probes. Using PCR amplification of 16S rRNA gene fragments and DGGE, the bacterioplankton community composition was shown to be constant with vertical depth in the water column. Specific bacterioplankton species identified through cloning and sequencing the DGGE products obtained were Flavobacterium xinjiangensis (a Flavobacterium), Leptothrix discophora (a beta-Proteobacterium), and a number of uncultured groups: two beta-Proteobacteria, an unclassified Proteobacterium, three sequences from Actinobacteria, and a Cyanobacterium. Fluorescence in situ hybridization (FISH), however, demonstrated that there were minor but significant fluctuations in different groups of bacteria with vertical depth in the water column. It showed that the beta-Proteobacteria accounted for between 26.4 and 71.5%, the alpha-Proteobacteria 2.3-10.6%, the gamma-Proteobacteria 0-29.6%, and the Cytophaga-Flavobacterium group 1.8-23.5% of cells hybridizing to a universal probe. This study reports the first description of the community structure of an oligotrophic Antarctic freshwater lake as determined by PCR-dependent and PCR-independent molecular techniques. It also suggests that the bacterioplankton community of Moss Lake contains classes of bacteria known to be important in freshwater systems elsewhere in the world. PMID:12739078

  5. Impacts of combined overfishing and oil spills on the plankton trophodynamics of the West Florida shelf over the last half century of 1965-2011: A two-dimensional simulation analysis of biotic state transitions, from a zooplankton- to a bacterioplankton-modulated ecosystem.

    NASA Astrophysics Data System (ADS)

    Walsh, J. J.; Lenes, J. M.; Darrow, B.; Parks, A.; Weisberg, R. H.

    2016-03-01

    Over 50 years of multiple anthropogenic perturbations, Florida zooplankton stocks of the northeastern Gulf of Mexico declined ten-fold, with increments of mainly dominant toxic dinoflagellate harmful algal blooms (HABs), rather than diatoms, and a shift in loci of nutrient remineralization and oxygen depletion by bacterioplankton, from the sea floor to near surface waters. Yet, lytic bacterial biomass and associated ammonification only increased at most five-fold over the same time period, with consequently little indication of new, expanded "dead zones" of diatom-induced hypoxia. After bacterial lysis of intact cells of these increased HABs, the remaining residues of zooplankton biomass decrements evidently instead exited the water column as malign aerosolized HAB asthma triggers, correlated by co-traveling mercury aerosols, within wind-borne sea sprays. To unravel the causal mechanisms of these inferred decadal food web transitions, a 36-state variable plankton model of algal, bacterial, protozoan, and copepod component communities replicated daily time series of each plankton group's representatives on the West Florida shelf (WFS) during 1965-2011. At the lower phytoplankton trophic levels, 52% of the ungrazed HAB increments, between 1965-1967 and 2001-2002 before recent oil spills, remained in the water column to kill fishes and fuel bacterioplankton. But, another 48% of the WFS primary production then left the ocean's surface as a harbinger of increased public health hazards during continuing sea spray exports of salts, HAB toxins, and Hg poisons. Following the Deepwater Horizon petroleum releases in 2010, little additional change of element partition among the altered importance of WFS food web components of the trophic pyramid then pertained between 2001-2002 and 2010-2011, despite when anomalous upwelled nutrient supplies instead favored retrograde benign, oil-tolerant diatoms over the HABs during 2010. Indeed, by 2011 HABs were back, with biomass

  6. The Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1996-04-01

    The authors are developing a computer application, called the Bayes Inference Engine, to provide the means to make inferences about models of physical reality within a Bayesian framework. The construction of complex nonlinear models is achieved by a fully object-oriented design. The models are represented by a data-flow diagram that may be manipulated by the analyst through a graphical programming environment. Maximum a posteriori solutions are achieved using a general, gradient-based optimization algorithm. The application incorporates a new technique of estimating and visualizing the uncertainties in specific aspects of the model.

  7. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria.

    PubMed Central

    Giovannoni, S J; Rappé, M S; Vergin, K L; Adair, N L

    1996-01-01

    Microorganisms play an important role in the biogeochemistry of the ocean surface layer, but spatial and temporal structures in the distributions of specific bacterioplankton species are largely unexplored, with the exceptions of those organisms that can be detected by either autofluorescence or culture methods. The use of rRNA genes as genetic markers provides a tool by which patterns in the growth, distribution, and activity of abundant bacterioplankton species can be studied regardless of the ease with which they can be cultured. Here we report an unusual cluster of related 16S rRNA genes (SAR202, SAR263, SAR279, SAR287, SAR293, SAR307) cloned from seawater collected at 250 m in the Sargasso Sea in August 1991, when the water column was highly stratified and the deep chlorophyll maximum was located at a depth of 120 m. Phylogenetic analysis and an unusual 15-bp deletion confirmed that the genes were related to the Green Non-Sulfur phylum of the domain Bacteria. This is the first evidence that representatives of this phylum occur in the open ocean. Oligonucleotide probes were used to examine the distribution of the SAR202 gene cluster in vertical profiles (0-250 m) from the Atlantic and Pacific Oceans, and in discrete (monthly) time series (O and 200 m) (over 30 consecutive months in the Western Sargasso Sea. The data provide robust statistical support for the conclusion that the SAR202 gene cluster is proportionately most abundant at the lower boundary of the deep chlorophyll maximum (P = 2.33 x 10(-5)). These results suggest that previously unsuspected stratification of microbial populations may be a significant factor in the ecology of the ocean surface layer. Images Fig. 4 PMID:8755588

  8. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage.

    PubMed

    Billerbeck, Sara; Wemheuer, Bernd; Voget, Sonja; Poehlein, Anja; Giebel, Helge-Ansgar; Brinkhoff, Thorsten; Gram, Lone; Jeffrey, Wade H; Daniel, Rolf; Simon, Meinhard

    2016-01-01

    The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments. PMID:27572966

  9. Bromodeoxyuridine (BrdU) labeling and subsequent fluorescence activated cell sorting for culture-independent identification of dissolved organic carbon-degrading bacterioplankton.

    PubMed

    Robbins, Steven; Jacob, Jisha; Lu, Xinxin; Moran, Mary Ann; Mou, Xiaozhen

    2011-01-01

    Microbes are major agents mediating the degradation of numerous dissolved organic carbon (DOC) substrates in aquatic environments. However, identification of bacterial taxa that transform specific pools of DOC in nature poses a technical challenge. Here we describe an approach that couples bromodeoxyuridine (BrdU) incorporation, fluorescence activated cell sorting (FACS), and 16S rRNA gene-based molecular analysis that allows culture-independent identification of bacterioplankton capable of degrading a specific DOC compound in aquatic environments. Triplicate bacterioplankton microcosms are set up to receive both BrdU and a model DOC compound (DOC amendments), or only BrdU (no-addition control). BrdU substitutes the positions of thymidine in newly synthesized bacterial DNA and BrdU-labeled DNA can be readily immunodetected. Through a 24-hr incubation, bacterioplankton that are able to use the added DOC compound are expected to be selectively activated, and therefore have higher levels of BrdU incorporation (HI cells) than non-responsive cells in the DOC amendments and cells in no-addition controls (low BrdU incorporation cells, LI cells). After fluorescence immunodetection, HI cells are distinguished and physically separated from the LI cells by fluorescence activated cell sorting (FACS). Sorted DOC-responsive cells (HI cells) are extracted for DNA and taxonomically identified through subsequent 16S rRNA gene-based analyses including PCR, clone library construction and sequencing. PMID:21931294

  10. Bromodeoxyuridine (BrdU) Labeling and Subsequent Fluorescence Activated Cell Sorting for Culture-independent Identification of Dissolved Organic Carbon-degrading Bacterioplankton

    PubMed Central

    Lu, Xinxin; Moran, Mary Ann; Mou, Xiaozhen

    2011-01-01

    Microbes are major agents mediating the degradation of numerous dissolved organic carbon (DOC) substrates in aquatic environments. However, identification of bacterial taxa that transform specific pools of DOC in nature poses a technical challenge. Here we describe an approach that couples bromodeoxyuridine (BrdU) incorporation, fluorescence activated cell sorting (FACS), and 16S rRNA gene-based molecular analysis that allows culture-independent identification of bacterioplankton capable of degrading a specific DOC compound in aquatic environments. Triplicate bacterioplankton microcosms are set up to receive both BrdU and a model DOC compound (DOC amendments), or only BrdU (no-addition control). BrdU substitutes the positions of thymidine in newly synthesized bacterial DNA and BrdU-labeled DNA can be readily immunodetected 1,2. Through a 24-hr incubation, bacterioplankton that are able to use the added DOC compound are expected to be selectively activated, and therefore have higher levels of BrdU incorporation (HI cells) than non-responsive cells in the DOC amendments and cells in no-addition controls (low BrdU incorporation cells, LI cells). After fluorescence immunodetection, HI cells are distinguished and physically separated from the LI cells by fluorescence activated cell sorting (FACS) 3. Sorted DOC-responsive cells (HI cells) are extracted for DNA and taxonomically identified through subsequent 16S rRNA gene-based analyses including PCR, clone library construction and sequencing. PMID:21931294

  11. Contrasting patterns of free-living bacterioplankton diversity in macrophyte-dominated versus phytoplankton blooming regimes in Dianchi Lake, a shallow lake in China

    NASA Astrophysics Data System (ADS)

    Wang, Yujing; Li, Huabing; Xing, Peng; Wu, Qinglong

    2016-04-01

    Freshwater shallow lakes typically exhibit two alternative stable states under certain nutrient loadings: macrophyte-dominated and phytoplankton-dominated water regimes. An ecosystem regime shift from macrophytes to phytoplankton blooming typically reduces the number of species of invertebrates and fishes and results in the homogenization of communities in freshwater lakes. We investigated how microbial biodiversity has responded to a shift of the ecosystem regime in Dianchi Lake, which was previously fully covered with submerged macrophytes but currently harbors both ecological states. We observed marked divergence in the diversity and community composition of bacterioplankton between the two regimes. Although species richness, estimated as the number of operational taxonomic units and phylogenetic diversity (PD), was higher in the phytoplankton dominated ecosystem after this shift, the dissimilarity of bacterioplankton community across space decreased. This decrease in beta diversity was accompanied by loss of planktonic bacteria unique to the macrophyte-dominated ecosystem. Mantel tests between bacterioplankton community distances and Euclidian distance of environmental parameters indicated that this reduced bacterial community diff erentiation primarily reflected the loss of environmental niches, particularly in the macrophyte regime. The loss of this small-scale heterogeneity in bacterial communities should be considered when assessing long-term biodiversity changes in response to ecosystem regime conversions in freshwater lakes.

  12. INFERENCES FROM ROSSI TRACES

    SciTech Connect

    KENNETH M. HANSON; JANE M. BOOKER

    2000-09-08

    The authors an uncertainty analysis of data taken using the Rossi technique, in which the horizontal oscilloscope sweep is driven sinusoidally in time ,while the vertical axis follows the signal amplitude. The analysis is done within a Bayesian framework. Complete inferences are obtained by tilting the Markov chain Monte Carlo technique, which produces random samples from the posterior probability distribution expressed in terms of the parameters.

  13. Active inference and learning.

    PubMed

    Friston, Karl; FitzGerald, Thomas; Rigoli, Francesco; Schwartenbeck, Philipp; O'Doherty, John; Pezzulo, Giovanni

    2016-09-01

    This paper offers an active inference account of choice behaviour and learning. It focuses on the distinction between goal-directed and habitual behaviour and how they contextualise each other. We show that habits emerge naturally (and autodidactically) from sequential policy optimisation when agents are equipped with state-action policies. In active inference, behaviour has explorative (epistemic) and exploitative (pragmatic) aspects that are sensitive to ambiguity and risk respectively, where epistemic (ambiguity-resolving) behaviour enables pragmatic (reward-seeking) behaviour and the subsequent emergence of habits. Although goal-directed and habitual policies are usually associated with model-based and model-free schemes, we find the more important distinction is between belief-free and belief-based schemes. The underlying (variational) belief updating provides a comprehensive (if metaphorical) process theory for several phenomena, including the transfer of dopamine responses, reversal learning, habit formation and devaluation. Finally, we show that active inference reduces to a classical (Bellman) scheme, in the absence of ambiguity. PMID:27375276

  14. Bayesian inference in physics

    NASA Astrophysics Data System (ADS)

    von Toussaint, Udo

    2011-07-01

    Bayesian inference provides a consistent method for the extraction of information from physics experiments even in ill-conditioned circumstances. The approach provides a unified rationale for data analysis, which both justifies many of the commonly used analysis procedures and reveals some of the implicit underlying assumptions. This review summarizes the general ideas of the Bayesian probability theory with emphasis on the application to the evaluation of experimental data. As case studies for Bayesian parameter estimation techniques examples ranging from extra-solar planet detection to the deconvolution of the apparatus functions for improving the energy resolution and change point estimation in time series are discussed. Special attention is paid to the numerical techniques suited for Bayesian analysis, with a focus on recent developments of Markov chain Monte Carlo algorithms for high-dimensional integration problems. Bayesian model comparison, the quantitative ranking of models for the explanation of a given data set, is illustrated with examples collected from cosmology, mass spectroscopy, and surface physics, covering problems such as background subtraction and automated outlier detection. Additionally the Bayesian inference techniques for the design and optimization of future experiments are introduced. Experiments, instead of being merely passive recording devices, can now be designed to adapt to measured data and to change the measurement strategy on the fly to maximize the information of an experiment. The applied key concepts and necessary numerical tools which provide the means of designing such inference chains and the crucial aspects of data fusion are summarized and some of the expected implications are highlighted.

  15. Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses.

    PubMed

    Voget, Sonja; Wemheuer, Bernd; Brinkhoff, Thorsten; Vollmers, John; Dietrich, Sascha; Giebel, Helge-Ansgar; Beardsley, Christine; Sardemann, Carla; Bakenhus, Insa; Billerbeck, Sara; Daniel, Rolf; Simon, Meinhard

    2015-02-01

    The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry. PMID:25083934

  16. Inferring the spatiotemporal DNA replication program from noisy data

    NASA Astrophysics Data System (ADS)

    Baker, A.; Bechhoefer, J.

    2014-03-01

    We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation rates from experimental data concerning replication in cell populations. Previous work based on curve fitting depended on arbitrarily chosen functional forms for the initiation rate, with free parameters that were constrained by the data. We introduce a nonparametric method of inference that is based on Gaussian process regression. The method replaces specific assumptions about the functional form of the initiation rate with more general prior expectations about the smoothness of variation of this rate, along the genome and in time. Using this inference method, we recover, with high precision, simulated replication schemes from noisy data that are typical of current experiments.

  17. Towards Context Sensitive Information Inference.

    ERIC Educational Resources Information Center

    Song, D.; Bruza, P. D.

    2003-01-01

    Discusses information inference from a psychologistic stance and proposes an information inference mechanism that makes inferences via computations of information flow through an approximation of a conceptual space. Highlights include cognitive economics of information processing; context sensitivity; and query models for information retrieval.…

  18. Regulon inference without arbitrary thresholds: three levels of sensitivity

    SciTech Connect

    Dubchak, Pavel Novichkov, Elena Stavrovskaya, Dmitry Rodionov, Andrey Mironov, Inna; Rodionov, Dmitry; Mironov, Andrey; Dubchak, Inna; Novichkov, P.S.

    2010-11-15

    Reconstruction of transcriptional regulatory networks is one of the major challenges facing the bioinformatics community in view of constantly growing number of complete genomes. The comparative genomics approach has been successfully used for the analysis of the transcriptional regulation of many metabolic systems in various bacteria taxa. The key step in this approach is given a position weight matrix, find an optimal threshold for the search of potential binding sites in genomes. In our previous work we proposed an approach for automatic selection of TFBS score threshold coupled with inference of regulon content. In this study we developed two modifications of this approach providing two additional levels of sensitivity.

  19. Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies

    PubMed Central

    Barbeau, Katherine A.

    2016-01-01

    Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages. PMID:26729720

  20. Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies.

    PubMed

    Hogle, Shane L; Thrash, J Cameron; Dupont, Chris L; Barbeau, Katherine A

    2016-03-01

    Heterotrophic bacteria in the SAR11 and Roseobacter lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and Roseobacter genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger Roseobacter genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and Roseobacter. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic Alphaproteobacteria of the SAR11 and Roseobacter lineages. PMID:26729720

  1. Visual Inference Programming

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin; Timucin, Dogan; Rabbette, Maura; Curry, Charles; Allan, Mark; Lvov, Nikolay; Clanton, Sam; Pilewskie, Peter

    2002-01-01

    The goal of visual inference programming is to develop a software framework data analysis and to provide machine learning algorithms for inter-active data exploration and visualization. The topics include: 1) Intelligent Data Understanding (IDU) framework; 2) Challenge problems; 3) What's new here; 4) Framework features; 5) Wiring diagram; 6) Generated script; 7) Results of script; 8) Initial algorithms; 9) Independent Component Analysis for instrument diagnosis; 10) Output sensory mapping virtual joystick; 11) Output sensory mapping typing; 12) Closed-loop feedback mu-rhythm control; 13) Closed-loop training; 14) Data sources; and 15) Algorithms. This paper is in viewgraph form.

  2. Genomics on a phylogeny: Evolution of genes and genomes in the genus Drosophila

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of inferences in evolutionary genomics. The genomes of 12 Drosophila species, nine of which are presented here for the first time (sechellia, yakuba, erecta, ananassae, persimili...

  3. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia. PMID:24065721

  4. Moment inference from tomograms

    USGS Publications Warehouse

    Day-Lewis, F. D.; Chen, Y.; Singha, K.

    2007-01-01

    Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error. Copyright 2007 by the American Geophysical Union.

  5. Quality of Computationally Inferred Gene Ontology Annotations

    PubMed Central

    Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-01-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

  6. Genome Size and Species Diversification

    PubMed Central

    2010-01-01

    Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone. PMID:22140283

  7. Betaproteobacteria Limnohabitans strains increase fecundity in the crustacean Daphnia magna: symbiotic relationship between major bacterioplankton and zooplankton in freshwater ecosystem.

    PubMed

    Peerakietkhajorn, Saranya; Kato, Yasuhiko; Kasalický, Vojtěch; Matsuura, Tomoaki; Watanabe, Hajime

    2016-09-01

    How symbioses between bacteria and aquatic animals influence food webs in freshwater ecosystems is a fundamental question in ecology. We investigated symbiosis between a crustacean zooplankton Daphnia magna and its dominant bacterial symbiont Limnohabitans, an abundant and globally distributed freshwater Betaproteobacteria. Aposymbiotic juvenile Daphnia were prepared and exposed to any of four Limnohabitans sp. - Limnohabitans strains DM1, 2KL-3, 2KL-7 and Limnohabitans planktonicus strain II-D5, all previously found in D. magna digestive tract or culture. Re-infected Daphnia were cultured until they produced the first clutch of juveniles. Limnohabitans strain DM1 and L. planktonicus strain II-D5 successfully re-infected Daphnia through single exposure at the first instar juvenile stage. In contrast to aposymbiotic Daphnia that produced non-viable juveniles, re-infected Daphnia produced viable juveniles and increased fecundity to levels of that of symbiotic Daphnia. Re-infected Daphnia did not increase their number of eggs nor growth rates. Limnohabitans strains 2KL-7 and 2KL-3 could not recover fecundity even in multiple exposures during culture. This study shows the functional evidence demonstrating that a single bacterium Limnohabitans regulates fecundity of the consumer Daphnia through symbiosis. Our results indicated that symbiotic relationship between major bacterioplankton and zooplankton is important for maintaining the population of zooplankton in freshwater ecosystems. PMID:26014379

  8. Seasonal dominance of CL500-11 bacterioplankton (phylum Chloroflexi) in the oxygenated hypolimnion of Lake Biwa, Japan.

    PubMed

    Okazaki, Yusuke; Hodoki, Yoshikuni; Nakano, Shin-ichi

    2013-01-01

    Uncultured bacteria affiliated with the CL500-11 cluster (phylum Chloroflexi) were first reported from the oxygenated hypolimnion of Crater Lake (USA) as a predominant bacterioplankton, although this dominance has not been reported in other environments. In this study, we showed that CL500-11 is also dominant in the oxygenated hypolimnion of Lake Biwa (Japan) and followed its spatiotemporal succession using fluorescent in situ hybridization. CL500-11 cells were almost absent [< 1% of 4',6-diamidino-2-phenylindole (DAPI)-stained cells] at the beginning of the stratification period, dominated (> 10% of DAPI-stained cells; maximum = 16.5%) in the hypolimnion during the stratification period, and decreased to below the detection limit with the collapse of the thermocline. This pattern was observed over two annual cycles. A longitudinal assessment also showed that CL500-11 was the dominant bacterium in the hypolimnion over the whole lake, but was generally undetectable in the stratified epilimnion. These data suggest that CL500-11 is acclimated to the oxygenated hypolimnion and is a potentially important component of the pelagic biogeochemical cycling of the lake. A comparative analysis of 16S rRNA gene sequences revealed that almost all CL500-11 sequences previously deposited in the database were detected from hypolimnion or holomictic water in deep oxic freshwater lakes, suggesting that the bacteria may form one of the common lineages residing in an aerobic hypolimnetic niche. PMID:22809435

  9. Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean oligotrophic lake.

    PubMed

    Fernández-Zenoff, María V; Estévez, María C; Farías, María E

    2014-01-01

    Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profiles showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment. PMID:25576421

  10. BIE: Bayesian Inference Engine

    NASA Astrophysics Data System (ADS)

    Weinberg, Martin D.

    2013-12-01

    The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates heta distributed according to P( heta|D) so moments are trivially obtained by summing of the ensemble of variates.

  11. Bayesian inference in geomagnetism

    NASA Technical Reports Server (NTRS)

    Backus, George E.

    1988-01-01

    The inverse problem in empirical geomagnetic modeling is investigated, with critical examination of recently published studies. Particular attention is given to the use of Bayesian inference (BI) to select the damping parameter lambda in the uniqueness portion of the inverse problem. The mathematical bases of BI and stochastic inversion are explored, with consideration of bound-softening problems and resolution in linear Gaussian BI. The problem of estimating the radial magnetic field B(r) at the earth core-mantle boundary from surface and satellite measurements is then analyzed in detail, with specific attention to the selection of lambda in the studies of Gubbins (1983) and Gubbins and Bloxham (1985). It is argued that the selection method is inappropriate and leads to lambda values much larger than those that would result if a reasonable bound on the heat flow at the CMB were assumed.

  12. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.

    2009-01-01

    Multimodel inference has two main themes: model selection, and model averaging. Model averaging is a means of making inference conditional on a model set, rather than on a selected model, allowing formal recognition of the uncertainty associated with model choice. The Bayesian paradigm provides a natural framework for model averaging, and provides a context for evaluation of the commonly used AIC weights. We review Bayesian multimodel inference, noting the importance of Bayes factors. Noting the sensitivity of Bayes factors to the choice of priors on parameters, we define and propose nonpreferential priors as offering a reasonable standard for objective multimodel inference.

  13. Homology-independent metrics for comparative genomics.

    PubMed

    Coutinho, Tarcisio José Domingos; Franco, Glória Regina; Lobo, Francisco Pereira

    2015-01-01

    A mainstream procedure to analyze the wealth of genomic data available nowadays is the detection of homologous regions shared across genomes, followed by the extraction of biological information from the patterns of conservation and variation observed in such regions. Although of pivotal importance, comparative genomic procedures that rely on homology inference are obviously not applicable if no homologous regions are detectable. This fact excludes a considerable portion of "genomic dark matter" with no significant similarity - and, consequently, no inferred homology to any other known sequence - from several downstream comparative genomic methods. In this review we compile several sequence metrics that do not rely on homology inference and can be used to compare nucleotide sequences and extract biologically meaningful information from them. These metrics comprise several compositional parameters calculated from sequence data alone, such as GC content, dinucleotide odds ratio, and several codon bias metrics. They also share other interesting properties, such as pervasiveness (patterns persist on smaller scales) and phylogenetic signal. We also cite examples where these homology-independent metrics have been successfully applied to support several bioinformatics challenges, such as taxonomic classification of biological sequences without homology inference. They where also used to detect higher-order patterns of interactions in biological systems, ranging from detecting coevolutionary trends between the genomes of viruses and their hosts to characterization of gene pools of entire microbial communities. We argue that, if correctly understood and applied, homology-independent metrics can add important layers of biological information in comparative genomic studies without prior homology inference. PMID:26029354

  14. Causal Inference in Retrospective Studies.

    ERIC Educational Resources Information Center

    Holland, Paul W.; Rubin, Donald B.

    1988-01-01

    The problem of drawing causal inferences from retrospective case-controlled studies is considered. A model for causal inference in prospective studies is applied to retrospective studies. Limitations of case-controlled studies are formulated concerning relevant parameters that can be estimated in such studies. A coffee-drinking/myocardial…

  15. Improving Inferences from Multiple Methods.

    ERIC Educational Resources Information Center

    Shotland, R. Lance; Mark, Melvin M.

    1987-01-01

    Multiple evaluation methods (MEMs) can cause an inferential challenge, although there are strategies to strengthen inferences. Practical and theoretical issues involved in the use by social scientists of MEMs, three potential problems in drawing inferences from MEMs, and short- and long-term strategies for alleviating these problems are outlined.…

  16. Causal Inference and Developmental Psychology

    ERIC Educational Resources Information Center

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  17. Learning to Observe "and" Infer

    ERIC Educational Resources Information Center

    Hanuscin, Deborah L.; Park Rogers, Meredith A.

    2008-01-01

    Researchers describe the need for students to have multiple opportunities and social interaction to learn about the differences between observation and inference and their role in developing scientific explanations (Harlen 2001; Simpson 2000). Helping children develop their skills of observation and inference in science while emphasizing the…

  18. INFERRING THE ECCENTRICITY DISTRIBUTION

    SciTech Connect

    Hogg, David W.; Bovy, Jo; Myers, Adam D.

    2010-12-20

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision-other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts-so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  19. Inferring the Eccentricity Distribution

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Myers, Adam D.; Bovy, Jo

    2010-12-01

    Standard maximum-likelihood estimators for binary-star and exoplanet eccentricities are biased high, in the sense that the estimated eccentricity tends to be larger than the true eccentricity. As with most non-trivial observables, a simple histogram of estimated eccentricities is not a good estimate of the true eccentricity distribution. Here, we develop and test a hierarchical probabilistic method for performing the relevant meta-analysis, that is, inferring the true eccentricity distribution, taking as input the likelihood functions for the individual star eccentricities, or samplings of the posterior probability distributions for the eccentricities (under a given, uninformative prior). The method is a simple implementation of a hierarchical Bayesian model; it can also be seen as a kind of heteroscedastic deconvolution. It can be applied to any quantity measured with finite precision—other orbital parameters, or indeed any astronomical measurements of any kind, including magnitudes, distances, or photometric redshifts—so long as the measurements have been communicated as a likelihood function or a posterior sampling.

  20. Social Inference Through Technology

    NASA Astrophysics Data System (ADS)

    Oulasvirta, Antti

    Awareness cues are computer-mediated, real-time indicators of people’s undertakings, whereabouts, and intentions. Already in the mid-1970 s, UNIX users could use commands such as “finger” and “talk” to find out who was online and to chat. The small icons in instant messaging (IM) applications that indicate coconversants’ presence in the discussion space are the successors of “finger” output. Similar indicators can be found in online communities, media-sharing services, Internet relay chat (IRC), and location-based messaging applications. But presence and availability indicators are only the tip of the iceberg. Technological progress has enabled richer, more accurate, and more intimate indicators. For example, there are mobile services that allow friends to query and follow each other’s locations. Remote monitoring systems developed for health care allow relatives and doctors to assess the wellbeing of homebound patients (see, e.g., Tang and Venables 2000). But users also utilize cues that have not been deliberately designed for this purpose. For example, online gamers pay attention to other characters’ behavior to infer what the other players are like “in real life.” There is a common denominator underlying these examples: shared activities rely on the technology’s representation of the remote person. The other human being is not physically present but present only through a narrow technological channel.

  1. Inference from aging information.

    PubMed

    de Oliveira, Evaldo Araujo; Caticha, Nestor

    2010-06-01

    For many learning tasks the duration of the data collection can be greater than the time scale for changes of the underlying data distribution. The question we ask is how to include the information that data are aging. Ad hoc methods to achieve this include the use of validity windows that prevent the learning machine from making inferences based on old data. This introduces the problem of how to define the size of validity windows. In this brief, a new adaptive Bayesian inspired algorithm is presented for learning drifting concepts. It uses the analogy of validity windows in an adaptive Bayesian way to incorporate changes in the data distribution over time. We apply a theoretical approach based on information geometry to the classification problem and measure its performance in simulations. The uncertainty about the appropriate size of the memory windows is dealt with in a Bayesian manner by integrating over the distribution of the adaptive window size. Thus, the posterior distribution of the weights may develop algebraic tails. The learning algorithm results from tracking the mean and variance of the posterior distribution of the weights. It was found that the algebraic tails of this posterior distribution give the learning algorithm the ability to cope with an evolving environment by permitting the escape from local traps. PMID:20421181

  2. Virioplankton and bacterioplankton in a shallow CO 2-dominated hydrothermal vent (Panarea Island, Tyrrhenian Sea)

    NASA Astrophysics Data System (ADS)

    Karuza, Ana; Celussi, Mauro; Cibic, Tamara; Del Negro, Paola; De Vittor, Cinzia

    2012-01-01

    Gas hydrothermal vents are used as a natural analogue for studying the effects of CO 2 leakage from hypothetical shallow marine storage sites on benthic and pelagic systems. This study investigated the interrelationships between planktonic prokaryotes and viruses in the Panarea Islands hydrothermal system (southern Tyrrhenian Sea, Italy), especially their abundance, distribution and diversity. No difference in prokaryotic abundance was shown between high-CO 2 and control sites. The community structure displayed differences between fumarolic field and the control, and between surface and bottom waters, the latter likely due to the presence of different water masses. Bacterial assemblages were qualitatively dominated by chemo- and photoautotrophic organisms, able to utilise both CO 2 and H 2S for their metabolic requirements. From significantly lower virioplankton abundance in the proximity of the exhalative area together with particularly low Virus-to-Prokaryotes Ratio, we inferred a reduced impact on prokaryotic abundance and proliferation. Even if the fate of viruses in this particular condition remains still unknown, we consider that lower viral abundance could reflect in enhancing the energy flow to higher trophic levels, thus largely influencing the overall functioning of the system.

  3. Functional Responses of Bacterioplankton Diversity and Metabolism to Experimental Bottom-Up and Top-Down Forcings.

    PubMed

    Pradeep Ram, A S; Chaibi-Slouma, S; Keshri, J; Colombet, J; Sime-Ngando, T

    2016-08-01

    We conducted an experimental approach using microcosms to simultaneously examine the functional response of natural freshwater bacterial assemblages to the impact of resources (nutrients) and top-down factors (viruses and grazers) on bacterial physiological state and their community structure. Addition of organic and inorganic nutrients led to the proliferation of high nucleic acid content bacterial cells accompanied by high bacterial growth efficiency (considered as proxy of bacterial carbon metabolism) estimates, suggesting that this subgroup represented the most active fraction of bacterial community and had a high capacity to incorporate carbon into its biomass. However, their rapid growth induced the pressure of viral lytic infection which led to their lysis toward the end of the experiment. In microcosms with flagellates plus viruses, and with viruses alone, the selective removal of metabolically active high nucleic acid cells through viral lysis benefitted the less active low nucleic acid content cells, perhaps via the use of lysis products for its growth and survival. Changes in bacterial physiological state in microcosms were reflected in their community structure which was examined using 16S ribosomal RNA (rRNA) gene sequencing by Illumina's Miseq platform. Chao estimator and Shannon diversity index values suggested that bacterial species richness was highest in the presence of both the top-down factors, indicating a tighter control of bacterioplankton dominants within a relatively stable bacterial community. The increase in bacterial metabolism with nutrient addition followed by subsequent lysis of bacterial dominants indicate that both resources and top-down factors work in concert for the sustenance of stable bacterial communities. PMID:27179523

  4. Combining Culture-Dependent and -Independent Methodologies for Estimation of Richness of Estuarine Bacterioplankton Consuming Riverine Dissolved Organic Matter

    PubMed Central

    Kisand, Veljo; Wikner, Johan

    2003-01-01

    Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated β-proteobacteria to be RDOM consumers. PMID:12788769

  5. Inferring Indel Parameters using a Simulation-based Approach.

    PubMed

    Levy Karin, Eli; Rabin, Avigayel; Ashkenazy, Haim; Shkedy, Dafna; Avram, Oren; Cartwright, Reed A; Pupko, Tal

    2015-12-01

    In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets. PMID:26537226

  6. Methods for causal inference from gene perturbation experiments and validation.

    PubMed

    Meinshausen, Nicolai; Hauser, Alain; Mooij, Joris M; Peters, Jonas; Versteeg, Philip; Bühlmann, Peter

    2016-07-01

    Inferring causal effects from observational and interventional data is a highly desirable but ambitious goal. Many of the computational and statistical methods are plagued by fundamental identifiability issues, instability, and unreliable performance, especially for large-scale systems with many measured variables. We present software and provide some validation of a recently developed methodology based on an invariance principle, called invariant causal prediction (ICP). The ICP method quantifies confidence probabilities for inferring causal structures and thus leads to more reliable and confirmatory statements for causal relations and predictions of external intervention effects. We validate the ICP method and some other procedures using large-scale genome-wide gene perturbation experiments in Saccharomyces cerevisiae The results suggest that prediction and prioritization of future experimental interventions, such as gene deletions, can be improved by using our statistical inference techniques. PMID:27382150

  7. Methods for causal inference from gene perturbation experiments and validation

    PubMed Central

    Meinshausen, Nicolai; Hauser, Alain; Mooij, Joris M.; Peters, Jonas; Versteeg, Philip; Bühlmann, Peter

    2016-01-01

    Inferring causal effects from observational and interventional data is a highly desirable but ambitious goal. Many of the computational and statistical methods are plagued by fundamental identifiability issues, instability, and unreliable performance, especially for large-scale systems with many measured variables. We present software and provide some validation of a recently developed methodology based on an invariance principle, called invariant causal prediction (ICP). The ICP method quantifies confidence probabilities for inferring causal structures and thus leads to more reliable and confirmatory statements for causal relations and predictions of external intervention effects. We validate the ICP method and some other procedures using large-scale genome-wide gene perturbation experiments in Saccharomyces cerevisiae. The results suggest that prediction and prioritization of future experimental interventions, such as gene deletions, can be improved by using our statistical inference techniques. PMID:27382150

  8. Inferring Indel Parameters using a Simulation-based Approach

    PubMed Central

    Levy Karin, Eli; Rabin, Avigayel; Ashkenazy, Haim; Shkedy, Dafna; Avram, Oren; Cartwright, Reed A.; Pupko, Tal

    2015-01-01

    In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets. PMID:26537226

  9. Chloroplast Phylogenomic Inference of Green Algae Relationships

    PubMed Central

    Sun, Linhua; Fang, Ling; Zhang, Zhenhua; Chang, Xin; Penny, David; Zhong, Bojian

    2016-01-01

    The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences. PMID:26846729

  10. Inference of fitness from genealogical trees

    NASA Astrophysics Data System (ADS)

    Vucelja, Marija; Dayarian, Adel; Shraiman, Boris

    2013-03-01

    Natural populations are fitness diverse and can have numerous genes under selection. The genealogical trees, that one obtains by sampling, often bear hallmarks of selection, such multiple mergers, asymmetric tree branches and long terminal branches (the trees are squished towards the root). These are qualitative differences compared to trees in the absence of selection. We propose a theoretical model that links the morphology of a tree with the fitness of the leaves. We obtain multipoint correlation functions of the fitness along the tree. In this way we are able extract some quantitative information about the strength of selection from data-reconstructed trees. The extensions of this approach can potentially be useful for inferring relative fitness of sequenced genomes of tumors and for predicting viral outbreaks.

  11. BINOCh: binding inference from nucleosome occupancy changes

    PubMed Central

    Meyer, Clifford A.; He, Housheng H.; Brown, Myles; Liu, X. Shirley

    2011-01-01

    Summary: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation. Availability: The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license. Contact: cliff@jimmy.harvard.edu; xsliu@jimmy.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21551136

  12. Pathway network inference from gene expression data

    PubMed Central

    2014-01-01

    Background The development of high-throughput omics technologies enabled genome-wide measurements of the activity of cellular elements and provides the analytical resources for the progress of the Systems Biology discipline. Analysis and interpretation of gene expression data has evolved from the gene to the pathway and interaction level, i.e. from the detection of differentially expressed genes, to the establishment of gene interaction networks and the identification of enriched functional categories. Still, the understanding of biological systems requires a further level of analysis that addresses the characterization of the interaction between functional modules. Results We present a novel computational methodology to study the functional interconnections among the molecular elements of a biological system. The PANA approach uses high-throughput genomics measurements and a functional annotation scheme to extract an activity profile from each functional block -or pathway- followed by machine-learning methods to infer the relationships between these functional profiles. The result is a global, interconnected network of pathways that represents the functional cross-talk within the molecular system. We have applied this approach to describe the functional transcriptional connections during the yeast cell cycle and to identify pathways that change their connectivity in a disease condition using an Alzheimer example. Conclusions PANA is a useful tool to deepen in our understanding of the functional interdependences that operate within complex biological systems. We show the approach is algorithmically consistent and the inferred network is well supported by the available functional data. The method allows the dissection of the molecular basis of the functional connections and we describe the different regulatory mechanisms that explain the network's topology obtained for the yeast cell cycle data. PMID:25032889

  13. Response of bacterioplankton activity in an Arctic fjord system to elevated pCO2: results from a mesocosm perturbation study

    NASA Astrophysics Data System (ADS)

    Piontek, J.; Borchard, C.; Sperling, M.; Schulz, K. G.; Riebesell, U.; Engel, A.

    2013-01-01

    The effect of elevated seawater carbon dioxide (CO2) on the activity of a natural bacterioplankton community in an Arctic fjord system was investigated by a mesocosm perturbation study in the frame of the European Project on Ocean Acidification (EPOCA). A pCO2 range of 175-1085 μatm was set up in nine mesocosms deployed in the Kongsfjorden (Svalbard). The activity of natural extracellular enzyme assemblages increased in response to acidification. Rates of β-glucosidase and leucine-aminopeptidase increased along the gradient of mesocosm pCO2. A decrease in seawater pH of 0.5 units almost doubled rates of both enzymes. Heterotrophic bacterial activity was closely coupled to phytoplankton productivity in this experiment. The bacterioplankton community responded to rising chlorophyll a concentrations after a lag phase of only a few days with increasing protein production and extracellular enzyme activity. Time-integrated primary production and bacterial protein production were positively correlated, strongly suggesting that higher amounts of phytoplankton-derived organic matter were assimilated by heterotrophic bacteria at increased primary production. Primary production increased under high pCO2 in this study, and it can be suggested that the efficient heterotrophic carbon utilisation had the potential to counteract the enhanced autotrophic CO2 fixation. However, our results also show that beneficial pCO2-related effects on bacterial activity can be mitigated by the top-down control of bacterial abundances in natural microbial communities.

  14. Ensemble Inference and Inferability of Gene Regulatory Networks

    PubMed Central

    Ud-Dean, S. M. Minhaz; Gunawan, Rudiyanto

    2014-01-01

    The inference of gene regulatory network (GRN) from gene expression data is an unsolved problem of great importance. This inference has been stated, though not proven, to be underdetermined implying that there could be many equivalent (indistinguishable) solutions. Motivated by this fundamental limitation, we have developed new framework and algorithm, called TRaCE, for the ensemble inference of GRNs. The ensemble corresponds to the inherent uncertainty associated with discriminating direct and indirect gene regulations from steady-state data of gene knock-out (KO) experiments. We applied TRaCE to analyze the inferability of random GRNs and the GRNs of E. coli and yeast from single- and double-gene KO experiments. The results showed that, with the exception of networks with very few edges, GRNs are typically not inferable even when the data are ideal (unbiased and noise-free). Finally, we compared the performance of TRaCE with top performing methods of DREAM4 in silico network inference challenge. PMID:25093509

  15. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

    PubMed

    Lindh, Markus V; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

    2015-01-01

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates. PMID

  16. Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

    PubMed Central

    Stewart, Frank J.; Dalsgaard, Tage; Young, Curtis R.; Thamdrup, Bo; Revsbech, Niels Peter; Ulloa, Osvaldo; Canfield, Don E.; DeLong, Edward F.

    2012-01-01

    metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations. PMID:22615914

  17. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

    PubMed Central

    Lindh, Markus V.; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

    2015-01-01

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates. PMID

  18. Algorithmic methods to infer the evolutionary trajectories in cancer progression.

    PubMed

    Caravagna, Giulio; Graudenzi, Alex; Ramazzotti, Daniele; Sanz-Pamplona, Rebeca; De Sano, Luca; Mauri, Giancarlo; Moreno, Victor; Antoniotti, Marco; Mishra, Bud

    2016-07-12

    The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next-generation sequencing data and machine learning for the inference of explanatory models of how the (epi)genomic events are choreographed in cancer initiation and development. However, despite the increasing availability of multiple additional -omics data, this quest has been frustrated by various theoretical and technical hurdles, mostly stemming from the dramatic heterogeneity of the disease. In this paper, we build on our recent work on the "selective advantage" relation among driver mutations in cancer progression and investigate its applicability to the modeling problem at the population level. Here, we introduce PiCnIc (Pipeline for Cancer Inference), a versatile, modular, and customizable pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes. The pipeline has many translational implications because it combines state-of-the-art techniques for sample stratification, driver selection, identification of fitness-equivalent exclusive alterations, and progression model inference. We demonstrate PiCnIc's ability to reproduce much of the current knowledge on colorectal cancer progression as well as to suggest novel experimentally verifiable hypotheses. PMID:27357673

  19. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparative Genomic Hybridization (CGH) with DNA microarrays has many biological applications including surveys of copy number changes in tumorigenesis, species detection and identification, and functional genomics studies among related organisms. Array CGH has also been used to infer phylogenetic r...

  20. From the Beauty of Genomic Landscapes to the Strength of Transcriptional Mechanisms.

    PubMed

    Natoli, Gioacchino

    2016-03-24

    Genomic analyses are commonly used to infer trends and broad rules underlying transcriptional control. The innovative approach by Tong et al. to interrogate genomic datasets allows extracting mechanistic information on the specific regulation of individual genes. PMID:27015303

  1. Bayesian Inference: with ecological applications

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2010-01-01

    This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

  2. Stimulation of viral infection of bacterioplankton during a mesoscale iron fertilization experiment in the Southern Ocean

    NASA Astrophysics Data System (ADS)

    Weinbauer, M. G.; Arrieta, J.-M.; Herndl, G. J.

    2003-04-01

    A mesoscale iron fertilization in the Southern Ocean (Eisenex ) induced a phytoplankton bloom within three weeks observation as well as in an increased bacterial abundance and production. Viral abundance and viral production were stimulated as well. A virus-dilution approach was used to estimate the frequency of infected cells (FIC) and the frequency of lysogenic cells (FLC), i.e. cells with a dormant viral genome. While the FLC did not vary strongly within the iron-enriched patch and did not differ from waters outside the patch, FIC increased significantly within the iron fertilized patch. This suggests that induction of the lytic cycle in lysogenic cells was not significant. Rather, the stimulated bacterial production and abundance within the patch resulted in higher and more successful encounters between viruses and hosts and thus in higher FIC values. Consequently, the iron fertilization enhanced the influence of viral infection in the microbial food web. According to the current model, this should result a stimulation of bacterial production, since lysed bacterial cells cannot be consumed up by protists and transferred to higher trophic level; lysis products can be taken up by bacteria and thus organic carbon spins within this viral loop. Viral infection is a significant and previously overlooked factor in the carbon flow during iron fertilization experiments.

  3. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

    PubMed Central

    Rivers, Adam R; Sharma, Shalabh; Tringe, Susannah G; Martin, Jeffrey; Joye, Samantha B; Moran, Mary Ann

    2013-01-01

    The Deepwater Horizon blowout released a massive amount of oil and gas into the deep ocean between April and July 2010, stimulating microbial blooms of petroleum-degrading bacteria. To understand the metabolic response of marine microorganisms, we sequenced ∼66 million community transcripts that revealed the identity of metabolically active microbes and their roles in petroleum consumption. Reads were assigned to reference genes from ∼2700 bacterial and archaeal taxa, but most assignments (39%) were to just six genomes representing predominantly methane- and petroleum-degrading Gammaproteobacteria. Specific pathways for the degradation of alkanes, aromatic compounds and methane emerged from the metatranscriptomes, with some transcripts assigned to methane monooxygenases representing highly divergent homologs that may degrade either methane or short alkanes. The microbial community in the plume was less taxonomically and functionally diverse than the unexposed community below the plume; this was due primarily to decreased species evenness resulting from Gammaproteobacteria blooms. Surprisingly, a number of taxa (related to SAR11, Nitrosopumilus and Bacteroides, among others) contributed equal numbers of transcripts per liter in both the unexposed and plume samples, suggesting that some groups were unaffected by the petroleum inputs and blooms of degrader taxa, and may be important for re-establishing the pre-spill microbial community structure. PMID:23902988

  4. Active inference, communication and hermeneutics.

    PubMed

    Friston, Karl J; Frith, Christopher D

    2015-07-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others--during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions--both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then--in principle--they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  5. Causal inference and developmental psychology.

    PubMed

    Foster, E Michael

    2010-11-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether the risk factor actually causes outcomes. Random assignment is not possible in many instances, and for that reason, psychologists must rely on observational studies. Such studies identify associations, and causal interpretation of such associations requires additional assumptions. Research in developmental psychology generally has relied on various forms of linear regression, but this methodology has limitations for causal inference. Fortunately, methodological developments in various fields are providing new tools for causal inference-tools that rely on more plausible assumptions. This article describes the limitations of regression for causal inference and describes how new tools might offer better causal inference. This discussion highlights the importance of properly identifying covariates to include (and exclude) from the analysis. This discussion considers the directed acyclic graph for use in accomplishing this task. With the proper covariates having been chosen, many of the available methods rely on the assumption of "ignorability." The article discusses the meaning of ignorability and considers alternatives to this assumption, such as instrumental variables estimation. Finally, the article considers the use of the tools discussed in the context of a specific research question, the effect of family structure on child development. PMID:20677855

  6. Active inference, communication and hermeneutics☆

    PubMed Central

    Friston, Karl J.; Frith, Christopher D.

    2015-01-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others – during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions – both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then – in principle – they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  7. hiHMM: Bayesian non-parametric joint inference of chromatin state maps

    PubMed Central

    Sohn, Kyung-Ah; Ho, Joshua W. K.; Djordjevic, Djordje; Jeong, Hyun-hwan; Park, Peter J.; Kim, Ju Han

    2015-01-01

    Motivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. Results: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. Conclusion: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis. Availability and implementation: Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/. Contact: peter_park@harvard.edu or juhan@snu.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25725496

  8. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples

    NASA Astrophysics Data System (ADS)

    Tuller, Tamir; Birin, Hadas; Kupiec, Martin; Ruppin, Eytan

    The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content.

  9. Optimal inference with suboptimal models: Addiction and active Bayesian inference

    PubMed Central

    Schwartenbeck, Philipp; FitzGerald, Thomas H.B.; Mathys, Christoph; Dolan, Ray; Wurst, Friedrich; Kronbichler, Martin; Friston, Karl

    2015-01-01

    When casting behaviour as active (Bayesian) inference, optimal inference is defined with respect to an agent’s beliefs – based on its generative model of the world. This contrasts with normative accounts of choice behaviour, in which optimal actions are considered in relation to the true structure of the environment – as opposed to the agent’s beliefs about worldly states (or the task). This distinction shifts an understanding of suboptimal or pathological behaviour away from aberrant inference as such, to understanding the prior beliefs of a subject that cause them to behave less ‘optimally’ than our prior beliefs suggest they should behave. Put simply, suboptimal or pathological behaviour does not speak against understanding behaviour in terms of (Bayes optimal) inference, but rather calls for a more refined understanding of the subject’s generative model upon which their (optimal) Bayesian inference is based. Here, we discuss this fundamental distinction and its implications for understanding optimality, bounded rationality and pathological (choice) behaviour. We illustrate our argument using addictive choice behaviour in a recently described ‘limited offer’ task. Our simulations of pathological choices and addictive behaviour also generate some clear hypotheses, which we hope to pursue in ongoing empirical work. PMID:25561321

  10. Effect of elevated CO2 on the dynamics of particle attached and free living bacterioplankton communities in an Arctic fjord

    NASA Astrophysics Data System (ADS)

    Sperling, M.; Piontek, J.; Gerdts, G.; Wichels, A.; Schunck, H.; Roy, A.-S.; La Roche, J.; Gilbert, J.; Bittner, L.; Romac, S.; Riebesell, U.; Engel, A.

    2012-08-01

    The increase in atmospheric carbon dioxide (CO2) results in acidification of the oceans, expected to lead to the fastest drop in ocean pH in the last 300 million years, if anthropogenic emissions are continued at present rate. Due to higher solubility of gases in cold waters and increased exposure to the atmosphere by decreasing ice cover, the Arctic Ocean will be among the areas most strongly affected by ocean acidification. Yet, the response of the plankton community of high latitudes to ocean acidification has not been studied so far. This work is part of the Arctic campaign of the European Project on Ocean Acidification (EPOCA) in 2010, employing 9 in situ mesocosms of about 45 000 l each to simulate ocean acidification in Kongsfjorden, Svalbard (78°56.2' N 11°53.6' E). In the present study, we investigated effects of elevated CO2 on the composition and richness of particle attached (PA; >3 μm) and free living (FL; <3 μm >0.2 μm) bacterial communities by Automated Ribosomal Intergenic Spacer Analysis (ARISA) in 6 of the mesocosms and the surrounding fjord, ranging from 185 to 1050 initial μatm pCO2. ARISA was able to resolve about 20-30 bacterial band-classes per sample and allowed for a detailed investigation of the explicit richness. Both, the PA and the FL bacterioplankton community exhibited a strong temporal development, which was driven mainly by temperature and phytoplankton development. In response to the breakdown of a picophytoplankton bloom (phase 3 of the experiment), number of ARISA-band classes in the PA-community were reduced at low and medium CO2 (∼180-600 μatm) by about 25%, while it was more or less stable at high CO2 (∼ 650-800 μatm). We hypothesise that enhanced viral lysis and enhanced availability of organic substrates at high CO2 resulted in a more diverse PA-bacterial community in the post-bloom phase. Despite lower cell numbers and extracellular enzyme activities in the post-bloom phase, bacterial protein production was

  11. Statistical inference and string theory

    NASA Astrophysics Data System (ADS)

    Heckman, Jonathan J.

    2015-09-01

    In this paper, we expose some surprising connections between string theory and statistical inference. We consider a large collective of agents sweeping out a family of nearby statistical models for an M-dimensional manifold of statistical fitting parameters. When the agents making nearby inferences align along a d-dimensional grid, we find that the pooled probability that the collective reaches a correct inference is the partition function of a nonlinear sigma model in d dimensions. Stability under perturbations to the original inference scheme requires the agents of the collective to distribute along two dimensions. Conformal invariance of the sigma model corresponds to the condition of a stable inference scheme, directly leading to the Einstein field equations for classical gravity. By summing over all possible arrangements of the agents in the collective, we reach a string theory. We also use this perspective to quantify how much an observer can hope to learn about the internal geometry of a superstring compactification. Finally, we present some brief speculative remarks on applications to the AdS/CFT correspondence and Lorentzian signature space-times.

  12. The small genome of an abundant coastal ocean methylotroph.

    PubMed

    Giovannoni, Stephen J; Hayakawa, Darin H; Tripp, H James; Stingl, Ulrich; Givan, Scott A; Cho, Jang-Cheon; Oh, Hyun-Myung; Kitner, Joshua B; Vergin, Kevin L; Rappé, Michael S

    2008-07-01

    OM43 is a clade of uncultured beta-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was obtained using new procedures for culturing cells in natural seawater. We found that this strain is an obligate methylotroph that cannot oxidize methane but can use the oxidized C1 compounds methanol and formaldehyde as sources of carbon and energy. Its complete genome is 1304 428 bp in length, the smallest yet reported for a free-living cell. The HTCC2181 genome includes genes for xanthorhodopsin and retinal biosynthesis, an auxiliary system for producing transmembrane electrochemical potentials from light. The discovery that HTCC2181 is an extremely simple specialist in C1 metabolism suggests an unanticipated, important role for oxidized C1 compounds as substrates for bacterioplankton productivity in coastal ecosystems. PMID:18393994

  13. Beyond the bounds of orthology: functional inference from metagenomic context.

    PubMed

    Vey, Gregory; Moreno-Hagelsieb, Gabriel

    2010-07-01

    The effectiveness of the computational inference of function by genomic context is bounded by the diversity of known microbial genomes. Although metagenomes offer access to previously inaccessible organisms, their fragmentary nature prevents the conventional establishment of orthologous relationships required for reliably predicting functional interactions. We introduce a protocol for the prediction of functional interactions using data sources without information about orthologous relationships. To illustrate this process, we use the Sargasso Sea metagenome to construct a functional interaction network for the Escherichia coli K12 genome. We identify two reliability metrics, target intergenic distance and source interaction count, and apply them to selectively filter the predictions retained to construct the network of functional interactions. The resulting network contains 2297 nodes with 10 072 edges with a positive predictive value of 0.80. The metagenome yielded 8423 functional interactions beyond those found using only the genomic orthologs as a data source. This amounted to a 134% increase in the total number of functional interactions that are predicted by combining the metagenome and the genomic orthologs versus the genomic orthologs alone. In the absence of detectable orthologous relationships it remains feasible to derive a reliable set of predicted functional interactions. This offers a strategy for harnessing other metagenomes and homologs in general. Because metagenomes allow access to previously unreachable microorganisms, this will result in expanding the universe of known functional interactions thus furthering our understanding of functional organization. PMID:20419183

  14. Thermodynamics of cellular statistical inference

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Fisher, Charles; Mehta, Pankaj

    2014-03-01

    Successful organisms must be capable of accurately sensing the surrounding environment in order to locate nutrients and evade toxins or predators. However, single cell organisms face a multitude of limitations on their accuracy of sensing. Berg and Purcell first examined the canonical example of statistical limitations to cellular learning of a diffusing chemical and established a fundamental limit to statistical accuracy. Recent work has shown that the Berg and Purcell learning limit can be exceeded using Maximum Likelihood Estimation. Here, we recast the cellular sensing problem as a statistical inference problem and discuss the relationship between the efficiency of an estimator and its thermodynamic properties. We explicitly model a single non-equilibrium receptor and examine the constraints on statistical inference imposed by noisy biochemical networks. Our work shows that cells must balance sample number, specificity, and energy consumption when performing statistical inference. These tradeoffs place significant constraints on the practical implementation of statistical estimators in a cell.

  15. Causal inference from observational data.

    PubMed

    Listl, Stefan; Jürges, Hendrik; Watt, Richard G

    2016-10-01

    Randomized controlled trials have long been considered the 'gold standard' for causal inference in clinical research. In the absence of randomized experiments, identification of reliable intervention points to improve oral health is often perceived as a challenge. But other fields of science, such as social science, have always been challenged by ethical constraints to conducting randomized controlled trials. Methods have been established to make causal inference using observational data, and these methods are becoming increasingly relevant in clinical medicine, health policy and public health research. This study provides an overview of state-of-the-art methods specifically designed for causal inference in observational data, including difference-in-differences (DiD) analyses, instrumental variables (IV), regression discontinuity designs (RDD) and fixed-effects panel data analysis. The described methods may be particularly useful in dental research, not least because of the increasing availability of routinely collected administrative data and electronic health records ('big data'). PMID:27111146

  16. We infer light in space.

    PubMed

    Schirillo, James A

    2013-10-01

    In studies of lightness and color constancy, the terms lightness and brightness refer to the qualia corresponding to perceived surface reflectance and perceived luminance, respectively. However, what has rarely been considered is the fact that the volume of space containing surfaces appears neither empty, void, nor black, but filled with light. Helmholtz (1866/1962) came closest to describing this phenomenon when discussing inferred illumination, but previous theoretical treatments have fallen short by restricting their considerations to the surfaces of objects. The present work is among the first to explore how we infer the light present in empty space. It concludes with several research examples supporting the theory that humans can infer the differential levels and chromaticities of illumination in three-dimensional space. PMID:23435628

  17. Eight challenges in phylodynamic inference

    PubMed Central

    Frost, Simon D.W.; Pybus, Oliver G.; Gog, Julia R.; Viboud, Cecile; Bonhoeffer, Sebastian; Bedford, Trevor

    2015-01-01

    The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data. PMID:25843391

  18. Inferring biotic interactions from proxies.

    PubMed

    Morales-Castilla, Ignacio; Matias, Miguel G; Gravel, Dominique; Araújo, Miguel B

    2015-06-01

    Inferring biotic interactions from functional, phylogenetic and geographical proxies remains one great challenge in ecology. We propose a conceptual framework to infer the backbone of biotic interaction networks within regional species pools. First, interacting groups are identified to order links and remove forbidden interactions between species. Second, additional links are removed by examination of the geographical context in which species co-occur. Third, hypotheses are proposed to establish interaction probabilities between species. We illustrate the framework using published food-webs in terrestrial and marine systems. We conclude that preliminary descriptions of the web of life can be made by careful integration of data with theory. PMID:25922148

  19. Inferring the Spatiotemporal DNA Replication Program from Noisy Biological Data

    NASA Astrophysics Data System (ADS)

    Bechhoefer, John; Baker, Antoine

    2014-03-01

    We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation rates from experimental data concerning replication in cell populations. Previous work based on curve fitting depended on arbitrarily chosen functional forms for the initiation rate, with free parameters that were constrained by the data. We introduce a model-free, non-parametric method of inference that is based on Gaussian process regression. The method replaces specific assumptions about the functional form of initiation rate with more general prior expectations about the smoothness of variation of this rate, along the genome and in time. Using this inference method, we show that we can recover with high precision simulated replication schemes with data that are typical of current experiments. The method of Gaussian process regression can be profitably applied to a wide range of physical and biological problems. Supported by NSERC (Canada).

  20. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

    PubMed Central

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-01-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  1. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

    PubMed

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-05-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  2. The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in Crete.

    PubMed

    Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis; Ladoukakis, Emmanuel D

    2014-07-01

    A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

  3. Response of bacterioplankton activity in an Arctic fjord system to elevated pCO2: results from a mesocosm perturbation study

    NASA Astrophysics Data System (ADS)

    Piontek, J.; Borchard, C.; Sperling, M.; Schulz, K. G.; Riebesell, U.; Engel, A.

    2012-08-01

    The effect of elevated seawater carbon dioxide (CO2) on the activity of a natural bacterioplankton community in an Arctic fjord system was investigated by a mesocosm perturbation study in the frame of the European Project on Ocean Acidification (EPOCA). A pCO2 range of 175-1085 μatm was set up in nine mesocosms deployed in the Kongsfjorden (Svalbard). The bacterioplankton communities responded to rising chlorophyll a concentrations after a lag phase of only a few days with increasing protein production and extracellular enzyme activity and revealed a close coupling of heterotrophic bacterial activity to phytoplankton productivity in this experiment. The natural extracellular enzyme assemblages showed increased activity in response to moderate acidification. A decrease in seawater pH of 0.5 units roughly doubled rates of β-glucosidase and leucine-aminopeptidase. Activities of extracellular enzymes in the mesocosms were directly related to both seawater pH and primary production. Also primary production and bacterial protein production in the mesocosms at different pCO2 were positively correlated. Therefore, it can be suggested that the efficient heterotrophic carbon utilization in this Arctic microbial food web had the potential to counteract increased phytoplankton production that was achieved under elevated pCO2 in this study. However, our results also show that the transfer of beneficial pCO2-related effects on the cellular bacterial metabolism to the scale of community activity and organic matter degradation can be mitigated by the top-down control of bacterial abundances in natural microbial communities.

  4. The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete

    PubMed Central

    Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis

    2014-01-01

    A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

  5. Science Shorts: Observation versus Inference

    ERIC Educational Resources Information Center

    Leager, Craig R.

    2008-01-01

    When you observe something, how do you know for sure what you are seeing, feeling, smelling, or hearing? Asking students to think critically about their encounters with the natural world will help to strengthen their understanding and application of the science-process skills of observation and inference. In the following lesson, students make…

  6. Sample Size and Correlational Inference

    ERIC Educational Resources Information Center

    Anderson, Richard B.; Doherty, Michael E.; Friedrich, Jeff C.

    2008-01-01

    In 4 studies, the authors examined the hypothesis that the structure of the informational environment makes small samples more informative than large ones for drawing inferences about population correlations. The specific purpose of the studies was to test predictions arising from the signal detection simulations of R. B. Anderson, M. E. Doherty,…

  7. Word Learning as Bayesian Inference

    ERIC Educational Resources Information Center

    Xu, Fei; Tenenbaum, Joshua B.

    2007-01-01

    The authors present a Bayesian framework for understanding how adults and children learn the meanings of words. The theory explains how learners can generalize meaningfully from just one or a few positive examples of a novel word's referents, by making rational inductive inferences that integrate prior knowledge about plausible word meanings with…

  8. The mechanisms of temporal inference

    NASA Technical Reports Server (NTRS)

    Fox, B. R.; Green, S. R.

    1987-01-01

    The properties of a temporal language are determined by its constituent elements: the temporal objects which it can represent, the attributes of those objects, the relationships between them, the axioms which define the default relationships, and the rules which define the statements that can be formulated. The methods of inference which can be applied to a temporal language are derived in part from a small number of axioms which define the meaning of equality and order and how those relationships can be propagated. More complex inferences involve detailed analysis of the stated relationships. Perhaps the most challenging area of temporal inference is reasoning over disjunctive temporal constraints. Simple forms of disjunction do not sufficiently increase the expressive power of a language while unrestricted use of disjunction makes the analysis NP-hard. In many cases a set of disjunctive constraints can be converted to disjunctive normal form and familiar methods of inference can be applied to the conjunctive sub-expressions. This process itself is NP-hard but it is made more tractable by careful expansion of a tree-structured search space.

  9. Perceptual Inference and Autistic Traits

    ERIC Educational Resources Information Center

    Skewes, Joshua C; Jegindø, Else-Marie; Gebauer, Line

    2015-01-01

    Autistic people are better at perceiving details. Major theories explain this in terms of bottom-up sensory mechanisms or in terms of top-down cognitive biases. Recently, it has become possible to link these theories within a common framework. This framework assumes that perception is implicit neural inference, combining sensory evidence with…

  10. Improving Explanatory Inferences from Assessments

    ERIC Educational Resources Information Center

    Diakow, Ronli Phyllis

    2013-01-01

    This dissertation comprises three papers that propose, discuss, and illustrate models to make improved inferences about research questions regarding student achievement in education. Addressing the types of questions common in educational research today requires three different "extensions" to traditional educational assessment: (1)…

  11. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

    PubMed Central

    Garcia, Sarahi L; McMahon, Katherine D; Martinez-Garcia, Manuel; Srivastava, Abhishek; Sczyrba, Alexander; Stepanauskas, Ramunas; Grossart, Hans-Peter; Woyke, Tanja; Warnecke, Falk

    2013-01-01

    Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria. PMID:22810059

  12. A genomic perspective on hybridization and speciation

    PubMed Central

    Payseur, Bret A.; Rieseberg, Loren H.

    2016-01-01

    Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns – which may contribute to reproductive barriers – are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation. PMID:26836441

  13. Homoeologs: What Are They and How Do We Infer Them?

    PubMed

    Glover, Natasha M; Redestig, Henning; Dessimoz, Christophe

    2016-07-01

    The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing projects under way, there is a pressing need for computational methods for homoeology inference. Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization. PMID:27021699

  14. Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages.

    PubMed

    Luo, Haiwei; Thompson, Luke R; Stingl, Ulrich; Hughes, Austin L

    2015-10-01

    The genomic G+C content of ocean bacteria varies from below 30% to over 60%. This broad range of base composition is likely shaped by distinct mutational processes, recombination, effective population size, and selection driven by environmental factors. A number of studies have hypothesized that depletion of G/C in genomes of marine bacterioplankton cells is an adaptation to the nitrogen-poor pelagic oceans, but they failed to disentangle environmental factors from mutational biases and population history. Here, we reconstructed the evolutionary changes of bases at synonymous sites in genomes of two marine SAR11 populations and a freshwater counterpart with its evolutionary origin rooted in the marine lineage. Although they all have similar genome sizes, DNA repair gene repertoire, and base compositions, there is a stronger bias toward A/T changes, a reduced frequency of nitrogenous amino acids, and an exclusive occurrence of polyamine, opine, and taurine transport systems in the ocean populations, consistent with a greater nitrogen stress in surface oceans compared with freshwater lakes. Furthermore, the ratio of nonsynoymous to synonymous nucleotide diversity is not statistically distinguishable among these populations, suggesting that population history has a limited effect. Taken together, the ecological transition of SAR11 from ocean to freshwater habitats makes nitrogen more available to these organisms, and thus relaxation of purifying selection drove a genome-wide reduction in the frequency of G/C to A/T changes in the freshwater population. PMID:26116859

  15. Reconstructing transcriptional regulatory networks through genomics data

    PubMed Central

    Sun, Ning; Zhao, Hongyu

    2013-01-01

    One central problem in biology is to understand how gene expression is regulated under different conditions. Microarray gene expression data and other high throughput data have made it possible to dissect transcriptional regulatory networks at the genomics level. Owing to the very large number of genes that need to be studied, the relatively small number of data sets available, the noise in the data and the different natures of the distinct data types, network inference presents great challenges. In this article, we review statistical and computational methods that have been developed in the last decade in response to genomics data for inferring transcriptional regulatory networks. PMID:20048387

  16. Homology-Independent Metrics for Comparative Genomics

    PubMed Central

    Coutinho, Tarcisio José Domingos; Franco, Glória Regina; Lobo, Francisco Pereira

    2015-01-01

    A mainstream procedure to analyze the wealth of genomic data available nowadays is the detection of homologous regions shared across genomes, followed by the extraction of biological information from the patterns of conservation and variation observed in such regions. Although of pivotal importance, comparative genomic procedures that rely on homology inference are obviously not applicable if no homologous regions are detectable. This fact excludes a considerable portion of “genomic dark matter” with no significant similarity — and, consequently, no inferred homology to any other known sequence — from several downstream comparative genomic methods. In this review we compile several sequence metrics that do not rely on homology inference and can be used to compare nucleotide sequences and extract biologically meaningful information from them. These metrics comprise several compositional parameters calculated from sequence data alone, such as GC content, dinucleotide odds ratio, and several codon bias metrics. They also share other interesting properties, such as pervasiveness (patterns persist on smaller scales) and phylogenetic signal. We also cite examples where these homology-independent metrics have been successfully applied to support several bioinformatics challenges, such as taxonomic classification of biological sequences without homology inference. They where also used to detect higher-order patterns of interactions in biological systems, ranging from detecting coevolutionary trends between the genomes of viruses and their hosts to characterization of gene pools of entire microbial communities. We argue that, if correctly understood and applied, homology-independent metrics can add important layers of biological information in comparative genomic studies without prior homology inference. PMID:26029354

  17. Bayesian Inference on Proportional Elections

    PubMed Central

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  18. Bayesian inference on proportional elections.

    PubMed

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  19. System Support for Forensic Inference

    NASA Astrophysics Data System (ADS)

    Gehani, Ashish; Kirchner, Florent; Shankar, Natarajan

    Digital evidence is playing an increasingly important role in prosecuting crimes. The reasons are manifold: financially lucrative targets are now connected online, systems are so complex that vulnerabilities abound and strong digital identities are being adopted, making audit trails more useful. If the discoveries of forensic analysts are to hold up to scrutiny in court, they must meet the standard for scientific evidence. Software systems are currently developed without consideration of this fact. This paper argues for the development of a formal framework for constructing “digital artifacts” that can serve as proxies for physical evidence; a system so imbued would facilitate sound digital forensic inference. A case study involving a filesystem augmentation that provides transparent support for forensic inference is described.

  20. Statistical learning and selective inference

    PubMed Central

    Taylor, Jonathan; Tibshirani, Robert J.

    2015-01-01

    We describe the problem of “selective inference.” This addresses the following challenge: Having mined a set of data to find potential associations, how do we properly assess the strength of these associations? The fact that we have “cherry-picked”—searched for the strongest associations—means that we must set a higher bar for declaring significant the associations that we see. This challenge becomes more important in the era of big data and complex statistical modeling. The cherry tree (dataset) can be very large and the tools for cherry picking (statistical learning methods) are now very sophisticated. We describe some recent new developments in selective inference and illustrate their use in forward stepwise regression, the lasso, and principal components analysis. PMID:26100887

  1. Network Plasticity as Bayesian Inference

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2015-01-01

    General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling. PMID:26545099

  2. Causal inference based on counterfactuals

    PubMed Central

    Höfler, M

    2005-01-01

    Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept. PMID:16159397

  3. Genomic Signals of Reoriented ORFs

    NASA Astrophysics Data System (ADS)

    Dan Cristea, Paul

    2004-12-01

    Complex representation of nucleotides is used to convert DNA sequences into complex digital genomic signals. The analysis of the cumulated phase and unwrapped phase of DNA genomic signals reveals large-scale features of eukaryote and prokaryote chromosomes that result from statistical regularities of base and base-pair distributions along DNA strands. By reorienting the chromosome coding regions, a "hidden" linear variation of the cumulated phase has been revealed, along with the conspicuous almost linear variation of the unwrapped phase. A model of chromosome longitudinal structure is inferred on these bases.

  4. Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

    PubMed Central

    Leyn, Semen A.; Kazanov, Marat D.; Sernova, Natalia V.; Ermakova, Ekaterina O.; Novichkov, Pavel S.

    2013-01-01

    The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium Bacillus subtilis and 10 related Bacillales species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in B. subtilis comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in B. subtilis and projected them to other Bacillales genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (http://regprecise.lbl.gov/) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis. PMID:23504016

  5. Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

    PubMed

    Leyn, Semen A; Kazanov, Marat D; Sernova, Natalia V; Ermakova, Ekaterina O; Novichkov, Pavel S; Rodionov, Dmitry A

    2013-06-01

    The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium Bacillus subtilis and 10 related Bacillales species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in B. subtilis comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in B. subtilis and projected them to other Bacillales genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (http://regprecise.lbl.gov/) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis. PMID:23504016

  6. Self-enforcing Private Inference Control

    NASA Astrophysics Data System (ADS)

    Yang, Yanjiang; Li, Yingjiu; Weng, Jian; Zhou, Jianying; Bao, Feng

    Private inference control enables simultaneous enforcement of inference control and protection of users' query privacy. Private inference control is a useful tool for database applications, especially when users are increasingly concerned about individual privacy nowadays. However, protection of query privacy on top of inference control is a double-edged sword: without letting the database server know the content of user queries, users can easily launch DoS attacks. To assuage DoS attacks in private inference control, we propose the concept of self-enforcing private inference control, whose intuition is to force users to only make inference-free queries by enforcing inference control themselves; otherwise, penalty will inflict upon the violating users.

  7. A Genome-Wide Landscape of Retrocopies in Primate Genomes

    PubMed Central

    Navarro, Fábio C.P.; Galante, Pedro A.F.

    2015-01-01

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. PMID:26224704

  8. A Genome-Wide Landscape of Retrocopies in Primate Genomes.

    PubMed

    Navarro, Fábio C P; Galante, Pedro A F

    2015-08-01

    Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. PMID:26224704

  9. Inferring genetic networks from DNA microarray data by multiple regression analysis.

    PubMed

    Kato, M; Tsunoda, T; Takagi, T

    2000-01-01

    Inferring gene regulatory networks by differential equations from the time series data of a DNA microarray is one of the most challenging tasks in the post-genomic era. However, there have been no studies actually inferring gene regulatory networks by differential equations from genome-level data. The reason for this is that the number of parameters in the equations exceeds the number of measured time points. We here succeeded in executing the inference, not by directly determining parameters but by applying multiple regression analysis to our equations. We derived our differential equations and steady state equations from the rate equations of transcriptional reactions in an organism. Verification with a number of genes related to respiration indicated the validity and effectiveness of our method. Moreover, the steady state equations were more appropriate than the differential equations for the microarray data used. PMID:11700593

  10. Inside the Pan-genome - Methods and Software Overview

    PubMed Central

    Guimarães, Luis Carlos; Florczak-Wyspianska, Jolanta; de Jesus, Leandro Benevides; Viana, Marcus Vinícius Canário; Silva, Artur; Ramos, Rommel Thiago Jucá; Soares, Siomar de Castro; Soares, Siomar de Castro

    2015-01-01

    The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be “open” as long as new genes are added significantly to the total repertoire for each new additional genome and “closed” when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification. PMID:27006628

  11. Assessing inhomogeneities in bacterial long genomic sequences

    SciTech Connect

    Karlin, S.

    1997-12-01

    Several complete prokaryotic and eukaryotic genomes are already at hand (S. cerevisiae, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, sp.) and many are forthcoming (e.g., E. coli, H, pylori, C. elegans). The comparative analysis of genomes generally strives to identify genes and characterize function/structure relationships inferred mostly via amino acid sequence comparisons. We describe concisely methods for comparing genomes (or long contigs) emphasizing sequence features other than gene comparisons. These center on the following measures of genomic organization and sequence heterogeneity: (i) compositional biases of short oligonucleotides; (ii) dinucleotide relative abundance distances within and between genomes; (iii) rare and frequent word (oligonucleotide) determinations and their distributional properties; (iv) r-scan statistics assessing clustering, overdispersion, or excessive evenness of various marker arrays; and (v) characterizations of repeat structures in the genome. 20 refs., 3 figs.

  12. Divergence and Shannon Information in Genomes

    NASA Astrophysics Data System (ADS)

    Chen, Hong-Da; Chang, Chang-Heng; Hsieh, Li-Ching; Lee, Hoong-Chien

    2005-05-01

    Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following: SI (but not divergence) is inversely proportional to sequence length for a random sequence but is length independent for genomes; the genomic SI is always greater and, for shorter words and longer sequences, hundreds to thousands times greater than the SI in a random sequence whose length and composition match those of the genome; genomic SIs appear to have word-length dependent universal values. The universality is inferred to be an evolution footprint of a universal mode for genome growth.

  13. Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

    PubMed Central

    Ames, Ryan M.; Money, Daniel; Lovell, Simon C.

    2014-01-01

    The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes. PMID:24921666

  14. The deepest divergences in land plants inferred from phylogenomic evidence.

    PubMed

    Qiu, Yin-Long; Li, Libo; Wang, Bin; Chen, Zhiduan; Knoop, Volker; Groth-Malonek, Milena; Dombrovska, Olena; Lee, Jungho; Kent, Livija; Rest, Joshua; Estabrook, George F; Hendry, Tory A; Taylor, David W; Testa, Christopher M; Ambros, Mathew; Crandall-Stotler, Barbara; Duff, R Joel; Stech, Michael; Frey, Wolfgang; Quandt, Dietmar; Davis, Charles C

    2006-10-17

    Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences. PMID:17030812

  15. Accurate inference of local phased ancestry of modern admixed populations.

    PubMed

    Ma, Yamin; Zhao, Jian; Wong, Jian-Syuan; Ma, Li; Li, Wenzhi; Fu, Guoxing; Xu, Wei; Zhang, Kui; Kittles, Rick A; Li, Yun; Song, Qing

    2014-01-01

    Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis. PMID:25052506

  16. sick: The Spectroscopic Inference Crank

    NASA Astrophysics Data System (ADS)

    Casey, Andrew R.

    2016-03-01

    There exists an inordinate amount of spectral data in both public and private astronomical archives that remain severely under-utilized. The lack of reliable open-source tools for analyzing large volumes of spectra contributes to this situation, which is poised to worsen as large surveys successively release orders of magnitude more spectra. In this article I introduce sick, the spectroscopic inference crank, a flexible and fast Bayesian tool for inferring astrophysical parameters from spectra. sick is agnostic to the wavelength coverage, resolving power, or general data format, allowing any user to easily construct a generative model for their data, regardless of its source. sick can be used to provide a nearest-neighbor estimate of model parameters, a numerically optimized point estimate, or full Markov Chain Monte Carlo sampling of the posterior probability distributions. This generality empowers any astronomer to capitalize on the plethora of published synthetic and observed spectra, and make precise inferences for a host of astrophysical (and nuisance) quantities. Model intensities can be reliably approximated from existing grids of synthetic or observed spectra using linear multi-dimensional interpolation, or a Cannon-based model. Additional phenomena that transform the data (e.g., redshift, rotational broadening, continuum, spectral resolution) are incorporated as free parameters and can be marginalized away. Outlier pixels (e.g., cosmic rays or poorly modeled regimes) can be treated with a Gaussian mixture model, and a noise model is included to account for systematically underestimated variance. Combining these phenomena into a scalar-justified, quantitative model permits precise inferences with credible uncertainties on noisy data. I describe the common model features, the implementation details, and the default behavior, which is balanced to be suitable for most astronomical applications. Using a forward model on low-resolution, high signal

  17. Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

    PubMed Central

    Martinez-Garcia, Manuel; Brazel, David M.; Swan, Brandon K.; Arnosti, Carol; Chain, Patrick S. G.; Reitenga, Krista G.; Xie, Gary; Poulton, Nicole J.; Gomez, Monica Lluesma; Masland, Dashiell E. D.; Thompson, Brian; Bellows, Wendy K.; Ziervogel, Kai; Lo, Chien-Chi; Ahmed, Sanaa; Gleasner, Cheryl D.; Detter, Chris J.; Stepanauskas, Ramunas

    2012-01-01

    Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation. PMID:22536372

  18. Plant functional genomics

    NASA Astrophysics Data System (ADS)

    Holtorf, Hauke; Guitton, Marie-Christine; Reski, Ralf

    2002-04-01

    Functional genome analysis of plants has entered the high-throughput stage. The complete genome information from key species such as Arabidopsis thaliana and rice is now available and will further boost the application of a range of new technologies to functional plant gene analysis. To broadly assign functions to unknown genes, different fast and multiparallel approaches are currently used and developed. These new technologies are based on known methods but are adapted and improved to accommodate for comprehensive, large-scale gene analysis, i.e. such techniques are novel in the sense that their design allows researchers to analyse many genes at the same time and at an unprecedented pace. Such methods allow analysis of the different constituents of the cell that help to deduce gene function, namely the transcripts, proteins and metabolites. Similarly the phenotypic variations of entire mutant collections can now be analysed in a much faster and more efficient way than before. The different methodologies have developed to form their own fields within the functional genomics technological platform and are termed transcriptomics, proteomics, metabolomics and phenomics. Gene function, however, cannot solely be inferred by using only one such approach. Rather, it is only by bringing together all the information collected by different functional genomic tools that one will be able to unequivocally assign functions to unknown plant genes. This review focuses on current technical developments and their impact on the field of plant functional genomics. The lower plant Physcomitrella is introduced as a new model system for gene function analysis, owing to its high rate of homologous recombination.

  19. Thinking laterally about genomes.

    PubMed

    Ragan, Mark A

    2009-10-01

    Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT. PMID:20180279

  20. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.

    PubMed

    Thrash, J Cameron; Temperton, Ben; Swan, Brandon K; Landry, Zachary C; Woyke, Tanja; DeLong, Edward F; Stepanauskas, Ramunas; Giovannoni, Stephan J

    2014-07-01

    Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size. PMID:24451205

  1. Quantum Inference on Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Yoder, Theodore; Low, Guang Hao; Chuang, Isaac

    2014-03-01

    Because quantum physics is naturally probabilistic, it seems reasonable to expect physical systems to describe probabilities and their evolution in a natural fashion. Here, we use quantum computation to speedup sampling from a graphical probability model, the Bayesian network. A specialization of this sampling problem is approximate Bayesian inference, where the distribution on query variables is sampled given the values e of evidence variables. Inference is a key part of modern machine learning and artificial intelligence tasks, but is known to be NP-hard. Classically, a single unbiased sample is obtained from a Bayesian network on n variables with at most m parents per node in time (nmP(e) - 1 / 2) , depending critically on P(e) , the probability the evidence might occur in the first place. However, by implementing a quantum version of rejection sampling, we obtain a square-root speedup, taking (n2m P(e) -1/2) time per sample. The speedup is the result of amplitude amplification, which is proving to be broadly applicable in sampling and machine learning tasks. In particular, we provide an explicit and efficient circuit construction that implements the algorithm without the need for oracle access.

  2. Genome walking.

    PubMed

    Shapter, Frances M; Waters, Daniel L E

    2014-01-01

    Genome walking is a method for determining the DNA sequence of unknown genomic regions flanking a region of known DNA sequence. The Genome walking has the potential to capture 6-7 kb of sequence in a single round. Ideal for identifying gene promoter regions where only the coding region. Genome walking also has significant utility for capturing homologous genes in new species when there are areas in the target gene with strong sequence conservation to the characterized species. The increasing use of next-generation sequencing technologies will see the principles of genome walking adapted to in silico methods. However, for smaller projects, PCR-based genome walking will remain an efficient method of characterizing unknown flanking sequence. PMID:24243201

  3. Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

    PubMed Central

    Harris, Kelley; Nielsen, Rasmus

    2013-01-01

    There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure. PMID:23754952

  4. Bayesian Inference of Tumor Hypoxia

    NASA Astrophysics Data System (ADS)

    Gunawan, R.; Tenti, G.; Sivaloganathan, S.

    2009-12-01

    Tumor hypoxia is a state of oxygen deprivation in tumors. It has been associated with aggressive tumor phenotypes and with increased resistance to conventional cancer therapies. In this study, we report on the application of Bayesian sequential analysis in estimating the most probable value of tumor hypoxia quantification based on immunohistochemical assays of a biomarker. The `gold standard' of tumor hypoxia assessment is a direct measurement of pO2 in vivo by the Eppendorf polarographic electrode, which is an invasive technique restricted to accessible sites and living tissues. An attractive alternative is immunohistochemical staining to detect proteins expressed by cells during hypoxia. Carbonic anhydrase IX (CAIX) is an enzyme expressed on the cell membrane during hypoxia to balance the immediate extracellular microenvironment. CAIX is widely regarded as a surrogate marker of chronic hypoxia in various cancers. The study was conducted with two different experimental procedures. The first data set was a group of three patients with invasive cervical carcinomas, from which five biopsies were obtained. Each of the biopsies was fully sectioned and from each section, the proportion of CAIX-positive cells was estimated. Measurements were made by image analysis of multiple deep sections cut through these biopsies, labeled for CAIX using both immunofluorescence and immunohistochemical techniques [1]. The second data set was a group of 24 patients, also with invasive cervical carcinomas, from which two biopsies were obtained. Bayesian parameter estimation was applied to obtain a reliable inference about the proportion of CAIX-positive cells within the carcinomas, based on the available biopsies. From the first data set, two to three biopsies were found to be sufficient to infer the overall CAIX percentage in the simple form: best estimate±uncertainty. The second data-set led to a similar result in 70% of the cases. In the remaining cases Bayes' theorem warned us

  5. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  6. Shannon Information in Complete Genomes

    NASA Astrophysics Data System (ADS)

    Hsieh, Li-Ching; Chang, Chang-Heng; Lee, Hoong-Chien

    2004-03-01

    Genomes are books of life and necessarily carry a huge amount of information. This study was first motivated by the question: "How much information do complete genomes have?" As an answer we measured a particular type of Shannon information in all prokaryotes and eukaryotes whose complete genomes have been sequenced and are available in publically assessible database. The Shannon information in complete genome sequences follow an extremely simple pattern. With the exception of one eukaryote the Shannon information in all (more than 200) complete sequences belong to a single universality class given by a simple geometric recursion formula. The data are interpreted in terms of models for genome growth and inferred to suggest that the ancestors of present day genomes began to grow, mainly by stochastic, selectively neutral, duplications and short mutations, most likely when they were not more than 300 nt long. This notion of selective neutralism independently corroborates Kimura's neutral theory of evolution which was based on the investigation of polymorphisms of genes.

  7. Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing.

    PubMed

    Klindworth, Anna; Mann, Alexander J; Huang, Sixing; Wichels, Antje; Quast, Christian; Waldmann, Jost; Teeling, Hanno; Glöckner, Frank Oliver

    2014-12-01

    A recent investigation of bacterioplankton communities in the German Bight towards the end of a diatom-dominated spring phytoplankton bloom revealed pronounced successions of distinct bacterial clades. A combination of metagenomics and metaproteomics indicated that these clades had distinct substrate spectra and consumed different algal substrates. In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing. This complementary approach provided new insights into the community composition and expressed genes as well as the assessment of metabolic activity levels of distinct clades. Flavobacteria (genera Ulvibacter, Formosa, and Polaribacter), Alphaproteobacteria (SAR11 clade and Rhodobacteraceae) and Gammaproteobacteria (genus Reinekea and SAR92 clade) were the most abundant taxa. Mapping of the metatranscriptome data on assembled and taxonomically classified metagenome data of the same samples substantiated that Formosa and Polaribacter acted as major algal polymer degraders, whereas Rhodobacteraceae and Reinekea spp. exhibited less specialized substrate spectra. In addition, we found that members of the Rhodobacteraceae and SAR92 clade showed high metabolic activity levels, which suggests that these clades played a more important role during the bloom event as indicated by their in situ abundances. PMID:25211053

  8. Enhanced viral production and virus-mediated mortality of bacterioplankton in a natural iron-fertilized bloom event above the Kerguelen Plateau

    NASA Astrophysics Data System (ADS)

    Malits, A.; Christaki, U.; Obernosterer, I.; Weinbauer, M. G.

    2014-07-01

    Above the Kerguelen Plateau in the Southern Ocean natural iron fertilization sustains a large phytoplankton bloom over three months during austral summer. During the KEOPS1 project (KErguelen Ocean and Plateau compared Study1) we sampled this phytoplankton bloom during its declining phase along with the surrounding HNLC waters to study the effect of natural iron fertilization on the role of viruses in the microbial food web. Bacterial and viral abundances were 1.7 and 2.1 times, respectively, higher within the bloom than in HNLC waters. Viral production and virus-mediated mortality of bacterioplankton was 4.1 and 4.9 times, respectively, higher in the bloom, while the fraction of infected cells (FIC) and the fraction of lysogenic cells (FLC) showed no significant differences between environments. The present study suggests viruses to be more important for bacterial mortality within the bloom and dominate over protozoan grazing during the late bloom phase. As a consequence, at least at a late bloom stage, viral lysis shunts part of the photosynthetically fixed carbon in iron-fertilized regions into the dissolved organic matter (DOM) pool with potentially less particulate organic carbon transfered to larger members of the food web or exported.

  9. Enhanced viral production and virus-mediated mortality of bacterioplankton in a natural iron-fertilized bloom event above the Kerguelen Plateau

    NASA Astrophysics Data System (ADS)

    Malits, A.; Christaki, U.; Obernosterer, I.; Weinbauer, M. G.

    2014-12-01

    Above the Kerguelen Plateau in the Southern Ocean natural iron fertilization sustains a large phytoplankton bloom over 3 months during austral summer. During the KEOPS1 project (KErguelen Ocean and Plateau compared Study1) we sampled this phytoplankton bloom during its declining phase along with the surrounding high-nutrient-low-chlorophyll (HNLC) waters to study the effect of natural iron fertilization on the role of viruses in the microbial food web. Bacterial and viral abundances were 1.7 and 2.1 times, respectively, higher within the bloom than in HNLC waters. Viral production and virus-mediated mortality of bacterioplankton were 4.1 and 4.9 times, respectively, higher in the bloom, while the fraction of infected cells (FIC) and the fraction of lysogenic cells (FLC) showed no significant differences between environments. The present study suggests viruses to be more important for bacterial mortality within the bloom and dominate over grazing of heterotrophic nanoflagellates (HNFs) during the late bloom phase. As a consequence, at least at a late bloom stage, viral lysis shunts part of the photosynthetically fixed carbon in iron-fertilized regions into the dissolved organic matter (DOM) pool with potentially less particulate organic carbon transferred to larger members of the food web or exported.

  10. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.

    PubMed Central

    Ovreås, L; Forney, L; Daae, F L; Torsvik, V

    1997-01-01

    The community structure of bacterioplankton in meromictic Lake Saelenvannet was examined by PCR amplification of the V3 region of 16S rRNA from microbial communities recovered from various depths in the water column. Two different primer sets were used, one for amplification of DNA from the domain Bacteria and another specific for DNA from the domain Archaea. Amplified DNA fragments were resolved by denaturing gradient gel electrophoresis (DGGE), and the resulting profiles were reproducible and specific for the communities from different depths. Bacterial diversity estimated from the number and intensity of specific fragments in DGGE profiles decreased with depth. The reverse was true for the Archaea, with the diversity increasing with depth. Hybridization of DGGE profiles with oligonucleotide probes specific for phylogenetic groups of microorganisms showed the presence of both sulfate-reducing bacteria and methanogens throughout the water column, but they appeared to be most abundant below the chemocline. Several dominant fragments in the DGGE profiles were excised and sequenced. Among the dominant populations were representatives related to Chlorobium phaeovibrioides, chloroplasts from eukaryotic algae, and unidentified Archaea. PMID:9292986

  11. Infering Networks From Collective Dynamics

    NASA Astrophysics Data System (ADS)

    Timme, Marc

    How can we infer direct physical interactions between pairs of units from only knowing the units' time series? Here we present a dynamical systems' view on collective network dynamics, and propose the concept of a dynamics' space to reveal interaction networks from time series. We present two examples: one, where the time series stem from standard ordinary differential equations, and a second, more abstract, where the time series exhibits only partial information about the units' states. We apply the latter to neural circuit dynamics where the observables are spike timing data, i.e. only a discrete, state-dependent outputs of the neurons. These results may help revealing network structure for systems where direct access to dynamics is simpler than to connectivity, cf.. This is work with Jose Casadiego, Srinivas Gorur Shandilya, Mor Nitzan, Hauke Haehne and Dimitra Maoutsa. Supported by Grants of the BMBF (Future Compliant Power Grids - CoNDyNet) and by the Max Planck Society to MT.

  12. Inferred properties of stellar granulation

    SciTech Connect

    Gray, D.F.; Toner, C.G.

    1985-06-01

    Apparent characteristics of stellar granulation in F and G main-sequence stars are inferred directly from observed spectral-line asymmetries and from comparisons of numerical simulations with the observations: (1) the apparent granulation velocity increases with effective temperature, (2) the dispersion of granule velocities about their mean velocity of rise increases with the apparent granulation velocity, (3) the mean velocity of rise of granules must be less than the total line broadening, (4) the apparent velocity difference between granules and dark lanes corresponds to the granulation velocity deduced from stellar line bisectors, (5) the dark lanes show velocities of fall approximately twice as large as the granule rise velocities, (6) the light contributed to the stellar flux by the granules is four to ten times more than the light from the dark lanes. Stellar rotation is predicted to produce distortions in the line bisectors which may give information on the absolute velocity displacements of the line bisectors. 37 references.

  13. Structural inference for uncertain networks

    NASA Astrophysics Data System (ADS)

    Martin, Travis; Ball, Brian; Newman, M. E. J.

    2016-01-01

    In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a certain probability. In this paper we develop methods for the analysis of such uncertain data, focusing particularly on the problem of community detection. We give a principled maximum-likelihood method for inferring community structure and demonstrate how the results can be used to make improved estimates of the true structure of the network. Using computer-generated benchmark networks we demonstrate that our methods are able to reconstruct known communities more accurately than previous approaches based on data thresholding. We also give an example application to the detection of communities in a protein-protein interaction network.

  14. Transdimensional inference in the geosciences.

    PubMed

    Sambridge, M; Bodin, T; Gallagher, K; Tkalcic, H

    2013-02-13

    Seismologists construct images of the Earth's interior structure using observations, derived from seismograms, collected at the surface. A common approach to such inverse problems is to build a single 'best' Earth model, in some sense. This is despite the fact that the observations by themselves often do not require, or even allow, a single best-fit Earth model to exist. Interpretation of optimal models can be fraught with difficulties, particularly when formal uncertainty estimates become heavily dependent on the regularization imposed. Similar issues occur across the physical sciences with model construction in ill-posed problems. An alternative approach is to embrace the non-uniqueness directly and employ an inference process based on parameter space sampling. Instead of seeking a best model within an optimization framework, one seeks an ensemble of solutions and derives properties of that ensemble for inspection. While this idea has itself been employed for more than 30 years, it is now receiving increasing attention in the geosciences. Recently, it has been shown that transdimensional and hierarchical sampling methods have some considerable benefits for problems involving multiple parameter types, uncertain data errors and/or uncertain model parametrizations, as are common in seismology. Rather than being forced to make decisions on parametrization, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Despite the relatively high computational burden involved, the number of areas where sampling methods are now feasible is growing rapidly. The intention of this article is to introduce concepts of transdimensional inference to a general readership and illustrate with particular seismological examples. A growing body of references provide necessary detail. PMID:23277604

  15. Bayesian Nonparametric Inference – Why and How

    PubMed Central

    Müller, Peter; Mitra, Riten

    2013-01-01

    We review inference under models with nonparametric Bayesian (BNP) priors. The discussion follows a set of examples for some common inference problems. The examples are chosen to highlight problems that are challenging for standard parametric inference. We discuss inference for density estimation, clustering, regression and for mixed effects models with random effects distributions. While we focus on arguing for the need for the flexibility of BNP models, we also review some of the more commonly used BNP models, thus hopefully answering a bit of both questions, why and how to use BNP. PMID:24368932

  16. Inference engine using optical array logic

    NASA Astrophysics Data System (ADS)

    Iwata, Masaya; Tanida, Jun; Ichioka, Yoshiki

    1990-07-01

    An implementation method for an inference engine using optical array logic is presented. Optical array logic is a technique for parallel neighborhood operation using spatial coding and 2-D correlation. For efficient execution of inference in artificial intelligence problems, a large number of data must be searched effectively. To achieve this demand, a template matching technique is applied to the inference operation. By introducing a new function of data conversion, the inference operation can be implemented with optical array logic, which utilizes parallelism in optical techniques.

  17. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  18. A new molecular approach to help conclude drowning as a cause of death: simultaneous detection of eight bacterioplankton species using real-time PCR assays with TaqMan probes.

    PubMed

    Uchiyama, Taketo; Kakizaki, Eiji; Kozawa, Shuji; Nishida, Sho; Imamura, Nahoko; Yukawa, Nobuhiro

    2012-10-10

    We developed a novel tool for concluding drowning as a cause of death. We designed nine primer pairs to detect representative freshwater or marine bacterioplankton (aquatic bacteria) and then used real-time PCR with TaqMan probes to rapidly and specifically detect them. We previously cultured the genus Aeromonas, which is a representative freshwater bacterial species, in blood samples from 94% of victims who drowned in freshwater and the genera Vibrio and/or Photobacterium that are representative marine bacteria in 88% of victims who drowned in seawater. Based on these results, we simultaneously detected eight species of bacterioplankton (Aeromonas hydrophila, A. salmonicida; Vibrio fischeri, V. harveyi, V. parahaemolyticus; Photobacterium damselae, P. leiognathi, P. phosphoreum) using three sets of triplex real-time PCR assays and TaqMan probes labelled with fluorophores (FAM, NED, Cy5). We assayed 266 specimens (109 blood, 157 tissues) from 43 victims, including 32 who had drowned in rivers, ditches, wells, sea or around estuaries. All lung samples of these 32 victims were TaqMan PCR-positive including the lung periphery into which water does not readily enter postmortem. On the other hand, findings in blood and/or closed organs (kidney or liver) were PCR-positive in 84% of the drowned victims (except for those who drowned in baths) although the conventional test detected diatoms in closed organs in only 44% of the victims. Thus, the results of the PCR assay reinforced those of diatom tests when only a few diatoms were detectable in organs due to the low density of diatoms in the water where they were found. Multiplex TaqMan PCR assays for bacterioplankton were rapid, less laborious and high-throughput as well as sensitive and specific. Therefore, these assays would be useful for routine forensic screening tests to estimate the amount and type of aspirated water. PMID:22682932

  19. Protein inference: A protein quantification perspective.

    PubMed

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/. PMID:26935399

  20. The Passive Yet Successful Way of Planktonic Life: Genomic and Experimental Analysis of the Ecology of a Free-Living Polynucleobacter Population

    PubMed Central

    Hahn, Martin W.; Scheuerl, Thomas; Jezberová, Jitka; Koll, Ulrike; Jezbera, Jan; Šimek, Karel; Vannini, Claudia; Petroni, Giulio; Wu, Qinglong L.

    2012-01-01

    Background The bacterial taxon Polynucleobacter necessarius subspecies asymbioticus represents a group of planktonic freshwater bacteria with cosmopolitan and ubiquitous distribution in standing freshwater habitats. These bacteria comprise <1% to 70% (on average about 20%) of total bacterioplankton cells in various freshwater habitats. The ubiquity of this taxon was recently explained by intra-taxon ecological diversification, i.e. specialization of lineages to specific environmental conditions; however, details on specific adaptations are not known. Here we investigated by means of genomic and experimental analyses the ecological adaptation of a persistent population dwelling in a small acidic pond. Findings The investigated population (F10 lineage) contributed on average 11% to total bacterioplankton in the pond during the vegetation periods (ice-free period, usually May to November). Only a low degree of genetic diversification of the population could be revealed. These bacteria are characterized by a small genome size (2.1 Mb), a relatively small number of genes involved in transduction of environmental signals, and the lack of motility and quorum sensing. Experiments indicated that these bacteria live as chemoorganotrophs by mainly utilizing low-molecular-weight substrates derived from photooxidation of humic substances. Conclusions Evolutionary genome streamlining resulted in a highly passive lifestyle so far only known among free-living bacteria from pelagic marine taxa dwelling in environmentally stable nutrient-poor off-shore systems. Surprisingly, such a lifestyle is also successful in a highly dynamic and nutrient-richer environment such as the water column of the investigated pond, which was undergoing complete mixis and pronounced stratification in diurnal cycles. Obviously, metabolic and ecological versatility is not a prerequisite for long-lasting establishment of abundant bacterial populations under highly dynamic environmental conditions. Caution

  1. Forward and Backward Inference in Spatial Cognition

    PubMed Central

    Penny, Will D.; Zeidman, Peter; Burgess, Neil

    2013-01-01

    This paper shows that the various computations underlying spatial cognition can be implemented using statistical inference in a single probabilistic model. Inference is implemented using a common set of ‘lower-level’ computations involving forward and backward inference over time. For example, to estimate where you are in a known environment, forward inference is used to optimally combine location estimates from path integration with those from sensory input. To decide which way to turn to reach a goal, forward inference is used to compute the likelihood of reaching that goal under each option. To work out which environment you are in, forward inference is used to compute the likelihood of sensory observations under the different hypotheses. For reaching sensory goals that require a chaining together of decisions, forward inference can be used to compute a state trajectory that will lead to that goal, and backward inference to refine the route and estimate control signals that produce the required trajectory. We propose that these computations are reflected in recent findings of pattern replay in the mammalian brain. Specifically, that theta sequences reflect decision making, theta flickering reflects model selection, and remote replay reflects route and motor planning. We also propose a mapping of the above computational processes onto lateral and medial entorhinal cortex and hippocampus. PMID:24348230

  2. Inferring Learners' Knowledge from Their Actions

    ERIC Educational Resources Information Center

    Rafferty, Anna N.; LaMar, Michelle M.; Griffiths, Thomas L.

    2015-01-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we…

  3. Local and Global Thinking in Statistical Inference

    ERIC Educational Resources Information Center

    Pratt, Dave; Johnston-Wilder, Peter; Ainley, Janet; Mason, John

    2008-01-01

    In this reflective paper, we explore students' local and global thinking about informal statistical inference through our observations of 10- to 11-year-olds, challenged to infer the unknown configuration of a virtual die, but able to use the die to generate as much data as they felt necessary. We report how they tended to focus on local changes…

  4. The Impact of Disablers on Predictive Inference

    ERIC Educational Resources Information Center

    Cummins, Denise Dellarosa

    2014-01-01

    People consider alternative causes when deciding whether a cause is responsible for an effect (diagnostic inference) but appear to neglect them when deciding whether an effect will occur (predictive inference). Five experiments were conducted to test a 2-part explanation of this phenomenon: namely, (a) that people interpret standard predictive…

  5. Causal Inferences during Text Comprehension and Production.

    ERIC Educational Resources Information Center

    Kemper, Susan

    As comprehension failure results whenever readers are unable to infer missing causal connections, recent comprehension research has focused both on assessing the inferential complexity of texts and on investigating students' developing ability to infer causal relationships. Studies have demonstrated that texts rely on four types of causal…

  6. Scalar Inferences in Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Chevallier, Coralie; Wilson, Deirdre; Happe, Francesca; Noveck, Ira

    2010-01-01

    On being told "John or Mary will come", one might infer that "not both" of them will come. Yet the semantics of "or" is compatible with a situation where both John and Mary come. Inferences of this type, which enrich the semantics of "or" from an "inclusive" to an "exclusive" interpretation, have been extensively studied in linguistic pragmatics.…

  7. Genetic Network Inference Using Hierarchical Structure.

    PubMed

    Kimura, Shuhei; Tokuhisa, Masato; Okada-Hatakeyama, Mariko

    2016-01-01

    Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives. Several researchers have attempted to reduce these erroneous regulations by proposing the use of a priori knowledge about the properties of genetic networks such as their sparseness, scale-free structure, and so on. This study focuses on another piece of a priori knowledge, namely, that biochemical networks exhibit hierarchical structures. Based on this idea, we propose an inference approach that uses the hierarchical structure in a target genetic network. To obtain a reasonable hierarchical structure, the first step of the proposed approach is to infer multiple genetic networks from the observed gene expression data. We take this step using an existing method that combines a genetic network inference method with a bootstrap method. The next step is to extract a hierarchical structure from the inferred networks that is consistent with most of the networks. Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations. Numerical experiments are also performed to demonstrate the effectiveness of using the hierarchical structure in the genetic network inference. The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods. PMID:26941653

  8. The Reasoning behind Informal Statistical Inference

    ERIC Educational Resources Information Center

    Makar, Katie; Bakker, Arthur; Ben-Zvi, Dani

    2011-01-01

    Informal statistical inference (ISI) has been a frequent focus of recent research in statistics education. Considering the role that context plays in developing ISI calls into question the need to be more explicit about the reasoning that underpins ISI. This paper uses educational literature on informal statistical inference and philosophical…

  9. Reinforcement learning or active inference?

    PubMed

    Friston, Karl J; Daunizeau, Jean; Kiebel, Stefan J

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  10. Reinforcement Learning or Active Inference?

    PubMed Central

    Friston, Karl J.; Daunizeau, Jean; Kiebel, Stefan J.

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain. PMID:19641614

  11. Causal Inference in Public Health

    PubMed Central

    Glass, Thomas A.; Goodman, Steven N.; Hernán, Miguel A.; Samet, Jonathan M.

    2014-01-01

    Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world. PMID:23297653

  12. Active inference and epistemic value.

    PubMed

    Friston, Karl; Rigoli, Francesco; Ognibene, Dimitri; Mathys, Christoph; Fitzgerald, Thomas; Pezzulo, Giovanni

    2015-01-01

    We offer a formal treatment of choice behavior based on the premise that agents minimize the expected free energy of future outcomes. Crucially, the negative free energy or quality of a policy can be decomposed into extrinsic and epistemic (or intrinsic) value. Minimizing expected free energy is therefore equivalent to maximizing extrinsic value or expected utility (defined in terms of prior preferences or goals), while maximizing information gain or intrinsic value (or reducing uncertainty about the causes of valuable outcomes). The resulting scheme resolves the exploration-exploitation dilemma: Epistemic value is maximized until there is no further information gain, after which exploitation is assured through maximization of extrinsic value. This is formally consistent with the Infomax principle, generalizing formulations of active vision based upon salience (Bayesian surprise) and optimal decisions based on expected utility and risk-sensitive (Kullback-Leibler) control. Furthermore, as with previous active inference formulations of discrete (Markovian) problems, ad hoc softmax parameters become the expected (Bayes-optimal) precision of beliefs about, or confidence in, policies. This article focuses on the basic theory, illustrating the ideas with simulations. A key aspect of these simulations is the similarity between precision updates and dopaminergic discharges observed in conditioning paradigms. PMID:25689102

  13. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  14. Inference-based constraint satisfaction supports explanation

    SciTech Connect

    Sqalli, M.H.; Freuder, E.C.

    1996-12-31

    Constraint satisfaction problems are typically solved using search, augmented by general purpose consistency inference methods. This paper proposes a paradigm shift in which inference is used as the primary problem solving method, and attention is focused on special purpose, domain specific inference methods. While we expect this approach to have computational advantages, we emphasize here the advantages of a solution method that is more congenial to human thought processes. Specifically we use inference-based constraint satisfaction to support explanations of the problem solving behavior that are considerably more meaningful than a trace of a search process would be. Logic puzzles are used as a case study. Inference-based constraint satisfaction proves surprisingly powerful and easily extensible in this domain. Problems drawn from commercial logic puzzle booklets are used for evaluation. Explanations are produced that compare well with the explanations provided by these booklets.

  15. Comparative genomics of protoploid Saccharomycetaceae.

    PubMed

    Souciet, Jean-Luc; Dujon, Bernard; Gaillardin, Claude; Johnston, Mark; Baret, Philippe V; Cliften, Paul; Sherman, David J; Weissenbach, Jean; Westhof, Eric; Wincker, Patrick; Jubin, Claire; Poulain, Julie; Barbe, Valérie; Ségurens, Béatrice; Artiguenave, François; Anthouard, Véronique; Vacherie, Benoit; Val, Marie-Eve; Fulton, Robert S; Minx, Patrick; Wilson, Richard; Durrens, Pascal; Jean, Géraldine; Marck, Christian; Martin, Tiphaine; Nikolski, Macha; Rolland, Thomas; Seret, Marie-Line; Casarégola, Serge; Despons, Laurence; Fairhead, Cécile; Fischer, Gilles; Lafontaine, Ingrid; Leh, Véronique; Lemaire, Marc; de Montigny, Jacky; Neuvéglise, Cécile; Thierry, Agnès; Blanc-Lenfle, Isabelle; Bleykasten, Claudine; Diffels, Julie; Fritsch, Emilie; Frangeul, Lionel; Goëffon, Adrien; Jauniaux, Nicolas; Kachouri-Lafond, Rym; Payen, Célia; Potier, Serge; Pribylova, Lenka; Ozanne, Christophe; Richard, Guy-Franck; Sacerdot, Christine; Straub, Marie-Laure; Talla, Emmanuel

    2009-10-01

    Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified. PMID:19525356

  16. Genomic Testing

    MedlinePlus

    ... Working Group Independent Web site Informing the effective integration of genomics into health practice—Lynch syndrome ACCE Model for Evaluating Genetic Tests Recommendations by the EGAPP Working Group Top of ... ...

  17. Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord

    NASA Astrophysics Data System (ADS)

    Sperling, M.; Piontek, J.; Gerdts, G.; Wichels, A.; Schunck, H.; Roy, A.-S.; La Roche, J.; Gilbert, J.; Nissimov, J. I.; Bittner, L.; Romac, S.; Riebesell, U.; Engel, A.

    2013-01-01

    In the frame of the European Project on Ocean Acidification (EPOCA), the response of an Arctic pelagic community (<3 mm) to a gradient of seawater pCO2 was investigated. For this purpose 9 large-scale in situ mesocosms were deployed in Kongsfjorden, Svalbard (78°56.2´ N, 11°53.6´ E), in 2010. The present study investigates effects on the communities of particle-attached (PA; >3 μm) and free-living (FL; < 3 μm > 0.2 μm) bacteria by Automated Ribosomal Intergenic Spacer Analysis (ARISA) in 6 of the mesocosms, ranging from 185 to 1050 μatm initial pCO2, and the surrounding fjord. ARISA was able to resolve, on average, 27 bacterial band classes per sample and allowed for a detailed investigation of the explicit richness and diversity. Both, the PA and the FL bacterioplankton community exhibited a strong temporal development, which was driven mainly by temperature and phytoplankton development. In response to the breakdown of a picophytoplankton bloom, numbers of ARISA band classes in the PA community were reduced at low and medium CO2 (~ 185-685 μatm) by about 25%, while they were more or less stable at high CO2 (~ 820-1050 μatm). We hypothesise that enhanced viral lysis and enhanced availability of organic substrates at high CO2 resulted in a more diverse PA bacterial community in the post-bloom phase. Despite lower cell numbers and extracellular enzyme activities in the post-bloom phase, bacterial protein production was enhanced in high CO2 mesocosms, suggesting a positive effect of community richness on this function and on carbon cycling by bacteria.

  18. Using ancient DNA and coalescent-based methods to infer extinction.

    PubMed

    Chang, Dan; Shapiro, Beth

    2016-02-01

    DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction. PMID:26864783

  19. The Inference of Gene Trees with Species Trees

    PubMed Central

    Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

    2015-01-01

    This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

  20. My sister's keeper?: genomic research and the identifiability of siblings

    PubMed Central

    Cassa, Christopher A; Schmidt, Brian; Kohane, Isaac S; Mandl, Kenneth D

    2008-01-01

    Background Genomic sequencing of SNPs is increasingly prevalent, though the amount of familial information these data contain has not been quantified. Methods We provide a framework for measuring the risk to siblings of a patient's SNP genotype disclosure, and demonstrate that sibling SNP genotypes can be inferred with substantial accuracy. Results Extending this inference technique, we determine that a very low number of matches at commonly varying SNPs is sufficient to confirm sib-ship, demonstrating that published sequence data can reliably be used to derive sibling identities. Using HapMap trio data, at SNPs where one child is homozygotic major, with a minor allele frequency ≤ 0.20, (N = 452684, 65.1%) we achieve 91.9% inference accuracy for sibling genotypes. Conclusion These findings demonstrate that substantial discrimination and privacy risks arise from use of inferred familial genomic data. PMID:18655711

  1. The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

    PubMed Central

    Nabhan, Ahmed Ragab

    2012-01-01

    Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis. PMID:21436145

  2. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis.

    PubMed

    Stahl, Eli A; Wegmann, Daniel; Trynka, Gosia; Gutierrez-Achury, Javier; Do, Ron; Voight, Benjamin F; Kraft, Peter; Chen, Robert; Kallberg, Henrik J; Kurreeman, Fina A S; Kathiresan, Sekar; Wijmenga, Cisca; Gregersen, Peter K; Alfredsson, Lars; Siminovitch, Katherine A; Worthington, Jane; de Bakker, Paul I W; Raychaudhuri, Soumya; Plenge, Robert M

    2012-05-01

    The genetic architectures of common, complex diseases are largely uncharacterized. We modeled the genetic architecture underlying genome-wide association study (GWAS) data for rheumatoid arthritis and developed a new method using polygenic risk-score analyses to infer the total liability-scale variance explained by associated GWAS SNPs. Using this method, we estimated that, together, thousands of SNPs from rheumatoid arthritis GWAS explain an additional 20% of disease risk (excluding known associated loci). We further tested this method on datasets for three additional diseases and obtained comparable estimates for celiac disease (43% excluding the major histocompatibility complex), myocardial infarction and coronary artery disease (48%) and type 2 diabetes (49%). Our results are consistent with simulated genetic models in which hundreds of associated loci harbor common causal variants and a smaller number of loci harbor multiple rare causal variants. These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases. PMID:22446960

  3. Linguistic Markers of Inference Generation While Reading.

    PubMed

    Clinton, Virginia; Carlson, Sarah E; Seipel, Ben

    2016-06-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students ([Formula: see text]) reading narrative texts were hand-coded for inferences. These data were also processed with a computer text analysis tool, Linguistic Inquiry and Word Count, for percentages of word use in the following categories: cognitive mechanism words, nonfluencies, and nine types of function words. Findings indicate that cognitive mechanisms were an independent, positive predictor of connections to background knowledge (i.e., elaborative inference generation) and nonfluencies were an independent, negative predictor of connections within the text (i.e., bridging inference generation). Function words did not provide unique variance towards predicting inference generation. These findings are discussed in the context of a cognitive reflection model and the differences between bridging and elaborative inference generation. In addition, potential practical implications for intelligent tutoring systems and computer-based methods of inference identification are presented. PMID:25833811

  4. Statistical Physics of High Dimensional Inference

    NASA Astrophysics Data System (ADS)

    Advani, Madhu; Ganguli, Surya

    To model modern large-scale datasets, we need efficient algorithms to infer a set of P unknown model parameters from N noisy measurements. What are fundamental limits on the accuracy of parameter inference, given limited measurements, signal-to-noise ratios, prior information, and computational tractability requirements? How can we combine prior information with measurements to achieve these limits? Classical statistics gives incisive answers to these questions as the measurement density α =N/P --> ∞ . However, modern high-dimensional inference problems, in fields ranging from bio-informatics to economics, occur at finite α. We formulate and analyze high-dimensional inference analytically by applying the replica and cavity methods of statistical physics where data serves as quenched disorder and inferred parameters play the role of thermal degrees of freedom. Our analysis reveals that widely cherished Bayesian inference algorithms such as maximum likelihood and maximum a posteriori are suboptimal in the modern setting, and yields new tractable, optimal algorithms to replace them as well as novel bounds on the achievable accuracy of a large class of high-dimensional inference algorithms. Thanks to Stanford Graduate Fellowship and Mind Brain Computation IGERT grant for support.

  5. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure.

    PubMed

    Hanemaaijer, Mark; Röling, Wilfred F M; Olivier, Brett G; Khandelwal, Ruchir A; Teusink, Bas; Bruggeman, Frank J

    2015-01-01

    Microbial communities play important roles in health, industrial applications and earth's ecosystems. With current molecular techniques we can characterize these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the genetic properties and the dynamic couplings between individual microorganisms give rise to their dynamic activities. Neither do they give insight into what we call "the community state", that is the fluxes and concentrations of nutrients within the community. This knowledge is a prerequisite for rational control and intervention in microbial communities. Therefore, the inference of the community structure from experimental data is a major current challenge. We will argue that this inference problem requires mathematical models that can integrate heterogeneous experimental data with existing knowledge. We propose that two types of models are needed. Firstly, mathematical models that integrate existing genomic, physiological, and physicochemical information with metagenomics data so as to maximize information content and predictive power. This can be achieved with the use of constraint-based genome-scale stoichiometric modeling of community metabolism which is ideally suited for this purpose. Next, we propose a simpler coarse-grained model, which is tailored to solve the inference problem from the experimental data. This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators. The simpler inference models are, in our opinion, key to understanding microbial ecosystems, yet until now, have received remarkably little attention. This has led to the situation where the modeling of microbial communities, using only genome-scale models is currently more a computational, theoretical exercise than a method useful to the experimentalist. PMID:25852671

  6. Inference and the introductory statistics course

    NASA Astrophysics Data System (ADS)

    Pfannkuch, Maxine; Regan, Matt; Wild, Chris; Budgett, Stephanie; Forbes, Sharleen; Harraway, John; Parsonage, Ross

    2011-10-01

    This article sets out some of the rationale and arguments for making major changes to the teaching and learning of statistical inference in introductory courses at our universities by changing from a norm-based, mathematical approach to more conceptually accessible computer-based approaches. The core problem of the inferential argument with its hypothetical probabilistic reasoning process is examined in some depth. We argue that the revolution in the teaching of inference must begin. We also discuss some perplexing issues, problematic areas and some new insights into language conundrums associated with introducing the logic of inference through randomization methods.

  7. An argument for mechanism-based statistical inference in cancer

    PubMed Central

    Ochs, Michael; Price, Nathan D.; Tomasetti, Cristian; Younes, Laurent

    2015-01-01

    Cancer is perhaps the prototypical systems disease, and as such has been the focus of extensive study in quantitative systems biology. However, translating these programs into personalized clinical care remains elusive and incomplete. In this perspective, we argue that realizing this agenda—in particular, predicting disease phenotypes, progression and treatment response for individuals—requires going well beyond standard computational and bioinformatics tools and algorithms. It entails designing global mathematical models over network-scale configurations of genomic states and molecular concentrations, and learning the model parameters from limited available samples of high-dimensional and integrative omics data. As such, any plausible design should accommodate: biological mechanism, necessary for both feasible learning and interpretable decision making; stochasticity, to deal with uncertainty and observed variation at many scales; and a capacity for statistical inference at the patient level. This program, which requires a close, sustained collaboration between mathematicians and biologists, is illustrated in several contexts, including learning bio-markers, metabolism, cell signaling, network inference and tumorigenesis. PMID:25381197

  8. Inferring admixture histories of human populations using linkage disequilibrium.

    PubMed

    Loh, Po-Ru; Lipson, Mark; Patterson, Nick; Moorjani, Priya; Pickrell, Joseph K; Reich, David; Berger, Bonnie

    2013-04-01

    Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese. PMID:23410830

  9. Degradation monitoring using probabilistic inference

    NASA Astrophysics Data System (ADS)

    Alpay, Bulent

    In order to increase safety and improve economy and performance in a nuclear power plant (NPP), the source and extent of component degradations should be identified before failures and breakdowns occur. It is also crucial for the next generation of NPPs, which are designed to have a long core life and high fuel burnup to have a degradation monitoring system in order to keep the reactor in a safe state, to meet the designed reactor core lifetime and to optimize the scheduled maintenance. Model-based methods are based on determining the inconsistencies between the actual and expected behavior of the plant, and use these inconsistencies for detection and diagnostics of degradations. By defining degradation as a random abrupt change from the nominal to a constant degraded state of a component, we employed nonlinear filtering techniques based on state/parameter estimation. We utilized a Bayesian recursive estimation formulation in the sequential probabilistic inference framework and constructed a hidden Markov model to represent a general physical system. By addressing the problem of a filter's inability to estimate an abrupt change, which is called the oblivious filter problem in nonlinear extensions of Kalman filtering, and the sample impoverishment problem in particle filtering, we developed techniques to modify filtering algorithms by utilizing additional data sources to improve the filter's response to this problem. We utilized a reliability degradation database that can be constructed from plant specific operational experience and test and maintenance reports to generate proposal densities for probable degradation modes. These are used in a multiple hypothesis testing algorithm. We then test samples drawn from these proposal densities with the particle filtering estimates based on the Bayesian recursive estimation formulation with the Metropolis Hastings algorithm, which is a well-known Markov chain Monte Carlo method (MCMC). This multiple hypothesis testing

  10. DINIES: drug–target interaction network inference engine based on supervised analysis

    PubMed Central

    Yamanishi, Yoshihiro; Kotera, Masaaki; Moriya, Yuki; Sawada, Ryusuke; Kanehisa, Minoru; Goto, Susumu

    2014-01-01

    DINIES (drug–target interaction network inference engine based on supervised analysis) is a web server for predicting unknown drug–target interaction networks from various types of biological data (e.g. chemical structures, drug side effects, amino acid sequences and protein domains) in the framework of supervised network inference. The originality of DINIES lies in prediction with state-of-the-art machine learning methods, in the integration of heterogeneous biological data and in compatibility with the KEGG database. The DINIES server accepts any ‘profiles’ or precalculated similarity matrices (or ‘kernels’) of drugs and target proteins in tab-delimited file format. When a training data set is submitted to learn a predictive model, users can select either known interaction information in the KEGG DRUG database or their own interaction data. The user can also select an algorithm for supervised network inference, select various parameters in the method and specify weights for heterogeneous data integration. The server can provide integrative analyses with useful components in KEGG, such as biological pathways, functional hierarchy and human diseases. DINIES (http://www.genome.jp/tools/dinies/) is publicly available as one of the genome analysis tools in GenomeNet. PMID:24838565

  11. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increa