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https://www.readbyqxmd.com/read/28923961/evolution-of-the-3-hydroxypropionate-bicycle-and-recent-transfer-of-anoxygenic-photosynthesis-into-the-chloroflexi
#1
Patrick M Shih, Lewis M Ward, Woodward W Fischer
Various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28923605/microbial-pathogenicity-and-virulence-mediated-by-integrons-on-gram-positive-microorganisms
#2
REVIEW
Yanmei Li, Ling Yang, Jie Fu, Muxia Yan, Dingqiang Chen, Li Zhang
Gram-positive microorganisms are one of leading pathogenic microorganisms in public health, including several typical "Super Bugs" as methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae carbapenemase and vancomycin-resistant enterococci, which caused a increasement of infections, clinical failures and expenses. Regarded as a common genetic element responsible for horizontal gene transfer, integrons are widely distributed in various pathogens considered as a determinant in the acquisition and evolution of antibiotic resistance...
September 15, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28923487/furcation-and-fusion-the-phylogenetics-of-evolutionary-novelty
#3
REVIEW
Todd H Oakley
Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study the history and provenance of novelty using phylogenetics, where key questions include when evolution occurs by tree-like branching and when it occurs by movement of distantly related parts in processes akin to horizontal transfer. Perfectly vertical inheritance, often an assumption of evolutionary trees, requires simultaneous co-duplication of the parts of a duplicating or speciating (processes I collectively call 'furcating') biological feature...
September 15, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28920507/navigating-the-structure-function-evolutionary-relationship-of-csaa-chaperone-in-archaea
#4
Archana Sharma, Shikha Rani, Manisha Goel
CsaA is a protein involved in the post-translational translocation of proteins across the cytoplasmic membrane. It is considered to be a functional homolog of SecB which participates in the Sec-dependent translocation pathway in an analogous manner. CsaA has also been reported to act as a molecular chaperone, preventing aggregation of unfolded proteins. It is essentially a prokaryotic protein which is absent in eukaryotes, but found extensively in bacteria and earlier thought to be widely present in archaea...
September 18, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28915794/genome-sequence-of-the-ectophytic-fungus-ramichloridium-luteum-reveals-unique-evolutionary-adaptations-to-plant-surface-niche
#5
Bo Wang, Xiaofei Liang, Mark L Gleason, Rong Zhang, Guangyu Sun
BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS: The R...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28914880/tremblaya-phenacola-pper-an-evolutionary-beta-gammaproteobacterium-collage
#6
Rosario Gil, Carlos Vargas-Chavez, Sergio López-Madrigal, Diego Santos-García, Amparo Latorre, Andrés Moya
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described...
September 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28912766/environmental-bacteriophages-of-the-emerging-enterobacterial-phytopathogen-dickeya-solani-show-genomic-conservation-and-capacity-for-horizontal-gene-transfer-between-their-bacterial-hosts
#7
Andrew Day, Jiyoon Ahn, Xinzhe Fang, George P C Salmond
Dickeya solani is an economically important phytopathogen widespread in mainland Europe that can reduce potato crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of this pathogen in the field, and limited field trials have been conducted. To date only a small number of bacteriophages capable of infecting D. solani have been isolated and characterized, and so there is a need to expand the repertoire of phages that may have potential utility in phage therapy strategies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28911112/integrative-and-conjugative-elements-and-their-hosts-composition-distribution-and-organization
#8
Jean Cury, Marie Touchon, Eduardo P C Rocha
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904264/zoonotic-potential-and-antibiotic-resistance-of-escherichia-coli-in-neonatal-calves-in-uruguay
#9
Ana Umpiérrez, Inés Bado, Martín Oliver, Sofía Acquistapace, Analía Etcheverría, Nora Lía Padola, Rafael Vignoli, Pablo Zunino
Escherichia coli is one of the main etiological agents of neonatal calf diarrhea (NCD). The objective of this study was to assess the presence of virulence genes, genetic diversity, and antibiotic resistance mechanisms in E. coli associated with NCD in Uruguay. PCR was used to assess the presence of intimin, Shiga-like toxin, and stable and labile enterotoxin genes. Resistance to fluoroquinolones and oxyimino-cephalosporins was estimated on Müller-Hinton agar plates. Further antibiotic disc-diffusion tests were performed to assess bacterial multi-resistance...
September 12, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28900256/genomic-and-transcriptomic-analysis-of-the-toluene-degrading-black-yeast-cladophialophora-immunda
#10
Barbara Blasi, Hakim Tafer, Christina Kustor, Caroline Poyntner, Ksenija Lopandic, Katja Sterflinger
Cladophialophora immunda is an ascomycotal species belonging to the group of the black yeasts. These fungi have a thick and melanized cell wall and other physiological adaptations that allows them to cope with several extreme physical and chemical conditions. Member of the group can colonize some of the most extremophilic environments on Earth. Cladophialophora immunda together with a few other species of the order Chaetothyriales show a special association with hydrocarbon polluted environments. The finding that the fungus is able to completely mineralize toluene makes it an interesting candidate for bioremediation purposes...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28899756/stability-based-sorting-the-forgotten-process-behind-not-only-biological-evolution
#11
Jan Toman, Jaroslav Flegr
Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities...
September 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28898777/different-impacts-of-manure-and-chemical-fertilizers-on-bacterial-community-structure-and-antibiotic-resistance-genes-in-arable-soils
#12
Peng Liu, Shuyu Jia, Xiwei He, Xuxiang Zhang, Lin Ye
Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash...
September 4, 2017: Chemosphere
https://www.readbyqxmd.com/read/28894459/a-preliminary-list-of-horizontally-transferred-genes-in-prokaryotes-determined-by-tree-reconstruction-and-reconciliation
#13
Hyeonsoo Jeong, Arshan Nasir
Genome-wide global detection of genes involved in horizontal gene transfer (HGT) remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA "reference" trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa) member of that tree...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28894204/novel-arsenic-transforming-bacteria-and-the-diversity-of-their-arsenic-related-genes-and-enzymes-arising-from-arsenic-polluted-freshwater-sediment
#14
Maria L S Suhadolnik, Ana P C Salgado, Larissa L S Scholte, Lucas Bleicher, Patrícia S Costa, Mariana P Reis, Marcela F Dias, Marcelo P Ávila, Francisco A R Barbosa, Edmar Chartone-Souza, Andréa M A Nascimento
Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893987/acidophilic-green-algal-genome-provides-insights-into-adaptation-to-an-acidic-environment
#15
Shunsuke Hirooka, Yuu Hirose, Yu Kanesaki, Sumio Higuchi, Takayuki Fujiwara, Ryo Onuma, Atsuko Era, Ryudo Ohbayashi, Akihiro Uzuka, Hisayoshi Nozaki, Hirofumi Yoshikawa, Shin-Ya Miyagishima
Some microalgae are adapted to extremely acidic environments in which toxic metals are present at high levels. However, little is known about how acidophilic algae evolved from their respective neutrophilic ancestors by adapting to particular acidic environments. To gain insights into this issue, we determined the draft genome sequence of the acidophilic green alga Chlamydomonas eustigma and performed comparative genome and transcriptome analyses between Ceustigma and its neutrophilic relative Chlamydomonas reinhardtii The results revealed the following features in Ceustigma that probably contributed to the adaptation to an acidic environment...
September 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28890711/horizontally-acquired-genes-are-often-shared-between-closely-related-bacterial-species
#16
Evgeni Bolotin, Ruth Hershberg
Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28888816/the-repeat-structure-of-two-paralogous-genes-yersinia-ruckeri-invasin-yrinv-and-a-y-ruckeri-invasin-like-molecule-yrilm-sheds-light-on-the-evolution-of-adhesive-capacities-of-a-fish-pathogen
#17
Agnieszka Wrobel, Claudio Ottoni, Jack C Leo, Snorre Gulla, Dirk Linke
Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule)...
September 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28886881/pahs-accelerate-the-propagation-of-antibiotic-resistance-genes-in-coastal-water-microbial-community
#18
Jing Wang, Jing Wang, Zelong Zhao, Jingwen Chen, Hong Lu, Guangfei Liu, Jiti Zhou, Xiaoyan Guan
Antibiotic resistance genes (ARGs) have been regarded as emerging contaminants and have attracted growing attention owing to their widespread presence in the environment. In addition to the well-documented selective pressure of antibiotics, ARGs have also become prevalent because of anthropogenic impacts. Coastal habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Excessive accumulation of polycyclic aromatic hydrocarbons (PAHs) has posed a serious threat to coastal habitats, but no information is available on the effect of PAHs on antibiotic resistance in the microbial community of coastal environments...
September 6, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28886679/microbial-expansins
#19
Daniel J Cosgrove
Expansins are small proteins that loosen plant cell walls and cellulosic materials without lytic activity. First discovered in plants, expansin genes are found in the genomes of numerous bacteria and fungi that interact with plants in pathogenic and mutualistic patterns, as well as in microbes that feed on plant debris. Horizontal gene transfer from plants to microbes and between microbes accounts for expansins' irregular taxonomic distribution. Expansins facilitate plant colonization by Bacillus, Clavibacter, and Trichoderma species, a list likely to grow as knowledge of microbial expansin function deepens...
September 8, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28877215/is-biotechnology-more-acceptable-when-it-enables-a-reduction-in-phytosanitary-treatments-a-european-comparison-of-the-acceptability-of-transgenesis-and-cisgenesis
#20
Damien Rousselière, Samira Rousselière
Reduced pesticide use is one of the reasons given by Europeans for accepting new genetic engineering techniques. According to the advocates of these techniques, consumers are likely to embrace the application of cisgenesis to apple trees. In order to verify the acceptability of these techniques, we estimate a Bayesian multilevel structural equation model, which takes into account the multidimensional nature of acceptability and individual, national, and European effects, using data from the Eurobarometer 2010 73...
2017: PloS One
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