Ancestry and Adaptive Radiation of Bacteroidetes As Assessed by Comparative Genomics
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Serial Horizontal Transfer of Vitamin-Biosynthetic Genes Enables the Establishment of New Nutritional Symbionts in Aphids’ Di-Symbiotic Systems
The ISME Journal (2020) 14:259–273 https://doi.org/10.1038/s41396-019-0533-6 ARTICLE Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems 1 1 1 2 2 Alejandro Manzano-Marıń ● Armelle Coeur d’acier ● Anne-Laure Clamens ● Céline Orvain ● Corinne Cruaud ● 2 1 Valérie Barbe ● Emmanuelle Jousselin Received: 25 February 2019 / Revised: 24 August 2019 / Accepted: 7 September 2019 / Published online: 17 October 2019 © The Author(s) 2019. This article is published with open access Abstract Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or 1234567890();,: 1234567890();,: carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera’s. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera’s. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Blattabacterium Genome: Structure, Function, and Evolution Austin Alleman
University of Texas at Tyler Scholar Works at UT Tyler Biology Theses Biology Spring 6-5-2014 Blattabacterium Genome: Structure, Function, and Evolution Austin Alleman Follow this and additional works at: https://scholarworks.uttyler.edu/biology_grad Part of the Biology Commons Recommended Citation Alleman, Austin, "Blattabacterium Genome: Structure, Function, and Evolution" (2014). Biology Theses. Paper 20. http://hdl.handle.net/10950/215 This Thesis is brought to you for free and open access by the Biology at Scholar Works at UT Tyler. It has been accepted for inclusion in Biology Theses by an authorized administrator of Scholar Works at UT Tyler. For more information, please contact [email protected]. BLATTABACTERIUM GENOME: STRUCTURE, FUNCTION, AND EVOLUTION by AUSTIN ALLEMAN A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Biology Srini Kambhampati, Ph. D., Committee Chair College of Arts and Sciences The University of Texas at Tyler May 2014 © Copyright by Austin Alleman 2014 All rights reserved Acknowledgements I would like to thank the Sam A. Lindsey Endowment, without whose support this research would not have been possible. I would also like to thank my research advisor, Dr. Srini Kambhampati, for his knowledge, insight, and patience; and my committee, Dr. John S. Placyk, Jr. and Dr. Blake Bextine, for their assistance and feedback. “It is the supreme art of the teacher to awaken joy in creative expression and knowledge.” --Albert Einstein Table of Contents Chapter -
Classification of Three Airborne Bacteria and Proposal Of
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 445–456 DOI: 10.1099/ijs.0.01682-0 Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. 1 Institut fu$ r Bakteriologie, Sandra Buczolits,1,2 Ewald B. M. Denner,2 Dietmar Vybiral,2 Mykologie und Hygiene, 1,2 3 1,2 Veterina$ rmedizinische Monika Wieser, Peter Ka$ mpfer and Hans-Ju$ rgen Busse Universita$ t, Veterina$ rplatz 1, A-1210 Wien, Austria 2 Author for correspondence: Hans-Ju$ rgen Busse. Tel: j43 1 25077 2128. Fax: j43 1 25077 2190. Institut fu$ r Mikrobiologie e-mail: Hans-Juergen.Busse!vu-wien.ac.at und Genetik, Universita$ t Wien, A-1030 Wien, Austria Three aerobic, Gram-negative, rod-shaped, non-spore-forming, red-pigmented, 3 Institut fu$ r Angewandte airborne bacteria (I/26-Cor1T, I/32A-Cor1 and I/74-Cor2) collected in the Museo Mikrobiologie, Justus- Liebig-Universita$ t Giessen, Correr (Venice, Italy) were investigated to determine their taxonomic status by D-35390 Giessen, Germany analysing their biochemical, physiological and chemotaxonomic features and the GMC content of genomic DNA and by comparing their genomic fingerprints. Additionally, the almost complete 16S rRNA gene sequence of strain I/26-Cor1T was analysed. The three strains were nearly identical in their morphological, physiological, biochemical and chemotaxonomic properties. The strains contained a menaquinone system with the predominant menaquinone MK-7 and a fatty acid profile with C15:0 anteiso, C15:0 iso and C16:1 predominant. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profiles. The polyamine pattern consisted of sym-homospermidine as the major compound. -
Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes Darwiniensis and Cryptocercus Wood Roaches
GBE Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches Yukihiro Kinjo1,2,3,4, Thomas Bourguignon3,5,KweiJunTong6, Hirokazu Kuwahara2,SangJinLim7, Kwang Bae Yoon7, Shuji Shigenobu8, Yung Chul Park7, Christine A. Nalepa9, Yuichi Hongoh1,2, Moriya Ohkuma1,NathanLo6,*, and Gaku Tokuda4,* 1Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan 2Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan 3Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan 4Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan 5Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic 6School of Life and Environmental Sciences, University of Sydney, NSW, Australia 7Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea 8National Institute for Basic Biology, NIBB Core Research Facilities, Okazaki, Japan 9Department of Entomology, North Carolina State University, Raleigh, North Carolina, USA *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: May 29, 2018 Data deposition: This project has been deposited in the International Nucleotide Sequence Database (GenBank/ENA/DDBJ) under the accession numbers given in Table 1. Abstract Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti.Onthebasisof genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of 630 kbp, with the exception of the termite Mastotermes darwiniensis (590 kbp) and Cryptocercus punctulatus (614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
The Cockroach Blattella Germanica Obtains Nitrogen from Uric Acid
Physiology The cockroach Blattella germanica obtains nitrogen from uric acid through a rsbl.royalsocietypublishing.org metabolic pathway shared with its bacterial endosymbiont Research Rafael Patin˜o-Navarrete1, Maria-Dolors Piulachs2, Xavier Belles2, Cite this article: Patin˜o-Navarrete R, Piulachs Andre´s Moya1, Amparo Latorre1 and Juli Pereto´1,3 M-D, Belles X, Moya A, Latorre A, Pereto´ J. 1 2014 The cockroach Blattella germanica obtains InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Vale`ncia, C/Catedra`tic Jose´ Beltra´nn8 2, Paterna 46980, Spain nitrogen from uric acid through a metabolic 2Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Cientı´ficas and Universitat Pompeu Fabra), pathway shared with its bacterial Passeig Marı´tim de la Barceloneta n8 37-49, Barcelona 08003, Spain endosymbiont. Biol. Lett. 10: 20140407. 3Departament de Bioquı´mica i Biologia Molecular, Universitat de Vale`ncia, Burjassot 46100, Spain http://dx.doi.org/10.1098/rsbl.2014.0407 Uric acid stored in the fat bodyof cockroaches is a nitrogen reservoir mobilized in times of scarcity. The discovery of urease in Blattabacterium cuenoti,theprimary endosymbiont of cockroaches, suggests that the endosymbiont may participate Received: 21 May 2014 in cockroach nitrogen economy. However, bacterial urease may only be one piece in the entire nitrogen recycling process from insect uric acid. Thus, Accepted: 2 July 2014 in addition to the uricolytic pathway to urea, there must be glutamine synthe- tase assimilating the released ammonia by the urease reaction to enable the stored nitrogen to be metabolically usable. None of the Blattabacterium genomes sequenced to date possess genes encoding for those enzymes. -
Thesis (PDF, 13.51MB)
Insects and their endosymbionts: phylogenetics and evolutionary rates Daej A Kh A M Arab The University of Sydney Faculty of Science 2021 A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Authorship contribution statement During my doctoral candidature I published as first-author or co-author three stand-alone papers in peer-reviewed, internationally recognised journals. These publications form the three research chapters of this thesis in accordance with The University of Sydney’s policy for doctoral theses. These chapters are linked by the use of the latest phylogenetic and molecular evolutionary techniques for analysing obligate mutualistic endosymbionts and their host mitochondrial genomes to shed light on the evolutionary history of the two partners. Therefore, there is inevitably some repetition between chapters, as they share common themes. In the general introduction and discussion, I use the singular “I” as I am the sole author of these chapters. All other chapters are co-authored and therefore the plural “we” is used, including appendices belonging to these chapters. Part of chapter 2 has been published as: Bourguignon, T., Tang, Q., Ho, S.Y., Juna, F., Wang, Z., Arab, D.A., Cameron, S.L., Walker, J., Rentz, D., Evans, T.A. and Lo, N., 2018. Transoceanic dispersal and plate tectonics shaped global cockroach distributions: evidence from mitochondrial phylogenomics. Molecular Biology and Evolution, 35(4), pp.970-983. The chapter was reformatted to include additional data and analyses that I undertook towards this paper. My role was in the paper was to sequence samples, assemble mitochondrial genomes, perform phylogenetic analyses, and contribute to the writing of the manuscript. -
Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus Punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities
GBE Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities Alexander Neef1,*, Amparo Latorre1,2,3, Juli Pereto´ 1,4, Francisco J. Silva1,2,3, Miguel Pignatelli2,5, and Downloaded from https://academic.oup.com/gbe/article-abstract/doi/10.1093/gbe/evr118/598520 by guest on 06 November 2018 Andre´ s Moya1,2,3,* 1Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Vale` ncia, Spain 2Unidad Mixta de Investigacio´ n en Geno´ mica y Salud—Centro Superior Investigacio´ n Salud Pu´ blica (Generalitat Valenciana)/Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Universitat de Vale` ncia, Spain 3Departament de Gene` tica, Universitat de Vale` ncia, Spain 4Departament de Bioquı´mica i Biologia Molecular, Universitat de Vale` ncia, Spain 5Present address: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK *Corresponding author: E-mail: [email protected]; [email protected]. Accepted: 9 November 2011 Data deposition: The complete sequences of chromosome and plasmid of Blattabacterium sp. (Cryptocercus punctulatus) BCpu were deposited at GenBank/DDBJ/EMBL and were assigned accession numbers CP003015 and CP003016, respectively. Abstract Cockroaches (Blattaria: Dictyoptera) harbor the endosymbiont Blattabacterium sp. in their abdominal fat body. This endosymbiont is involved in nitrogen recycling and amino acid provision to its host. In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam, respectively. The BCpu genome consists of a chromosome of 605.7 kb and a plasmid of 3.8 kb and is therefore approximately 31 kb smaller than the other two aforementioned genomes. -
Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. -
View and Research Objectives
University of Alberta Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis by Jonathan Lee Klassen A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Cell Biotechnology Department of Biological Sciences ©Jonathan Lee Klassen Fall 2009 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Examining Committee Dr. Julia Foght, Department of Biological Science Dr. Phillip Fedorak, Department of Biological Sciences Dr. Brenda Leskiw, Department of Biological Sciences Dr. David Bressler, Department of Agriculture, Food and Nutritional Science Dr. Jeffrey Lawrence, Department of Biological Sciences, University of Pittsburgh Abstract Many diverse microbes have been detected in or isolated from glaciers, including novel taxa exhibiting previously unrecognized physiological properties with significant biotechnological potential. Of 29 unique phylotypes isolated from Victoria Upper Glacier, Antarctica (VUG), 12 were related to the poorly studied bacterial genus Hymenobacter including several only distantly related to previously described taxa.