Wedding Higher Taxonomic Ranks with Metabolic Signatures Coded in Prokaryotic Genomes
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Eubacteria Fabia U. Battistuzzia,b,* and S. Blair Hedgesa shown increasing support for lower-level phylogenetic Department of Biology, 208 Mueller Laboratory, The Pennsylvania clusters (e.g., classes and below), they have also shown the State University, University Park, PA 16802-5301, USA; bCurrent susceptibility of eubacterial phylogeny to biases such as address: Center for Evolutionary Functional Genomics, The Biodesign horizontal gene transfer (HGT) (20, 21). Institute, Arizona State University, Tempe, AZ 85287-5301, USA In recent years, three major approaches have been used *To whom correspondence should be addressed (Fabia.Battistuzzi@ asu.edu) for studying prokaryote phylogeny with data from com- plete genomes: (i) combining gene sequences in a single analysis of multiple genes (e.g., 7, 9, 10), (ii) combining Abstract trees from individual gene analyses into a single “super- tree” (e.g., 22, 23), and (iii) using the presence or absence The ~9400 recognized species of prokaryotes in the of genes (“gene content”) as the raw data to investigate Superkingdom Eubacteria are placed in 25 phyla. Their relationships (e.g., 17, 18). While the results of these dif- relationships have been diffi cult to establish, although ferent approaches have not agreed on many details of some major groups are emerging from genome analyses. relationships, there have been some points of agreement, A molecular timetree, estimated here, indicates that most such as support for the monophyly of all major classes (85%) of the phyla and classes arose in the Archean Eon and some phyla (e.g., Proteobacteria and Firmicutes). (4000−2500 million years ago, Ma) whereas most (95%) of 7 ese A ndings, although criticized by some (e.g., 24, 25), the families arose in the Proterozoic Eon (2500−542 Ma). -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Bacterial Communities Associated with the Pine Wilt Disease Vector Monochamus Alternatus (Coleoptera: Cerambycidae) During Different Larval Instars
Journal of Insect Science, (2017)17(6): 115; 1–7 doi: 10.1093/jisesa/iex089 Research Article Bacterial Communities Associated With the Pine Wilt Disease Vector Monochamus alternatus (Coleoptera: Cerambycidae) During Different Larval Instars Xia Hu,1 Ming Li,1 Kenneth F. Raffa,2 Qiaoyu Luo,1 Huijing Fu,1 Songqing Wu,1 Guanghong Liang,1 Rong Wang,1 and Feiping Zhang1,3 1College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China, 2Department of Entomology, University of Wisconsin-Madison, 345 Russell Labs 1630 Linden Dr., Madison, WI 53706, and 3Corresponding author, e-mail: [email protected] Subject Editor: Campbell Mary and Lancette Josh Received 14 June 2017; Editorial decision 20 September 2017 Abstract We investigated the influence of larval instar on the structure of the gut bacterial community in the Japanese pine sawyer, Monochamus alternatus (Hope; Coleoptera: Cerambycidae). The diversity of the gut bacterial community in early, phloem-feeding larvae is significantly higher than in later, wood-feeding larvae. Many of these associates were assigned into a few taxonomic groups, of which Enterobacteriaceae was the most abundant order. The predominant bacterial genus varied during the five instars of larval development.Erwinia was the most abundant genus in the first and fifth instars,Enterobacter was predominant in the third and fourth instars, and the predominant genus in the second instars was in the Enterobacteriaceae (genus unclassified). Actinobacteria were reported in association with M. alternatus for the first time in this study. Cellulomonadaceae (Actinobacteria) was the second most abundant family in the first instar larvae (10.6%). These data contribute to our understanding of the relationships among gut bacteria and M. -
Identification of Glucose Non-Fermenting Gram Negative Rods
UK Standards for Microbiology Investigations Identification of Glucose Non-Fermenting Gram Negative Rods REVIEW UNDER Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 1 of 24 © Crown copyright 2014 Identification of Glucose Non-Fermenting Gram Negative Rods Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website http://www.hpa.org.uk/SMI/Partnerships. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see http://www.hpa.org.uk/SMI/WorkingGroups). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: http://www.hpa.org.uk/SMI UK Standards for Microbiology Investigations are produced in association with: REVIEW UNDER Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 2 of 24 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Glucose Non-Fermenting Gram Negative Rods Contents ACKNOWLEDGMENTS .......................................................................................................... 2 AMENDMENT TABLE ............................................................................................................. 4 UK STANDARDS FOR MICROBIOLOGY INVESTIGATIONS: SCOPE AND PURPOSE ...... -
Molecular Detection of Tick-Borne Pathogens in Ticks Collected from Hainan Island, China
Molecular Detection of Tick-Borne Pathogens in Ticks Collected From Hainan Island, China Miao Lu National Institute for Communicable Disease Control and Prevention Guangpeng Tang PHLIC: Centers for Disease Control and Prevention Xiaosong Bai Congjiang CDC Xincheng Qin National Institute for Communicable Disease Control and Prevention Wenping Guo Chengde Medical University Kun Li ( [email protected] ) National Institute for Communicable Disease Control and Prevention Research Keywords: Ticks, Rickettsiales bacteria, Protozoa, Coxiellaceae bacteria, Tick-borne disease, China Posted Date: December 1st, 2020 DOI: https://doi.org/10.21203/rs.3.rs-114641/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/29 Abstract Background Kinds of pathogens such as viruses, bacteria and protozoa are transmitted by ticks as vectors, and they have deeply impact on human and animal health worldwide. Methods To better understand the genetic diversity of bacteria and protozoans carried by ticks in Chengmai county of Hainan province, China, 285 adult hard ticks belonging to two species (Rhipicephalus sanguineus: 183, 64.21% and R. microplus: 102, 35.79%) from dogs, cattle, and goats were colleted. Rickettsiales bacteria, Coxiellaceae bacteria, Babesiidae, and Hepatozoidae were identied in these ticks by amplifying the 18S rRNA, 16S rRNA (rrs), citrate synthase (gltA), and heat shock protein (groEL) genes. Results Our data revealed the presence of four recognized species and two Candidatus spp. of Anaplasmataceae and Coxiellaceae in locality. Conclusions In sum, these data reveal an extensive diversity of Anaplasmataceae bacteria, Coxiellaceae bacteria, Babesiidae, and Hepatozoidae in ticks from Chengmai county, highlighting the need to understand the tick-borne pathogen infection in local animals and humans. -
Abstract Betaproteobacteria Alphaproteobacteria
Abstract N-210 Contact Information The majority of the soil’s biosphere containins biodiveristy that remains yet to be discovered. The occurrence of novel bacterial phyla in soil, as well as the phylogenetic diversity within bacterial phyla with few cultured representatives (e.g. Acidobacteria, Anne Spain Dr. Mostafa S.Elshahed Verrucomicrobia, and Gemmatimonadetes) have been previously well documented. However, few studies have focused on the Composition, Diversity, and Novelty within Soil Proteobacteria Department of Botany and Microbiology Department of Microbiology and Molecular Genetics novel phylogenetic diversity within phyla containing numerous cultured representatives. Here, we present a detailed University of Oklahoma Oklahoma State University phylogenetic analysis of the Proteobacteria-affiliated clones identified in a 13,001 nearly full-length 16S rRNA gene clones 770 Van Vleet Oval 307 LSE derived from Oklahoma tall grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised Norman, OK 73019 Stillwater, OK 74078 25% of total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, which comprised 405 325 5255 405 744 6790 39% of Proteobacteria clones, followed by the Deltaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, which made Anne M. Spain (1), Lee R. Krumholz (1), Mostafa S. Elshahed (2) up 37, 16, and 8% of Proteobacteria clones, respectively. Members of the Epsilonproteobacteria were not detected in the dataset. [email protected] [email protected] Detailed phylogenetic analysis indicated that 14% of the Proteobacteria clones belonged to 15 novel orders and 50% belonged (1) Dept. of Botany and Microbiology, University of Oklahoma, Norman, OK to orders with no described cultivated representatives or were unclassified. -
Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp. -
Relative Genetic Diversity of the Rare and Endangered Agave Shawii Ssp
Received: 17 July 2020 | Revised: 9 December 2020 | Accepted: 14 December 2020 DOI: 10.1002/ece3.7172 ORIGINAL RESEARCH Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve Jeanne P. Vu1 | Miguel F. Vasquez1 | Zuying Feng1 | Keith Lombardo2 | Sora Haagensen1,3 | Goran Bozinovic1,4 1Boz Life Science Research and Teaching Institute, San Diego, CA, USA Abstract 2Southern California Research Learning Shaw's Agave (Agave shawii ssp. shawii) is an endangered maritime succulent growing Center, National Park Services, San Diego, along the coast of California and northern Baja California. The population inhabiting CA, USA 3University of California San Diego Point Loma Peninsula has a complicated history of transplantation without documen- Extended Studies, La Jolla, CA, USA tation. The low effective population size in California prompted agave transplanting 4 Biological Sciences, University of California from the U.S. Naval Base site (NB) to Cabrillo National Monument (CNM). Since 2008, San Diego, La Jolla, CA, USA there are no agave sprouts identified on the CNM site, and concerns have been raised Correspondence about the genetic diversity of this population. We sequenced two barcoding loci, rbcL Goran Bozinovic, Boz Life Science Research and Teaching Institute, 3030 Bunker Hill St, and matK, of 27 individual plants from 5 geographically distinct populations, includ- San Diego CA 92109, USA. ing 12 individuals from California (NB and CNM). Phylogenetic analysis revealed the Emails: [email protected]; gbozinovic@ ucsd.edu three US and two Mexican agave populations are closely related and have similar ge- netic variation at the two barcoding regions, suggesting the Point Loma agave popu- Funding information National Park Services (NPS) Pacific West lation is not clonal. -
Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Downloaded 13 April 2017); Using Diamond
bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Microbial Biofilms – Veronica Lazar and Eugenia Bezirtzoglou
MEDICAL SCIENCES – Microbial Biofilms – Veronica Lazar and Eugenia Bezirtzoglou MICROBIAL BIOFILMS Veronica Lazar University of Bucharest, Faculty of Biology, Dept. of Microbiology, 060101 Aleea Portocalelor No. 1-3, Sector 6, Bucharest, Romania; Eugenia Bezirtzoglou Democritus University of Thrace - Faculty of Agricultural Development, Dept. of Microbiology, Orestiada, Greece Keywords: Microbial adherence to cellular/inert substrata, Biofilms, Intercellular communication, Quorum Sensing (QS) mechanism, Dental plaque, Tolerance to antimicrobials, Anti-biofilm strategies, Ecological and biotechnological significance of biofilms Contents 1. Introduction 2. Definition 3. Microbial Adherence 4. Development, Architecture of a Mature Biofilm and Properties 5. Intercellular Communication: Intra-, Interspecific and Interkingdom Signaling, By QS Mechanism and Implications 6. Medical Significance of Microbial Biofilms Formed on Cellular Substrata and Medical Devices 6.1. Microbial Biofilms on Medical Devices 6.2. Microorganisms - Biomaterial Interactions 6.3. Phenotypical Resistance or Tolerance to Antimicrobials; Mechanisms of Tolerance 7. New Strategies for Prevention and Treatment of Biofilm Associated Infections 8. Ecological Significance 9. Biotechnological / Industrial Applications 10. Conclusion Acknowledgments Glossary Bibliography Biographical Sketches UNESCO – EOLSS Summary A biofilm is a sessileSAMPLE microbial community coCHAPTERSmposed of cells embedded in a matrix of exopolysaccharide matrix attached to a substratum or interface. Biofilms